year author title publication issue link extra pmid doi category
1998 Ashburner M On the representation of gene function in genetic databases. Unpublished http://www.geneontology.org/gene.ontology.discussion.shtml|full 1
2000 Adams MD|etAl The genome sequence of Drosophila melanogaster. Science 287: 2185-2195. Drosophila genomic 10731132 1,4
2000 Lewis S, Ashburner M, Reese MG Annotating eukaryote genomes. Curr Opin Struct Biol 10: 349-354. 10851187 1,4,14
2000 Rison SC, Hodgman TC, Thornton JM Comparison of functional annotation schemes for genomes. Funct Integr Genomics 1: 56-69. 11793222 14
2000 Stevens R, Goble CA, Bechhofer S Ontology-based knowledge representation for bioinformatics. Brief Bioinform 1: 398-414. 11465057 14
2000 The Gene Ontology Consortium Gene Ontology: tool for the unification of biology. Nat Genet 25: 25-29. http://www.geneontology.org/GO_nature_genetics_2000.pdf|pdf 10802651 1,2
2001 Bard J, Winter R Ontologies of developmental anatomy: their current and future roles. Briefings Bioinformatics 2: 289-299. 11589589 15
2001 Berriman M, Aslett M, Ivens A, Hall N Parasites are GO. Trends Parasitol 17: 463-464. Parasites 11642257 1,3
2001 Hill DP, Davis AP, Richardson JE, Corradi JP, Ringwald M, Eppig JT, Blake JA Program description: Strategies for biological annotation of mammalian systems: implementing gene ontologies in mouse genome informatics. Genomics 74: 121-128. Mouse 11374909 1,4,11
2001 Jenssen TK, Laegreid A, Komorowski J, Hovig E A literature network of human genes for high-throughput analysis of gene expression. Nat Genet 28: 21-28. 11326270 9,12
2001 Juty NS, Spence HD, Hotz HR, Tang H, Goryanin I, Hodgman TC Simultaneous modelling of metabolic, genetic and product-interaction networks. Brief Bioinform 2: 223-232. 11589583 13,17
2001 Kawai J|etAl Functional annotation of a full-length mouse cDNA collection. Nature 409: 685-690. Mouse cDNAs 11217851 3
2001 Pouliot Y, Gao J, Su QJ, Liu GG, Ling XB DIAN: a novel algorithm for genome ontological classification. Genome Res 11: 1766-1779. 11591654 9
2001 The Gene Ontology Consortium Creating the gene ontology resource: design and implementation. Genome Res 11: 1425-1433. http://www.genome.org/cgi/content/full/11/8/1425|full 11483584 1,2
2002 Ashburner M, Lewis SE On ontologies for biologists: the Gene Ontology - uncoupling the web. Novartis Found Symp 247: 66-80; discussion 80-3, 84-90, 244-52. 12539950 1,2
2002 Berger A, Mutch DM, Bruce German J, Roberts MA Dietary effects of arachidonate-rich fungal oil and fish oil on murine hepatic and hippocampal gene expression. Lipids Health Dis 1: 2. Mouse liver and hippocampal genes 12617750 7
2002 Biswas M|etAl Applications of InterPro in protein annotation and genome analysis. Brief Bioinform 3: 285-295. 12230037 13,6
2002 Blake JA, Harris MA The Gene Ontology (GO) project: structured vocabularies for molecular biology and their application to genome and expression analysis. Curr Protoc Bioinformatics Chapter 7: Unit 7.2. 18792943 1,2
2002 Bodenreider O, Mitchell JA, McCray AT Evaluation of the UMLS as a terminology and knowledge resource for biomedical informatics. Proc AMIA Symp 2002: 61-65. 12463787 14
2002 Bono H, Kasukawa T, Furuno M, Hayashizaki Y, Okazaki Y FANTOM DB: database of functional annotation of RIKEN mouse cDNA clones. Nucleic Acids Res 30: 116-118. Mouse cDNAs 11752270 3,11
2002 Brenner S Life sentences: Ontology recapitulates philology. Genome Biol 3: comment1006.1-comment1006.2. 11983049 14
2002 Carlton JM|etAl Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature 419: 512-519. Plasmodium yoelii 12368865 4
2002 Dwight SS|etAl Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res 30: 69-72. Saccharomyces 11752257 1,4,11
2002 Enright AJ, van Dongen S, Ouzounis C An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30: 1575-1585. 11917018 9
2002 Gardner MJ|etAl Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419: 498-511. Plasmodium falciparum 12368864 4
2002 Gardner MJ|etAl Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14. Nature 419: 531-534. Plasmodium falciparum, chromosomes 2, 10, 11 and 14 12368868 4
2002 Glockner G|etAl Sequence and analysis of chromosome 2 of Dictyostelium discoideum. Nature 418: 79-85. Dictyostelium chromosome 2 genomic 12097910 4
2002 Goff SA|etAl A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100. Rice genomic 11935018 4
2002 Hall N|etAl Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13. Nature 419: 527-531. Plasmodium falciparum, chromosomes 1, 3-9 and 13 12368867 4
2002 Harrison PM, Hegyi H, Balasubramanian S, Luscombe NM, Bertone P, Echols N, Johnson T, Gerstein M Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res 12: 272-280. Human pseudogenes 11827946 13,3
2002 Hill DP, Blake JA, Richardson JE, Ringwald M Extension and Integration of the Gene Ontology (GO): Combining GO vocabularies with external vocabularies. Genome Res 12: 1982-1991. http://www.genome.org/cgi/content/full/12/12/1982|full 12466303 1
2002 Hodges PE, Carrico PM, Hogan JD, O'Neill KE, Owen JJ, Mangan M, Davis BP, Brooks JE, Garrels JI Annotating the human proteome: the Human Proteome Survey Database (HumanPSD) and an in-depth target database for G protein-coupled receptors (GPCR-PD) from Incyte Genomics. Nucleic Acids Res 30: 137-141. Human GPCRs 11752275 6,8,11
2002 Holt RA|etAl The genome sequence of the malaria mosquito Anopheles gambiae. Science 298: 129-149. Anopheles gambiae 12364791 4
2002 Hunter L Ontologies for programs, not people. Genome Biol 3: INTERACTIONS1002. 12093368 14
2002 Hvidsten TR, Komorowski J, Sandvik AK, Laegreid A Predicting gene function from gene expressions and ontologies. Pac Symp Biocomput 7: 299-310. 11262949 7,9
2002 Hyman|etAl Sequence of Plasmodium falciparum chromosome 12. Nature 419: 534-537. Plasmodium falciparum, chromosome 12 12368869 4
2002 Jaiswal P|etAl Gramene: development and integration of trait and gene ontologies for rice. Comp Funct Genomics 3: 132-136. Rice genome 18628886 1,4,11,15
2002 Khatri P, Draghici S, Ostermeier GC, Krawetz SA Profiling gene expression using onto-express. Genomics 79: 266-270. Onto-Express 11829497 10
2002 Kohler J, Schulze-Kremer S The semantic metadatabase (SEMEDA): ontology based integration of federated molecular biological data sources. In Silico Biol 2: 219-231. 12542408 14
2002 Liu YG, Gano J, Huang R, Lin Y, Wang SM, Huang RP Analysis of gene expression in Egr-1 transfected human fibrosarcoma cells. J Surg Oncol 80: 190-196. Human fibrosarcoma cells 12210033 7
2002 Martinez-Chantar ML, Corrales FJ, Martinez-Cruz LA, Garcia-Trevijano ER, Huang ZZ, Chen L, Kanel G, Avila MA, MatoJ M, Lu SC Spontaneous oxidative stress and liver tumors in mice lacking methionine adenosyltransferase 1A. FASEB J 16: 1292-1294. Mouse tumors 12060674 7,16
2002 McConnell P, Johnson K, Lin S Applications of Tree-Maps to hierarchical biological data. Bioinformatics 18: 1278-1279. 12217926 10
2002 McCray AT, Browne AC, Bodenreider O The lexical properties of the gene ontology. Proc AMIA Symp 2002: 504-508. 12463875 14
2002 Michalickova K, Bader GD, Dumontier M, Lieu HC, Betel D, Isserlin R, Hogue CW SeqHound: biological sequence and structure database as a platform for bioinformatics research. BMC Bioinformatics 3: 32. 12401134 11
2002 Nembaware V, Crum K, Kelso J, Seoighe C Impact of the presence of paralogs on sequence divergence in a set of mouse-human orthologs. Genome Res 12: 1370-1376. 12213774 13,18
2002 Nene V, Lee D, Quackenbush J, Skilton R, Mwaura S, Gardner MJ, Bishop R AvGI, an index of genes transcribed in the salivary glands of the ixodid tick Amblyomma variegatum. Int J Parasitol 32: 1447. Amblyomma variegatum ESTs 12392910 3,11
2002 Perez-Iratxeta C, Bork P, Andrade, MA Association of genes to genetically inherited diseases using data mining. Nat Genet 31: 316-319. 12006977 12
2002 Pletcher SD, Macdonald SJ, Marguerie R, Certa U, Stearns SC, Goldstein DB, Partridge L Genome-wide transcript profiles in aging and calorically restricted Drosophila melanogaster. Curr Biol 12: 712-723. Drosophila genes during aging 12007414 7
2002 Raychaudhuri S, Chang JT, Sutphin PD, Altman RB Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature. Genome Res 12: 203-214. 11779846 9,12
2002 Rector AL, Rogers J, Roberts A, Wroe C Scale and CONTEXT: Issues in ontologies to link health- and bio-informatics. Proc AMIA Symp 2002: 642-646. 12463902 14
2002 Schug J, Diskin S, Mazzarelli J, Brunk BP, Stoeckert CJ Jr Predicting Gene Ontology functions from ProDom and CDD protein domains. Genome Res 12: 648-655. 11932249 9
2002 Schulze-Kremer S Ontologies for molecular biology and bioinformatics. In Silico Biol 2: 179-193. 12542404 14
2002 Simin K, Scuderi A, Reamey J, Dunn D, Weiss R, Metherall JE, Letsou A Profiling patterned transcripts in Drosophila embryos. Genome Res 12: 1040-1047. Drosophila embryos 12097340 7
2002 Sonstegard TS|etAl Analysis of bovine mammary gland EST and functional annotation of the Bos taurus gene index. Mamm Genome 13: 373-379. Bovine ESTs 12140684 5
2002 Tanoue J, Yoshikawa M, Uemura S The GeneAround GO viewer. Bioinformatics 18: 1705-1706. GeneAround 12490464 10
2002 The Plant Ontology Consortium The plant ontology consortium and plant ontologies. Comp Funct Genomics 3: 137-142. 18628842 15
2002 The Plant OntologyTM Consortium The Plant OntologyTM Consortium and Plant Ontologies. Comp Funct Genomics 3: 137-142. Conference Review. http://www3.interscience.wiley.com/cgi-bin/abstract/91016119/START|abs 15
2002 Ware DH|etAl Gramene, a tool for grass genomics. Plant Physiol 130: 1606-1613. 12481044 15
2002 Whitfield CW, Band MR, Bonaldo MF, Kumar CG, Liu L, Pardinas JR, Robertson HM, Soares MB, Robinson GE Annotated expressed sequence tags and cDNA microarrays for studies of brain and behavior in the honey bee. Genome Res 12: 555-566. Honey bee ESTs 11932240 5
2002 Wood V, Bahler J How to get the best from fission yeast genome data. Comp Funct Genomics 3: 282-288. http://www3.interscience.wiley.com/cgi-bin/abstract/93520677/START|abs Schizosaccharomyces pombe 1,4
2002 Xie H, Wasserman A, Levine Z, Novik A, Grebinskiy V, Shoshan A, Mintz Large scale protein annotation through Gene Ontology. Genome Res 12: 785-794. 11997345 9
2002 Yu J|etAl A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79-92. Rice genomic 11935017 4
2002 Zdobnov|etAl Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science 298: 149-159. Anopheles gambiae 12364792 4,6,8
2003 Aerts S, Van Loo P, Thijs G, Moreau Y, De Moor B Computational detection of cis-regulatory modules. Bioinformatics 19 Suppl 2: ii5-14. 14534164 7,10,17,19
2003 Ahn WS, Kim KW, Bae SM, Yoon JH, Lee JM, Namkoong SE, Kim JH, Kim CK, Lee YJ, Kim YW Targeted cellular process profiling approach for uterine leiomyoma using cDNA microarray, proteomics and gene ontology analysis. Int J Exp Pathol 84: 267-279. Human uterine tumor cells 14748746 7,16
2003 Arciero C, Somiari SB, Shriver CD, Brzeski H, Jordan R, Hu H, Ellsworth DL, Somiari RI Functional relationship and gene ontology classification of breast cancer biomarkers. Int J Biol Markers 18: 241-272. Human breast cancer markers 14756541 7,16
2003 Ashburner M, Mungall CJ, Lewis SE Ontologies for biologists: a community model for the annotation of genomic data. Cold Spring Harb Symp Quant Biol 68: 227-235. 15338622 1,2,11,14,15
2003 Badea L Functional discrimination of gene expression patterns in terms of the Gene Ontology. Pac Symp Biocomput 8: 565-576. 12603058 7,13
2003 Bard J Ontologies: Formalising biological knowledge for bioinformatics. Bioessays 25: 501-506. 12717820 14
2003 Bernardi L, Rojas I, van der Vet P The ESF programme on Integrated Approaches to Functional Genomics. Workshop on Ontology for Biology. Comp Funct Genomics 4: 68-70. Conference Report. http://www3.interscience.wiley.com/cgi-bin/abstract/102531164/START|ws 14
2003 Berriz GF, King OD, Bryant B, Sander C, Roth FP Characterizing gene sets with FuncAssociate. Bioinformatics 19: 2502-2504. FuncAssociate 14668247 10
2003 Berriz GF, White JV, King OD, Roth FP GoFish finds genes with combinations of Gene Ontology attributes. Bioinformatics 19: 788-789. GoFish 12691998 10
2003 Blake JA, Harris M The Gene Ontology Project: Structured vocabularies for molecular biology and their application to genome and expression analysis. Current Protocols in Bioinformatics. [A.D. Baxevanis, D.B. Davison, R.D.M. Page, G.A. Petsko, L.D. Stein, and G.D. Stormo (eds.), Wiley and Sons, Inc., New York.] 1,2
2003 Blaschke C, Valencia A Automatic classification of protein functions from the literature. Comp Funct Genomics 4: 75-79. Conference Review. http://www3.interscience.wiley.com/cgi-bin/abstract/102531166/START|abs 9
2003 Bodenreider O, Burgun A, Mitchell JA Evaluation of WordNet as a source of lay knowledge for molecular biology and genetic diseases: a feasibility study. Stud Health Technol Inform 95: 379-384. Analysis of ontologies 14664016 13
2003 Bono H, Nikaido I, Kasukawa T, Hayashizaki Y, Okazaki Y Comprehensive analysis of the mouse metabolome based on the transcriptome. Genome Res 13: 1345-1349. 12819132 13
2003 Bono H|etAl Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays. Genome Res 13: 1318-1323. Mouse transcripts 12819129 7
2003 Camon E, Barrell D, Brooksbank C, Magrane M, Apweiler R The Gene Ontology Annotation (GOA) project-application of GO in SWISS-PROT, TrEMBL and InterPro. Comp Funct Genomics 4: 71-74. Swiss-Prot proteins 18629103 1,6
2003 Camon E, Barrell D, Lee V, Dimmer E, Apweiler R The Gene Ontology Annotation (GOA) Database - An integrated resource of GO annotations to the UniProt Knowledgebase. In Silico Biol 4: 5-6. UniProt 15089749 1,6,11
2003 Camon E|etAl The Gene Ontology Annotation (GOA) Project: Implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res 13: 662-672. Swiss-Prot/TrEMBL 12654719 1,6,11
2003 Cantor MN, Lussier YA Putting data integration into practice: using biomedical terminologies to add structure to existing data sources. Proc AMIA Symp 2003: 125-129. 14728147 14
2003 Cantor MN, Sarkar IN, Gelman R, Hartel F, Bodenreider O, Lussier YA An evaluation of hybrid methods for matching biomedical terminologies: mapping the gene ontology to the UMLS. Stud Health Technol Inform 95: 62-67. Analysis of ontologies 14663964 13
2003 Carinci F|etAl Genetic expression profiling of six odontogenic tumors. J Dent Res 82: 551-557. Human odontogenic tumors 12821718 7,16
2003 Chen JY, Sivachenko AY, Bell R, Kurschner C, Ota I, Sahasrabudhe S Initial large-scale exploration of protein-protein interactions in human brain. Proc IEEE Comput Soc Bioinform Conf 2: 229-234. Human brain proteins 16452797 8
2003 Chen Y, Li S, Ye L, Geng J, Deng Y, Hu S Gene expression profiling in porcine fetal thymus. Genomics Proteomics Bioinformatics 1: 171-172. Porcine ESTs 15626347 7
2003 Chiang JH, Yu HC MeKE: discovering the functions of gene products from biomedical literature via sentence alignment. Bioinformatics 19: 1417-1422. 12874055 12
2003 Chou KC, Cai YD A new hybrid approach to predict subcellular localization of proteins by incorporating gene ontology. Biochem Biophys Res Commun 311: 743-747. 14623335 9
2003 Clerch LB, Baras AS, Massaro GD, Hoffman EP, Massaro D DNA microarray analysis of neonatal mouse lung connects regulation of KDR with dexamethasone-induced inhibition of alveolar formation. Am J Physiol Lung Cell Mol Physiol 286: L411-L419. Mouse lung transcripts 14607780 7
2003 Cornell M, Paton NW, Hedeler C, Kirby P, Delneri D, Hayes A, Oliver SG GIMS: an integrated data storage and analysis environment for genomic and functional data. Yeast 20: 1291-1306. 14618567 11,13,10,7
2003 Cunliffe HE, Ringner M, Bilke S, Walker RL, Cheung JM, Chen Y, Meltzer PS The gene expression response of breast cancer to growth regulators: patterns and correlation with tumor expression profiles. Cancer Res 63: 7158-7166. Human breast cancer cells 14612509 7,16
2003 Dellaire G, Farrall R, Bickmore WA The Nuclear Protein Database (NPD): sub-nuclear localisation and functional annotation of the nuclear proteome. Nucleic Acids Res 31: 328-330. Vertebrate nuclear proteins 12520015 6,8,11
2003 Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4: P3. DAVID 12734009 10,11
2003 Doniger SW, Salomonis N, Dahlquist, KD, Vranizan K, Lawlor, SC and Conklin, BR MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol 4: R7. http://www.genomebiology.com/2003/4/1/R7|full MAPPFinder 12540299 7,10
2003 Draghici S, Khatri P, Bhavsar P, Shah A, Krawetz SA, Tainsky MA Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Nucleic Acids Res 31: 3775-3781. Onto-Tools 12824416 10
2003 Draghici S, Khatri P, Martins RP, Ostermeier GC, Krawetz SA Global profiling of gene expression. Genomics 81: 98-104. 12620386 7,10
2003 Draghici S, Khatri P, Shah A, Tainsky MA Assessing the functional bias of commercial microarrays using the onto-compare database. Biotechniques Mar;Suppl: 55-61. Onto-Compare 12664686 7,10,13
2003 Edwards AD, Chaussabel D, Tomlinson S, Schulz O, Sher A, Reis E Sousa C Relationships among murine CD11c(high) dendritic cell subsets as revealed by baseline gene expression patterns. J Immunol 171: 47-60. Mouse dendritic cells 12816982 7
2003 Felipe MS|etAl Transcriptome characterization of the dimorphic and pathogenic fungus Paracoccidioides brasiliensis by EST analysis. Yeast 20: 263-271. Paracoccidioides brasiliensis 12557278 5,7
2003 Feng W, Wang G, Zeeberg BR, Guo K, Fojo AT, Kane DW, Reinhold WC, Lababidi S, Weinstein JN, Wang MD Development of gene ontology tool for biological interpretation of genomic and proteomic data. Proc AMIA Symp 2003: 839. 14728344 10
2003 Gallagher PG, Bao Y, Serrano SM, Kamiguti AS, Theakston RD, Fox JW Use of microarrays for investigating the subtoxic effects of snake venoms: insights into venom-induced apoptosis in human umbilical vein endothelial cells. Toxicon 41: 429-440. Human endothelial cells 12657312 7,16
2003 Garavelli JS The RESID Database of Protein Modifications: 2003 developments. Nucleic Acids Res 31: 499-501. RESID 12520062 6,11
2003 Guettler S, Jackson EN, Lucchese SA, Honaas L, Green A, Hittinger CT, Tian Y, Lilly WW, Gathman AC ESTs from the basidiomycete Schizophyllum commune grown on nitrogen-replete and nitrogen-limited media. Fungal Genet Biol 39: 191-198. Schizophyllum commune 12781677 5
2003 Haft DH, Selengut JD, White O The TIGRFAMs database of protein families. Nucleic Acids Res 31: 371-373. TIGRFAMs protein families 12520025 6
2003 Harhay GP, Keele JW Positional candidate gene selection from livestock EST databases using Gene Ontology. Bioinformatics 19: 249-255. Livestock (cattle and swine) ESTs 12538246 4,13,5
2003 Harris MA, Parkinson H Standards and ontologies for functional genomics: towards unified ontologies for biology and biomedicine. Comp Funct Genomics 4: 116-120. Conference Report. http://www3.interscience.wiley.com/cgi-bin/abstract/102531180/START|ws 14
2003 Hauser P, Schwarz C, Mitterbauer C, Regele HM, Muhlbacher F, Mayer G, Perco P, Mayer B, Meyer TW, Oberbauer R Genome-wide gene-expression patterns of donor kidney biopsies distinguish primary allograft function. Lab Invest 84: 353-361. Human kidney transcripts 14704720 7,16
2003 Hawse JR, Hejtmancik JF, Huang Q, Sheets NL, Hosack DA, Lempicki RA, Horwitz J, Kantorow M Identification and functional clustering of global gene expression differences between human age-related cataract and clear lenses. Mol Vis 9: 515-537. Human lens epithelial cells 14551530 7,16
2003 Hennig S, Groth D, Lehrach H Automated Gene Ontology annotation for anonymous sequence data. Nucleic Acids Res 31: 3712-3715. 12824400 9
2003 Herrero J, Al-Shahrour F, Diaz-Uriarte R, Mateos A, Vaquerizas JM, Santoyo J, Dopazo J GEPAS: a web-based resource for microarray gene expression data analysis. Nucleic Acids Res 31: 3461-3467. GEPAS 12824345 7,10
2003 Hunter A, Kaufman MH, McKay A, Baldock R, Simmen MW, Bard JB An ontology of human developmental anatomy. J Anat 203: 347-355. 14620375 15
2003 Hunter WB, Dang PM, Bausher MG, Chaparro JX, McKendree W, Shatters RG Jr, McKenzie CL, Sinisterra XH Aphid biology: expressed genes from alate Toxoptera citricida, the brown citrus aphid. J Insect Sci 3: 23. Aphid ESTs 15841239 5
2003 Hvidsten TR, Laegreid A, Komorowski J Learning rule-based models of biological process from gene expression time profiles using Gene Ontology. Bioinformatics 19: 1116-1123. 12801872 7,9
2003 Isokpehi RD, Hide WA Integrative analysis of intraerythrocytic differentially expressed transcripts yields novel insights into the biology of Plasmodium falciparum. Malar J 2: 38. Plasmodium falciparum transcripts 14617379 7
2003 Jensen LJ, Gupta R, Staerfeldt HH, Brunak S Prediction of human protein function according to Gene Ontology categories. Bioinformatics 19: 635-642. 12651722 9
2003 Kanapin A|etAl Mouse proteome analysis. Genome Res 13: 1335-1344. Mouse proteome 12819131 8
2003 Khan S, Situ G, Decker K, Schmidt CJ GoFigure: Automated Gene Ontology(TM) annotation. Bioinformatics 19: 2484-2485. GoFigure 14668239 10
2003 King OD, Foulger, RE, Dwight SS, White JV, and Roth FP Predicting gene function from patterns of annotation. Genome Res 13: 896-904. 12695322 9
2003 King OD, Lee JC, Dudley AM, Janse DM, Church GM, Roth FP Predicting phenotype from patterns of annotation. Bioinformatics 19: I183-I189. 12855456 13,19
2003 Kislinger T, Rahman K, Radulovic D, Cox B, Rossant J, Emili A PRISM, a generic large scale proteomic investigation strategy for mammals. Mol Cell Proteomics 2: 96-106. Mouse proteome (lung and liver) 12644571 6,8
2003 Kohler J, Philippi S, Lange M SEMEDA: ontology based semantic integration of biological databases. Bioinformatics 19: 2420-2427. 14668226 14
2003 Krebs WG, Bourne PE Statistical and visual morph movie analysis of crystallographic mutant selection bias in protein mutation resource data. Proc IEEE Comput Soc Bioinform Conf 2: 180-189. 16452792 12,13
2003 Kumar A, Smith B The Unified Medical Language System and the Gene Ontology: Some critical reflections. KI 2003: Advances in Artificial Intelligence [A. Gunter, R. Kruse, and B. Neumann (eds.), Lecture Notes in Artificial Intelligence 2821, Springer, Berlin] http://ontology.buffalo.edu/medo/UMLS_GO.pdf|pdf 14
2003 Lagreid A, Hvidsten TR, Midelfart H, Komorowski J, Sandvik AK Predicting Gene Ontology biological process from temporal gene expression patterns. Genome Res 13: 965-979. 12695321 7,9
2003 Lambrix P, Edberg A Evaluation of ontology merging tools in bioinformatics. Pac Symp Biocomput 8: 589-600. 12603060 10,13,10,7
2003 Lambrix P, Habbouche M, Perez M Evaluation of ontology development tools for bioinformatics. Bioinformatics 19: 1564-1571. 12912838 10,13,10,7
2003 Lan N, Montelione GT, Gerstein M Ontologies for proteomics: towards a systematic definition of structure and function that scales to the genome level. Curr Opin Chem Biol 7: 44-54. 12547426 8,14
2003 Landgraf C, Panni S, Montecchi-Palazzi L, Castagnoli L, Schneider-Mregener J, Volkmer-Engert R, Cesareni G Protein interaction networks by proteome peptide scanning. PLoS Biol 1: e14. Saccharomyces proteins 14737190 10.1371/journal.pbio.0020014 8
2003 Lee RY, Sternberg PW Building a cell and anatomy ontology of caenorhabditis elegans. Comp Funct Genomics 4: 121-126. 18629098 1,15
2003 Lee Y, Quackenbush J Using the TIGR gene index databases for biological discovery. Curr Protoc Bioinformatics Chapter 1: Unit 1.6. TIGR Gene Index 18428690 1,3,11
2003 Lehane MJ, Aksoy S, Gibson W, Kerhornou A, Berriman M, Hamilton J, Soares MB, Bonaldo MF, Lehane S, Hall N Adult midgut expressed sequence tags from the tsetse fly Glossina morsitans morsitans and expression analysis of putative immune response genes. Genome Biol 4: R63. Glossina morsitans ESTs 14519198 1,5
2003 Letovsky S, Kasif S Predicting protein function from protein/protein interaction data: a probabilistic approach. Bioinformatics 19: I197-I204. 12855458 9
2003 Liu G, Loraine AE, Shigeta R, Cline M, Cheng J, Valmeekam V, Sun S, Kulp D, Siani-Rose MA NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res 31: 82-86. Affymetrix probes 12519953 3
2003 Lord PW, Stevens RD, Brass A, Goble CA Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 19: 1275-1283. Analysis of ontologies 12835272 13
2003 Lord PW, Stevens RD, Brass A, Goble CA Semantic similarity measures as tools for exploring the Gene Ontology. Pac Symp Biocomput 8: 601-612. Analysis of ontologies 12603061 13
2003 Marquet G, Burgun A, Moussouni F, Guerin E, Le Duff F, Loreal O BioMeKe: an ontology-based biomedical knowledge extraction system devoted to transcriptome analysis. Stud Health Technol Inform 95: 80-85. 14663967 13,10,7
2003 Martinez-Cruz LA, Rubio A, Martinez-Chantar ML, Labarga A, Barrio I, Podhorski A, Segura V, Sevilla Campo JL, Avila MA, Mato JM GARBAN: genomic analysis and rapid biological annotation of cDNA microarray and proteomic data. Bioinformatics 19: 2158-2160. GARBAN 14594726 10
2003 Mazzolini G, Narvaiza I, Martinez-Cruz LA, Arina A, Barajas M, Galofre JC, Qian C, Mato JM, Prieto J, Melero I Pancreatic cancer escape variants that evade immunogene therapy through loss of sensitivity to IFNgamma-induced apoptosis. Gene Ther 10: 1067-1078. Human pancreatic carcinoma cells 12808437 7,16
2003 McCarter JP|etAl Analysis and functional classification of transcripts from the nematode Meloidogyne incognita. Genome Biol 4: R26. http://genomebiology.com/render/render.asp?arx_id=2003-4-4-R26&type=&item=&pubtype=core|full Meloidogyne incognita 12702207 5
2003 McCray AT An upper-level ontology for the biomedical domain. Comp Funct Genomics 4: 80-84. 18629109 13
2003 McRedmond JP, Park SD, Reilly DF, Coppinger JA, Maguire PB, Shields DC, Fitzgerald DJ Integration of proteomics and genomics in platelets: a profile of platelet proteins and platelet-specific genes. Mol Cell Proteomics 286: L411-L419. Platelet-specific transcripts 14645502 6,8
2003 Merino EF, Fernandez-Becerra C, Madeira AM, Machado AL, Durham A, Gruber A, Hall N, Del Portillo HA Pilot survey of expressed sequence tags (ESTs) from the asexual blood stages of Plasmodium vivax in human patients. Malar J 2: 21. Plasmodium vivax ESTs 12914668 5
2003 Mi H, Vandergriff J, Campbell M, Narechania A, Majoros W, Lewis S, Thomas PD, Ashburner M Assessment of genome-wide protein function classification for Drosophila melanogaster. Genome Res 13: 2118-2128. Drosophila melanogaster 12952880 1,4,6
2003 Mita K|etAl The construction of an EST database for Bombyx mori and its application. Proc Natl Acad Sci U S A 100: 14121-14126. Silkworm ESTs 14614147 5
2003 Palmer LE, O'Shaughnessy AL, Preston RR, Santos L, Balija VS, Nascimento LU, Zutavern TL, Henthorn PS, Hannon GJ, McCombie WR A survey of canine expressed sequence tags and a display of their annotations through a flexible web-based interface. J Hered 94: 15-22. Canine ESTs 12692157 5
2003 Peng Y, Kang Q, Cheng H, Li X, Sun MH, Jiang W, Luu HH, Park JY, Haydon RC, He TC Transcriptional characterization of bone morphogenetic proteins (BMPs)-mediated osteogenic signaling. J Cell Biochem 90: 1149-1165. Human osteoblast progenitor cells 14635189 7
2003 Poustka AJ, Groth D, Hennig S, Thamm S, Cameron A, Beck A, Reinhardt R, Herwig R, Panopoulou G, Lehrach H Generation, annotation, evolutionary analysis, and database integration of 20,000 unique sea urchin EST clusters. Genome Res 13: 2736-2746. Sea urchin ESTs 14656975 5
2003 Raychaudhuri S, Altman RB A literature-based method for assessing the functional coherence of a gene group. Bioinformatics 19: 396-401. 12584126 9,12
2003 Rhee SY|etAl The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res 31: 224-228. Arabidopsis thaliana 12519987 1,4,11
2003 Sarkar IN, Cantor MN, Gelman R, Hartel F, Lussier YA Linking biomedical language information and knowledge resources in the 21st century: GO and UMLS. Pac Symp Biocomput 8: 427-450. 12603048 14
2003 Shakhnovich BE, Dokholyan NV, DeLisi C, Shakhnovich EI Functional fingerprints of folds: evidence for correlated structure-function evolution. J Mol Biol 326: 1-9. 12547186 13,18
2003 Sharov AA|etAl Transcriptome analysis of mouse stem cells and early embryos. PLoS Biol 1: e74. Mouse transcripts 14691545 10.1371/journal.pbio.0000074 7
2003 Smith B, Williams J, Schulze-Kremer S The ontology of the Gene Ontology. Proc AMIA Symp 2003: 609-613. 14728245 14
2003 Sprague J, Clements D, Conlin T, Edwards P, Frazer K, Schaper K, Segerdell E, Song P, Sprunger B, Westerfield M The Zebrafish Information Network (ZFIN): the zebrafish model organism database. Nucleic Acids Res 31: 241-243. Danio rerio 12519991 1,4,11
2003 Stark A, Brennecke J, Russell RB, Cohen SM Identification of Drosophila MicroRNA targets. PLoS Biol 1: e60 14691535 10.1371/journal.pbio.0000060 13,3
2003 Stein L|etAl The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol 1: e45. Caenorhabditis briggsae 14624247 10.1371/journal.pbio.0000045 4
2003 Stevens R, Wroe C, Bechhofer S, Lord P, Rector A, Goble C Building Ontologies in DAML + OIL. Comp Funct Genomics 4: 133-141. 18629114 13
2003 Stoeckert CJ, Parkinson H The MGED Ontology: A framework for describing functional genomics experiments. Comp Funct Genomics 4: 127-132. 18629093 15
2003 Thomas PD|etAl PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic Acids Res 31: 334-341. PANTHER (human, Drosophila) 12520017 4,11
2003 Toppo S, Cannata N, Fontana P, Romualdi C, Laveder P, Bertocco E, Lanfranchi G, Valle G TRAIT (TRAnscript Integrated Table): a knowledgebase of human skeletal muscle transcripts. Bioinformatics 19: 661-662. Human skeletal muscle transcripts 12651729 11
2003 Troyanskaya OG, Dolinski K, Owen AB, Altman RB, Botstein D A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci U S A 100: 8348-8353. 12826619 9
2003 Tulipano PK, Millar W, Cimino JJ Linking molecular imaging terminology to the Gene Ontology (GO). Pac Symp Biocomput 8: 613-623. Analysis of ontologies 12603062 13
2003 Vincent PL, Coe EH, Polacco ML Zea mays ontology--a database of international terms. Trends Plant Sci 8: 517-520. 14607095 15
2003 Williams J, Andersen W Bringing ontology to the gene ontology. Comp Funct Genomics 4: 90-93. 18629099 14
2003 Wroe CJ, Stevens R, Goble CA, Ashburner M A methodology to migrate the Gene Ontology to a description logic environment using DAML+OIL. Pac Symp Biocomput 8: 624-635. 12603063 14
2003 Xu H, He L, Zhu Y, Huang W, Fang L, Tao L, Zhu Y, Cai L, Xu H, Zhang L, Xu H, Zhou Y EST pipeline system: detailed and automated EST data processing and mining. Genomics Proteomics Bioinformatics 1: 236-242. 15629036 5,10,12
2003 Yang E, Van Nimwegen E, Zavolan M, Rajewsky N, Schroeder M, Magnasco M, Darnell JE Jr Decay rates of human mRNAs: Correlation with functional characteristics and sequence attributes. Genome Res 13: 1863-1872. Human mRNAs during decay 12902380 13
2003 Yeh I, Karp PD, Noy NF, Altman RB Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO). Bioinformatics 19: 241-248. Annotation consistency analysis 12538245 3,13
2003 Zeeberg BR|etAl GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol 4: R28. http://genomebiology.com/render/render.asp?arx_id=2003-4-4-R28&type=&item=&pubtype=core|full 12702209 10
2003 Zehetner G OntoBlast function: from sequence similarities directly to potential functional annotations by ontology terms. Nucleic Acids Res 31: 3799-3803. 12824422 9,10
2003 Zhang J, Carey V, Gentleman R An extensible application for assembling annotation for genomic data. Bioinformatics 19: 155-156. 12499308 13,10,7
2003 Zhong S, Li C, Wong WH ChipInfo: software for extracting gene annotation and gene ontology information for microarray analysis. Nucleic Acids Res 31: 3483-3486. ChipInfo 12824349 7,10
2003 Zhou Y, Zhou C, Ye L, Dong J, Xu H, Cai L, Zhang L, Wei L Database and analyses of known alternatively spliced genes in plants. Genomics 82: 584-595. Plant alternatively spliced genes 14611800 11
2003 Zhou Y|etAl Gene identification and expression analysis of 86,136 expressed sequence tags (EST) from the rice genome. Genomics Proteomics Bioinformatics 1: 26-42. Rice ESTs 15626331 5,7
2004 Aavik E, Mahapatra A, Boldrick J, Chen X, Barry C, Dutoit D, Sarwal M, Hayry P Correlation between gene expression and morphological alterations in baboon carotid after balloon dilatation injury. FASEB J 19: 130-132. Baboon cDNAs 15496494 7,16
2004 Adryan B, Schuh R Gene ontology-based clustering of gene expression data. Bioinformatics 20: 2851-2852. 15117760 7,10
2004 Ahn WS, Bae SM, Lee JM, Namkoong SE, Han SJ, Cho YL, Nam GH, Seo JS, Kim CK, Kim YW Searching for pathogenic gene functions to cervical cancer. Gynecol Oncol 93: 41-48. Human cervical cancer 15047212 7,16
2004 Ahn WS|etAl Comparison of effects of As2O3 and As4O6 on cell growth inhibition and gene expression profiles by cDNA microarray analysis in SiHa cells. Oncol Rep 12: 573-580. Human cervical cancer 15289840 7,16
2004 Aitken JS, Webber BL, Bard JB Part-of relations in anatomy ontologies: a proposal for RDFS and OWL formalisations. Pac Symp Biocomput 9: 166-177. 14992501 15
2004 Aitken S, Korf R, Webber B, Bard J COBrA: a bio-ontology editor. Bioinformatics 21: 825-826. COBrA 15513995 10
2004 Al-Shahrour F, Diaz-Uriarte R, Dopazo J FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics 20: 578-580. FatiGO 14990455 10
2004 Anderson NL|etAl The human plasma proteome: A non-redundant list developed by combination of four separate sources. Mol Cell Proteomics 3: 311-326. Human plasma proteins 14718574 6,8
2004 Aris-Brosou S Determinants of adaptive evolution at the molecular level: the extended complexity hypothesis. Mol Biol Evol 22: 200-209. 15483330 13,18
2004 Asamizu E, Nakamura Y, Sato S, Tabata S Characteristics of the Lotus japonicus gene repertoire deduced from large-scale expressed sequence tag (EST) analysis. Plant Mol Biol 54: 405-414. Lotus ESTs 15284495 5
2004 Bada M, Stevens R, Goble C, Gil Y, Ashburner M, Blake JA, Cherry JM, Harris M, Lewis S A short study on the success of the Gene Ontology J Web Semantics 1: 235-240. http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B758F-4BT0VM4-9&_coverDate=02%2F29%2F2004&_alid=318078867&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=12925&_sort=d&view=c&_acct=C000042238&_version=1&_urlVersion=0&_userid=776054&md5=cf3fa144f8ea41fc0734c526a8f1cd86|abs 1,2
2004 Bada M, Turi D, McEntire R, Stevens R Using reasoning to guide annotation with Gene Ontology terms in GOAT SIGMOD Record 33: 27-32. 3,10
2004 Baehrecke EH, Dang N, Babaria K, Shneiderman B Visualization and analysis of microarray and gene ontology data with treemaps. BMC Bioinformatics 5: 84. 15222902 7,10
2004 Balasubramanian R, LaFramboise T, Scholtens D, Gentleman R A graph theoretic approach to testing associations between disparate sources of functional genomics data. Bioinformatics 18: 3353-3362. Graph theoretical analysis 15256415 13
2004 Baldock RA|etAl EMAP and EMAGE: a framework for understanding spatially organized data. Nueroinformatics 1: 309-325. 15043218 15
2004 Bard JB, Rhee SY Ontologies in biology: design, applications and future challenges. Nat Rev Genet 5: 213-222. 14970823 14
2004 Beissbarth T, Speed T GOstat: Find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 20: 1464-1465. GOstat 14962934 10
2004 Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D Ultraconserved elements in the human genome. Science 304: 1321-1325. 15131266 13,18
2004 Ben-Shaul Y, Bergman H, Soreq H Identifying subtle interrelated changes in functional gene categories using continuous measures of gene expression. Bioinformatics 21: 1129-1137. Mouse brain transcripts 15550480 7
2004 Berardini TZ|etAl Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol 135: 745-755. Arabidopsis thaliana 15173566 1,4,11
2004 Berriman M, Harris M Annotation of parasite genomes. Methods Mol Biol 270: 17-44. Parasite genomes 15153621 1,4
2004 Blackshaw S|etAl Genomic analysis of mouse retinal development. PLoS Biol 2: e247. Mouse retinal transcripts 15226823 10.1371/journal.pbio.0020247 7
2004 Blake J Bio-ontologies-fast and furious. Nat Biotechnol 22: 773-774. 15175701 1,14
2004 Blanc G, Wolfe KH Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16: 1679-1691. Arabidopsis, duplicated genes 15208398 3
2004 Blomberg LA, Long EL, Sonstegard TS, Van Tassell CP, Dobrinsky JR, Zuelke KA Serial analysis of gene expression (SAGE) during elongation of the peri-implantation porcine trophectoderm (conceptus). Physiol Genomics 20: 188-194. Porcine trophectoderm transcripts 15536174 7
2004 Blonder J|etAl A proteomic characterization of the plasma membrane of human epidermis by high-throughput mass spectrometry. J Invest Dermatol 123: 691-699. Human membrane proteins 15373774 6,8
2004 Bodenreider O The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res 32: D267-D270. http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D267|full 14681409 14
2004 Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G GO::TermFinder - open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 20: 3710-3715. GO::TermFinder 15297299 10
2004 Breslin T, Eden P, Krogh M Comparing functional annotation analyses with Catmap. BMC Bioinformatics 5: 193. Catmap 15588298 10
2004 Burger A, Davidson D, Baldock R Formalization of mouse embryo anatomy. Bioinformatics 20: 259-267. 14734318 15
2004 Burger A, Davidson D, Yang Y, Baldock R Integrating partonomic hierarchies in anatomy ontologies. BMC Bioinformatics 5: 184. 15566564 15
2004 Cai YD, Chou KC Predicting protein localization in budding yeast. Bioinformatics 21: 944-950. 15513989 9
2004 Cai YD, Chou KC Predicting subcellular localization of proteins in a hybridization space. Bioinformatics 20: 1151-1156. 14764553 9
2004 Camon E, Magrane M, Barrell D, Lee V, Dimmer E, Maslen J, Binns D, Harte N, Lopez R, Apweiler R The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res 32: D262-D266. http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D262|full UniProt 14681408 1,6,11
2004 Cao SL, Qin L, He WZ, Zhong Y, Zhu YY, Li YX Semantic search among heterogeneous biological databases based on Gene Ontology. Acta Biochim Biophys Sin (Shanghai) 36: 365-370. Data integration using ontologies 15156279 11,13
2004 Carey VJ Ontology concepts and tools for statistical genomics. J Multivariate Anal 90: 213-228. http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK9-4C47MGH-5&_user=776054&_handle=B-WA-A-W-AW-MsSAYWA-UUA-AUEYYZACBZ-AUEZVVWBBZ-ZVBUVCADD-AW-U&_fmt=summary&_coverDate=07%2F31%2F2004&_rdoc=11&_orig=browse&_srch=%23toc%236901%232004%23999099998%23503475!&_cdi=6901&view=c&_acct=C000042238&_version=1&_urlVersion=0&_userid=776054&md5=2502d44b306979b249c3103c4854c3dc|abs 14
2004 Castresana J, Guigo R, Alba MM Clustering of genes coding for DNA binding proteins in a region of atypical evolution of the human genome. J Mol Evol 59: 72-79. Human and mouse genes 15383909 13,18
2004 Catona E, Srinivasan P, Street WN Protein annotation with GO codes. Medinfo 2004(CD): 1543. Swiss-Prot 15360372 6
2004 Chang HY, Sneddon JB, Alizadeh AA, Sood R, West RB, Montgomery K, Chi JT, van de Rijn M, Botstein D, Brown PO Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS Biol 2: E7. Human fibroblast transcripts 14737219 10.1371/journal.pbio.0020007 7,16
2004 Chen G, Hata N, Zhang MQ Transcription factor binding element detection using functional clustering of mutant expression data. Nucleic Acids Res 32: 2362-2371. Saccharomyces transcription factor mutants 15115798 7
2004 Chen J, Sun M, Kent WJ, Huang X, Xie H, Wang W, Zhou G, Shi RZ, Rowley JD Over 20% of human transcripts might form sense-antisense pairs. Nucleic Acids Res 32: 4812-4820. Human sense-antisense transcripts 15356298 3,13
2004 Chen YA, McKillen DJ, Wu S, Jenny MJ, Chapman R, Gross PS, Warr GW, Almeida JS Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information. BMC Bioinformatics 5: 191. Litopenaeus setiferus ESTs 15585062 7
2004 Cheng J, Cline M, Martin J, Finkelstein D, Awad T, Kulp D, Siani-Rose MA A knowledge-based clustering algorithm driven by Gene Ontology. J Biopharm Stat 14: 687-700. 15468759 13,10,7
2004 Cheng J|etAl NetAffx Gene Ontology Mining Tool: a visual approach for microarray data analysis. Bioinformatics 20: 1462-1463. NetAffx Gene Ontology Mining Tool 14962933 7,10
2004 Cheung KH, Hager J, Pan D, Srivastava R, Mane S, Li Y, Miller P, Williams KR KARMA: a web server application for comparing and annotating heterogeneous microarray platforms. Nucleic Acids Res 32: W441-W444. KARMA 15215426 10
2004 Choi JK, Choi JY, Kim DG, Choi DW, Kim BY, Lee KH, Yeom YI, Yoo HS, Yoo OJ, Kim S Integrative analysis of multiple gene expression profiles applied to liver cancer study. FEBS Lett 565: 93-9100. Human liver transcripts 15135059 7,16
2004 Chou KC, Cai YD Predicting enzyme family class in a hybridization space. Protein Sci 13: 2857-2863. 15498934 9
2004 Chou KC, Cai YD Prediction of protein subcellular locations by GO-FunD-PseAA predictor. Biochem Biophys Res Commun 320: 1236-1239. 15249222 9
2004 Chuang JH, Li H Functional bias and spatial organization of genes in mutational hot and cold regions in the human genome. PLoS Biol 2: e29. Human genes in mutational hot and cold spots; Genomic analysis 14966531 10.1371/journal.pbio.0020029 3,13
2004 Conde L, Vaquerizas JM, Santoyo J, Al-Shahrour F, Ruiz-Llorente S, Robledo M, Dopazo J PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level. Nucleic Acids Res 32: W242-W248. PupaSNP Finder 15215388 10
2004 Corà D, Di Cunto F, Provero P, Silengo L, Caselle M Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrepresented upstream motifs. BMC Bioinformatics 5: 57. Saccharomyces; Genomic analysis 15137914 13
2004 Crangle C, Zbyslaw A Identifying gene ontology concepts in natural-language text. Conf Proc IEEE Eng Med Biol Soc 4: 2821-2823. 17270864 10,12
2004 Cras-Meneur C, Inoue H, Zhou Y, Ohsugi M, Bernal-Mizrachi E, Pape D, Clifton SW, Permutt MA An expression profile of human pancreatic islet mRNAs by Serial Analysis of Gene Expression (SAGE). Diabetologia 47: 284-299. Human pancreatic transcripts 14722648 7
2004 D'Ascenzo MD, Collmer A, Martin GB PeerGAD: a peer-review-based and community-centric web application for viewing and annotating prokaryotic genome sequences. Nucleic Acids Res 32: 3124-3125. PeerGAD 15184545 10
2004 Dahlquist KD Using GenMAPP and MAPPFinder to view microarray data on biological pathways and identify global trends in the data. Curr Protoc Bioinformatics Chapter 7: Unit 7.5. 18428731 7,10
2004 Datson NA, Meijer L, Steenbergen PJ, Morsink MC, van der Laan S, Meijer OC, de Kloet ER Expression profiling in laser-microdissected hippocampal subregions in rat brain reveals large subregion-specific differences in expression. Eur J Neurosci 20: 2541-2554. Rat brain transcripts 15548198 7
2004 Degtyarenko K, Contrino S COMe: the ontology of bioinorganic proteins. BMC Struct Biol 4: 3. http://www.biomedcentral.com/content/pdf/1472-6807-4-3.pdf|pdf 15113423 15
2004 Dejongh M, Van Dort P, Ramsay B Linking molecular function and biological process terms in the ontology for gene expression data analysis. Conf Proc IEEE Eng Med Biol Soc 4: 2984-2986. 17270905 7,13
2004 Demir E, Babur O, Dogrusoz U, Gursoy A, Ayaz A, Gulesir G, Nisanci G, Cetin-Atalay R An ontology for collaborative construction and analysis of cellular pathways. Bioinformatics 20: 349-356. 14960461 14
2004 Deng M, Tu Z, Sun F, Chen T Mapping gene ontology to proteins based on protein-protein interaction data. Bioinformatics 20: 895-902. 14751964 9
2004 Desagher S, Severac D, Lipkin A, Bernis C, Ritchie W, Le Digarcher A, Journot L Genes regulated in neurons undergoing transcription-dependent apoptosis belong to signaling pathways rather than the apoptotic machinery. J Biol Chem 280: 5693-5702. Mouse neuronal transcripts 15542599 7
2004 Diener SE, Dunn-Coleman N, Foreman P, Houfek TD, Teunissen PJ, van Solingen P, Dankmeyer L, Mitchell TK, Ward M, Dean RA Characterization of the protein processing and secretion pathways in a comprehensive set of expressed sequence tags from Trichoderma reesei. FEMS Microbiol Lett 230: 275-282. Trichoderma reesei ESTs 14757250 5
2004 Diez-Tascon C, Keane OM, Wilson T, Zadissa A, Hyndman DL, Baird DB, McEwan JC, Crawford AM Microarray analysis of selection lines from outbred populations to identify genes involved with nematode parasite resistance in sheep. Physiol Genomics 21: 59-69. Bovine transcripts 15623564 7
2004 Ding C, He X, Meraz RF, Holbrook SR A unified representation of multiprotein complex data for modeling interaction networks. Proteins 57: 99-108. 15326596 13,17
2004 Eggert US, Kiger AA, Richter C, Perlman ZE, Perrimon N, Mitchison TJ, Field CM Parallel chemical genetic and genome-wide RNAi screens identify cytokinesis inhibitors and targets. PLoS Biol 2: e379. 15547975 10.1371/journal.pbio.0020379 13
2004 Eilbeck K, Lewis SE Sequence ontology annotation guide. Comp Funct Genomics 5: 642-647. 18629179 1,15
2004 Evsikov AV|etAl Systems biology of the 2-cell mouse embryo. Cytogenet Genome Res 105: 240-250. Mouse embryo 15237213 13
2004 Feng W, Henning P, Wang M EGOMiner: a comprehensive genomics and proteomics data analysis and biological function interpretation system. Conf Proc IEEE Eng Med Biol Soc 4: 2809-2812. 17270861 10
2004 Fortna A, Kim Y, MacLaren E, Marshall K, Hahn G, Meltesen L, Brenton M, Hink R, Burgers S, Hernandez-Boussard T, Karimpour-Fard A, Glueck D, McGavran L, Berry R, Pollack J, Sikela JM Lineage-specific gene duplication and loss in human and great ape evolution. PLoS Biol 2: e207. 15252450 10.1371/journal.pbio.0020207 18
2004 Franke L, Bakel Hv H, Diosdado B, Belzen Mv M, Wapenaar M, Wijmenga C TEAM: a tool for the integration of expression, and linkage and association maps. Eur J Hum Genet 12: 633-638. TEAM 15114375 10
2004 Fraser AG, Marcotte EM A probabilistic view of gene function. Nat Genet 36: 559-564. 15167932 9,13
2004 Friedman N Inferring cellular networks using probabilistic graphical models. Science 303: 799-805. 14764868 13,17
2004 Garavelli JS The RESID Database of Protein Modifications as a resource and annotation tool. Proteomics 4: 1527-1533. RESID 15174122 6,11
2004 Gerber AP, Herschlag D, Brown PO Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol 2: e79. Saccharomyces mRNAs; Gene family analysis 15024427 10.1371/journal.pbio.0020079 13
2004 Gkoutos GV, Green EC, Greenaway S, Blake A, Mallon AM, Hancock JM CRAVE: a database, middleware and visualisation system for phenotype ontologies. Bioinformatics 21: 1257-1262. 15550481 15
2004 Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D Building mouse phenotype ontologies. Pac Symp Biocomput 9: 178-189. 14992502 15
2004 Goeman JJ, Van De Geer SA, De Kort F, Van Houwelingen HC A global test for groups of genes: testing association with a clinical outcome. Bioinformatics 20: 93-99. 14693814 7,10,13,19,16
2004 Groth D, Lehrach H, Hennig S GOblet: a platform for Gene Ontology annotation of anonymous sequence data. Nucleic Acids Res 32: W313-W317. GOblet 15215401 10
2004 Guan H, Arany E, van Beek JP, Chamson-Reig A, Thyssen S, Hill DJ, Yang K Adipose tissue gene expression profiling reveals distinct molecular pathways that define visceral adiposity in the offspring of maternal protein restricted rats. Am J Physiol Endocrinol Metab 288: E663-E673. Rat adipose tissue transcripts 15562247 7,16
2004 Hanisch D, Sohler F, Zimmer R ToPNet--an application for interactive analysis of expression data and biological networks. Bioinformatics 20: 1470-1471. ToPNet 14962941 10
2004 Hansen C, Fu A, Meng Y, Okine E, Hawken R, Barris W, Li C, Moore SS Gene expression profiling of the bovine gastrointestinal tract. Genome 47: 639-649. Bovine gastrointestinal tract ESTs 15284868 7
2004 Harris TW|etAl WormBase: a multi-species resource for nematode biology and genomics. Nucleic Acids Res 32: D411-D417. Caenorhabditis 14681445 1,4,11
2004 Haverty PM, Frith MC, Weng Z CARRIE web service: automated transcriptional regulatory network inference and interactive analysis. Nucleic Acids Res 32: W213-W216. CARRIE web service 15215383 10
2004 Haverty PM, Hansen U, Weng Z Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification. Nucleic Acids Res 32: 179-188. 14704355 13,17
2004 Hazbun TR|etAl Assigning function to yeast proteins by integration of technologies. Mol cell 12: 1353-1365. Saccharomyces proteins 14690591 6
2004 Hematti P|etAl Distinct genomic integration of MLV and SIV vectors in primate hematopoietic stem and progenitor cells. PLoS Biol 2: e423. 15550989 10.1371/journal.pbio.0020423 13
2004 Henrich T, Ramialison M, Segerdell E, Westerfield M, Furutani-Seiki M, Wittbrodt J, Kondoh H GSD: a genetic screen database. Mech Dev 121: 959-963. 15210199 15
2004 Hermoso A, Aguilar D, Aviles FX, Querol E TrSDB: a proteome database of transcription factors. Nucleic Acids Res 32: D171-D173. http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D171|full Eukaryotic transcription factors 14681387 6,8,11
2004 Herrero J, Vaquerizas JM, Al-Shahrour F, Conde L, Mateos A, Diaz-Uriarte JS, Dopazo J New challenges in gene expression data analysis and the extended GEPAS. Nucleic Acids Res 32: W485-W491. GEPAS 15215434 10
2004 Hill DP|etAl The mouse Gene Expression Database (GXD): updates and enhancements. Nucleic Acids Res 32: D568-D571. http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D568|full Mouse 14681482 1,3,11
2004 Hillier LW|etAl Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716. 15592404 18
2004 Holmes C, Brown SD All systems GO for understanding mouse gene function. J Biol 3: 20. 15610553 13,3
2004 Hu Z, Mellor J, DeLisi C Analyzing networks with VisANT. Curr Protoc Bioinformatics Chapter 8: Unit 8.8. 18428738 10,17
2004 Hu ZZ, Mani I, Hermoso V, Liu H, Wu CH iProLINK: an integrated protein resource for literature mining. Comput Biol Chem 28: 409-416. 15556482 11,13,10,7
2004 Huang TW, Tien AC, Huang WS, Lee YC, Peng CL, Tseng HH, Kao CY, Huang CY POINT: a database for the prediction of protein-protein interactions based on the orthologous interactome. Bioinformatics 20: 3273-3276. Interacting human proteins 15217821 11,13,19
2004 Imanishi T|etAl Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol 2: e162. Human cDNAs 15103394 10.1371/journal.pbio.0020162 3
2004 International Chicken Genome Sequencing Consortium Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716. http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v432/n7018/full/nature03154_fs.html|full Chicken (Gallus gallus) genomic 15592404 4
2004 Jansen RC, Nap JP Regulating gene expression: surprises still in store. Trends Genet 20: 223-225. Saccharomyces transcripts 15109773 7
2004 Jensen P, Magdaleno S, Lehman KM, Rice DS, Lavallie ER, Collins-Racie L, McCoy JM, Curran T A neurogenomics approach to gene expression analysis in the developing brain. Brain Res Mol Brain Res 132: 116-127. Mouse embryonic brain transcripts 15582152 7
2004 Jiang H|etAl Large-scale generation and analysis of expressed sequence tags from porcine ovary. Biol Reprod 71: 1991-2002. Porcine ESTs 15306552 5
2004 John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS Human microRNA targets. PLoS Biol 2: e363. 15502875 10.1371/journal.pbio.0020363 13,3
2004 Joshi T, Chen Y, Alexandrov N, Xu D Cellular function prediction and biological pathway discovery in Arabidopsis thaliana using microarray data. Conf Proc IEEE Eng Med Biol Soc 4: 2881-2884. 17270879 7,9
2004 Joshi T, Chen Y, Becker JM, Alexandrov N, Xu D Genome-scale gene function prediction using multiple sources of high-throughput data in yeast Saccharomyces cerevisiae. OMICS 8: 322-333. 15703749 9,12
2004 Joslyn CA, Mniszewski SM, Fulmer A, Heaton G The gene ontology categorizer. Bioinformatics 20 Suppl 1: I169-I177. 15262796 10
2004 Kaab S|etAl Global gene expression in human myocardium-oligonucleotide microarray analysis of regional diversity and transcriptional regulation in heart failure. J Mol Med 82: 308-316. Human myocardial transcripts 15103417 7,16
2004 Kanamori M, Konno H, Osato N, Kawai J, Hayashizaki Y, Suzuki H A genome-wide and nonredundant mouse transcription factor database. Biochem Biophys Res Commun 322: 787-793. Mouse transcription factors 15336533 11,13,6
2004 Kang L, Chen X, Zhou Y, Liu B, Zheng W, Li R, Wang J, Yu J The analysis of large-scale gene expression correlated to the phase changes of the migratory locust. Proc Natl Acad Sci U S A 101: 17611-17615. Locust ESTs 15591108 5,7
2004 Kappler R, Hess I, Schlegel J, Hahn H Transcriptional up-regulation of Gadd45a in Patched-associated medulloblastoma. Int J Oncol 25: 113-120. Mouse medulloblastoma 15201996 7,16
2004 Karaoz U, Murali TM, Letovsky S, Zheng Y, Ding C, Cantor CR, Kasif S Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci U S A 101: 2888-2893. 14981259 9
2004 Karp PD, Paley S, Krieger CJ, Zhang P An evidence ontology for use in pathway/genome databases. Pac Symp Biocomput 9: 190-201. 14992503 14
2004 Kelso RJ, Buszczak M, Quinones AT, Castiblanco C, Mazzalupo S, Cooley L Flytrap, a database documenting a GFP protein-trap insertion screen in Drosophila melanogaster. Nucleic Acids Res 32: D418-D420. http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D418|full Drosophila transposon insertions 14681446 11,13,10,7
2004 Kestler HA, Muller A, Gress TM, Buchholz M Generalized Venn diagrams: a new method of visualizing complex genetic set relations. Bioinformatics 21: 1592-1595. 15572472 10,13,10,7
2004 Khatri P, Bhavsar P, Bawa G, Draghici S Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments. Nucleic Acids Res 32: W449-W456. Onto-Tools 15215428 10
2004 Kim JJ, Park JC BioIE: Retargetable information extraction and ontological annotation of biological interactions from the literature. J Bioinform Comput Biol 2: 551-568. BioIE 15359426 10,13,12
2004 Kim TH, Jeon YJ, Yi JM, Kim DS, Huh JW, Hur CG, Kim HS The distribution and expression of HERV families in the human genome. Mol Cells 18: 87-93. Human endogenous retroviruses; Gene family analysis 15359128 3,13
2004 Kinser S, Jia Q, Li M, Laughter A, Cornwell P, Corton J, Pestka J Gene expression profiling in spleens of deoxynivalenol-exposed mice: immediate early genes as primary targets. J Toxicol Environ Health A 67: 1423-1441. Mouse spleen genes 15371230 7,16
2004 Kloster M, Tang C, Wingreen NS Finding regulatory modules through large-scale gene-expression data analysis. Bioinformatics 21: 1172-1179. Saccharomyces transcripts 15513996 7
2004 Kluger Y|etAl Lineage specificity of gene expression patterns. Proc Natl Acad Sci U S A 101: 6508-6513. Human hematopoeitic cells 15096607 7
2004 Kobayashi MS, Takahashi Y, Nagata T, Nishida Y, Murata A, Ishikawa K, Asai S Screening for control genes in rat global cerebral ischemia using high-density oligonucleotide array. J Neurosci Res 76: 512-518. Rat transcripts in cerebral ischemia 15114623 7,16
2004 Koike A, Niwa Y, Takagi T Automatic extraction of gene/protein biological functions from biomedical text. Bioinformatics 21: 1227-1236. 15509601 12
2004 Kong SW, Bodyak N, Yue P, Liu Z, Brown J, Izumo S, Kang PM Genetic expression profiles during physiologic and pathologic cardiac hypertrophy and heart failure in rats. Physiol Genomics 21: 34-42. Rat heart transcripts 15623566 7,16
2004 Koskinen H, Pehkonen P, Vehniainen E, Krasnov A, Rexroad C, Afanasyev S, Molsa H, Oikari A Response of rainbow trout transcriptome to model chemical contaminants. Biochem Biophys Res Commun 320: 745-753. Rainbow trout transcripts 15240111 7
2004 Krasnoselsky AL, Whiteford CC, Wei JS, Bilke S, Westermann F, Chen QR, Khan J Altered expression of cell cycle genes distinguishes aggressive neuroblastoma. Oncogene 24: 1533-1541. Human neuroblastoma transcripts 15592497 7,16
2004 Krebs WG, Bourne PE Statistical and visual morph movie analysis of crystallographic mutant selection bias in protein mutation resource data. J Bioinform Comput Biol 2: 61-75. 15272433 12,13
2004 Krebs WG, Bourne PE Statistically rigorous automated protein annotation. Bioinformatics 20: 1066-1073. PDB; PMR 14764575 6
2004 Kudo Y, Boyd CA, Sargent IL, Redman CW, Lee JM, Freeman TC An analysis using DNA microarray of the time course of gene expression during syncytialization of a human placental cell line (BeWo). Placenta 25: 479-488. Human placental cells 15135230 7
2004 Kumar CG, Leduc R, Gong G, Roinishivili L, Lewin HA, Liu L ESTIMA, a tool for EST management in a multi-project environment. BMC Bioinformatics 5: 176. ESTIMA 15527510 10
2004 Larkin JE, Frank BC, Gaspard RM, Duka I, Gavras H, Quackenbush J Cardiac transcriptional response to acute and chronic angiotensin II treatments. Physiol Genomics 18: 152-166. Mouse heart transcripts 15126644 7,16
2004 Le Novere N, Donizelli M The Molecular Pages of the mesotelencephalic dopamine consortium (DopaNet). BMC Bioinformatics 5: 174. 15518589 11,13,10,7
2004 Lee SG, Hur JU, Kim YS A graph-theoretic modeling on GO space for biological interpretation of gene clusters. Bioinformatics 20: 381-388. Graph theoretical analysis 14960465 13
2004 Lefebvre C, Aude JC, Glemet E, Neri C Balancing protein similarity and gene co-expression reveals new links between genetic conservation and developmental diversity in invertebrates. Bioinformatics 21: 1550-1558. 15598835 13
2004 Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP, Bork P SMART 4.0: towards genomic data integration. Nucleic Acids Res 32: D142-D144. http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D142|full SMART domains 14681379 11,13
2004 Li R, Rimmer R, Buchwaldt L, Sharpe AG, Seguin-Swartz G, Coutu C, Hegedus DD Interaction of Sclerotinia sclerotiorum with a resistant Brassica napus cultivar: expressed sequence tag analysis identifies genes associated with fungal pathogenesis. Fungal Genet Biol 41: 735-753. Sclerotinia sclerotiorum ESTs 15219559 5,7
2004 Li S, Becich MJ, Gilbertson J Microarray data mining using gene ontology. Medinfo 2004: 778-782. 15360918 10,12
2004 Liang F|etAl ORFDB: an information resource linking scientific content to a high-quality Open Reading Frame (ORF) collection. Nucleic Acids Res 32: D595-D599. http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D595|full Human and mouse ORFs 14681490 11
2004 Lin N, Wu B, Jansen R, Gerstein M, Zhao H Information assessment on predicting protein-protein interactions. BMC Bioinformatics 5: 154. 15491499 13,19
2004 Liu J, Wang W, Yang J Gene Ontology friendly biclustering of expression profiles. Proc IEEE Comput Syst Bioinform Conf 3: 436-447. 16448036 7,13
2004 Lomax J, McCray AT Mapping the gene ontology into the unified medical language system. Comp Funct Genomics 5: 354-361. 18629164 1,13
2004 Long F, Liu H, Hahn C, Sumazin P, Zhang MQ, Zilberstein A Genome-wide prediction and analysis of function-specific transcription factor binding sites. In Silico Biol 4: 395-410. Genomic analysis 15506990 13
2004 Louis LS, Shi T, Duan ZH, Sadhukhan P, Der SD, Novick AC, Hissong J, Skacel M, Almasan A, DiDonato JA Microarray gene expression profiling and analysis in renal cell carcinoma. BMC Urol 4: 9. human renal cell carcinoma 15212686 7,16
2004 Love CG, Batley J, Lim G, Robinson AJ, Savage D, Singh D, Spangenberg GC, Edwards D New computational tools for brassica genome research. Comp Funct Genomics 5: 276-280. 18629157 3,10
2004 Lu X, Zhai C, Gopalakrishnan V, Buchanan BG Automatic annotation of protein motif function with Gene Ontology terms. BMC Bioinformatics 5: 122. 15345032 9
2004 Lu X, Zhang W, Qin ZS, Kwast KE, Liu JS Statistical resynchronization and Bayesian detection of periodically expressed genes. Nucleic Acids Res 32: 447-455. Saccharomyces transcripts 14739237 7
2004 Luo X, Ding L, Xu J, Chegini N Gene expression profiling of leiomyoma and myometrial smooth muscle cells in response to TGF-beta. Endocrinology 146: 1097-1118. Human smooth muscle transcripts 15604209 7,16
2004 Malek RL, Sajadi H, Abraham J, Grundy MA, Gerhard GS The effects of temperature reduction on gene expression and oxidative stress in skeletal muscle from adult zebrafish. Comp Biochem Physiol C Toxicol Pharmacol 138: 363-373. Zebrafish skeletal muscle transcripts 15533794 7
2004 Malmstrom J|etAl Proteome annotations and identifications of the human pulmonary fibroblast. J Proteome Res 3: 525-537. Human pulmonary fibroblasts 15253434 6,7,8
2004 Martin D, Brun C, Remy E, Mouren P, Thieffry D, Jacq B GOToolBox: functional analysis of gene datasets based on Gene Ontology. Genome Biol 5: R101. GOToolBox 15575967 10
2004 Martin DM, Berriman M, Barton GJ GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics 5: 178. GOtcha 15550167 9,10
2004 Martucci D, Masseroli M, Pinciroli F Gene ontology application to genomic functional annotation, statistical analysis and knowledge mining. Stud Health Technol Inform 102: 108-131. 15853267 10,12,13,4
2004 Masseroli M, Martucci D, Pinciroli F Towards biological knowledge mining by statistical analysis of gene ontology annotations. Medinfo 2004(CD): 1745. 15360573 12
2004 McCarroll SA, Murphy CT, Zou S, Pletcher SD, Chin CS, Jan YN, Kenyon C, Bargmann CI, Li H Comparing genomic expression patterns across species identifies shared transcriptional profile in aging. Nat Genet 36: 197-204. Transcripts during aging (several species) 14730301 7
2004 Midford PE Ontologies for behavior. Bioinformatics 20: 3700-3701. 15284105 15
2004 Mitreva M, Elling AA, Dante M, Kloek AP, Kalyanaraman A, Aluru S, Clifton SW, Bird DM, Baum TJ, McCarter JP A survey of SL1-spliced transcripts from the root-lesion nematode Pratylenchus penetrans. Mol Genet Genomics 272: 138-148. Pratylenchus penetrans transcripts 15338281 5
2004 Moggs JG|etAl Phenotypic anchoring of gene expression changes during estrogen-induced uterine growth. Environ Health Perspect 112: 1589-1606. Rodent uterine transcripts 15598610 7,16
2004 Monks SA, Leonardson A, Zhu H, Cundiff P, Pietrusiak P, Edwards S, Phillips JW, Sachs A, Schadt EE Genetic inheritance of gene expression in human cell lines. Am J Hum Genet 75: 1094-1105. Human cell lines 15514893 7
2004 Muller HM, Kenny EE, Sternberg PW Textpresso: An ontology-based information retrieval and extraction system for biological literature. PLoS Biol 2: e309. Textpresso 15383839 10.1371/journal.pbio.0020309 1,10,12
2004 Mungall CJ Obol: integrating language and meaning in bio-ontologies. Comp Funct Genomics 5: 509-520. 18629143 1,13,14
2004 Munkvold JD|etAl Group 3 chromosome bin maps of wheat and their relationship to rice chromosome 1. Genetics 168: 639-650. Wheat ESTs 15514041 5
2004 Mutch DM, Simmering R, Donnicola D, Fotopoulos G, Holzwarth JA, Williamson G, Corthesy-Theulaz I Impact of commensal microbiota on murine gastrointestinal tract gene ontologies. Physiol Genomics 19: 22-31. Mouse gastrointestinal tract cells 15226484 7
2004 Nene V, Lee D, Kang'a S, Skilton R, Shah T, de Villiers E, Mwaura S, Taylor D, Quackenbush J, Bishop R Genes transcribed in the salivary glands of female Rhipicephalus appendiculatus ticks infected with Theileria parva. Insect Biochem Mol Biol 34: 1117-1128. Rhipicephalus appendiculatus ESTs 15475305 5
2004 Nishimura M, Yokoi N, Miki T, Horikawa Y, Yoshioka H, Takeda J, Ohara O, Seino S Construction of a multi-functional cDNA library specific for mouse pancreatic islets and its application to microarray. DNA Res 11: 315-323. Mouse pancreatic islet cDNAs 15747579 3,7
2004 Ochs MF, Moloshok TD, Bidaut G, Toby G Bayesian decomposition: analyzing microarray data within a biological context. Ann N Y Acad Sci 1020: 212-216. 15208194 7
2004 Odom DT|etAl Control of pancreas and liver gene expression by HNF transcription factors. Science 303: 1378-1381. Human liver and pancreas transcripts 14988562 7
2004 Ogren PV, Cohen KB, Acquaah-Mensah GK, Eberlein J, Hunter L The compositional structure of Gene Ontology terms. Pac Symp Biocomput 9: 214-215. 14992505 14
2004 Ohsugi M, Cras-Meneur C, Zhou Y, Warren W, Bernal-Mizrachi E, Permutt MA Glucose and insulin treatment of insulinoma cells results in transcriptional regulation of a common set of genes. Diabetes 53: 1496-1508. Mouse insulinoma cells 15161754 7
2004 Oliver MJ, Dowd SE, Zaragoza J, Mauget SA, Payton PR The rehydration transcriptome of the desiccation-tolerant bryophyte Tortula ruralis: Transcript classification and analysis. BMC Genomics 5: 89. Tortula ruralis transcripts 15546486 7
2004 Osier MV, Zhao H, Cheung KH Handling multiple testing while interpreting microarrays with the Gene Ontology Database. BMC Bioinformatics 5: 124. 15350198 7,10,13
2004 Ovcharenko I, Loots GG, Nobrega MA, Hardison RC, Miller W, Stubbs L Evolution and functional classification of vertebrate gene deserts. Genome Res 15: 137-145. Verebrate genes 15590943 13,18
2004 Packer BR|etAl SNP500Cancer: a public resource for sequence validation and assay development for genetic variation in candidate genes. Nucleic Acids Res 32: D528-D532. http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D528|full Human SNPs 14681474 11,13,16
2004 Pan H|etAl Dragon TF Association Miner: a system for exploring transcription factor associations through text-mining. Nucleic Acids Res 32: W230-W234. Dragon TF Association Miner 15215386 10,12
2004 Park YR, Park CH, Kim JH GOChase: correcting errors from gene ontology-based annotations for gene products. Bioinformatics 21: 829-831. GOChase; Annotation consistency analysis 15513987 3,10,13
2004 Paschall JE, Oleksiak MF, Vanwye JD, Roach JL, Whitehead A, Wykoff GJ, Kolell KJ, Crawford DL FunnyBase: a systems level functional annotation of Fundulus ESTs for the analysis of gene expression. BMC Genomics 5: 96. Fundulus heteroclitus 15610557 5,11
2004 Pasquier C, Girardot F, Jevardat de Fombelle K, Christen R THEA: ontology-driven analysis of microarray data. Bioinformatics 20: 2636-2643. 15130932 7,13
2004 Pavlidis P, Qin J, Arango V, Mann JJ, Sibille E Using the gene ontology for microarray data mining: a comparison of methods and application to age effects in human prefrontal cortex. Neurochem Res 29: 1213-1222. 15176478 7,12,16
2004 Pazos F, Sternberg MJ Automated prediction of protein function and detection of functional sites from structure. Proc Natl Acad Sci U S A 101: 14754-14759. 15456910 9
2004 Pedra JH, McIntyre LM, Scharf ME, Pittendrigh BR Genome-wide transcription profile of field- and laboratory-selected dichlorodiphenyltrichloroethane (DDT)-resistant Drosophila. Proc Natl Acad Sci U S A 101: 7034-7039. Drosophila transcripts 15118106 7
2004 Pellegrino M, Provero P, Silengo L, Di Cunto F CLOE: Identification of putative functional relationships among genes by comparison of expression profiles between two species. BMC Bioinformatics 5: 179. 15550177 13
2004 Perez A, Davis PB Gene profile changes after Pseudomonas aeruginosa exposure in immortalized airway epithelial cells. J Struct Funct Genomics 5: 179-194. Human airway epithelial cells 15263834 7,16
2004 Perez AJ, Perez-Iratxeta C, Bork P, Thode G, Andrade MA Gene annotation from scientific literature using mappings between keyword systems. Bioinformatics 20: 2084-2091. 15059832 9,12
2004 Philip-Couderc|etAl Uncomplicated human obesity is associated with a specific cardiac transcriptome: involvement of the Wnt pathway. FASEB J 18: 1539-1540. Human heart transcripts 15289443 7,16
2004 Pinto FR, Cowart LA, Hannun YA, Rohrer B, Almeida JS Local correlation of expression profiles with gene annotations - proof of concept for a general conciliatory method. Bioinformatics 21: 1037-1045. Yeast and mouse transcripts 15509607 7,13
2004 Popesco MC, Frostholm A, Rejniak K, Rotter A Digital transcriptome analysis in the aging cerebellum. Ann N Y Acad Sci 1019: 58-63. Mouse cerebellar transcripts 15246995 7
2004 Prlic A, Domingues FS, Lackner P, Sippl MJ WILMA-automated annotation of protein sequences. Bioinformatics 20: 127-128. 14693821 9
2004 Puga A, Sartor MA, Huang MY, Kerzee JK, Wei YD, Tomlinson CR, Baxter CS, Medvedovic M Gene expression profiles of mouse aorta and cultured vascular smooth muscle cells differ widely, yet show common responses to dioxin exposure. Cardiovasc Toxicol 4: 385-404. Mouse vascular cell transcripts 15531781 7,16
2004 Racunas SA, Shah NH, Albert I, Fedoroff NV HyBrow: a prototype system for computer-aided hypothesis evaluation. Bioinformatics 20 Suppl 1: I257-I264. 15262807 13,19
2004 Reneker J, Shyu CR, Zeng P, Polacco JC, Gassmann W ACMES: fast multiple-genome searches for short repeat sequences with concurrent cross-species information retrieval. Nucleic Acids Res 32: W649-W653. ACMES 15215469 10
2004 Reverter A, Wang YH, Byrne KA, Tan SH, Harper GS, Lehnert SA Joint analysis of multiple cDNA microarray studies via multivariate mixed models applied to genetic improvement of beef cattle. J Anim Sci 82: 3430-3439. Bovine transcripts 15537761 7
2004 Rhodes DR, Chinnaiyan AM Bioinformatics strategies for translating genome-wide expression analyses into clinically useful cancer markers. Ann N Y Acad Sci 1020: 32-40. 15208181 13,16
2004 Ringner M, Veerla S, Andersson S, Staaf J, Hakkinen J ACID: a database for microarray clone information. Bioinformatics 20: 2305-2306. Microarray clones 14962935 11
2004 Robinson PN, Bohme U, Lopez R, Mundlos S, Nurnberg P Gene-ontology analysis reveals association of tissue-specific 5' CpG-island genes with development and embryogenesis. Hum Mol Genet 13: 1969-1978. Human genes with CpG islands; Genomic analysis 15254011 13
2004 Robinson PN, Wollstein A, Bohme U, Beattie B Ontologizing gene-expression microarray data: characterizing clusters with gene ontology. Bioinformatics 20: 979-981. 14764576 7,10
2004 Rohrer B, Pinto FR, Hulse KE, Lohr HR, Zhang L, Almeida JS Multi-destructive pathways triggered in photoreceptor cell death of the RD mouse as determined through gene expression profiling. J Biol Chem 279: 41903-41910. Mouse retinal cells 15218024 7
2004 Rojas I, Ratsch E, Saric J, Wittig U Notes on the use of ontologies in the biochemical domain. In Silico Biol 4: 89-96. 15089756 14
2004 Ruse CI, Tan FL, Kinter M, Bond M Intregrated analysis of the human cardiac transcriptome, proteome and phosphoproteome. Proteomics 4: 1505-1516. Human transcripts and proteins 15188417 6,8,11
2004 Sadlier DM, Connolly SB, Kieran NE, Roxburgh S, Brazil DP, Kairaitis L, Wang Y, Harris DC, Doran P, Brady HR Sequential extracellular matrix-focused and baited-global cluster analysis of serial transcriptomic profiles identifies candidate modulators of renal tubulointerstitial fibrosis in murine adriamycin induced nephropathy. J Biol Chem 279: 29670-29680. Mouse renal tubule cells 15033991 7,16
2004 Schlosser I, Holzel M, Hoffmann R, Burtscher H, Kohlhuber F, Schuhmacher M, Chapman R, Weidle UH, Eick D Dissection of transcriptional programmes in response to serum and c-Myc in a human B-cell line. Oncogene 24: 520-524. Human B-cells 15516975 7
2004 Schoenroth LJ, Hart DA, Pollard KM, Fritzler MJ The effect of the phytoestrogen coumestrol on the NZB/W F1 murine model of systemic lupus. J Autoimmun 23: 323-332. Mouse kidney transcripts 15571926 7,16
2004 Schofield PN|etAl Pathbase: a database of mutant mouse pathology. Nucleic Acids Res 32: D512-D515. http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D512|full 14681470 15
2004 Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, Huhn G, Schomburg D BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res 32: D431-D433. BRENDA 14681450 11
2004 Schonbach C, Nagashima T, Konagaya A Textmining in support of knowledge discovery for vaccine development. Methods 4: 488-495. 15542375 12
2004 Scott LK, Vachharajani V, Mynatt RL, Minagar A, Conrad SA Brain RNA expression in obese vs lean mice after LPS-induced systemic inflammation. Front Biosci 9: 2686-2696. Mouse brain transcripts 15353306 7,16
2004 Shah NH, Fedoroff NV CLENCH: a program for calculating CLuster ENriCHment using the Gene Ontology. Bioinformatics 20: 1196-1197. CLENCH 14764555 10
2004 Shi T, Liou LS, Sadhukhan P, Duan ZH, Novick AC, Hissong JG, Almasan A, DiDonato JA Effects of resveratrol on gene expression in renal cell carcinoma. Cancer Biol Ther 3: 882-888. Human renal carcinoma cells 15280659 7,16
2004 Shim MH, Hoover A, Blake N, Drachman JG, Reems JA Gene expression profile of primary human CD34(+)CD38(lo) cells differentiating along the megakaryocyte lineage. Exp Hematol 32: 638-648. Human hematopoietic cells 15246160 7
2004 Shoop E, Casaes P, Onsongo G, Lesnett L, Petursdottir EO, Donkor EK, Tkach D, Cosimini M Data exploration tools for the gene ontology database. Bioinformatics 18: 3442-3454. 15271779 10
2004 Smid M, Dorssers LC GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms. Bioinformatics 20: 2851-2852. GO-Mapper 15130934 10
2004 Speer N, Spieth C, Zell A A memetic clustering algorithm for the functional partition of genes based on the Gene Ontology. Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2004) 252-259. 13
2004 Speer N, Spieth C, Zell A A memetic co-clustering algorithm for gene expression profiles and biological annotation. Proceedings of the 2004 Congress on Evolutionary Computation (CEC 2004) 2: 1631-1638. 12
2004 Spin JM, Nallamshetty S, Tabibiazar R, Ashley EA, King JY, Chen M, Tsao PS, Quertermous T Transcriptional profiling of in vitro smooth muscle cell differentiation identifies specific patterns of gene and pathway activation. Physiol Genomics 19: 292-302. Mouse smooth muscle transcripts 15340120 7
2004 Stolc V|etAl A gene expression map for the euchromatic genome of Drosophila melanogaster Science 306:655-660. 15499012 7
2004 Sulman EP, White PS, Brodeur GM Genomic annotation of the meningioma tumor suppressor locus on chromosome 1p34. Oncogene 23: 1014-1020. Human meningioma suppressor locus 14749765 13,3
2004 Szafron D|etAl Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations. Nucleic Acids Res 32: W365-W371. Proteome Analyst 15215412 8,9,10
2004 Tang X, Shen L, Dickerson JA BarleyExpress: a web-based submission tool for enriched microarray database annotations. Bioinformatics 21: 399-401. 15347571 15
2004 The Gene Ontology Consortium The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32: D258-D261. http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D258|full 14681407 1,2
2004 Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY, Stitt M MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 37: 914-939. 14996223 9,10
2004 Tong AH|etAl Global mapping of the yeast genetic interaction network. Science 303: 808-813. 14764870 12
2004 Tu K, Yu H, Guo Z, Li X Learnability-based further prediction of gene functions in Gene Ontology. Genomics 84: 922-928. 15533709 9
2004 Vemula M, Berthiaume F, Jayaraman A, Yarmush ML Expression profiling analysis of the metabolic and inflammatory changes following burn-injury in rats. Physiol Genomics 18: 87-98. Rat transcripts following burn injury 15114001 7,16
2004 Venezia TA, Merchant AA, Ramos CA, Whitehouse NL, Young AS, Shaw CA, Goodell MA Molecular signatures of proliferation and quiescence in hematopoietic stem cells. PLoS Biol 2: e301. Mouse hematopoeitic stem cell transcripts 15459755 10.1371/journal.pbio.0020301 7
2004 Viguerie N|etAl In vivo epinephrine-mediated regulation of gene expression in human skeletal muscle. J Clin Endocrinol Metab 89: 2000-2014. Human skeletal muscle transcripts 15126512 7,16
2004 Vinayagam A, Koenig R, Moormann J, Schubert F, Eils R, Glatting KH, Suhai S Applying Support Vector Machines for Gene Ontology based gene function prediction. BMC Bioinformatics 5: 116. 15333146 9
2004 Volinia S, Evangelisti R, Francioso F, Arcelli D, Carella M, Gasparini P GOAL: automated Gene Ontology analysis of expression profiles. Nucleic Acids Res 32: W492-W499. GOAL 15215435 7,9,10
2004 Wagner RA, Tabibiazar R, Powers J, Bernstein D, Quertermous T Genome-wide expression profiling of a cardiac pressure overload model identifies major metabolic and signaling pathway responses. J Mol Cell Cardiol 37: 1159-1170. Mouse heart transcripts 15572046 7,16
2004 Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 337: 635-645. Saccharomyces proteins containing disordered regions 15019783 6,13,18
2004 Weitzman JB Co-regulation of mouse genes predicts function. J Biol 3: 19. 15588313 9,13
2004 Wolstencroft KJ, Stevens R, Tabernero L, Brass A PhosphaBase: An ontology-driven database resource for protein phosphatases. Proteins 58: 290-294. Gene family analysis 15558746 11,13
2004 Wren JD Extending the mutual information measure to rank inferred literature relationships. BMC Bioinformatics 5: 145. 15471547 13,12
2004 Wren JD, Garner HR Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network. Bioinformatics 20: 191-198. 14734310 9,12
2004 Wu CH, Huang H, Nikolskaya A, Hu Z, Barker WC The iProClass integrated database for protein functional analysis. Comput Biol Chem 28: 87-96. iProClass protein database 15022647 6,11
2004 Yan W|etAl System-based proteomic analysis of the interferon response in human liver cells. Genome Biol 5: R54. Human liver proteins 15287976 7,8,16
2004 Yao G, Craven M, Drinkwater N, Bradfield CA Interaction networks in yeast define and enumerate the signaling steps of the vertebrate aryl hydrocarbon receptor. PLoS Biol 2: E65. 15024417 10.1371/journal.pbio.0020065 17
2004 Young A, Whitehouse N, Cho J, Shaw C OntologyTraverser: an R package for GO analysis. Bioinformatics 21: 275-276. OntologyTraverser 15333457 10
2004 Yu J, Whitelaw CA, Nierman WC, Bhatnagar D, Cleveland TE Aspergillus flavus expressed sequence tags for identification of genes with putative roles in aflatoxin contamination of crops. FEMS Microbiol Lett 237: 333-340. Aspergillus flavus ESTs 15321681 5
2004 Zhang B, Jin W, Zeng Y, Su Z, Hu S, Yu J EST-based analysis of gene expression in the porcine brain. Genomics Proteomics Bioinformatics 2: 237-244. Porcine ESTs 15901252 5,7
2004 Zhang B, Schmoyer D, Kirov S, Snoddy J GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. BMC Bioinformatics 5: 16. GOTree Machine 14975175 10
2004 Zhang W|etAl The functional landscape of mouse gene expression. J Biol 3: 21. Mouse transcripts 15588312 7
2004 Zhong S, Tian L, Li C, Storch KF, Wong WH Comparative analysis of gene sets in the Gene Ontology space under the multiple hypothesis testing framework. Proc IEEE Comput Syst Bioinform Conf 3: 425-435. 16448035 7,10,13
2004 Zhou M, Cui Y GeneInfoViz: Constructing and visualizing gene relation networks. In Silico Biol 4: 323-333. GeneInfoViz 15724283 10
2004 Zhou Y, Young JA, Santrosyan A, Chen K, Yan FS, Winzeler EA In silico gene function prediction using ontology-based pattern identification. Bioinformatics 21: 1237-1245. 15531612 9,12
2005 Abba MC, Hu Y, Sun H, Drake JA, Gaddis S, Baggerly K, Sahin A, Aldaz CM Gene expression signature of estrogen receptor alpha status in breast cancer. BMC Genomics 6: 37. Human breast tumor transcripts 15762987 7,16
2005 Abbas AR|etAl Immune response in silico (IRIS): immune-specific genes identified from a compendium of microarray expression data. Genes Immun 6: 319-331. Human immune cell transcripts 15789058 7,16
2005 Agbemafle BM, Oesterreicher TJ, Shaw CA, Henning SJ Immediate early genes of glucocorticoid action on the developing intestine. Am J Physiol Gastrointest Liver Physiol 288: G897-G906. Mouse intestinal transcripts 15826934 7
2005 Ahn WS, Seo MJ, Bae SM, Lee JM, Namkoong SE, Kim CK, Kim YW Cellular process classification of human papillomavirus-16-positive SiHa cervical carcinoma cell using Gene Ontology. Int J Gynecol Cancer 15: 94-106. Human cell line transcripts 15670303 7,16
2005 Aidinis V|etAl Cytoskeletal rearrangements in synovial fibroblasts as a novel pathophysiological determinant of modeled rheumatoid arthritis. PLoS Genet 1: e48 Mouse transcriptsn; rheumatoid arthritis 16254600 10.1371/journal.pgen.0010048 7,16
2005 Aitken S Formalising concepts of species, sex and developmental stage in anatomical ontologies. Bioinformatics 21: 2773-2779. 15797906 15
2005 Al-Shahrour F, Minguez P, Vaquerizas JM, Conde L, Dopazo J BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments Nucleic Acids Res 33: W460-W464. 15980512 10
2005 Alm EJ, Huang KH, Price MN, Koche RP, Keller K, Dubchak IL, Arkin AP The MicrobesOnline Web site for comparative genomics Genome Res 15: 1015-1022. Microbial genomic 4,10,11,13
2005 Anderle P, Sengstag T, Mutch DM, Rumbo M, Praz V, Mansourian R, Delorenzi M, Williamson G, Roberts MA Changes in the transcriptional profile of transporters in the intestine along the anterior-posterior and crypt-villus axes. BMC Genomics 6: 69. Mouse intestinal transcripts 15882471 7
2005 Armand F, Bucher P, Jongeneel CV, Farmer EE Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge. Bioinformatics 21: 2906-2908. 15817689 10
2005 Arnaud MB, Costanzo MC, Skrzypek MS, Binkley G, Lane C, Miyasato SR, Sherlock G The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information. Nucleic Acids Res 33: D358-D363. Candida albicans 15608216 1,4,11
2005 Baird K, Davis S, Antonescu CR, Harper UL, Walker RL, Chen Y, Glatfelter AA, Duray PH, Meltzer PS Gene expression profiling of human sarcomas: insights into sarcoma biology. Cancer Res 65: 9226-9235. Human sarcoma transcripts 16230383 7,16
2005 Baldwin NE, Chesler EJ, Kirov S, Langston MA, Snoddy JR, Williams RW, Zhang B Computational, integrative, and comparative methods for the elucidation of genetic coexpression networks. J Biomed Biotechnol 2005: 172-180. Mouse transcripts 16046823 7,13,17
2005 Ballester B|etAl Gene expression profiling identifies molecular subgroups among nodal peripheral T-cell lymphomas. Oncogene 25: 1560-1570. Human lymphoma transcripts 16288225 7,16
2005 Bammler T|etAl Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods 2: 351-356. Mouse transcripts 15846362 7,13
2005 Bard J, Rhee SY, Ashburner M An ontology for cell types. Genome Biol 6: R21. 15693950 15
2005 Bard JB Anatomics: the intersection of anatomy and bioinformatics. J Anat 206: 1-16. 15679867 15
2005 Barry WT, Nobel AB, Wright FA Significance analysis of functional categories in gene expression studies: a structured permutation approach. Bioinformatics 21: 1943-1949. 15647293 7,10,13
2005 Barth AS|etAl Functional profiling of human atrial and ventricular gene expression. Pflugers Arch 450: 201-208. Human heart transcripts 15877233 7
2005 Barth AS|etAl Reprogramming of the human atrial transcriptome in permanent atrial fibrillation. Expression of a ventricular-like genomic signature. Circ Res 96: 1022-1029. Human atrial transcripts 15817885 7,16
2005 Basu S, Bremer E, Zhou C, Bogenhagen DF MiGenes: a searchable interspecies database of mitochondrial proteins curated using Gene Ontology annotation. Bioinformatics 22: 485-492. Mitochondrial proteins 16368773 6,11
2005 Baudot A, Martin D, Mouren P, Chevenet F, Guenoche A, Jacq B, Brun C PRODISTIN web site: a tool for the functional classification of proteins from interaction networks. Bioinformatics 22: 248-250. 16269417 8,9,10
2005 Bauersachs S|etAl Gene expression profiling of bovine endometrium during the oestrous cycle: detection of molecular pathways involved in functional changes J Mol Endocrinol 34: 889-908. Bovine endometrial transcripts 15956356 7
2005 Bechhofer SK, Stevens RD, Lord PW Ontology driven dynamic linking of biology resources. Pac Symp Biocomput 10: 79-90. Data integration using ontologies 15759616 13
2005 Beckett P, Bancroft I, Trick M Computational tools for Brassica-Arabidopsis comparative genomics. Comp Funct Genomics 6: 147-152. http://www3.interscience.wiley.com/cgi-bin/abstract/110473755/ABSTRACT|abs Brassica genomic survey sequence 4
2005 Behbod F, Xian W, Shaw CA, Hilsenbeck SG, Tsimelzon A, Rosen JM Transcriptional profiling of mammary gland side population cells. Stem Cells 24: 1065-1074. Mammary gland transcripts 16282442 7
2005 Beltrao P, Serrano L Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions. PLoS Comput Biol 1: e26. 16110343 10.1371/journal.pcbi.0010026 18,19
2005 Ben-Hur A, Noble WS Kernel methods for predicting protein-protein interactions Bioinformatics 21 Suppl 1: i38-i46. 15961482 13,19
2005 Best CJ|etAl Molecular alterations in primary prostate cancer after androgen ablation therapy. Clin Cancer Res 11: 6823-6834. Human prostate transcripts 16203770 7,16
2005 Bjorklund SK, Ekman D, Light S, Frey-Skott J, Elofsson A Domain rearrangements in protein evolution. J Mol Biol 353: 911-923. 16198373 13,18
2005 Blaschke C, Leon EA, Krallinger M, Valencia A Evaluation of BioCreAtIvE assessment of task 2 BMC Bioinformatics 6 Suppl 1: S16. 15960828 9,12
2005 Blaschke C, Yeh A, Camon E, Colosimo M, Apweiler R, Hirschman L, Valencia A Do you do text? Bioinformatics 21: 4199-4200. 16195360 12
2005 Bluthgen N, Brand K, Cajavec B, Swat M, Herzel H, Beule D Biological profiling of gene groups utilizing gene ontology. Genome Inform Ser Workshop Genome Inform 16: 106-115. 16362912 7,10
2005 Bluthgen N, Kielbasa SM, Herzel H Inferring combinatorial regulation of transcription in silico. Nucleic Acids Res 33: 272-279. 15647509 13,19
2005 Bodenreider O, Aubry M, Burgun A Non-lexical approaches to identifying associative relations in the gene ontology. Pac Symp Biocomput 10: 91-102. Analysis of ontologies 15759617 13
2005 Bolshakova N, Azuaje F, Cunningham P A knowledge-driven approach to cluster validity assessment. Bioinformatics 21: 2546-2547. 15713738 10,13,19
2005 Boorsma A, Foat BC, Vis D, Klis F, Bussemaker HJ T-profiler: scoring the activity of predefined groups of genes using gene expression data Nucleic Acids Res 33: W33: W592-W595. 15980543 7,10
2005 Boyle J Gene Expression Omnibus integration and clustering tools in SeqExpress. Bioinformatics 21: 2550-2551. SeqExpress 15746290 7,10,11
2005 Braun BR|etAl A human-curated annotation of the Candida albicans genome. PLoS Genet 1: 36-57. Candida albicans genome 16103911 10.1371/journal.pgen.0010001 4,11
2005 Brors B Microarray annotation and biological information on function. Methods Inf Med 44: 468-472. 16113775 7
2005 Brown KR, Jurisica I Online Predicted Human Interaction Database. Bioinformatics 21: 2076-2082. 15657099 11,13,19
2005 Burgun A Desiderata for domain reference ontologies in biomedicine. J Biomed Inform 39: 307-313. 16266830 14
2005 Busold CH, Winter S, Hauser N, Bauer A, Dippon J, Hoheisel JD, Fellenberg K Integration of GO annotations in Correspondence Analysis: facilitating the interpretation of microarray data. Bioinformatics 21: 2424-2429. 15746280 7,10
2005 Cai H, Kauffman S, Naider F, Becker JM Genome-wide screen reveals a wide regulatory network for di/tri-peptide utilization in Saccharomyces cerevisiae. Genetics 172: 1459-1476. Saccharomyces deletion analysis 16361226 13
2005 Camon EB, Barrell DG, Dimmer EC, Lee V, Magrane M, Maslen J, Binns D, Apweiler R An evaluation of GO annotation retrieval for BioCreAtIvE and GOA BMC Bioinformatics 6 Suppl 1: S17. Human proteins 15960829 3,9,12
2005 Cannata N, Merelli E, Altman RB Time to organize the bioinformatics resourceome. PLoS Comput Biol 1: e76. 16738704 10.1371/journal.pcbi.0010076 2
2005 Cantor MN, Sarkar IN, Bodenreider O, Lussier YA Genestrace: phenomic knowledge discovery via structured terminology. Pac Symp Biocomput 10: 103-114. 15759618 13,19
2005 Carinci F|etAl Potential markers of tongue tumor progression selected by cDNA microarray. Int J Immunopathol Pharmacol 18: 513-524. Human transcripts in tongue tumors 16164832 7,16
2005 Chalmel F, Lardenois A, Thompson JD, Muller J, Sahel JA, Leveillard T, Poch O GOAnno: GO annotation based on multiple alignment. Bioinformatics 21: 2095-2096. 15647299 9
2005 Chan CS, Elemento O, Tavazoie S Revealing posttranscriptional regulatory elements through network-level conservation. PLoS Comput Biol 1: e69. Drosophila, Caenorhabditis mRNA 16355253 10.1371/journal.pcbi.0010069 7,13,17,18
2005 Chen Y, Xu D Genome-scale protein function prediction in yeast Saccharomyces cerevisiae through integrating multiple sources of high-throughput data. Pac Symp Biocomput 10: 471-482. 15759652 9
2005 Chen Y, Zhang Y, Yin Y, Gao G, Li S, Jiang Y, Gu X, Luo J SPD--a web-based secreted protein database. Nucleic Acids Res 33: D169-D173. Secreted proteins 15608170 6,11
2005 Chen Z, Liu L RealSpot: software validating results from DNA microarray data analysis with spot images. Physiol Genomics 21: 284-291. RealSpot 15687483 10
2005 Chimpanzee Sequencing and Analysis Consortium Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87. Chimpanzee genomic 16136131 4
2005 Chin CS, Chuang JH, Li H Genome-wide regulatory complexity in yeast promoters: Separation of functionally conserved and neutral sequence. Genome Res 15: 205-213. Genomic analysis 15653830 13
2005 Cho YL|etAl Array comparative genomic hybridization analysis of uterine leiomyosarcoma. Gynecol Oncol 99: 545-551. 16125217 12
2005 Chou KC, Cai YD Using GO-PseAA predictor to identify membrane proteins and their types. Biochem Biophys Res Commun 327: 845-847. 15649422 9
2005 Chung HJ, Park CH, Han MR, Lee S, Ohn JH, Kim J, Kim J, Kim JH ArrayXPath II: mapping and visualizing microarray gene-expression data with biomedical ontologies and integrated biological pathway resources using Scalable Vector Graphics Nucleic Acids Res 33: W621-W626. 15980549 7,10
2005 Chute JP, Muramoto GG, Dressman HK, Wolfe G, Chao NJ, Lin S Molecular profile and partial functional analysis of novel endothelial cell derived growth factors that regulate hematopoiesis. Stem Cells 24: 1315-1327 Human endothelial cell transcripts 16373696 7
2005 Clark JI, Brooksbank C, Lomax J It's all GO for plant scientists. Plant Physiol 138: 1268-1279. http://www.plantphysiol.org/cgi/content/full/138/3/1268?ijkey=93fZcsdipUr6E&keytype=ref&siteid=plant|pdf 16010001 1,2
2005 Clemente JC, Satou K, Valiente G Reconstruction of phylogenetic relationships from metabolic pathways based on the enzyme hierarchy and the gene ontology. Genome Inform 16: 45-55. 16901088 17,18
2005 Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676. 16081474 10
2005 Cora D, Herrmann C, Dieterich C, Di Cunto F, Provero P, Caselle M Ab initio identification of putative human transcription factor binding sites by comparative genomics. BMC Bioinformatics 6: 110. 15865625 13,18
2005 Costello CM|etAl Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays. PLoS Med 2: e199. Human colon transcripts; inflammatory bowel disease 16107186 10.1371/journal.pmed.0020199 7,16
2005 Couto FM, Silva MJ, Coutinho PM Finding genomic ontology terms in text using evidence content BMC Bioinformatics 6 Suppl 1: S21. 15960834 9,12
2005 Covarrubias MY, Khan RL, Vadigepalli R, Hoek JB, Schwaber JS Chronic alcohol exposure alters transcription broadly in a key integrative brain nucleus for homeostasis: the nucleus tractus solitarius. Physiol Genomics 24: 45-58. rat brain transcripts 16189278 7,16
2005 Crockett DK, Seiler CE, Elenitoba-Johnson KS, Lim MS Annotated proteome of a human T-cell lymphoma. J Biomol Tech 16: 341-346. Human proteins; T-cell lymphoma 16522855 8,16
2005 Currie RA, Bombail V, Oliver JD, Moore DJ, Lim FL, Gwilliam V, Kimber I, Chipman K, Moggs JG, Orphanides G Gene ontology mapping as an unbiased method for identifying molecular pathways and processes affected by toxicant exposure: application to acute effects caused by the rodent non-genotoxic carcinogen diethylhexylphthalate. Toxicol Sci 86: 453-469. Mouse liver genes 15901911 7,13,16,16
2005 Currie RA, Orphanides G, Moggs JG Mapping molecular responses to xenoestrogens through Gene Ontology and pathway analysis of toxicogenomic data. Reprod Toxicol 20: 433-440. 15964738 7,16
2005 Dahia PL|etAl A HIF1alpha regulatory loop links hypoxia and mitochondrial signals in pheochromocytomas. PLoS Genet 1: 72-80. Human transcripts; pheochromocytoma 16103922 10.1371/journal.pgen.0010008 7,16
2005 Dai C, Liu J Inducing pairwise gene interactions from time-series data by EDA based Bayesian network. Conf Proc IEEE Eng Med Biol Soc 7: 7746-7749. 17282077 7,17
2005 Dang H, Trempus C, Malarkey DE, Wei SJ, Humble M, Morris RJ, Tennant RW Identification of genes and gene ontology processes critical to skin papilloma development in Tg.AC transgenic mice. Mol Carcinog 45: 126-140. Mouse skin transcipts 16329151 7,16
2005 De Biase A, Knoblach SM, Di Giovanni S, Fan C, Molon A, Hoffman EP, Faden AI Gene expression profiling of experimental traumatic spinal cord injury as a function of distance from impact site and injury severity. Physiol Genomics 22: 368-381. Rat spinal cord transcripts 15942019 7,16
2005 Deng DX|etAl Differences in vascular bed disease susceptibility reflect differences in gene expression response to atherogenic stimuli. Circ Res 98: 200-208. Human blood vessel genes 16373601 7,16
2005 Dhahbi JM, Mote PL, Fahy GM, Spindler SR Identification of potential caloric restriction mimetics by microarray profiling. Physiol Genomics 23:343-350. mouse transcripts 16189280 7,16
2005 Dieguez-Acuna FJ, Gerber SA, Kodama S, Elias JE, Beausoleil SA, Faustman D, Gygi SP Characterization of mouse spleen cells by subtractive proteomics. Mol Cell Proteomics 4: 1459-1470. Mouse spleen proteins 16037072 8
2005 Diener SE, Houfek TD, Kalat SE, Windham DE, Burke M, Opperman C, Dean RA Alkahest NuclearBLAST : a user-friendly BLAST management and analysis system BMC Bioinformatics 6: 147. 15958161 9,10
2005 Dingare S, Nissim M, Finkel J, Manning C, Grover C A system for identifying named entities in biomedical text: how results from two evaluations reflect on both the system and the evaluations. Comp Funct Genomics 6: 77-85. Conference Report. http://www3.interscience.wiley.com/cgi-bin/abstract/109932711/ABSTRACT|abs 12
2005 Dolan ME, Ni L, Camon E, Blake JA A procedure for assessing GO annotation consistency Bioinformatics 21 Suppl 1: i134-i143. Annotation consistency analysis 15961450 3
2005 Doms A, Schroeder M GoPubMed: exploring PubMed with the Gene Ontology Nucleic Acids Res 33: W783-W786. 15980585 10,12
2005 Dong Q, Lawrence CJ, Schlueter SD, Wilkerson MD, Kurtz S, Lushbough C, Brendel V Comparative plant genomics resources at PlantGDB. Plant Physiol 139: 610-618. Plant EST and genomic sequences 16219921 4,5,11
2005 Donker RB, Asgeirsdottir SA, Gerbens F, van Pampus MG, Kallenberg CG, Te Meerman GJ, Aarnoudse JG, Molema G Plasma factors in severe early-onset preeclampsia do not substantially alter endothelial gene expression in vitro. J Soc Gynecol Investig 12: 98-106. Human endothelial transcripts 15695104 7,16
2005 Drabkin HJ, Hollenbeck C, Hill DP, Blake JA Ontological visualization of protein-protein interactions. BMC Bioinformatics 6: 29. Mouse 15707487 1,12
2005 Du P, Gong J, Syrkin Wurtele E, Dickerson JA Modeling gene expression networks using fuzzy logic. IEEE Trans Syst Man Cybern B Cybern 35: 1351-1359. Arabidopsis genes 16366260 7,13
2005 Duan KB, Rajapakse JC, Wang H, Azuaje F Multiple SVM-RFE for gene selection in cancer classification with expression data. IEEE Trans Nanobioscience 4: 228-234. 16220686 7,16
2005 Dunn R, Dudbridge F, Sanderson CM The use of edge-betweenness clustering to investigate biological function in protein interaction networks. BMC Bioinformatics 6: 39. 15740614 13,17
2005 Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, Brazma A, Huber W BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 21: 3439-3440. 16082012 3,7,10
2005 Dvorak CM, Hyland KA, Machado JG, Zhang Y, Fahrenkrug SC, Murtaugh MP Gene discovery and expression profiling in porcine Peyer's patch. Vet Immunol Immunopathol 105: 301-315. Porcine transcripts 15808308 7
2005 Eckfeldt CE, Mendenhall EM, Flynn CM, Wang TF, Pickart MA, Grindle SM, Ekker SC, Verfaillie CM Functional analysis of human hematopoietic stem cell gene expression using zebrafish. PLoS Biol 3: e254. Human hematopoietic stem cell transcripts 16089502 10.1371/journal.pbio.0030254 7,16
2005 Edlundh-Rose E, Kupershmidt I, Gustafsson AC, Parasassi T, Serafino A, Bracci-Laudiero L, Greco G, Krasnowska EK, Romano MC, Lundeberg T, Nilsson P, Lundeberg J Gene expression analysis of human epidermal keratinocytes after N-acetyl L-cysteine treatment demonstrates cell cycle arrest and increased differentiation. Pathobiology 72: 203-212. Human epidermal keratinocyte transcripts 16127296 7,16
2005 Ehrler F, Geissbuhler A, Jimeno A, Ruch P Data-poor categorization and passage retrieval for Gene Ontology Annotation in Swiss-Prot BMC Bioinformatics 6 Suppl 1: S23. 15960836 9,12
2005 Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, Ashburner M The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol 6: R44. 15892872 15
2005 Engelhardt BE, Jordan MI, Muratore KE, Brenner SE Protein molecular function prediction by Bayesian phylogenomics. PLoS Comput Biol 1: e45. 16217548 10.1371/journal.pcbi.0010045 9,10
2005 Ernst J, Nau GJ, Bar-Joseph Z Clustering short time series gene expression data Bioinformatics 21 Suppl 1: i159-i168. 15961453 7,10
2005 Espadaler J, Romero-Isart O, Jackson RM, Oliva B Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships. Bioinformatics 21: 3360-3368. 15961445 13,19
2005 Everts RE, Band MR, Liu ZL, Kumar CG, Liu L, Loor JJ, Oliveira R, Lewin HA A 7872 cDNA microarray and its use in bovine functional genomics. Vet Immunol Immunopathol 105: 235-245. Bovine cDNAs 15808303 3
2005 Faccioli P, Provero P, Herrmann C, Stanca AM, Morcia C, Terzi V From Single Genes to Co-Expression Networks: Extracting Knowledge from Barley Functional Genomics. Plant Mol Biol 58: 739-750. Barley cDNAs 16158246 7
2005 Fang Z, Yang J, Li Y, Luo Q, Liu L Knowledge guided analysis of microarray data. J Biomed Inform 39:401-411. 16214421 7
2005 Faux NG, Bottomley SP, Lesk AM, Irving JA, Morrison JR, de la Banda MG, Whisstock JC Functional insights from the distribution and role of homopeptide repeat-containing proteins. Genome Res 15: 537-551. Human proteins 15805494 6
2005 Finocchiaro G, Mancuso F, Muller H Mining published lists of cancer related microarray experiments: Identification of a gene expression signature having a critical role in cell-cycle control. BMC Bioinformatics 6 Suppl 4: S14. Human transcripts, cancer 16351740 7,12,16
2005 Fontenot JD, Rasmussen JP, Gavin MA, Rudensky AY A function for interleukin 2 in Foxp3-expressing regulatory T cells. Nat Immunol 6: 1142-1151. Mouse T cell transcripts 16227984 7,16
2005 Forsberg EC, Prohaska SS, Katzman S, Heffner GC, Stuart JM, Weissman IL Differential expression of novel potential regulators in hematopoietic stem cells. PLoS Genet 1: e28. Mouse transcripts; hematopoiesis 16151515 10.1371/journal.pgen.0010028 7,16
2005 Fraser HB, Khaitovich P, Plotkin JB, Paabo S, Eisen MB Aging and gene expression in the primate brain. PLoS Biol 3: e274. Human, chimpanzee brain transcripts; aging 16048372 10.1371/journal.pbio.0030274 7,16
2005 Friedberg I, Godzik A Connecting the protein structure universe by using sparse recurring fragments. Structure (Camb) 13: 1213-1224. 16084393 13,6
2005 Friedberg I, Godzik A Fragnostic: walking through protein structure space Nucleic Acids Res 33: W249-W251. 15980462 10
2005 Gennari JH, Silberfein A, Wiley JC Integrating genomic knowledge sources through an anatomy ontology. Pac Symp Biocomput 10: 115-126. Knowledge integration using ontologies 15759619 13
2005 Gharib SA, Liles WC, Matute-Bello G, Glenny RW, Martin TR, Altemeier WA Computational identification of key biologic modules and transcription factors in acute lung injury. Am J Respir Crit Care Med 173: 653-658. Mouse lung transcripts 16387799 7,16,17
2005 Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D Using ontologies to describe mouse phenotypes. Genome Biol 6: R8. 15642100 15
2005 Goble C, Wroe C The Montagues and the Capulets. Comp Funct Genomics 5: 623-632. Conference Report. http://www3.interscience.wiley.com/cgi-bin/abstract/109925284/ABSTRACT|abs 14
2005 Goeman JJ, Oosting J, Cleton-Jansen AM, Anninga JK, van Houwelingen HC Testing association of a pathway with survival using gene expression data. Bioinformatics 21: 1950-1957. 15657105 7,10,13,16
2005 Goes da Silva F|etAl Characterizing the grape transcriptome. Analysis of expressed sequence tags from multiple Vitis species and development of a compendium of gene expression during berry development. Plant Physiol 139: 574-597. Grape ESTs 16219919 5
2005 Griffith OL, Pleasance ED, Fulton DL, Oveisi M, Ester M, Siddiqui AS, Jones SJ Assessment and integration of publicly available SAGE, cDNA microarray, and oligonucleotide microarray expression data for global coexpression analyses. Genomics 86: 476-488. Human genes 16098712 7
2005 Grun D, Wang Y, Langenberger D, Gunsalus KC, Rajewsky N microRNA target predictions across seven Drosophila species and comparison to mammalian targets Plos Comput Biol 1: e13. 16103902 10.1371/journal.pcbi.0010013 13,18
2005 Guenther R, Krenn V, Morawietz L, Dankof A, Melcher I, Schaser KD, Kasper HU, Kuban RJ, Ungethum U, Sers C Giant cell tumors of the bone: molecular profiling and expression analysis of Ephrin A1 receptor, Claudin 7, CD52, FGFR3 and AMFR. Pathol Res Pract 201: 649-663. Human bone transcripts 16325507 7,16
2005 Guo X, Shriver CD, Hu H, Liebman MN Analysis of Metabolic and Regulatory Pathways through Gene Ontology-Derived Semantic Similarity Measures. AMIA Annu Symp Proc 2005:972. 16779259 13
2005 Guo Z, Zhang T, Li X, Wang Q, Xu J, Yu H, Zhu J, Wang H, Wang C, Topol EJ, Wang Q, Rao S Towards precise classification of cancers based on robust gene functional expression profiles. BMC Bioinformatics 6: 58. 15774002 7,13,16,16
2005 Gustafsson M, Hornquist M, Lombardi A Constructing and analyzing a large-scale gene-to-gene regulatory network--lasso-constrained inference and biological validation. IEEE/ACM Trans Comput Biol Bioinform 2: 254-261. Saccharomyces gene expression 17044188 7,17
2005 Haas BJ|etAl Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. BMC Biol 3: 7. Arabidopsis thaliana 15784138 1,4
2005 Hagen-Larsen H, Laerdahl JK, Panitz F, Adzhubei A, Hoyheim B An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar). BMC Genomics 6: 171. Salmon ESTs 16321156 5
2005 Handfield M, Mans JJ, Zheng G, Lopez MC, Mao S, Progulske-Fox A, Narasimhan G, Baker HV, Lamont RJ Distinct transcriptional profiles characterize oral epithelium-microbiota interactions. Cell Microbiol 7: 811-823. Human gingival epithelial cell transcripts 15888084 7,16
2005 Hannah MA, Heyer AG, Hincha DK A global survey of gene regulation during cold acclimation in Arabidopsis thaliana. PLoS Genet 1: e26. Arabidopsis transcripts 16121258 10.1371/journal.pgen.0010026 7
2005 Hao P, He WZ, Huang Y, Ma LX, Xu Y, Xi H, Wang C, Liu BS, Wang JM, Li YX, Zhong Y MPSS: an integrated database system for surveying a set of proteins. Bioinformatics 21: 2142-2143. 15699026 11,13,6
2005 Harkema H, Roberts I, Gaizauskas R. Hepple M A web service for biomedical term look-up. Comp Funct Genomics 6: 86-93. Conference Report. http://www3.interscience.wiley.com/cgi-bin/abstract/109932712/ABSTRACT|abs 12
2005 Harris MA, Lomax J, Ireland A, Clark JI The Gene Ontology project. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Part 4, Bioinformatics [Subramaniam S (ed.), Wiley and Sons, Inc., New York.] http://www.mrw.interscience.wiley.com/ggpb/articles/g408202/abstract.html|abs 1,2
2005 Harris MA, Parkinson H Standards and Ontologies for Functional Genomics 2. Comp Funct Genomics 5: 618-622. Conference Report. http://www3.interscience.wiley.com/cgi-bin/abstract/109925300/START|ws 14
2005 Hauck SM, Schoeffmann S, Deeg CA, Gloeckner CJ, Swiatek-de Lange M, Ueffing M Proteomic analysis of the porcine interphotoreceptor matrix. Proteomics 5: 3623-3636. 16127731 8
2005 Hayamizu TF, Mangan M, Corradi JP, Kadin JA, Ringwald M The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data. Genome Biol 6: R29. 15774030 15
2005 Hayete B, Bienkowska JR Gotrees: predicting go associations from protein domain composition using decision trees. Pac Symp Biocomput 10: 127-138. 15759620 9
2005 Henrich T|etAl MEPD: a resource for medaka gene expression patterns. Bioinformatics 21: 3195-3197. Medaka genes 15879458 3,7,11,15
2005 Hirschman L, Blaschke C, Valencia A The BioLink SIG workshop at ISMB2004. Comp Funct Genomics 6: 58-60. Conference Report. http://www3.interscience.wiley.com/cgi-bin/abstract/109932715/ABSTRACT|abs 12
2005 Hirschman L, Yeh A, Blaschke C, Valencia A Overview of BioCreAtIvE: critical assessment of information extraction for biology BMC Bioinformatics 16 Suppl 1: S 15960821 12
2005 Ho Sui SJ, Mortimer JR, Arenillas DJ, Brumm J, Walsh CJ, Kennedy BP, Wasserman WW oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes Nucleic Acids Res 33: 3154-3164. 15933209 7,10,11,13,10,7
2005 Horan K, Lauricha J, Bailey-Serres J, Raikhel N, Girke T Genome cluster database. A sequence family analysis platform for Arabidopsis and rice. Plant Physiol 138: 47-54. 15888677 11,13,10,7
2005 Horn R|etAl Candidate gene database and transcript map for peach, a model species for fruit trees. Theor Appl Genet 110: 1419-1428. Peach ESTs 15846479 5,11
2005 Hsiao A, Ideker T, Olefsky JM, Subramaniam S VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data Nucleic Acids Res 33: W627-W632. 15980550 7,10
2005 Hu X, Friedman D, Hill S, Caprioli R, Nicholson W, Powers AC, Hunter L, Limbird LE Proteomic exploration of pancreatic islets in mice null for the alpha2A adrenergic receptor. J Mol Endocrinol 35: 73-88. Mouse pancreatic islet proteins 16087723 8
2005 Hu Z, Mellor J, Wu J, Yamada T, Holloway D, Delisi C VisANT: data-integrating visual framework for biological networks and modules Nucleic Acids Res 33: W352-W357. 15980487 10
2005 Huang HD, Horng JT, Lin FM, Chang YC, Huang CC SpliceInfo: an information repository for mRNA alternative splicing in human genome. Nucleic Acids Res 33: D80-D85. Human alternatively spliced transcripts 15608290 3,11
2005 Huang JC, Morris QD, Hughes TR, Frey BJ GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data Bioinformatics 21 Suppl 1: i222-i231. 15961461 7
2005 Huang R, Wallqvist A, Covell DG Comprehensive analysis of pathway or functionally related gene expression in the National Cancer Institute's anticancer screen. Genomics 87: 315-328. NCI tumor cell line genes 16386875 7,16,17
2005 Huang R, Wallqvist A, Thanki N, Covell DG Linking pathway gene expressions to the growth inhibition response from the National Cancer Institute's anticancer screen and drug mechanism of action. Pharmacogenomics J 5: 381-399. 16103895 7,13,16,16
2005 Huang Y, Yan J, Lubet R, Kensler TW, Sutter TR Identification of novel transcriptional networks in response to treatment with the anticarcinogen 3H-1, 2-dithiole-3-thione. Physiol Genomics 24: 144-153. Rat liver transcripts 16317079 7,16
2005 Huang ZW, Chen P, Mei L, Fan QJ, Xiao BK, Wu ZY [Differentially expressed gene profiles of cochlea in rats induced by acute and chronic sodium salicylate injection.] [Article in Chinese] Zhonghua Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 40: 27-32. Rat cochlear transcripts 15906514 7
2005 Hvidsten TR, Wilczynski B, Kryshtafovych A, Tiuryn J, Komorowski J, Fidelis K Discovering regulatory binding-site modules using rule-based learning. Genome Res 15: 856-866. 15930496 13,19
2005 Ihmels J, Bergmann S, Berman J, Barkai N Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program. PLoS Genet 1: e39. Candida transcripts 16470937 10.1371/journal.pgen.0010039 7
2005 Jaiswal P|etAl Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages. Comp Funct Genomics 6: 388-397. 18629207 15
2005 Jiang T, Keating AE AVID: An integrative framework for discovering functional relationships among proteins. BMC Bioinformatics 6: 136. 15929793 9
2005 Johnson RJ, Williams JM, Schreiber BM, Elfe CD, Lennon-Hopkins KL, Skrzypek MS, White RD Analysis of Gene Ontology features in microarray data using the Proteome BioKnowledge Library. In Silico Biol 5: 0035. Rat vascular transcripts 16268783 7,11
2005 Jones CE, Baumann U, Brown AL Automated methods of predicting the function of biological sequences using GO and BLAST. BMC Bioinformatics 6: 272. 16288652 9
2005 Joshi T, Chen Y, Alexandrov NN, Xu D Cellular function prediction and biological pathway discovery in Arabidopsis thaliana using microarray data. Int J Bioinform Res Appl 1: 335-350. Eisenia fetida ESTs 18048140 5,7
2005 Jung S, Abbott A, Jesudurai C, Tomkins J, Main D Frequency, type, distribution and annotation of simple sequence repeats in Rosaceae ESTs. Funct Integr Genomics 5: 136-143. Rosaceae (almond, peach, rose) ESTs 15761705 5
2005 Kan Z, Garrett-Engele PW, Johnson JM, Castle JC Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles. Nucleic Acids Res 33: 5659-5666. 16195578 13,18
2005 Kaplan T, Friedman N, Margalit H Ab initio prediction of transcription factor targets using structural knowledge Plos Comput Biol 1: e1. 16103898 10.1371/journal.pcbi.0010001 13,19
2005 Karsan A, Blonder J, Law J, Yaquian E, Lucas DA, Conrads TP, Veenstra T Proteomic analysis of lipid microdomains from lipopolysaccharide-activated human endothelial cells. J Proteome Res 4: 349-357. 15822910 8
2005 Kasamatsu A, Endo Y, Uzawa K, Nakashima D, Koike H, Hashitani S, Numata T, Urade M, Tanzawa H Identification of candidate genes associated with salivary adenoid cystic carcinomas using combined comparative genomic hybridization and oligonucleotide microarray analyses. Int J Biochem Cell Biol 37: 1869-1880. Human salivary gland transcripts 15908262 7,13,16,16
2005 Kato K, Yamashita R, Matoba R, Monden M, Noguchi S, Takagi T, Nakai K Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues. Nucleic Acids Res 33: D533-D536. Human tumor genes 15608255 7,11,16
2005 Kato M, Nagasaki M, Doi A, Miyano S Automatic drawing of biological networks using cross cost and subcomponent data. Genome Inform 16: 22-31. 16901086 10,17
2005 Katsel P, Davis KL, Haroutunian V Variations in myelin and oligodendrocyte-related gene expression across multiple brain regions in schizophrenia: A gene ontology study. Schizophr Res 79: 157-173. Human brain transcripts 16139990 7,16
2005 Kawaura K, Mochida K, Yamazaki Y, Ogihara Y Transcriptome analysis of salinity stress responses in common wheat using a 22k oligo-DNA microarray. Funct Integr Genomics 6: 132-142. Wheat transcripts 16328439 7
2005 Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, Haussler D Exploring relationships and mining data with the UCSC Gene Sorter. Genome Res 15: 737-741. 15867434 10,11
2005 Khatri P, Done B, Rao A, Done A, Draghici S A semantic analysis of the annotations of the human genome. Bioinformatics 21: 3416-3421. 15955782 9,12
2005 Khatri P, Draghici S Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 21: 3587-3595. 15994189 10
2005 Khatri P, Sellamuthu S, Malhotra P, Amin K, Done A, Draghici S Recent additions and improvements to the Onto-Tools Nucleic Acids Res 33: W762-W765. 15980579 7,10
2005 Kim DK, Lim D, Lee BR, Shin JH, Kim H, Han JY Analysis of testis-specific transcripts in the chicken. Anim Genet 36: 232-234. Chicken transcripts 15932403 7
2005 Kim SN|etAl Age-dependent changes of gene expression in the Drosophila head. Neurobiol Aging 26: 1083-1091. Drosophila transcripts 15748788 7
2005 King JY|etAl Pathway analysis of coronary atherosclerosis Physiol Genomics 23: 103-118. Human heart transcripts 15942018 7,16
2005 Klink VP, Alkharouf N, Macdonald M, Matthews B Laser capture microdissection (LCM) and expression analyses of Glycine max (soybean) syncytium containing root regions formed by the plant pathogen Heterodera glycines (soybean cyst nematode). Plant Mol Biol 59: 965-979. Soybean ESTs 16307369 5,7
2005 Ko D, Xu W, Windle B Gene function classification using NCI-60 cell line gene expression profiles. Comput Biol Chem 29: 412-419. NCI-60 cell line genes 16290039 7,9,16
2005 Koike A, Takagi T PRIME: automatically extracted PRotein Interactions and Molecular Information databasE In Silico Biol 5: 9-20. 15972002 11,12
2005 Kornberg LJ, Villaret D, Popp M, Lui L, McLaren R, Brown H, Cohen D, Yun J, McFadden M Gene expression profiling in squamous cell carcinoma of the oral cavity shows abnormalities in several signaling pathways. Laryngoscope 115: 690-698. Human squamous cell transcripts 15805883 7,16
2005 Kramer-Hammerle S, Hahn A, Brack-Werner R, Werner T Elucidating effects of long-term expression of HIV-1 Nef on astrocytes by microarray, promoter, and literature analyses Gene 358: 31-38. Human astrocyte transcripts 15958282 7,16
2005 Krasnov A, Koskinen H, Pehkonen P, Rexroad CE 3rd, Afanasyev S, Molsa H Gene expression in the brain and kidney of rainbow trout in response to handling stress. BMC Genomics 6: 3. Rainbow trout transcripts 15634361 7
2005 Krasnov A, Koskinen H, Rexroad C, Afanasyev S, Molsa H, Oikari A Transcriptome responses to carbon tetrachloride and pyrene in the kidney and liver of juvenile rainbow trout (Oncorhynchus mykiss). Aquat Toxicol 74: 70-81. Rainbow trout transcripts 15963578 7
2005 Kreeft AJ, Moen CJ, Porter G, Kasanmoentalib S, Sverdlov R, van Gorp PJ, Havekes LM, Frants RR, Hofker MH Genomic analysis of the response of mouse models to high-fat feeding shows a major role of nuclear receptors in the simultaneous regulation of lipid and inflammatory genes. Atherosclerosis 182: 249-257. Mouse liver transcripts 16159597 7,16
2005 Kriventseva EV, Koutsos AC, Blass C, Kafatos FC, Christophides GK, Zdobnov EM AnoEST: Toward A. gambiae functional genomics. Genome Res 6: 893-899. Anopheles ESTs 15899967 5,11
2005 Kuffner R, Fundel K, Zimmer R Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts. Bioinformatics 21 Suppl 2: ii259-ii267. 16204115 7,12
2005 Kunne C, Lange M, Funke T, Miehe H, Thiel T, Grosse I, Scholz U CR-EST: a resource for crop ESTs. Nucleic Acids Res 33: D619-D621. Crop plant ESTs 15608274 5,11
2005 LaCount DJ|etAl A protein interaction network of the malaria parasite Plasmodium falciparum. Nature 438: 103-107. Plasmodium falciparum proteins 16267556 8
2005 Lang D, Eisinger J, Reski R, Rensing SA Representation and high-quality annotation of the Physcomitrella patens transcriptome demonstrates a high proportion of proteins involved in metabolism in mosses. Plant Biol 7: 238-250. Physcomitrella patens transcripts 15912443 5
2005 Larsson O, Wahlestedt C, Timmons JA Considerations when using the significance analysis of microarrays (SAM) algorithm. BMC Bioinformatics 6: 129. 15921534 14
2005 Law GL, Bickel KS, MacKay VL, Morris DR The undertranslated transcriptome reveals widespread translational silencing by alternative 5' transcript leaders. Genome Biol 6: R111. Saccharomyces transcripts; translation rates 16420678 7,13
2005 Lazareva-Ulitsky B, Diemer K, Thomas PD On the quality of tree-based protein classification. Bioinformatics 21: 1876-1890. 15647305 7
2005 Lazzari B, Caprera A, Vecchietti A, Stella A, Milanesi L, Pozzi C ESTree db: a tool for peach functional genomics. BMC Bioinformatics 6 Suppl 4: S16. Peach ESTs 16351742 5,11
2005 Lee HK, Braynen W, Keshav K, Pavlidis P ErmineJ: Tool for functional analysis of gene expression data sets. BMC Bioinformatics 6: 269. 16280084 10
2005 Lee JS, Katari G, Sachidanandam R GObar: A Gene Ontology based analysis and visualization tool for gene sets. BMC Bioinformatics 6: 189. 16042800 10
2005 Lee V, Camon E, Dimmer E, Barrell D, Apweiler R Who tangos with GOA? - Use of Gene Ontology Annotation (GOA) for biological interpretation of '-omics' data and for validation of automatic annotation tools In Silico Biol 5: 5-8. 15972001 6,12
2005 Lee W, St Onge RP, Proctor M, Flaherty P, Jordan MI, Arkin AP, Davis RW, Nislow C, Giaever G Genome-wide requirements for resistance to functionally distinct DNA-damaging agents. PLoS Genet 1: e24. Saccharomyces deletion mutants 16121259 10.1371/journal.pgen.0010024 13
2005 Lee YH, Nair S, Rousseau E, Allison DB, Page GP, Tataranni PA, Bogardus C, Permana PA Microarray profiling of isolated abdominal subcutaneous adipocytes from obese vs non-obese Pima Indians: increased expression of inflammation-related genes. Diabetologia 48: 1776-1783. Human adipocyte transcripts 16059715 7,16
2005 Lemos B, Meiklejohn CD, Caceres M, Hartl DL Rates of divergence in gene expression profiles of primates, mice, and flies: stabilizing selection and variability among functional categories. Evolution Int J Org Evolution 59: 126-137. 15792233 13,18
2005 Lewis SE Gene Ontology: looking backwards and forwards. Genome Biol 6: 103. http://genomebiology.com/2004/6/1/103|full 15642104 1,2
2005 Lim DA, Suarez-Farinas M, Naef F, Hacker CR, Menn B, Takebayashi H, Magnasco M, Patil N, Alvarez-Buylla A In vivo transcriptional profile analysis reveals RNA splicing and chromatin remodeling as prominent processes for adult neurogenesis. Mol Cell Neurosci 31: 131-148 Mouse brain transcipts 16330219 7,16
2005 Liu F, Vantoai T, Moy LP, Bock G, Linford LD, Quackenbush J Global transcription profiling reveals comprehensive insights into hypoxic response in Arabidopsis. Plant Physiol 137: 1115-1129. Arabidopsis transcripts 15734912 7
2005 Liu H, Hu Z, Wu CH DynGO: A tool for browsing and mining Gene Ontology and its associations. BMC Bioinformatics 6: 201. 16091147 10
2005 Liu Y, Liu N, Zhao H Inferring protein-protein interactions through high-throughput interaction data from diverse organisms. Bioinformatics 117: 267-274. 15905281 13,19
2005 Loftus BJ|etAl The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science 307: 1321-1324. Cryptococcus neoformans genomic 15653466 4,6,18
2005 Lomax J, The Gene Ontology Consortium Get ready to GO! A biologist's guide to the Gene Ontology. Brief Bioinform 6: 298-304. ftp://ftp.geneontology.org/pub/go/teaching_resources/tutorials/2005-09_BiB-journal-tutorial_jlomax.pdf|pdf 16212777 1,2
2005 Lopez-Bigas N, Blencowe BJ, Ouzounis CA Highly consistent patterns for inherited human diseases at the molecular level. Bioinformatics 22: 269-277. Human disease gene classification 16287936 13,16
2005 Lord P, Stevens R, Butler JA, McEntire R The eighth annual bio-ontologies meeting. PLoS Comput Biol 1: e77. Conference review 16758004 10.1371/journal.pcbi.0010077 2
2005 Lorenzini DM, Silva PI, Soares MB, Arruda P, Setubal J, Daffre S Discovery of immune-related genes expressed in hemocytes of the tarantula spider Acanthoscurria gomesiana. Dev Comp Immunol 30: 545-556. Tarantula ESTs 16386302 5,7
2005 Lottaz C, Spang R Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data. Bioinformatics 21: 1971-1978. 15677704 7,10,13,16
2005 Love CG, Robinson AJ, Lim GA, Hopkins CJ, Batley J, Barker G, Spangenberg GC, Edwards D Brassica ASTRA: an integrated database for Brassica genomic research. Nucleic Acids Res 33: D656-D659. Brassica species 15608282 11
2005 Lu J, Izvolsky KI, Qian J, Cardoso WV Identification of FGF10 targets in the embryonic lung epithelium during bud morphogenesis. J Biol Chem 280: 4834-4841. Mouse embryonic lung transcripts 15556938 7
2005 Lu P, Szafron D, Greiner R, Wishart DS, Fyshe A, Pearcy B, Poulin B, Eisner R, Ngo D, Lamb N PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization. Nucleic Acids Res 33: D147-D153. Proteome Analyst proteins 15608166 6,11
2005 Lu Z, Hunter L Go molecular function terms are predictive of subcellular localization. Pac Symp Biocomput 10: 151-161. 15759622 9
2005 Mackay TF, Heinsohn SL, Lyman RF, Moehring AJ, Morgan TJ, Rollmann SM Genetics and genomics of Drosophila mating behavior. Proc Natl Acad Sci U S A 102 Suppl 1: 6622-6629. Drosophila transcripts 15851659 7
2005 Mackenzie S, Iliev D, Liarte C, Koskinen H, Planas JV, Goetz FW, Molsa H, Krasnov A, Tort L Transcriptional analysis of LPS-stimulated activation of trout (Oncorhynchus mykiss) monocyte/macrophage cells in primary culture treated with cortisol. Mol Immunol 43: 1340-1348. Trout tanscripts 16239032 7
2005 Maere S, Heymans K, Kuiper M BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21: 3448-3449. 15972284 10
2005 Mahalingam R, Shah N, Scrymgeour A, Fedoroff N Temporal evolution of the Arabidopsis oxidative stress response Plant Mol Biol 57:709-730 Arabidopsis transcripts 15988565 7
2005 Mao X, Cai T, Olyarchuk JG, Wei L Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21: 3787-3793. 15817693 14
2005 Martin AC Mapping PDB chains to UniProtKB entries. Bioinformatics 21: 4297-4301. PDB chains 16188924 6
2005 Massar JP, Travers M, Elhai J, Shrager J BioLingua: a programmable knowledge environment for biologists. Bioinformatics 21: 199-207. 15308539 10,13,17
2005 Masseroli M, Pinciroli F Using Gene Ontology and genomic controlled vocabularies to analyze high-throughput gene lists: Three tool comparison. Comput Biol Med 36: 731-747. 16165121 10
2005 Mathavan S|etAl Transcriptome analysis of zebrafish embryogenesis using microarrays. PLoS Genet 1: 260-276. Zebrafish transcripts 16132083 10.1371/journal.pgen.0010029 7
2005 McNutt MC, Tongbai R, Cui W, Collins I, Freebern WJ, Montano I, Haggerty CM, Chandramouli GV, Gardner K Human promoter genomic composition demonstrates non-random groupings that reflect general cellular function. BMC Bioinformatics 6: 259. human transciption factor binding sites; Genomic analysis 16232321 13
2005 Meinel T, Krause A, Luz H, Vingron M, Staub E The SYSTERS Protein Family Database in 2005. Nucleic Acids Res 33: D226-D229. SYSTERS protein families 15608183 6,11
2005 Mi H|etAl The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res 33: D284-D288. PANTHER protein families 15608197 6
2005 Miles RR, Crockett DK, Lim MS, Elenitoba-Johnson KS Analysis of BCL6 interacting proteins by tandem mass spectrometry. Mol Cell Proteomics 4: 1898-1909. 16147992 8
2005 Moggs JG Molecular responses to xenoestrogens: Mechanistic insights from toxicogenomics. Toxicology 213: 177-193. mammalian transcipts 15996808 7,16
2005 Moyle RL, Crowe ML, Ripi-Koia J, Fairbairn DJ, Botella JR PineappleDB: An online pineapple bioinformatics resource. BMC Plant Biol 5: 21. Pineapple ESTs 16202174 5,11
2005 Mulder NJ|etAl InterPro, progress and status in 2005. Nucleic Acids Res 33: D201-D205. InterPro 15608177 6,11
2005 Nagano K, Taoka M, Yamauchi Y, Itagaki C, Shinkawa T, Nunomura K, Okamura N, Takahashi N, Izumi T, Isobe T Large-scale identification of proteins expressed in mouse embryonic stem cells. Proteomics 5: 1346-1361. Mouse stem cell proteins 15742316 6,7,8
2005 Niculescu MD, Craciunescu CN, Zeisel SH Gene expression profiling of choline-deprived neural precursor cells isolated from mouse brain. Brain Res Mol Brain Res 134: 309-322. Mouse brain transcripts 15836926 7
2005 O'Dushlaine CT, Edwards RJ, Park SD, Shields DC Tandem repeat copy-number variation in protein-coding regions of human genes. Genome Biol 6: R69. Genomic analysis 16086851 13
2005 Ogren PV, Cohen KB, Hunter L Implications of compositionality in the gene ontology for its curation and usage. Pac Symp Biocomput 10: 174-185. 15759624 14
2005 Ohya Y|etAl High-dimensional and large-scale phenotyping of yeast mutants. Proc Natl Acad Sci U S A 102: 19015-19020. Saccharomyces morphology 16365294 9,13
2005 Omenn GS|etAl Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics 5: 3226-3245. Human plasma proteome 16104056 8
2005 Ovcharenko I, Nobrega MA Identifying synonymous regulatory elements in vertebrate genomes Nucleic Acids Res 33: W403-W407. 15980499 10,13,18
2005 Pal D, Eisenberg D Inference of protein function from protein structure. Structure (Camb) 13: 121-130. 15642267 9
2005 Papanicolaou A, Joron M, McMillan WO, Blaxter ML, Jiggins CD Genomic tools and cDNA derived markers for butterflies. Mol Ecol 14: 2883-2897. Heliconius spp. ESTs 16029486 5,11
2005 Patil A, Nakamura H Filtering high-throughput protein-protein interaction data using a combination of genomic features. BMC Bioinformatics 6: 100. 15833142 13,6
2005 Patil MA|etAl An integrated data analysis approach to characterize genes highly expressed in hepatocellular carcinoma. Oncogene 24: 3737-3747. Human liver transcripts 15735714 7,16
2005 Pavy N|etAl Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters. BMC Genomics 6: 144. Spruce ESTs 16236172 5
2005 Perez-Rey D, Maojo V, Garcia-Remesal M, Alonso-Calvo R, Billhardt H, Martin-Sanchez F, Sousa A ONTOFUSION: Ontology-based integration of genomic and clinical databases. Comput Biol Med 36: 712-730. 16144697 14
2005 Persico M, Ceol A, Gavrila C, Hoffmann R, Florio A, Cesareni G HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. BMC Bioinformatics 6 Suppl 4: S21. Human proteins 16351748 8
2005 Petkov PM, Graber JH, Churchill GA, DiPetrillo K, King BL, Paigen K Evidence of a large-scale functional organization of mammalian chromosomes. PLoS Genet 1: e33. 16163395 10.1371/journal.pgen.0010033 13
2005 Petrusz P, Jeyaraj AD, Grossman G Microarray analysis of androgen-regulated gene expression in testis: the use of the androgen-binding protein (ABP)-transgenic mouse as a model. Reprod Biol Endocrinol 3: 70. Mouse testis transcripts 16336681 7
2005 Phuc Le P, Friedman JR, Schug J, Brestelli JE, Parker JB, Bochkis IM, Kaestner KH Glucocorticoid receptor-dependent gene regulatory networks. PLoS Genet 1: e16. Mouse liver transcripts 16110340 10.1371/journal.pgen.0010016 7,17
2005 Pina C, Pinto F, Feijo JA, Becker JD Gene family analysis of the Arabidopsis pollen transcriptome reveals biological implications for cell growth, division control, and gene expression regulation. Plant Physiol 138: 744-756. Arabidopsis pollen transcripts 15908605 7
2005 Pollet N, Muncke N, Verbeek B, Li Y, Fenger U, Delius H, Niehrs C An atlas of differential gene expression during early Xenopus embryogenesis. Mech Dev 122: 365-439. Xenopus embryonic cDNAs 15763213 7
2005 Psarros M, Heber S, Sick M, Thoppae G, Harshman K, Sick B RACE: Remote Analysis Computation for gene Expression data Nucleic Acids Res 33: W638-W643. 15980552 7,10
2005 Ray S, Craven M Learning statistical models for annotating proteins with function information using biomedical text BMC Bioinformatics 6 Suppl 1: S17. 15960830 9,12
2005 Rebholz-Schuhmann D, Kirsch H, Couto F Facts from text-is text mining ready to deliver? PLoS Biol 3: e65. 15719064 10.1371/journal.pbio.0030065 12
2005 Reghunathan R, Jayapal M, Hsu LY, Chng HH, Tai D, Leung BP, Melendez AJ Expression profile of immune response genes in patients with Severe Acute Respiratory Syndrome. BMC Immunol 6: 2. Human blood cell transcripts; immune response; SARS 15655079 7,16
2005 Rendl M, Lewis L, Fuchs E Molecular dissection of mesenchymal-epithelial interactions in the hair follicle. PLoS Biol 3: e331. Mouse hair follicle transcripts 16162033 10.1371/journal.pbio.0030331 7
2005 Reneker J, Shyu CR Refined repetitive sequence searches utilizing a fast hash function and cross species information retrievals. BMC Bioinformatics 6: 111. 15869708 13,10,7
2005 Rensink W, Hart A, Liu J, Ouyang S, Zismann V, Buell CR Analyzing the potato abiotic stress transcriptome using expressed sequence tags. Genome 48: 598-605. Potato ESTs 16094426 5,7
2005 Ribichich KF, Salem-Izacc SM, Georg RC, Vencio RZ, Navarro LD, Gomes SL Gene discovery and expression profile analysis through sequencing of expressed sequence tags from different developmental stages of the chytridiomycete Blastocladiella emersonii. Eukaryot Cell 4: 455-464. Blastocladiella emersonii ESTs 15701807 5
2005 Rice SB, Nenadic G, Stapley BJ Mining protein function from text using term-based support vector machines BMC Bioinformatics 6 Suppl 1: S22. 15960835 9,12
2005 Ringner M, Krogh M Folding free energies of 5'-UTRs impact post-transcriptional regulation on a genomic scale in yeast. PLoS Comput Biol 1: e72. Saccharomyces mRNA 16355254 10.1371/journal.pcbi.0010072 7,13
2005 Robins H, Press WH Human microRNAs target a functionally distinct population of genes with AT-rich 3' UTRs. Proc Natl Acad Sci U S A 102: 15557-15562. Human microRNAs; Genomic analysis 16230613 13
2005 Roche JP, Wackym PA, Cioffi JA, Kwitek AE, Erbe CB, Popper P In silico analysis of 2085 clones from a normalized rat vestibular periphery 3' cDNA library. Audiol Neurootol 10: 310-322. Rat vestibular cDNAs 16103642 3
2005 Roy S|etAl Human genome screen to identify the genetic basis of the anti-inflammatory effects of Boswellia in microvascular endothelial cells. DNA Cell Biol 24: 244-255. Human microvascular endothelial transcripts 15812241 7,13,16,16
2005 Ruch P Automatic assignment of biomedical categories: toward a generic approach. Bioinformatics 22: 658-664. 16287934 9,12
2005 Rudd MF, Williams RD, Webb EL, Schmidt S, Sellick GS, Houlston RS The predicted impact of coding single nucleotide polymorphisms database. Cancer Epidemiol Biomarkers Prev 14: 2598-2604. 16284384 13,10,7
2005 Rudic RD, McNamara P, Reilly D, Grosser T, Curtis AM, Price TS, Panda S, Hogenesch JB, Fitzgerald GA Bioinformatic analysis of circadian gene oscillation in mouse aorta. Circulation 112: 2716-2724. Mouse aortic transcripts 16230482 7
2005 Salasznyk RM, Westcott AM, Klees RF, Ward DF, Xiang Z, Vandenberg S, Bennett K, Plopper GE Comparing the protein expression profiles of human mesenchymal stem cells and human osteoblasts using gene ontologies. Stem Cells Dev 14: 354-366. Human stem cell proteome 16137224 8
2005 Satou K, Yamamoto K Utilizing weakly controlled vocabulary for sentence segmentation in biomedical literature In Silico Biol 5: 67-79. 15972007 12
2005 Schaaf GJ, Ruijter JM, van Ruissen F, Zwijnenburg DA, Waaijer R, Valentijn LJ, Benit-Deekman J, van Kampen AH, Baas F, Kool M Full transcriptome analysis of rhabdomyosarcoma, normal and fetal skeletal muscle: statistical comparison of multiple SAGE libraries. FASEB J 19: 404-406. Human skeletal muscle transcripts 15629888 7,16
2005 Schindler J, Lewandrowski U, Sickmann A, Friauf E, Nothwang HG Proteome analysis of brain plasma membranes isolated by affinity two-phase partitioning. Mol Cell Proteomics 5: 390-400. Rat brain plasma membrane proteins 16249173 8
2005 Schmidt-Ott|etAl Novel regulators of kidney development from the tips of the ureteric bud. J Am Soc Nephrol 16: 1993-2002. Rodent kidney transcripts 15917337 7
2005 Scott LK, Vachharajani V, Minagar A, Mynatt RL, Conrad SA Differential RNA expression of hepatic tissue in lean and obese mice after LPS-induced systemic inflammation. Front Biosci 10: 1828-1834. Mouse liver transcripts 15769670 7,16
2005 Semeiks JR, Grate LR, Mian IS Text-based analysis of genes, proteins, aging, and cancer. Mech Ageing Dev 126: 193-208. 15610779 13,16
2005 Seo MJ, Bae SM, Kim YW, Kim YW, Hur SY, Ro DY, Lee JM, Namkoong SE, Kim CK, Ahn WS New approaches to pathogenic gene function discovery with human squamous cell cervical carcinoma by gene ontology. Gynecol Oncol 96: 621-629. Human cervical cell transcripts 15721403 7,13,16,16
2005 Sethupathy P, Corda B, Hatzigeorgiou AG TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA 12:192-197 Animal microRNA targets 16373484 3,11
2005 Sevilla JL, Segura V, Podhorski A, Guruceaga E, Mato JM, Martinez-Cruz LA, Corrales FJ, Rubio A Correlation between gene expression and GO semantic similarity. IEEE/ACM Trans Comput Biol Bioinform 2: 330-338. 17044170 7,13
2005 Shah SP, Huang Y, Xu T, Yuen MM, Ling J, Ouellette BF Atlas - a data warehouse for integrative bioinformatics. BMC Bioinformatics 6: 34. 15723693 11
2005 Shakhnovich BE Improving the precision of the structure-function relationship by considering phylogenetic context Plos Comput Biol 1: e9. 16103910 10.1371/journal.pcbi.0010009 9,13
2005 Shamir R, Maron-Katz A, Tanay A, Linhart C, Steinfeld I, Sharan R, Shiloh Y, Elkon R EXPANDER - an integrative program suite for microarray data analysis. BMC Bioinformatics 6: 232. 16176576 10
2005 Sharon I, Birkland A, Chang K, El-Yaniv R, Yona G Correcting BLAST e-Values for Low-Complexity Segments. J Comput Biol 12: 980-1003. 16201917 13,10,7
2005 Shegogue D, Zheng WJ Integration of the Gene Ontology into an object-oriented architecture. BMC Bioinformatics 6: 113. 15885145 13,10,7
2005 Smith B, Ceusters W, Klagges B, Kohler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector AL, Rosse C Relations in biomedical ontologies. Genome Biol 6: R46. 15892874 14,15
2005 Smith CL, Anthony S, Hubank M, Leiper JM, Vallance P Effects of ADMA upon gene expression: an insight into the pathophysiological significance of raised plasma ADMA. PLoS Med 2: e264. Human endothelial cell transcripts; ADMA exposure 16190779 10.1371/journal.pmed.0020264 7,16
2005 Smith CL, Goldsmith CA, Eppig JT The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol 6: R7. 15642099 15
2005 Song B, Tang JW, Wang B, Cui XN, Zhou CH, Hou L [Screening for Lymphatic Metastasis-associated Genes in Mouse Hepatocarcinoma Cell Lines Hca-F and Hca-P Using Gene Chip.] [Article in Chinese] Ai Zheng 24: 774-780. Mouse liver transcripts 16004799 7,16
2005 Song B|etAl Identify lymphatic metastasis-associated genes in mouse hepatocarcinoma cell lines using gene chip. World J Gastroenterol 11: 1463-1472. Mouse hepatocarcinoma transcripts 15770722 7,16
2005 Song J, Xu Q, Olsen R, Loomis WF, Shaulsky G, Kuspa A, Sucgang R Comparing the Dictyostelium and Entamoeba genomes reveals an ancient split in the Conosa lineage. PLoS Comput Biol 1: e71. 16362072 10.1371/journal.pcbi.0010071 18
2005 Song MO, Freedman JH Expression of copper-responsive genes in HepG2 cells. Mol Cell Biochem 279: 141-147. HepG2 (human) cell transcripts 16283523 7
2005 Spasic I, Ananiadou S, McNaught J, Kumar A Text mining and ontologies in biomedicine: making sense of raw text. Brief Bioinform 6: 239-251. 16212772 12
2005 Speer N, Frohlich H, Spieth C, Zell A Functional distances for genes based on GO feature maps and their application to clustering Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2005) 142-149. 13
2005 Speer N, Frohlich H, Spieth C, Zell A Functional grouping of genes using spectral clustering and Gene Ontology Proceedings of the IEEE International Joint Conference on Neural Networks (IJCNN 2005) 298-303. 13,17
2005 Speer N, Spieth C, Zell A Biological cluster validity indices based on the Gene Ontology Lecture Notes in Computer Science (LNCS) 3646: 429-439. 13
2005 Speer N, Spieth C, Zell A. Spectral clustering Gene Ontology terms to group genes by function Lecture Notes in Bioinformatics (LNBI) 3692: 1-12. 9,13
2005 Staib F|etAl The p53 tumor suppressor network is a key responder to microenvironmental components of chronic inflammatory stress. Cancer Res 65: 10255-10264. Human cell line transcripts during inflammation 16288013 7,16
2005 Steigele S, Nieselt K Open reading frames provide a rich pool of potential natural antisense transcripts in fungal genomes. Nucleic Acids Res 33: 5034-5044. Fungal antisense transcripts 16147987 3
2005 Stein A, Russell RB, Aloy P 3did: interacting protein domains of known three-dimensional structure. Nucleic Acids Res 33: D413-D417. Protein domains 15608228 6,11
2005 Steinau M, Lee DR, Rajeevan MS, Vernon SD, Ruffin MT 4th, Unger ER Gene expression profile of cervical tissue compared to exfoliated cells: Impact on biomarker discovery. BMC Genomics 6: 64. Human cervical cell transcripts 15876354 7,16
2005 Storvik M, Tiikkainen P, van Iersel M, Wong G Distinct gene expression profiles in adult rat brains after acute MK-801 and cocaine treatments. Eur Neuropsychopharmacol 16: 211-219. Rat brain transcripts 16242920 7,16
2005 Sukumaran B, Carlyon JA, Cai JL, Berliner N, Fikrig E Early transcriptional response of human neutrophils to Anaplasma phagocytophilum infection. Infect Immun 73: 8089-8099. Human neutrophil transcripts; anaplasmosis 16299303 7,16
2005 Sullivan CJ, Teal TH, Luttrell IP, Tran KB, Peters MA, Wessells H Microarray analysis reveals novel gene expression changes associated with erectile dysfunction in diabetic rats. Physiol Genomics 23: 192-205. Rat penile transcripts 16118269 7,16
2005 Sun XT, Ding YT, Wu LY, Li Q, Cheng N, Qiu YD, Zhang MY [Gene expression profiling of microvascular endothelial cells during capillary morphogenesis in an in vitro model of angiogenesis.] [Article in Chinese] Zhonghua Wai Ke Za Zhi 43: 37-41. Human microvascular endothelial transcipts 15774172 7,16
2005 Suthram S, Sittler T, Ideker T The Plasmodium protein network diverges from those of other eukaryotes. Nature 438: 108-112. Plasmodium proteins 16267557 8
2005 Sweet-Cordero A, Tseng GC, You H, Douglass M, Huey B, Albertson D, Jacks T Comparison of gene expression and DNA copy number changes in a murine model of lung cancer. Genes Chromosomes Cancer 45: 338-348. Mouse lung genes & transcripts 16323170 7,13,16,16
2005 Tabibiazar R|etAl Signature patterns of gene expression in mouse atherosclerosis and their correlation to human coronary disease. Physiol Genomics 22: 213-226. Mouse transcipts 15870398 7,13,16,16
2005 Taghavi M, Siermala M, Lehtinen TO, Vihinen M Dynamic covariation between gene expression and proteome characteristics. BMC Bioinformatics 6: 215. 16131395 7,8
2005 Takai-Igarashi T, Takagi T, Michael H, Wingender E Third "Ontology Workshop on Ontology and Genomes" - Preface In Silico Biol 5: 1-4. 14
2005 Talbi S|etAl Molecular phenotyping of human endometrium distinguishes menstrual cycle phases and underlying biological processes in normo-ovulatory women. Endocrinology 47: 1097-1121. Human endometrial transcripts 16306079 7,16
2005 Tan FK|etAl Classification analysis of the transcriptosome of nonlesional cultured dermal fibroblasts from systemic sclerosis patients with early disease. Arthritis Rheum 52: 865-876. Human dermal fibroblast transcripts 15751056 7,16
2005 Tan Q, Christensen K, Christiansen L, Frederiksen H, Bathum L, Dahlgaard J, Kruse TA Genetic dissection of gene expression observed in whole blood samples of elderly Danish twins. Hum Genet 117: 267-274. Human transcripts 15906095 7,16
2005 Tari L, Baral C, Dasgupta P Understanding the global properties of functionally-related gene networks using the gene ontology. Pac Symp Biocomput 10: 209-220. 15759627 13,17
2005 Thomas DM, Francescutti-Verbeem DM, Kuhn DM Gene expression profile of activated microglia under conditions associated with dopamine neuronal damage. FASEB J 20: 515-517. Mouse microglial transcripts 16384912 7,16
2005 Tian B, Hu J, Zhang H, Lutz CS A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res 33: 201-212. Genomic analysis 15647503 13
2005 Tiffin N, Kelso JF, Powell AR, Pan H, Bajic VB, Hide WA Integration of text- and data-mining using ontologies successfully selects disease gene candidates. Nucleic Acids Res 33: 1544-1552. 15767279 15
2005 Timmons JA|etAl Human muscle gene expression responses to endurance training provide a novel perspective on Duchenne muscular dystrophy. FASEB J 19: 750-760. Human skeletal muscle transcripts 15857889 7,16
2005 Tobias CM, Twigg P, Hayden DM, Vogel KP, Mitchell RM, Lazo GR, Chow EK, Sarath G Analysis of expressed sequence tags and the identification of associated short tandem repeats in switchgrass. Theor Appl Genet 111: 956-964. Switchgrass ESTs 16049706 5
2005 Trissl S, Rother K, Mueller H, Steinke T, Koch I, Preissner R, Froemmel C, Leser U Columba: an integrated database of proteins, structures, and annotations. BMC Bioinformatics 6: 81. Protein structures 15801979 6,11
2005 Troadec MB|etAl Hepatocyte iron loading capacity is associated with differentiation and repression of motility in the HepaRG cell line. Genomics 87: 91-103. Human hepatocyte transcripts 16325370 7,16
2005 Tu K, Yu H, Zhu M MEGO: gene functional module expression based on gene ontology. Biotechniques 38: 277-283. 15727134 10
2005 Tuikkala J, Elo L, Nevalainen OS, Aittokallio T Improving missing value estimation in microarray data with gene ontology. Bioinformatics 22: 566-672. Analysis of Saccharomyces transcript data 16377613 7
2005 Ule J|etAl Nova regulates brain-specific splicing to shape the synapse. Nat Genet 37: 844-852. Mouse brain transcripts; alternative splicing 16041372 7,13
2005 Vaquerizas JM, Conde L, Yankilevich P, Cabezon A, Minguez P, Diaz-Uriarte R, Al-Shahrour F, Herrero J, Dopazo J GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data. Nucleic Acids Res 33: W616-620. 15980548 10
2005 Verspoor K Towards a semantic lexicon for biological language processing. Comp Funct Genomics 6: 61-66. Conference Report. http://www3.interscience.wiley.com/cgi-bin/abstract/109932698/ABSTRACT|abs 14
2005 Verspoor K, Cohn J, Joslyn C, Mniszewski S, Rechtsteiner A, Rocha LM, Simas T Protein annotation as term categorization in the gene ontology using word proximity networks BMC Bioinformatics 6 Suppl 1: S18. 15960833 9,12
2005 Volz DC, Bencic DC, Hinton DE, Law JM, Kullman SW 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) induces organ-specific differential gene expression in male Japanese medaka (Oryzias latipes). Toxicol Sci 85: 572-584. Medaka transcripts 15703262 7
2005 Wagner RA, Tabibiazar R, Liao A, Quertermous T Genome-wide expression dynamics during mouse embryonic development reveal similarities to Drosophila development. Dev Biol 288: 595-611. Mouse embryonic transcripts 16310180 7,18
2005 Wang ET, Kodama G, Baldi P, Moyzis RK Global landscape of recent inferred Darwinian selection for Homo sapiens. Proc Natl Acad Sci U S A 103: 135-140 Human linkage disequilibrium analysis 16371466 13
2005 Wang JY, Yeh CS, Tzou WS, Hsieh JS, Chen FM, Lu CY, Yu FJ, Cheng TL, Huang TJ, Lin SR Analysis of progressively overexpressed genes in tumorigenesis of colorectal cancers using cDNA microarray Oncol Rep 14: 65-72. human colorectal transcripts 15944769 7,16
2005 Wang J|etAl SilkDB: a knowledgebase for silkworm biology and genomics. Nucleic Acids Res 33: D399-D402. Bombyx mori 15608225 4,11
2005 Watson JD, Laskowski RA, Thornton JM Predicting protein function from sequence and structural data Curr Opin Struct Biol 15: 275-284. 15963890 9
2005 Weng JK, Tanurdzic M, Chapple C Functional analysis and comparative genomics of expressed sequence tags from the lycophyte Selaginella moellendorffii BCM Genomics 6: 85. Selaginella moellendorffii 15938755 5
2005 Weng Y, Dirusso CC, Reilly AA, Black PN, Ding X Hepatic gene expression changes in mouse models with liver-specific deletion or global suppression of the NADPH-cytochrome P450 reductase gene: Mechanistic implications for the regulation of microsomal cytochrome P450 and the fatty liver phenotype. J Biol Chem 280: 31686-31698. Mouse liver transcripts 16006652 7,16
2005 Wennmalm K, Wahlestedt C, Larsson O The expression signature of in vitro senescence resembles mouse but not human aging. Genome Biol 6: R109. Mammalian cell culture transcripts; aging 16420669 7,18
2005 Whistler T, Jones JF, Unger ER, Vernon SD Exercise responsive genes measured in peripheral blood of women with chronic fatigue syndrome and matched control subjects. BMC Physiol 5: 5. Human exercise-responsive transcripts 15790422 7,16
2005 Wild PJ|etAl RNA expression profiling of normal and tumor cells following photodynamic therapy with 5-aminolevulinic acid-induced protoporphyrin IX in vitro. Mol Cancer Ther 4: 516-528. Human endothelial cell line transcripts 15827324 7,16
2005 Williams DR, Epperson LE, Li W, Hughes MA, Taylor R, Rogers J, Martin SL, Cossins AR, Gracey AY The seasonally hibernating phenotype assessed through transcript screening. Physiol Genomics 24: 13-22. Ground squirrel transcripts 16249311 7
2005 Willinger T, Freeman T, Hasegawa H, McMichael AJ, Callan MF Molecular signatures distinguish human central memory from effector memory CD8 T cell subsets. J Immunol 175: 5895-5903. Human T cell transcripts 16237082 7,16
2005 Wiwatwattana N, Kumar A Organelle DB: a cross-species database of protein localization and function. Nucleic Acids Res 33: D598-D604. Organellar proteins 15608270 6,11
2005 Wolfe CJ, Kohane IS, Butte AJ Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks. BMC Bioinformatics 6: 227. Mammalian coexpression networks 16162296 7,9,13
2005 Wolstencroft K, McEntire R, Stevens R, Tabernero L, Brass A Constructing ontology-driven protein family databases. Bioinformatics 21: 1685-1692. 15564301 11,13,6
2005 Wong CE, Li Y, Whitty BR, Diaz-Camino C, Akhter SR, Brandle JE, Golding GB, Weretilnyk EA, Moffatt BA, Griffith M Expressed sequence tags from the Yukon ecotype of Thellungiella reveal that gene expression in response to cold, drought and salinity shows little overlap. Plant Mol Biol 58: 561-574. Thellungiella salsuginea ESTs 16021339 5
2005 Wong YF|etAl Genome-wide gene expression profiling of cervical cancer in Hong Kong women by oligonucleotide microarray. Int J Cancer 118: 2461-2469. Human cervical transcripts 16353136 7,16
2005 Woolfe A|etAl Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol 3: e7. 15630479 10.1371/journal.pbio.0030007 13
2005 Wu H, Mao F, Su Z, Olman V, Xu Y Prediction of functional modules based on gene distributions in microbial genomes. Genome Inform 16: 247-259. 16901107 17,18,19
2005 Wu H, Su Z, Mao F, Olman V, Xu Y Prediction of functional modules based on comparative genome analysis and Gene Ontology application. Nucleic Acids Res 33: 2822-2837. 15901854 13,19
2005 Xie K, Zhang J, Xiang Y, Feng Q, Han B, Chu Z, Wang S, Zhang Q, Xiong L Isolation and annotation of 10828 putative full length cDNAs from indica rice. Sci China C Life Sci 48: 445-451. Rice cDNAs 16315595 3
2005 Xie L, Bourne PE Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models. PLoS Comput Biol 1: e31. 16118666 10.1371/journal.pcbi.0010031 13,4
2005 Xiong H, He X, Ding C, Zhang Y, Kumar V, Holbrook SR Identification of functional modules in protein complexes via hyperclique pattern discovery. Pac Symp Biocomput 10: 221-232. 15759628 13,17
2005 Xu Q, Shaulsky G GOAT: An R tool for analysing Gene Ontology term enrichment. Appl Bioinformatics 4: 281-283. 16309346 10
2005 Yamakawa H, Maruhashi K, Nakao Y, Yamaguchi M Multi-aspect gene relation analysis. Pac Symp Biocomput 10: 233-244. Gene family analysis 15759629 13
2005 Yamamoto Y, Teratani T, Yamamoto H, Quinn G, Murata S, Ikeda R, Kinoshita K, Matsubara K, Kato T, Ochiya T Recapitulation of in vivo gene expression during hepatic differentiation from murine embryonic stem cells. Hepatology 42: 558-567. Mouse hepatocyte transcripts 16104048 7
2005 Yamashita R, Suzuki Y, Sugano S, Nakai K Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity. Gene 350: 129-136. Genomic analysis 15784181 13
2005 Yamazaki Y, Jaiswal P Biological ontologies in rice databases. An introduction to the activities in Gramene and Oryzabase. Plant Cell Physiol 46: 63-68. 15659431 11,15
2005 Yang C, Zeng E, Li T, Narasimhan G Clustering genes using gene expression and text literature data. Proc IEEE Comput Syst Bioinform Conf 4: 329-340. 16447990 7,12
2005 Yang F, Foekens JA, Yu J, Sieuwerts AM, Timmermans M, Klijn JG, Atkins D, Wang Y, Jiang Y Laser microdissection and microarray analysis of breast tumors reveal ER-alpha related genes and pathways. Oncogene 25: 1413-1419. Human breast tumor transcripts 16261164 7,16
2005 Yang SX, Simon RM, Tan AR, Nguyen D, Swain SM Gene expression patterns and profile changes pre- and post-erlotinib treatment in patients with metastatic breast cancer. Clin Cancer Res 11: 6226-6232. Human genes in breast cancer 16144925 7,16
2005 Yap YL, Wong MP, Zhang XW, Hernandez D, Gras R, Smith DK, Danchin A Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays. Nucleic Acids Res 33: 409-421. Human lung transcripts: 15653641 13,16
2005 Yeh CS, Wang JY, Cheng TL, Juan CH, Wu CH, Lin SR Fatty acid metabolism pathway play an important role in carcinogenesis of human colorectal cancers by Microarray-Bioinformatics analysis. Cancer Lett 233: 297-308. Human colorectal transcipts 15885896 7,16
2005 Yoon S, Benini L, De Micheli G Finding co-clusters of genes and clinical parameters. Conf Proc IEEE Eng Med Biol Soc 1: 906-912. 17282331 13,16
2005 Yoon S, De Micheli G Prediction and analysis of human microRNA regulatory modules. Conf Proc IEEE Eng Med Biol Soc 5: 4799-4802. 17281315 17,19
2005 Yoon S, De Micheli G Prediction of regulatory modules comprising microRNAs and target genes. Bioinformatics 21 Suppl 2: ii93-ii100. 16204133 13,19
2005 Young JA, Fivelman QL, Blair PL, de la Vega P, Le Roch KG, Zhou Y, Carucci DJ, Baker DA, Winzeler EA The Plasmodium falciparum sexual development transcriptome: A microarray analysis using ontology-based pattern identification. Mol Biochem Parasitol 143: 67-79. Plasmodium falciparum transcripts 16005087 7
2005 Yu AC Methods in biomedical ontology. J Biomed Inform 39: 252-266. 16387553 14
2005 Yu H, Gao L, Tu K, Guo Z Broadly predicting specific gene functions with expression similarity and taxonomy similarity. Gene 352: 75-81. 15927423 7,9
2005 Yu J|etAl The genomes of Oryza sativa: a history of duplications. PLoS Biol 3: e38. Rice genomic 15685292 10.1371/journal.pbio.0030038 4
2005 Yu P, Ma D, Xu M Nested genes in the human genome. Genomics 86: 414-422. Nested human genes 16084061 3,13,4
2005 Yu U, Choi YJ, Choi JK, Kim S TO-GO: a Java-based Gene Ontology navigation environment. Bioinformatics 21: 3580-3581. 15994194 10
2005 Zayas RM, Hernandez A, Habermann B, Wang Y, Stary JM, Newmark PA The planarian Schmidtea mediterranea as a model for epigenetic germ cell specification: Analysis of ESTs from the hermaphroditic strain. Proc Natl Acad Sci U S A 102: 18491-18496. Schmidtea mediterranea (planarian) ESTs 16344473 5,7
2005 Zeeberg BR|etAl High-Throughput GoMiner, an 'industrial-strength' integrative Gene Ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID). BMC Bioinformatics 6: 168. 15998470 7,10,16
2005 Zhang B, Kirov S, Snoddy J WebGestalt: an integrated system for exploring gene sets in various biological context Nucleic Acids Res 33: W741-W748. 15980575 7,10,12,13
2005 Zhang P, Foerster H, Tissier CP, Mueller L, Paley S, Karp PD, Rhee SY MetaCyc and AraCyc. Metabolic pathway databases for plant research. Plant Physiol 138: 27-37. 15888675 1,3,11
2005 Zindy P, Andrieux L, Bonnier D, Musso O, Langouet S, Campion JP, Turlin B, Clement B, Theret N Upregulation of DNA repair genes in active cirrhosis associated with hepatocellular carcinoma. FEBS Lett 579: 95-99. Human liver transcripts 15620696 7,16
2005 de la Cruz N|etAl The Rat Genome Database (RGD): developments towards a phenome database. Nucleic Acids Res 33: D485-D491. Rat 15608243 1,4,11
2005 van Lunteren E, Moyer M, Leahy P Gene expression profiling of diaphragm muscle in alpha2-laminin (merosin) deficient dy/dy dystrophic mice. Physiol Genomics 25: 85-95. Mouse transcripts 16368874 7,16
2006 Insights into social insects from the genome of the honeybee Apis mellifera. Nature 443: 931-949. Honeybee genomic 17073008 4
2006 Abdel-Aziz HO, Takasaki I, Tabuchi Y, Nomoto K, Murai Y, Tsuneyama K, Takano Y High-density oligonucleotide microarrays and functional network analysis reveal extended lung carcinogenesis pathway maps and multiple interacting genes in NNK [4-(methylnitrosamino)-1-(3-pyridyle)-1-butanone] induced CD1 mouse lung tumor. J Cancer Res Clin Oncol 133: 107-115. Mouse lung transcripts; tobacco smoke; lung cancer 16977459 7,16
2006 Adachi J, Kumar C, Zhang Y, Olsen JV, Mann M The human urinary proteome contains more than 1500 proteins including a large proportion of membranes proteins. Genome Biol 7: R80. Human urinary proteins 16948836 8
2006 Adryan B, Teichmann SA FlyTF: a systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster. Bioinformatics 22: 1532-1533. 16613907 11,13
2006 Alexa A, Rahnenfuhrer J, Lengauer T Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22: 1600-1607. 16606683 7,10
2006 Alonso-Calvo R, Maojo V, Billhardt H, Martin-Sanchez F, Garcia-Remesal M, Perez-Rey D An agent- and ontology-based system for integrating public gene, protein, and disease databases. J Biomed Inform 40: 17-29. 16621723 10,13
2006 Altenhein B, Becker A, Busold C, Beckmann B, Hoheisel JD, Technau GM Expression profiling of glial genes during Drosophila embryogenesis. Dev Biol 296: 545-560. Drosophila glial cell transcripts 16762338 7
2006 Alterovitz G, Xiang M, Mohan M, Ramoni MF GO PaD: the Gene Ontology Partition Database. Nucleic Acids Res 35: D322-D327. 17098937 11,13
2006 Altheide TK, Hayakawa T, Mikkelsen TS, Diaz SL, Varki NM, Varki A Systemwide genomic and biochemical comparisons of sialic acid biology amongst primates and rodents - evidence for two modes of rapid evolution. J Biol Chem 281: 25689-25702. 16769723 18
2006 Amariglio N, Jacob-Hirsch J, Shimoni A, Leiba M, Rechavi G, Nagler A Changes in gene expression pattern following granulocyte colony-stimulating factor administration to normal stem cell sibling donors. Acta Haematol 117: 68-73. Human hematopoietic stem cell transcripts; G-CSF treatment 17106189 7,16
2006 Ameur A, Yankovski V, Enroth S, Spjuth O, Komorowski J The LCB DataWareHouse. Bioinformatics 22: 1024-1026. 16455749 7,10,11,17
2006 Andreopoulos B, An A, Wang X Bi-level clustering of mixed categorical and numerical biomedical data. Int J Data Min Bioinform 1: 19-56. 18402041 10,12
2006 Aparicio G, Gotz S, Conesa A, Segrelles D, Blanquer I, Garcia JM, Hernandez V, Robles M, Talon M Blast2GO goes Grid: Developing a Grid-enabled prototype for functional genomics analysis. Stud Health Technol Inform 120: 194-204. 16823138 10
2006 Arbiza L, Dopazo J, Dopazo H Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome. PLoS Comput Biol 2: e38. 16683019 10.1371/journal.pcbi.0020038 18
2006 Argos M, Kibriya MG, Parvez F, Jasmine F, Rakibuz-Zaman M, Ahsan H Gene expression profiles in peripheral lymphocytes by arsenic exposure and skin lesion status in a Bangladeshi population. Cancer Epidemiol Biomarkers Prev 15: 1367-1375. Human transcripts; arsenic exposure 16835338 7,16
2006 Arnaiz O, Cain S, Cohen J, Sperling L ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. Nucleic Acids Res 35: D439-D444. Paramecium genome 17142227 4,11
2006 Ashley EA|etAl Network analysis of human in-stent restenosis. Circulation 114: 2644-2654. Human transcripts; coronary atheroma; in-stent restenosis 17145989 7,16
2006 Aslett M, Wood V Gene Ontology annotation status of the fission yeast genome: preliminary coverage approaches 100% Yeast 23: 913-919. Schizosaccharomyces pombe genomic 17072883 1,4,11
2006 Au AP, Li X, Gennari JH Differences Among Cell-structure Ontologies: FMA, GO, & CCO. AMIA Annu Symp Proc 2006:16-20. 17238294 14,15
2006 Aubry M, Monnier A, Chicault C, de Tayrac M, Galibert MD, Burgun A, Mosser J Combining evidence, biomedical literature and statistical dependence: new insights for functional annotation of gene sets. BMC Bioinformatics 7: 241. 16674810 7,9,12
2006 Azuaje F, Al-Shahrour F, Dopazo J Ontology-driven approaches to analyzing data in functional genomics. Methods Mol Biol 316: 67-86. 16671401 7,13,14,19
2006 Bachtiary B|etAl Gene expression profiling in cervical cancer: an exploration of intratumor heterogeneity. Clin Cancer Res 12: 5632-5640. Human cervical transcripts; cervical cancer 17020965 7,16
2006 Bahir I, Linial M Functional grouping based on signatures in protein termini. Proteins 63: 996-1004. 16475191 9,18
2006 Baitaluk M, Qian X, Godbole S, Raval A, Ray A, Gupta A PathSys: integrating molecular interaction graphs for systems biology. BMC Bioinformatics 7: 55. 16464251 10,11,17
2006 Bajic VB|etAl Mice and men: their promoter properties. PLoS Genet 2: e54. Human and mouse promoters 16683032 10.1371/journal.pgen.0020054 7,18
2006 Bakheet T, Williams BR, Khabar KS ARED 3.0: the large and diverse AU-rich transcriptome. Nucleic Acids Res 34: D111-D114. AU-rich element analysis 16381826 11,13
2006 Balasubramanian S, Sureshkumar S, Lempe J, Weigel D Potent induction of Arabidopsis thaliana flowering by elevated growth temperature. PLoS Genet 2: e106. Arabidopsis transcripts 16839183 10.1371/journal.pgen.0020106 7
2006 Ball CA, Brazma A MGED standards: Work in progress. OMICS 10: 138-144. 16901218 15
2006 Bandapalli OR|etAl Global analysis of host tissue gene expression in the invasive front of colorectal liver metastases. Int J Cancer 118: 74-89. Human & mouse liver transcripts 16080196 7,16
2006 Bandyopadhyay D, Huan J, Liu J, Prins J, Snoeyink J, Wang W, Tropsha A Structure-based function inference using protein family-specific fingerprints. Protein Sci 15: 1537-1543. 16731985 9
2006 Bao L|etAl Combining gene expression QTL mapping and phenotypic spectrum analysis to uncover gene regulatory relationships. Mamm Genome 17: 575-583. 16783639 15
2006 Barrey E, Mucher E, Robert C, Amiot F, Gidrol X Gene expression profiling in blood cells of endurance horses completing competition or disqualified due to metabolic disorder. Equine Vet J Suppl 36:43-49. Horse leukocyte transcripts 17402390 7
2006 Barth AS|etAl Identification of a common gene expression signature in dilated cardiomyopathy across independent microarray studies. J Am Coll Cardiol 48: 1610-1617. Human cardiac transcripts; dilated cardiomyopathy 17045896 7,16
2006 Barutcuoglu Z, Schapire RE, Troyanskaya OG Hierarchical multi-label prediction of gene function. Bioinformatics 22: 830-836. 16410319 9
2006 Batada NN, Hurst LD, Tyers M Evolutionary and physiological importance of hub proteins. PLoS Comput Biol 2: e88. Saccharomyces proteins 16839197 10.1371/journal.pcbi.0020088 8,17
2006 Begg AC Can the severity of normal tissue damage after radiation therapy be predicted? PLoS Med 3: e440. 17076565 10.1371/journal.pmed.0030440 16
2006 Beissbarth T [18] Interpreting experimental results using gene ontologies. Methods Enzymol 411: 340-352. 16939799 7,8,10,11,12
2006 Beisvag V, Junge FK, Bergum H, Jolsum L, Lydersen S, Gunther CC, Ramampiaro H, Langaas M, Sandvik AK, Laegreid A GeneTools--application for functional annotation and statistical hypothesis testing. BMC Bioinformatics 7: 470. 17062145 10
2006 Beisvag V, Lehre PK, Midelfart H, Aass H, Geiran O, Sandvik AK, Laegreid A, Komorowski J, Ellingsen O Aetiology-specific patterns in end-stage heart failure patients identified by functional annotation and classification of microarray data. Eur J Heart Fail 8: 381-389. Human heart transcripts; heart disease 16753336 7,16
2006 Beyer A, Workman C, Hollunder J, Radke D, Moller U, Wilhelm T, Ideker T Integrated assessment and prediction of transcription factor binding. PLoS Comput Biol 2: e70. Saccharomyces transcription factor binding sites 16789814 10.1371/journal.pcbi.0020070 7,13,19
2006 Bidaut G, Suhre K, Claverie JM, Ochs MF Determination of strongly overlapping signaling activity from microarray data. BMC Bioinformatics 7: 99. 16507110 7
2006 Blake JA, Bult CJ Beyond the data deluge: Data integration and bio-ontologies. J Biomed Inform 39: 314-320. 16564748 1,2,11,14,18
2006 Blanchard Y, Le Meur N, Le Cunff M, Blanchard P, Leger J, Jestin A Cellular gene expression survey of PseudoRabies Virus (PRV) infected Human Embryonic Kidney cells (HEK-293). Vet Res 37: 705-723. Human embryonic kidney cell transcripts; PRV infection 16820135 7,16
2006 Blei DM, Franks K, Jordan MI, Mian IS Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to life span. BMC Bioinformatics 7: 250. 16681860 12
2006 Bonnet A, Frappart PO, Dehais P, Tosser-Klopp G, Hatey F Identification of differential gene expression in in vitro FSH treated pig granulosa cells using suppression subtractive hybridization. Reprod Biol Endocrinol 4: 35. Pig granulosa cell genes 16827936 7
2006 Booms P|etAl A fibrillin-1-fragment containing the elastin-binding-protein GxxPG consensus sequence upregulates matrix metalloproteinase-1: biochemical and computational analysis. J Mol Cell Cardiol 40: 234-246. Human proteome 16442122 8,16
2006 Bosco MC, Puppo M, Santangelo C, Anfosso L, Pfeffer U, Fardin P, Battaglia F, Varesio L Hypoxia modifies the transcriptome of primary human monocytes: modulation of novel immune-related genes and identification of CC-chemokine ligand 20 as a new hypoxia-inducible gene. J Immunol 177: 1941-1955. Human monocyte transcripts; hypoxia 16849508 7,16
2006 Boverhof DR, Burgoon LD, Tashiro C, Sharratt B, Chittim B, Harkema JR, Mendrick DL, Zacharewski TR Comparative toxicogenomic analysis of the hepatotoxic effects of TCDD in Sprague Dawley rats and C57BL/6 mice. Toxicol Sci 94: 398-416. Mouse and rat liver transcripts; TCDD exposure 16960034 7,16
2006 Brameier M, Wiuf C Co-clustering and visualization of gene expression data and gene ontology terms for Saccharomyces cerevisiae using self-organizing maps. J Biomed Inform 40: 160-173. Saccharomyces genes 16824804 7,9
2006 Bresell A, Servenius B, Persson B Ontology annotation treebrowser: an interactive tool where the complementarity of medical subject headings and gene ontology improves the interpretation of gene lists. Appl Bioinformatics 5: 225-236. 17140269 10
2006 Brooksbank C, Quackenbush J Data standards: a call to action. OMICS 10: 94-99. 16901212 14
2006 Brown D, Sjolander K Functional classification using phylogenomic inference. PLoS Comput Biol 2: e77. 16846248 10.1371/journal.pcbi.0020077 3
2006 Brown M, Davies IM, Moffat CF, Craft JA Application of SSH and a macroarray to investigate altered gene expression in Mytilus edulis in response to exposure to benzo[a]pyrene. Mar Environ Res 62 Suppl 1: S128-S135. Mussel ESTs; benzo[a]pyrene exposure 16712918 7
2006 Brown SD, Hancock JM, Gates H Understanding Mammalian Genetic Systems: The Challenge of Phenotyping in the Mouse. PLoS Genet 2: e118. 16933996 10.1371/journal.pgen.0020118 15
2006 Buchholz DR, Heimeier RA, Das B, Washington T, Shi YB Pairing morphology with gene expression in thyroid hormone-induced intestinal remodeling and identification of a core set of TH-induced genes across tadpole tissues. Dev Biol 303: 576-590. Xenopus tadpole intestinal transcripts 17214978 7
2006 Buettner P, Mosig S, Lechtermann A, Funke H, Mooren FC Exercise affects the gene expression profiles of human white blood cells. J Appl Physiol 102: 26-36. Human white blood cell transcripts; exercise 16990507 7,16
2006 Bukowski R, Hankins GD, Saade GR, Anderson GD, Thornton S Labor-associated gene expression in the human uterine fundus, lower segment, and cervix. PLoS Med 3: e169. Human uterine and cervical transcripts; labor 16768543 10.1371/journal.pmed.0030169 7,16
2006 Buttner P, Mosig S, Funke H Gene expression profiles of T lymphocytes are sensitive to the influence of heavy smoking: a pilot study. Immunogenetics 59: 37-43. Human T cell transcripts; cigarette smoke 17149619 7,16
2006 Cai Z, Mao X, Li S, Wei L Genome comparison using Gene Ontology (GO) with statistical testing. BMC Bioinformatics 7: 374. 16901353 18
2006 Camon E, Barrell D, Dimmer E, Lee V. The Gene Ontology Annotation (GOA) database. In Silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins. [N. Mulder (ed.), Nova Science Publishers, New York.] 1,3,11
2006 Cao D, Cheng H, Wu W, Meng Soo H, Peng J Gibberllin mobilizes distinct DELLA-dependent transcriptomes to regulate seed germination and floral development in Arabidopsis. Plant Physiol 142: 509-525. Arabidopsis transcripts 16920880 7
2006 Cao R, Li X, Liu Z, Peng X, Hu W, Wang X, Chen P, Xie J, Liang S Integration of a two-phase partition method into proteomics research on rat liver plasma membrane proteins. J Proteome Res 5: 634-642. Rat liver membrane proteins 16512679 8
2006 Capurso G|etAl Gene expression profiles of progressive pancreatic endocrine tumours and their liver metastases reveal potential novel markers and therapeutic targets. Endocr Relat Cancer 13: 541-558. Human transcripts; pancreatic endocrine cancer 16728581 7,16
2006 Carmona-Saez P, Chagoyen M, Rodriguez A, Trelles O, Carazo JM, Pascual-Montano A Integrated analysis of gene expression by association rules discovery. BMC Bioinformatics 7: 54. 16464256 7,10,12
2006 Carroll S, Pavlovic V Protein classification using probabilistic chain graphs and the Gene Ontology structure. Bioinformatics 22: 1871-1878. 16705013 9
2006 Cashion A, Driscoll C, Conley Y, Xu L, Mandrell B, Homayouni R Pilot study examining the utility of microarray data to identify genes associated with weight in transplant recipients. Nurs Health Sci 8: 125. Human transcripts; obesity; transplants 16764567 7,16
2006 Chagoyen M, Carmona-Saez P, Gil C, Carazo JM, Pascual-Montano A A literature-based similarity metric for biological processes. BMC Bioinformatics 7: 363. 16872502 12,13
2006 Che D, Li G, Mao F, Wu H, Xu Y Detecting uber-operons in prokaryotic genomes. Nucleic Acids Res 34: 2418-2427. 16682449 18,19
2006 Chen CF, Feng X, Szeto J Identification of critical genes in microarray experiments by a Neuro-Fuzzy approach. Comput Biol Chem 30: 372-381. 16987708 7,13
2006 Chen CH, Lin EC, Cheng WT, Sun HS, Mersmann HJ, Ding ST Abundantly expressed genes in pig adipose tissue: an expressed sequence tag approach. J Anim Sci 84: 2673-2683. Pig adipose tissue ESTs 16971568 5,7
2006 Chen G, Larsen P, Almasri E, Dai Y Sample scale-free gene regulatory network using gene ontology. Conf Proc IEEE Eng Med Biol Soc 1: 5523-5526. 17946312 17
2006 Chen JY, Shen C, Yan Z, Brown DP, Wang M A systems biology case study of ovarian cancer drug resistance. Comput Syst Bioinformatics Conf 2006: 389-398. Human ovarian cell line proteins; ovarian cancer; drug resistance 17369659 8,16,17
2006 Chen T, Guo L, Zhang L, Shi L, Fang H, Sun Y, Fuscoe JC, Mei N Gene expression profiles distinguish the carcinogenic effects of aristolochic acid in target (kidney) and non-target (liver) tissues in rats. BMC Bioinformatics 7 Suppl 2: S20. Rat liver and kidney transcripts; aristolochic acid exposure 17118142 7,16
2006 Chen X, Wu JM, Hornischer K, Kel A, Wingender E TiProD: the Tissue-specific Promoter Database. Nucleic Acids Res 34: D104-D107. Tissue-specific promoters 16381824 3,11
2006 Chen Z, Wang W, Ling XB, Liu JJ, Chen L GO-Diff: Mining functional differentiation between EST-based transcriptomes. BMC Bioinformatics 7: 72. EST libraries 16480524 7,10
2006 Cheng SL, Huang Liu R, Sheu JN, Chen ST, Sinchaikul S, Tsay GJ Toxicogenomics of kojic acid on gene expression profiling of a375 human malignant melanoma cells. Biol Pharm Bull 29: 655-669. Human skin cell transcripts; melanoma 16595896 7,16
2006 Cheng SL, Liu RH, Sheu JN, Chen ST, Sinchaikul S, Tsay GJ Toxicogenomics of A375 human malignant melanoma cells treated with arbutin. J Biomed Sci 14: 87-8105. Human transcripts; malignant melanoma; arbutin treatment 17103032 7,16
2006 Cheng TC, Manorek G, Samimi G, Lin X, Berry CC, Howell SB Identification of genes whose expression is associated with cisplatin resistance in human ovarian carcinoma cells. Cancer Chemother Pharmacol 58: 384-395. Human ovarian transcripts 16404635 7,16
2006 Cherry S, Kunte A, Wang H, Coyne C, Rawson RB, Perrimon N COPI activity coupled with fatty acid biosynthesis is required for viral replication. PLoS Pathog 2: e102. 17040126 10.1371/journal.ppat.0020102 13,16
2006 Cheung F, Haas BJ, Goldberg SM, May GD, Xiao Y, Town CD Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology. BMC Genomics 7: 272. Medicago ESTs 17062153 5
2006 Chiang JH, Shin JW, Liu HH, Chin CL GeneLibrarian: an effective gene-information summarization and visualization system. BMC Bioinformatics 7: 392. 16939640 10,12
2006 Cho EM, Boucias D, Keyhani NO EST analysis of cDNA libraries from the entomopathogenic fungus Beauveria (Cordyceps) bassiana. II. Fungal cells sporulating on chitin and producing oosporein. Microbiology 152: 2855-2864. Beauveria ESTs 16946279 5
2006 Cho EM, Liu L, Farmerie W, Keyhani NO EST analysis of cDNA libraries from the entomopathogenic fungus Beauveria (Cordyceps) bassiana. I. Evidence for stage-specific gene expression in aerial conidia, in vitro blastospores and submerged conidia. Microbiology 152: 2843-2854. Beauveria ESTs 16946278 5
2006 Chou KC, Cai YD Predicting protein-protein interactions from sequences in a hybridization space. J Proteome Res 5: 316-322. Saccharomyces proteins 16457597 8,17
2006 Chou KC, Shen HB Hum-PLoc: A novel ensemble classifier for predicting human protein subcellular localization. Biochem Biophys Res Commun 347: 150-157. 16808903 9,10
2006 Chou KC, Shen HB Large-scale predictions of gram-negative bacterial protein subcellular locations. J Proteome Res 5: 3420-3428. 17137343 9,10
2006 Chow LS, Greenlund LJ, Asmann YW, Short KR, McCrady S, Levine JA, Nair KS Impact of endurance training on murine spontaneous activity, muscle mitochondrial dna abundance, gene transcripts and function. J Appl Physiol 102: 1078-1089. Mouse transcripts; endurance training 17110513 7,16
2006 Choy KW|etAl Molecular characterization of the developmental gene in eyes: Through data-mining on integrated transcriptome databases. Clin Biochem 39: 224-230. Human fetal eye ESTs 16427038 5,7,12,16
2006 Chun CK|etAl An annotated cDNA library of juvenile Euprymna scolopes with and without colonization by the symbiont Vibrio fischeri. BMC Genomics 7: 154. Euprymna scolopes ESTs 16780587 5,13
2006 Cimino JJ, Zhu X The practical impact of ontologies on biomedical informatics. Methods Inf Med 45 Suppl 1: 124-135. 17051306 14
2006 Clare A, Karwath A, Ougham H, King RD Functional bioinformatics for Arabidopsis thaliana. Bioinformatics 22: 1130-1136. 16481336 9
2006 Clemente EJ, Furlong RA, Loveland KL, Affara NA Gene expression study in the juvenile mouse testis: identification of stage-specific molecular pathways during spermatogenesis. Mamm Genome 17: 956-975. Mouse testis transcripts 16964443 7
2006 Cochrane G|etAl EMBL Nucleotide Sequence Database: developments in 2005. Nucleic Acids Res 34: D10-15. EMBL-Bank 16381823 11
2006 Coller HA, Sang L, Roberts JM A new description of cellular quiescence. PLoS Biol 4: e83. Human fibroblast transcripts 16509772 10.1371/journal.pbio.0040083 7
2006 Coppola G, Choi SH, Santos MM, Miranda CJ, Tentler D, Wexler EM, Pandolfo M, Geschwind DH Gene expression profiling in frataxin deficient mice: Microarray evidence for significant expression changes without detectable neurodegeneration. Neurobiol Dis 22: 302-311. Mouse transcripts 16442805 7,16
2006 Corton M, Botella-Carretero JI, Benguria A, Villuendas G, Zaballos A, San Millan JL, Escobar-Morreale HF, Peral B Differential gene expression profile in omental adipose tissue in women with polycystic ovary syndrome. J Clin Endocrinol Metab 92: 328-337. Human adipose tissue transcripts; polycystic ovary syndrome 17062763 7,16
2006 Couto FM, Silva MJ, Lee V, Dimmer E, Camon E, Apweiler R, Kirsch H, Rebholz-Schuhmann D GOAnnotator: linking protein GO annotations to evidence text. J Biomed Discov Collab 1: 19. 17181854 9,10,12
2006 Coyle DE Spinal cord transcriptional profile analysis reveals protein trafficking and RNA processing as prominent processes regulated by tactile allodynia. Neuroscience 144: 144-156. Rat spinal cord transcripts; tactile allodynia 17069981 7,16
2006 Cristino AS, Nascimento AM, Costa Lda F, Simoes ZL A comparative analysis of highly conserved sex-determining genes between Apis mellifera and Drosophila melanogaster. Genet Mol Res 5: 154-168. 16755507 18,19
2006 Cristino AS, Nunes FM, Lobo CH, Bitondi MM, Simoes ZL, da Fontoura Costa L, Lattorff HM, Moritz RF, Evans JD, Hartfelder K Caste development and reproduction: a genome-wide analysis of hallmarks of insect eusociality. Insect Mol Biol 15: 703-714. Honeybee ESTs 17069641 5
2006 Cui Q, Yu Z, Pan Y, Purisima EO, Wang E MicroRNAs preferentially target the genes with high transcriptional regulation complexity. Biochem Biophys Res Commun 352: 733-738. 17141185 7,17
2006 Cui XS, Li XY, Shen XH, Bae YJ, Kang JJ, Kim NH Transcription profile in mouse four-cell, morula, and blastocyst: Genes implicated in compaction and blastocoel formation. Mol Reprod Dev 74: 133-143. Mouse embryonic transcripts 16998848 7
2006 Dang VH, Choi KC, Hyun SH, Jeung EB Analysis of gene expression profiles in the offspring of rats following maternal exposure to xenoestrogens. Reprod Toxicol 23: 42-54. Rat uterine transcripts; xenoestrogen exposure 17011747 7,16
2006 Datta S, Datta S Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes. BMC Bioinformatics 7: 397. 16945146 7
2006 Davis MJ|etAl Differential use of signal peptides and membrane domains is a common occurrence in the protein output of transcriptional units. PLoS Genet 2: e46. Mouse transcripts and proteins 16683029 10.1371/journal.pgen.0020046 7,13
2006 Delongchamp R, Lee T, Velasco C A method for computing the overall statistical significance of a treatment effect among a group of genes. BMC Bioinformatics 7 Suppl 2: S11. 17118132 7
2006 Diehn M, Bhattacharya R, Botstein D, Brown PO Genome-scale identification of membrane-associated human mRNAs. PLoS Genet 2: e11. Human mRNAs 16415983 10.1371/journal.pgen.0020011 7,13
2006 Dieterich DC, Link AJ, Graumann J, Tirrell DA, Schuman EM Selective identification of newly synthesized proteins in mammalian cells using bioorthogonal noncanonical amino acid tagging (BONCAT). Proc Natl Acad Sci U S A 103: 9482-9487. Mammalian proteins 16769897 8
2006 Doherty JM, Carmichael LK, Mills JC GOurmet: A tool for quantitative comparison and visualization of gene expression profiles based on gene ontology (GO) distributions. BMC Bioinformatics 7: 151. 16545118 7,10
2006 Dong Y, Aguilar R, Xi Z, Warr E, Mongin E, Dimopoulos G Anopheles gambiae immune responses to human and rodent Plasmodium parasite species. PLoS Pathog 2: e52. Plasmodium transcripts; malaria 16789837 10.1371/journal.ppat.0020052 7,16
2006 Draghici S, Sellamuthu S, Khatri P Babel's tower revisited: a universal resource for cross-referencing across annotation databases. Bioinformatics 22: 2934-2939. 17068090 10
2006 Duan ZH, Hughes B, Reichel L, Perez DM, Shi T The relationship between protein sequences and their gene ontology functions. BMC Bioinformatics 7 Suppl 4: S11. 17217503 8,9
2006 Edwards AC, Rollmann SM, Morgan TJ, Mackay TF Quantitative genomics of aggressive behavior in Drosophila melanogaster. PLoS Genet 2: e154. Drosophila transcripts; aggressive behavior 17044737 10.1371/journal.pgen.0020154 7,18
2006 Eisele L, Klein-Hitpass L, Chatzimanolis N, Opalka B, Boes T, Seeber S, Moritz T, Flasshove M Differential expression of drug resistance-related genes between sensitive and resistant blasts in acute myeloid leukemia. Acta Haematol 117: 8-15. Human transcripts; acute myeloid leukemia 17095854 7,16
2006 Eisen JA|etAl Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote. PLoS Biol 4: e286. Tetrahymena genome 16933976 10.1371/journal.pbio.0040286 4,11
2006 Eklind S, Hagberg H, Wang X, Savman K, Leverin AL, Hedtjarn M, Mallard C Effect of lipopolysaccharide on global gene expression in the immature rat brain. Pediatr Res 60: 161-168. Rat brain transcripts; lipopolysaccharide exposure 16864697 7
2006 Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE The mouse genome database (MGD): new features facilitating a model system. Nucleic Acids Res 35: D630-D637. Mouse genome 17135206 1,4,11,15
2006 Ernst J, Bar-Joseph Z STEM: a tool for the analysis of short time series gene expression data. BMC Bioinformatics 7: 191. 16597342 7,10
2006 Espadaler J, Querol E, Aviles FX, Oliva B Identification of function-associated loop motifs and application to protein function prediction. Bioinformatics 22: 2237-2243. 16870939 9
2006 Estrada B, Choe SE, Gisselbrecht SS, Michaud S, Raj L, Busser BW, Halfon MS, Church GM, Michelson AM An integrated strategy for analyzing the unique developmental programs of different myoblast subtypes. PLoS Genet 2: e16. Drosophila embryonic mesoderm transcripts 16482229 10.1371/journal.pgen.0020016 7,13
2006 Falcon S, Gentleman R Using GOstats to test gene lists for GO term association. Bioinformatics 23: 257-258. 17098774 10
2006 Fang Z, Liu L, Yang J, Luo QM, Li YX Comparisons of Graph-structure Clustering Methods for Gene Expression Data. Acta Biochim Biophys Sin (Shanghai) 38: 379-384. 16761095 7,12,13
2006 Felitti S|etAl Transcriptome analysis of Neotyphodium and Epichloo grass endophytes. Fungal Genet Biol 43: 465-475. Grass endophyte genes and transcripts 16554176 3,7
2006 Field D, Morrison N, Selengut J, Sterk P Meeting report: eGenomics: Cataloguing our complete genome collection II. OMICS 10: 100-104. 16901213 15
2006 Field D, Sansone SA A special issue on data standards. OMICS 10: 84-93. 16901211 14
2006 Fischer M, Oberthuer A, Brors B, Kahlert Y, Skowron M, Voth H, Warnat P, Ernestus K, Hero B, Berthold F Differential expression of neuronal genes defines subtypes of disseminated neuroblastoma with favorable and unfavorable outcome. Clin Cancer Res 12: 5118-5128. Human neuronal transcripts; neuroblastoma 16951229 7,16
2006 Fitzgerald PC, Sturgill D, Shyakhtenko A, Oliver B, Vinson C Comparative genomics of Drosophila and human core promoters. Genome Biol 7: R53. Drosophila and human promoters 16827941 7,13
2006 Fleming K, Kelley LA, Islam SA, MacCallum RM, Muller A, Pazos F, Sternberg MJ The proteome: structure, function and evolution. Philos Trans R Soc Lond B Biol Sci 361: 441-451. 16524832 8,9,18
2006 Flores S, Echols N, Milburn D, Hespenheide B, Keating K, Lu J, Wells S, Yu EZ, Thorpe M, Gerstein M The Database of Macromolecular Motions: new features added at the decade mark. Nucleic Acids Res 34: D296-D301. Macromolecular motions 16381870 6,11
2006 Forbus J, Spratt H, Wiktorowicz J, Wu Z, Boldogh I, Denner L, Kurosky A, Brasier RC, Luxon B, Brasier AR Functional analysis of the nuclear proteome of human A549 alveolar epithelial cells by HPLC-high resolution 2-D gel electrophoresis. Proteomics 6: 2656-2672. Human nuclear proteins 16586437 8,16
2006 Franke L, Bakel H, Fokkens L, de Jong ED, Egmont-Petersen M, Wijmenga C Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. Am J Hum Genet 78: 1011-1025. Hmuan disease genes 16685651 16,17
2006 Fridman AL, Tang L, Kulaeva OI, Ye B, Li Q, Nahhas F, Roberts PC, Land SJ, Abrams J, Tainsky MA Expression profiling identifies three pathways altered in cellular immortalization: interferon, cell cycle, and cytoskeleton. J Gerontol A Biol Sci Med Sci 61: 879-889. Human cell line transcripts; immortalization 16960018 7,16
2006 Friedman C, Borlawsky T, Shagina L, Xing HR, Lussier YA Bio-ontology and text: bridging the modeling gap. Bioinformatics 22: 2421-2429. 16870928 12
2006 Frith MC, Forrest AR, Nourbakhsh E, Pang KC, Kai C, Kawai J, Carninci P, Hayashizaki Y, Bailey TL, Grimmond SM The abundance of short proteins in the mammalian proteome. PLoS Genet 2: e52. Mouse proteins 16683031 10.1371/journal.pgen.0020052 6,8
2006 Fu C, Hickey M, Morrison M, McCarter R, Han ES Tissue specific and non-specific changes in gene expression by aging and by early stage CR. Mech Ageing Dev 127: 905-916. Mouse genes; caloric restriction 17092546 7
2006 Fujita H, Samejima H, Kitagawa N, Mitsuhashi T, Washio T, Yonemoto J, Tomita M, Takahashi T, Kosaki K Genome-wide screening of dioxin-responsive genes in fetal brain: bioinformatic and experimental approaches. Congenit Anom (Kyoto) 46: 135-143. Mouse fetal transcripts; dioxin exposure 16922920 7,16
2006 Fukushima K, Ueno Y Bioinformatic approach for understanding the heterogeneity of cholangiocytes. World J Gastroenterol 12: 3481-3486. Moune cholangiocyte transcripts 16773705 7
2006 Gaffney DJ, Keightley PD Genomic selective constraints in murid noncoding DNA. PLoS Genet 2: e204. 17166057 10.1371/journal.pgen.0020204 18
2006 Galamb O, Sipos F, Dinya E, Spisak S, Tulassay Z, Molnar B mRNA expression, functional profiling and multivariate classification of colon biopsy specimen by cDNA overall glass microarray. World J Gastroenterol 12: 6998-7006. Human colon transcripts; inflammatory and neoplastic diseases 17109495 7,16
2006 Gamberoni G, Storari S, Volinia S Finding biological process modifications in cancer tissues by mining gene expression correlations. BMC Bioinformatics 7: 6. Human liver cell transcripts; liver cancer 16401337 7,16
2006 Gao G, Zhong Y, Guo A, Zhu Q, Tang W, Zheng W, Gu X, Wei L, Luo J DRTF: a database of rice transcription factors. Bioinformatics 22: 1286-1287. Rice transcription factors 16551659 6,11
2006 Garcia O, Saveanu C, Cline M, Fromont-Racine M, Jacquier A, Schwikowski B, Aittokallio T GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. Bioinformatics 23: 394-396. 17127678 10
2006 Ghazalpour A|etAl Integrating Genetic and Network Analysis to Characterize Genes Related to Mouse Weight. PLoS Genet 2: e130. Mouse QTLs and transcripts; weight 16934000 10.1371/journal.pgen.0020130 7,16,17
2006 Giannakis M|etAl Molecular properties of adult mouse gastric and intestinal epithelial progenitors in their niches. J Biol Chem 281: 11292-11300. Mouse gastric and epithelial genes 16464855 5,7,17
2006 Giorgi RR, Correa-Giannella ML, Casarini AP, Machado MC, Bronstein MD, Cescato VA, Giannella-Neto D Metallothionein Isoform 3 gene is differentially expressed in corticotropin-producing pituitary adenomas. Neuroendocrinology 82: 208-214. Human pituitary transcripts; pituitary adenoma 16601360 7,16
2006 Giusti B|etAl A model of anti-angiogenesis: Differential transcriptosome profiling of microvascular endothelial cells from diffuse systemic sclerosis patients. Arthritis Res Ther 8: R115. Human endothelial cell transcripts; systemic sclerosis 16859528 7,16
2006 Glebov OK, Rodriguez LM, Lynch P, Patterson S, Lynch H, Nakahara K, Jenkins J, Cliatt J, Humbyrd CJ, Denobile J, Soballe P, Gallinger S, Buchbinder A, Gordon G, Hawk E, Kirsch IR Celecoxib treatment alters the gene expression profile of normal colonic mucosa. Cancer Epidemiol Biomarkers Prev 15: 1382-1391. Human colonic mucosal transcripts; celecoxib treatment 16835340 7,16
2006 Glover CH, Marin M, Eaves CJ, Helgason CD, Piret JM, Bryan J Meta-analysis of differentiating mouse embryonic stem cell gene expression kinetics reveals early change of a small gene set. PLoS Comput Biol 2: e158. Mouse embryonic stem cell transcripts 17121458 10.1371/journal.pcbi.0020158 7
2006 Glover CH, Marin M, Eaves CJ, Helgason CD, Piret JM, Bryan J Meta-analysis of differentiating mouse embryonic stem cell gene expression kinetics reveals early change of a small gene set. PLoS Comput Biol 2: e158. Mouse transcripts 17121458 10.1371/journal.pcbi.0020158 7
2006 Glyn-Jones S, Song S, Black MA, Phillips AR, Choong SY, Cooper GJ Transcriptomic Analysis of the Cardiac Left Ventricle in a Rodent Model of Diabetic Cardiomyopathy Molecular Snapshot of a Severe Myocardial Disease. Physiol Genomics 28: 284-293. Rat heart transcripts; diabetic cardiomyopathy 17062650 7,16
2006 Goffard N, Weiller G Extending MapMan: application to legume genome arrays. Bioinformatics 22: 2958-2959. 17046975 9,10
2006 Gold DL, Coombes KR, Wang J, Mallick B Enrichment analysis in high-throughput genomics--accounting for dependency in the NULL. Brief Bioinform 8: 71-77. 17077137 7,13
2006 Goodstadt L, Ponting CP Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human. PLoS Comput Biol 2: e133. 17009864 10.1371/journal.pcbi.0020133 18
2006 Gorter JA, van Vliet EA, Aronica E, Breit T, Rauwerda H, Lopes da Silva FH, Wadman WJ Potential new antiepileptogenic targets indicated by microarray analysis in a rat model for temporal lobe epilepsy. J Neurosci 26: 11083-11110. Rat brain transcripts; epilepsy 17065450 7,16
2006 Grigoryev DN, Liu M, Cheadle C, Barnes KC, Rabb H Genomic profiling of kidney ischemia-reperfusion reveals expression of specific alloimmunity-associated genes: linking "immune" and "nonimmune" injury events. Transplant Proc 38: 3333-3336. Mouse kidney transcripts; ischemia-reperfusion 17175265 7,16
2006 Grinde B, Gayorfar M, Rinaldo CH Impact of a polyomavirus (BKV) infection on mRNA expression in human endothelial cells. Virus Res 123: 86-94. Human endothelial cell transcripts; polyoma virus infection 16996634 7,16
2006 Groth P, Pavlova N, Kalev I, Tonov S, Georgiev G, Pohlenz HD, Weiss B PhenomicDB: a new cross-species genotype/phenotype resource. Nucleic Acids Res 35: D696-D699. 16982638 11,15
2006 Guisbert KS, Li H, Guthrie C Alternative 3' pre-mRNA processing in Saccharomyces cerevisiae is modulated by Nab4/Hrp1 in vivo. PLoS Biol 5: e6. Saccharomyces transcripts 17194212 10.1371/journal.pbio.0050006 7
2006 Guo L|etAl Rat toxicogenomic study reveals analytical consistency across microarray platforms. Nat Biotechnol 24: 1162-1169. Rat transcripts 17061323 7,13
2006 Guo L|etAl Rat toxicogenomic study reveals analytical consistency across microarray platforms. Nat Biotechnol 24: 1162-1169. Rat transcripts; toxicogenomics 16964230 7,16
2006 Guo X, Liu R, Shriver CD, Hu H, Liebman MN Assessing semantic similarity measures for the characterization of human regulatory pathways. Bioinformatics 22: 967-973. 16492685 13,17
2006 Haarer B, Viggiano S, Hibbs MA, Troyanskaya OG, Amberg DC Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies. Genes Dev 21: 148-159. 17167106 13,17
2006 Haas CS, Creighton CJ, Pi X, Maine I, Koch AE, Haines GK, Ling S, Chinnaiyan AM, Holoshitz J Identification of genes modulated in rheumatoid arthritis using complementary DNA microarray analysis of lymphoblastoid B cell lines from disease-discordant monozygotic twins. Arthritis Rheum 54: 2047-2060. Human transcripts; rheumatoid arthritis 16804865 7,16
2006 Haddad R, Tromp G, Kuivaniemi H, Chaiworapongsa T, Kim YM, Mazor M, Romero R Human spontaneous labor without histologic chorioamnionitis is characterized by an acute inflammation gene expression signature. Am J Obstet Gynecol 195: 394.e1-24. Human chorioamniotic membrane transcripts; labor 16890549 7,16
2006 Han JY, Park TS, Kim JN, Kim MA, Lim D, Lim JM, Kim H Gene expression profiling of chicken primordial germ cell ESTs. BMC Genomics 7: 220. Chicken ESTs 16939661 7
2006 Harrison RA, Ibison F, Wilbraham D, Wagstaff SC Identification of cDNAs encoding viper venom hyaluronidases: Cross-generic sequence conservation of full-length and unusually short variant transcripts. Gene 392: 22-33. Viper ESTs 17210232 5
2006 Hasegawa Y|etAl A flexible representation of omic knowledge for thorough analysis of microarray data. Plant Methods 2: 5. 16509996 7,13
2006 Hassan SS, Romero R, Haddad R, Hendler I, Khalek N, Tromp G, Diamond MP, Sorokin Y, Malone J The transcriptome of the uterine cervix before and after spontaneous term parturition. Am J Obstet Gynecol 195: 778-786. Human uterine cervical transcripts; labor 16949412 7,16
2006 Haston CK, Cory S, Lafontaine L, Dorion G, Hallett MT Strain-dependent pulmonary gene expression profiles of a cystic fibrosis mouse model. Physiol Genomics 25: 336-345. Mouse lung genes & ESTs; cystic fibrosis 16614460 7,16
2006 Hawkins T, Luban S, Kihara D Enhanced automated function prediction using distantly related sequences and contextual association by PFP. Protein Sci 15: 1550-1556. 16672240 9
2006 Hayashizaki Y, Carninci P Genome Network and FANTOM3: assessing the complexity of the transcriptome. PLoS Genet 2: e63. Mouse genome 16683037 10.1371/journal.pgen.0020063 4
2006 Haynes C, Oldfield CJ, Ji F, Klitgord N, Cusick ME, Radivojac P, Uversky VN, Vidal M, Iakoucheva LM Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes. PLoS Comput Biol 2: e100. Eukaryotic proteins 16884331 10.1371/journal.pcbi.0020100 8,17
2006 Hecht J|etAl Detection of novel skeletogenesis target genes by comprehensive analysis of a Runx2(-/-) mouse model. Gene Expr Patterns 7: 102-112. Mouse embryonic bone transcripts 16829211 7,16
2006 Higo M|etAl Enhancement of SPHK1 in vitro by carbon ion irradiation in oral squamous cell carcinoma. Int J Radiat Oncol Biol Phys 65: 867-875. Human transcripts; oral squamous cell carcinoma 16751068 7,16
2006 Hinrichs AS|etAl The UCSC Genome Browser Database: update 2006. Nucleic Acids Res 34: D590-598. UCSC Genome Browser 16381938 11
2006 Hirschman JE|etAl Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res 34: D442-445. Saccharomyces genomic 16381907 1,4,11
2006 Hoffmann JL, Torontali SP, Thomason RG, Lee DM, Brill JL, Price BB, Carr GJ, Versteeg DJ Hepatic gene expression profiling using Genechips in zebrafish exposed to 17alpha-ethynylestradiol. Aquat Toxicol 79: 233-246. Zebrafish transcripts; steroid exposure 16872691 7
2006 Hook SE, Skillman AD, Small JA, Schultz IR Temporal changes in gene expression in rainbow trout exposed to ethynyl estradiol. Comp Biochem Physiol C Toxicol Pharmacol 145: 73-85. Rainbow trout transcripts; ethynyl estradiol exposure 17215170 7
2006 Horsman S, Moorhouse MJ, de Jager VC, van der Spek P, Grosveld F, Strouboulis J, Katsantoni EZ TF Target Mapper: A BLAST search tool for the identification of Transcription Factor target genes. BMC Bioinformatics 7: 120. 16524462 7,10,19
2006 Hou WJ, Lin KH, Chen HH Gene ontology annotation by density and gravitation models. Genome Inform 17: 110-120. 17503384 3,9
2006 Houde M|etAl Wheat EST resources for functional genomics of abiotic stress. BMC Genomics 7: 149. Wheat ESTs 16772040 5,7
2006 Huang D, Wei P, Pan W Combining gene annotations and gene expression data in model-based clustering: weighted method. OMICS 10: 28. 16584316 7
2006 Huang GS, Hong MY Functional and molecular characterization for the damp-obstructed rat model in chinese medicine. Am J Chin Med 34: 323-340. Rat transcripts 16552842 7
2006 Huttenhower C, Hibbs M, Myers C, Troyanskaya OG A scalable method for integration and functional analysis of multiple microarray data sets. Bioinformatics 22: 2890-2897. 17005538 7,10
2006 Hwang YY, Li MD Proteins differentially expressed in response to nicotine in five rat brain regions: Identification using a 2-DE/MS-based proteomics approach. Proteomics 6: 3138-3153. Rat transcripts & proteins; nicotine 16622831 7,8,16
2006 Ilic K|etAl Plant Structure Ontology. Unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiol 143: 587-599. 17142475 15
2006 Ivanovski S, Lichanska AM, D'Aniello E, Xiao Y, Waters MJ Gene expression profiling of cells involved in periodontal regeneration. Tissue Eng 13: 393-404. Human transcripts; periodontal regeneration 17518572 7,16
2006 Jacob RJ, Cramer R PIGOK: Linking protein identity to Gene Ontology and function. J Proteome Res 5: 3429-3432. 17137344 11
2006 Jarvinen AK, Autio R, Haapa-Paananen S, Wolf M, Saarela M, Grenman R, Leivo I, Kallioniemi O, Makitie AA, Monni O Identification of target genes in laryngeal squamous cell carcinoma by high-resolution copy number and gene expression microarray analyses. Oncogene 25: 6997-7008. Human transcripts; laryngeal cancer 16715129 7,16
2006 Ji W, Li Y, Li J, Dai CH, Wang X, Bai X, Cai H, Yang L, Zhu YM Generation and analysis of expressed sequence tags from NaCl-treated Glycine soja. BMC Plant Biol 6: 4. Soybean ESTs 16504061 5,7
2006 Jia Y, Anderson JV, Horvath DP, Gu YQ, Lym RG, Chao WS Subtractive cDNA libraries identify differentially expressed genes in dormant and growing buds of leafy spurge (Euphorbia esula). Plant Mol Biol 61: 329-344. Leafy spurge cDNAs 16786310 7
2006 Jin R, Si L, Srivastava S, Li Z, Chan C A knowledge driven regression model for gene expression and microarray analysis. Conf Proc IEEE Eng Med Biol Soc 1: 5326-5329. 17945892 7
2006 Johns MA, Mao L Differentiation of the two rice subspecies indica and japonica: a Gene Ontology perspective. Funct Integr Genomics 7: 135-151. 17131138 18
2006 Johnson HL, Cohen KB, Baumgartner WA, Lu Z, Bada M, Kester T, Kim H, Hunter L Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies. Pac Symp Biocomput 2006: 28-39. 17094225 12,15
2006 Johnsson A, Xue-Franzen Y, Lundin M, Wright AP Stress-specific role of fission yeast Gcn5 histone acetyltransferase in programming a subset of stress response genes. Eukaryot Cell 5: 1337-1346. Saccharomyces and Schizosaccharomyces genes 16896217 7,18
2006 Ju Z, Wells MC, Heater SJ, Walter RB Multiple tissue gene expression analyses in Japanese medaka (Oryzias latipes) exposed to hypoxia. Comp Biochem Physiol C Toxicol Pharmacol 145: 134-144. Medaka transcripts; hypoxia 16916623 7
2006 Jung WH, Sham A, White R, Kronstad JW Iron regulation of the major virulence factors in the AIDS-associated pathogen Cryptococcus neoformans. PLoS Biol 4: e410. Cryptococcus transcripts 17121456 10.1371/journal.pbio.0040410 7,16
2006 Juuti-Uusitalo KM, Kaukinen K, Maki M, Tuimala J, Kainulainen H Gene expression in TGFbeta-induced epithelial cell differentiation in a three-dimensional intestinal epithelial cell differentiation model. BMC Genomics 7: 279. Human epithelial cell transcripts; differentiation 17074098 7
2006 Kalita MK, Ramasamy G, Duraisamy S, Chauhan VS, Gupta D ProtRepeatsDB: A database of amino acid repeats in genomes. BMC Bioinformatics 7: 336. 16827924 8,11
2006 Kankainen M, Brader G, Toronen P, Palva ET, Holm L Identifying functional gene sets from hierarchically clustered expression data: map of abiotic stress regulated genes in Arabidopsis thaliana. Nucleic Acids Res 34: e124. Arabidopsis transcripts 17003050 7,10
2006 Kawada J, Kimura H, Kamachi Y, Nishikawa K, Taniguchi M, Nagaoka K, Kurahashi H, Kojima S, Morishima T Analysis of gene-expression profiles by oligonucleotide microarray in children with influenza. J Gen Virol 87: 1677-1683. Human transcripts; influenza 16690933 7,16
2006 Keating DT, Sadlier DM, Patricelli A, Smith SM, Walls D, Egan JJ, Doran PP Microarray identifies ADAM family members as key responders to TGF-beta1 in alveolar epithelial cells. Respir Res 7: 114. Human alveolar epithelial cell transcripts; pulmonary fibrosis 16948840 7,16
2006 Kerr JR, Boschetti N Short regions of sequence identity between the genomes of human and rodent parvoviruses and their respective hosts occur within host genes for the cytoskeleton, cell adhesion and Wnt signalling. J Gen Virol 87: 3567-3575. 17098972 13,16,18
2006 Kim BH, von Arnim AG The early dark-response in Arabidopsis thaliana revealed by cDNA microarray analysis. Plant Mol Biol 60: 321-342. Arabidopsis transcripts 16514558 7
2006 Kim H, Lim D, Han BK, Sung S, Jeon M, Moon S, Kang Y, Nam J, Han JY ChickGCE: A novel germ cell EST database for studying the early developmental stage in chickens. Genomics 88:252-257. Chicken ESTs 16714094 5,11
2006 Kim SK, Nam JW, Rhee JK, Lee WJ, Zhang BT miTarget: microRNA target-gene prediction using a Support Vector Machine. BMC Bioinformatics 7: 411. Human miRNA target prediction 16978421 19
2006 Kim TH|etAl Generation and analysis of large-scale expressed sequence tags (ESTs) from a full-length enriched cDNA library of porcine backfat tissue. BMC Genomics 7: 36. Porcine ESTS 16504160 5
2006 Kirac M, Ozsoyoglu G, Yang J Annotating proteins by mining protein interaction networks. Bioinformatics 22: e260-270. 16873481 8,9,10,12
2006 Knowles DG, McLysaght A high rate of recent intron gain and loss in simultaneously duplicated Arabidopsis genes. Mol Biol Evol 23: 1548-1557. 16720694 18
2006 Kohler J, Munn K, Ruegg A, Skusa A, Smith B Quality control for terms and definitions in ontologies and taxonomies. BMC Bioinformatics 7: 212. 16623942 13,14
2006 Koide T, Salem-Izacc SM, Gomes SL, Vencio RZ SpotWhatR: a user-friendly microarray data analysis system. Genet Mol Res 5: 93-9107. 16755501 7,10
2006 Kong SW, Pu WT, Park PJ A multivariate approach for integrating genome-wide expression data and biological knowledge. Bioinformatics 22: 2373-2380. 16877751 7
2006 Korostynski M, Kaminska-Chowaniec D, Piechota M, Przewlocki R Gene expression profiling in the striatum of inbred mouse strains with distinct opioid-related phenotypes. BMC Genomics 7: 146. Mouse transcripts; opioid response 16772024 7,16
2006 Kouranov A, Xie L, de la Cruz J, Chen L, Westbrook J, Bourne PE, Berman HM The RCSB PDB information portal for structural genomics. Nucleic Acids Res 34: D302-D305. PDB 16381872 6,11
2006 Kristensen VN|etAl Genetic variation in putative regulatory loci controlling gene expression in breast cancer. Proc Natl Acad Sci U S A 103: 7735-7740 Human transcripts and SNPs; breast cancer 16684880 7,16
2006 Kurokawa Y|etAl Central genetic alterations common to all HCV-positive, HBV-positive and non-B, non-C hepatocellular carcinoma: A new approach to identify novel tumor markers. Int J Oncol 28: 383-391. Human liver transcripts 16391793 7,16
2006 Kushida T, Takagi T, Fukuda KI Event ontology: a pathway-centric ontology for biological processes. Pac Symp Biocomput 2006: 152-163. 17094236 13,15
2006 Kustikova OS|etAl Retroviral vector insertion sites associated with dominant hematopoietic clones mark "stemness" pathways. Blood 109: 1897-1907. Mouse retroviral insertion sites 17119121 11,13,16
2006 Kustra R, Shioda R, Zhu M A factor analysis model for functional genomics. BMC Bioinformatics 7: 216. 16630343 7,19
2006 Kutchma A, Quayum N, Jensen J GeneSpeed: protein domain organization of the transcriptome. Nucleic Acids Res 35: D674-D679. 17132830 7,11
2006 Lan H|etAl Combined expression trait correlations and expression quantitative trait locus mapping. PLoS Genet 2: e6. Mouse transcripts; obesity; diabetes 16424919 10.1371/journal.pgen.0020006 7,16,17
2006 Lee BW, Kim TH, Kim SK, Kim SS, Ryu GC, Bhak J Functional annotation and analysis of korean patented biological sequences using bioinformatics. Mol Cells 21: 269-275. Human genes; Korean patents 16682823 3,13
2006 Lee H, Deng M, Sun F, Chen T An integrated approach to the prediction of domain-domain interactions. BMC Bioinformatics 7: 269. Protein domain-domain interactions 16725050 8,18
2006 Lee HS, Park MH, Yang SJ, Park KC, Kim NS, Kim YS, Kim DI, Yoo HS, Choi EJ, Yeom YI Novel candidate targets of Wnt/beta-catenin signaling in hepatoma cells. Life Sci 80: 690-698. Human hepatoma cell transcripts 17157329 7,16
2006 Lee JA|etAl Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation. BMC Bioinformatics 7: 237. Murine B cell transcripts 16670020 7,16
2006 Lee JB, Kim JJ, Park JC Automatic extension of gene ontology with flexible identification of candidate terms. Bioinformatics 22: 665-670. 16428805 12,13,19
2006 Lee MS, Jun DH, Hwang CI, Park SS, Kang JJ, Park HS, Kim J, Seo JS, Park WY Selection of neural differentiation-specific genes by comparing profiles of random differentiation. Stem Cells 24: 1946-1955. Mouse ES cell transcripts during differentiation 16627687 7
2006 Lee S|etAl Gene expression profiles in acute myeloid leukemia with common translocations using SAGE. Proc Natl Acad Sci U S A 103: 1030-1035. Human myeloid progenitor cell transcripts 16418266 7,16
2006 Lee TL, Alba D, Baxendale V, Rennert OM, Chan WY Application of transcriptional and biological network analyses in mouse germ-cell transcriptomes. Genomics 88: 18-33. Mouse transcripts; spermatogenesis 16678385 7,17
2006 Lee WP, Jeng BC, Pai TW, Tsai CP, Yu CY, Tzou WS Differential evolutionary conservation of motif modes in a yeast protein interaction network. BMC Genomics 7: 89. Interacting Saccharomyces proteins 16638125 8,17,18
2006 Lee Y, Lee Y, Kim B, Shin Y, Nam S, Kim P, Kim N, Chung WH, Kim J, Lee S ECgene: an alternative splicing database update. Nucleic Acids Res 35: D99-D103. 17132829 7,11
2006 Lei Z, Dai Y Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction. BMC Bioinformatics 7: 491. 17090318 9,13
2006 Lemay DG, Hwang DH Genome-wide identification of peroxisome proliferator response elements using integrated computational genomics. J Lipid Res 47: 1583-1587. Human PPRAR target genes 16585784 7,19
2006 Leontis NB|etAl The RNA Ontology Consortium: An open invitation to the RNA community. RNA 12: 533-541. 16484377 15
2006 Leung AK, Trinkle-Mulcahy L, Lam YW, Andersen JS, Mann M, Lamond AI NOPdb: Nucleolar Proteome Database. Nucleic Acids Res 34: D218-D220. Nucleolar proteins 16381850 6,11
2006 Leupin N, Kuhn A, Hugli B, Grob TJ, Jaggi R, Tobler A, Delorenzi M, Fey MF Gene expression profiling reveals consistent differences between clinical samples of human leukaemias and their model cell lines. Br J Haematol 135: 520-523. Human white blood cells; leukemia 17061979 7,16
2006 Levesque MP|etAl Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. PLoS Biol 4: e143. Arabidopsis transcripts 16640459 10.1371/journal.pbio.0040143 7
2006 Lewin A, Grieve IC Grouping Gene Ontology terms to improve the assessment of gene set enrichment in microarray data. BMC Bioinformatics 7: 426. 17018143 7
2006 Lewin A, Richardson S, Marshall C, Glazier A, Aitman T Bayesian modeling of differential gene expression. Biometrics 62: 10-18. 16542224 7
2006 Li J, Liu Q, Qiu M, Pan Y, Li Y, Shi T Identification and analysis of the mouse basic/Helix-Loop-Helix transcription factor family. Biochem Biophys Res Commun 350: 648-656. Mouse basic/Helix-Loop-Helix (bHLH) proteins 17027923 8
2006 Li JM|etAl Temporal evolution of gene expression in rat carotid artery following balloon angioplasty. J Cell Biochem 101: 399-410. Rat carotid artery transcripts; balloon angioplasty 17171642 7,16
2006 Li S, Ehrhardt DW, Rhee SY Systematic analysis of Arabidopsis organelles and a protein localization database for facilitating fluorescent tagging of full-length Arabidopsis proteins. Plant Physiol 141: 527-539. 16617091 1,8,11,13
2006 Li XY, Cui XS, Kim NH Transcription profile during maternal to zygotic transition in the mouse embryo. Reprod Fertil Dev 18: 635-645. Mouse embryonic transcripts 16930510 7
2006 Li YY, Yu H, Guo ZM, Guo TQ, Tu K, Li YX Systematic analysis of head-to-head gene organization: evolutionary conservation and potential biological relevance. PLoS Comput Biol 2: e74. 16839196 10.1371/journal.pcbi.0020074 13,18
2006 Li Y|etAl Mapping determinants of gene expression plasticity by genetical genomics in C. elegans. PLoS Genet 2: e222. Caenorhabditis transcripts 17196041 10.1371/journal.pgen.0020222 7,18
2006 Lindberg J, Af Klint E, Catrina AI, Nilsson P, Klareskog L, Ulfgren AK, Lundeberg J Effect of infliximab on mRNA expression profiles in synovial tissue of RA patients. Arthritis Res Ther 8: R179. Human transcripts; rheumatoid arthritis 17134501 7,16
2006 Lindberg J, Af Klint E, Ulfgren AK, Stark A, Andersson T, Nilsson P, Klareskog L, Lundeberg J Variability in synovial inflammation in rheumatoid arthritis investigated by microarray technology. Arthritis Res Ther 8: R47. Human transcripts; arthritis 16507157 7,16
2006 Lindqvist C, Scheen AC, Yoo MJ, Grey P, Oppenheimer DG, Leebens-Mack JH, Soltis DE, Soltis PS, Albert VA An expressed sequence tag (EST) library from developing fruits of an Hawaiian endemic mint (Stenogyne rugosa, Lamiaceae): characterization and microsatellite markers. BMC Plant Biol 6: 16. Stenogyne rugosa ESTs 16928278 5
2006 Lisewski AM, Lichtarge O Rapid detection of similarity in protein structure and function through contact metric distances. Nucleic Acids Res 34: e152. 17130161 13
2006 Liu CC, Lin CC, Chen WS, Chen HY, Chang PC, Chen JJ, Yang PC CRSD: a comprehensive web server for composite regulatory signature discovery. Nucleic Acids Res 34: W571-577. 16845073 7,10
2006 Liu F|etAl New perspectives on host-parasite interplay by comparative transcriptomic and proteomic analyses of Schistosoma japonicum. PLoS Pathog 2: e29. Schistosoma transcripts and proteins 16617374 10.1371/journal.ppat.0020029 5,7,8
2006 Liu Y, Li J, Sam L, Goh CS, Gerstein M, Lussier YA An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits. PLoS Comput Biol 2: e159. 17112314 10.1371/journal.pcbi.0020159 12,13,17,19
2006 Lo SL, You T, Lin Q, Joshi SB, Chung MC, Hew CL SPLASH: Systematic proteomics laboratory analysis and storage hub. Proteomics 6: 1758-1769. 16456885 8,11,12
2006 Lockyer AE, Spinks JN, Walker AJ, Kane RA, Noble LR, Rollinson D, Dias-Neto E, Jones CS Biomphalaria glabrata transcriptome: Identification of cell-signalling, transcriptional control and immune-related genes from open reading frame expressed sequence tags (ORESTES). Dev Comp Immunol 31: 763-782. Biomphalaria glabrata ESTs 17208299 5
2006 Loewe R, Valero T, Kremling S, Pratscher B, Kunstfeld R, Pehamberger H, Petzelbauer P Dimethylfumarate impairs melanoma growth and metastasis. Cancer Res 66: 11888-11896. Mouse skin transcripts; melanoma 17178886 7,16
2006 Loots GG, Chain PS, Mabery S, Rasley A, Garcia E, Ovcharenko I Array2BIO: from microarray expression data to functional annotation of co-regulated genes. BMC Bioinformatics 7: 307. 16780584 7,10
2006 Lu B, Xu J, Zhu Y, Zhang H, Lai M Systemic analysis of the differential gene expression profile in a colonic adenoma-normal SSH library. Clin Chim Acta 378: 42-47. Human colonic mucosa ESTs; colonic adenoma 17184759 7,16
2006 Lu G, Nguyen TV, Xia Y, Fromm M AffyMiner: mining differentially expressed genes and biological knowledge in GeneChip microarray data. BMC Bioinformatics 7 Suppl 4: S26. 17217519 7,10
2006 Lu Z, Cohen KB, Hunter L Finding generifs via gene ontology annotations. Pac Symp Biocomput 2006: 52-63. 17094227 12,19
2006 Lubovac Z, Gamalielsson J, Olsson B Combining functional and topological properties to identify core modules in protein interaction networks. Proteins 64: 948-959. Yeast proteins 16794996 8
2006 Lukas TJ, Luo WW, Mao H, Cole N, Siddique T Informatics assisted protein profiling in a transgenic mouse model of amyotrophic lateral sclerosis. Mol Cell Proteomics 5: 1233-1244. Mouse CNS transcripts and proteins 16571896 7,8,16
2006 Lunardi C, Dolcino M, Peterlana D, Bason C, Navone R, Tamassia N, Beri R, Corrocher R, Puccetti A Antibodies against human cytomegalovirus in the pathogenesis of systemic sclerosis: a gene array approach. PLoS Med 3: e2. Human endothelial cell transcripts; cytomegalovirus; systemic sclerosis 16318412 10.1371/journal.pmed.0030002 7,16
2006 Lussier Y, Borlawsky T, Rappaport D, Liu Y, Friedman C Phenogo: assigning phenotypic context to gene ontology annotations with natural language processing. Pac Symp Biocomput 2006:64-75. 17094228 10,11,12,15
2006 Lv BJ, Cui J, Xu J, Zhang H, Luo MJ, Zhu YM, Lai MD [Bioinformatic analysis of adenoma-normal mucosa SSH library of colon.] [Article in Chinese] Yi Chuan 28: 385-392. Human colon ESTs 16606587 7,16
2006 Ma J Building an ontology-driven database for clinical immune research. AMIA Annu Symp Proc 2006: 1018. 17238637 11,13
2006 Ma J, Morrow DJ, Fernandes J, Walbot V Comparative profiling of the sense and antisense transcriptome of maize lines. Genome Biol 7: R22. Maize transcripts 16542496 7
2006 Ma Z, Yu J, Kang L LocustDB: a relational database for the transcriptome and biology of the migratory locust (Locusta migratoria). BMC Genomics 7: 11. Locust ESTs 16426458 5,11,18
2006 MacCallum C, Hill E Being positive about selection. PLoS Biol 4: e87. 16524343 10.1371/journal.pbio.0040087 18
2006 Maeda N|etAl Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genet 2: e62. Mouse genome; cDNAs 16683036 10.1371/journal.pgen.0020062 4
2006 Magdaleno S|etAl BGEM: an in situ hybridization database of gene expression in the embryonic and adult mouse nervous system. PLoS Biol 4: e86. Mouse transcripts 16602821 10.1371/journal.pbio.0040086 7,11
2006 Makrantonaki E, Adjaye J, Herwig R, Brink TC, Groth D, Hultschig C, Lehrach H, Zouboulis CC Age-specific hormonal decline is accompanied by transcriptional changes in human sebocytes in vitro. Aging Cell 5: 331-344. Human sebocyte transcripts; aging 16805856 7,16
2006 Malik R, Franke L, Siebes A Combination of text-mining algorithms increases the performance. Bioinformatics 22: 2151-2157. 16766558 10,12
2006 Mans JJ, Baker HV, Oda D, Lamont RJ, Handfield M Distinctive characteristics of transcriptional profiles from two epithelial cell lines upon interaction with Actinobacillus actinomycetemcomitans. Oral Microbiol Immunol 21: 261-267. Human epithelial cell lines; Actinobacillus exposure 16842512 7,16
2006 Marino-Ramirez L, Bodenreider O, Kantz N, Jordan IK Co-evolutionary rates of functionally related yeast genes. Evol Bioinform Online 2: 295-300. 18345352 18
2006 Martinez G, Georgas K, Challen GA, Rumballe B, Davis MJ, Taylor D, Teasdale RD, Grimmond SM, Little MH Definition and spatial annotation of the dynamic secretome during early kidney development. Dev Dyn 235: 1709-1719. Mouse kidney transcripts, secreted proteins 16538671 7
2006 Massjouni N, Rivera CG, Murali TM VIRGO: computational prediction of gene functions. Nucleic Acids Res 34: W340-344. 16845022 9,10
2006 McCarthy FM, Bridges SM, Wang N, Magee GB, Williams WP, Luthe DS, Burgess SC AgBase: a unified resource for functional analysis in agriculture. Nucleic Acids Res 35: D599-D603. Agricultural genomes 17135208 1,3,11
2006 McCarthy FM|etAl AgBase: a functional genomics resource for agriculture. BMC Genomics 7: 229. AgBase; farm animal genomes and ESTs 16961921 1,4,5,10,11
2006 Mendoza G|etAl A new locus for autosomal dominant amelogenesis imperfecta on chromosome 8q24.3. Hum Genet 120: 653-662. Mouse dental tissue transcripts; amelogenesis imperfecta 17024372 7,16
2006 Mense SM, Sengupta A, Zhou M, Lan C, Bentsman G, Volsky DJ, Zhang L Gene expression profiling reveals the profound up-regulation of hypoxia-responsive genes in primary human astrocytes. Physiol Genomics 25: 435-449 Human astrocyte transcripts 16507782 7,16
2006 Merrick BA|etAL Alterations in the rat serum proteome during liver injury from acetaminophen exposure. J Pharmacol Exp Ther 318: 792-802. Rat proteins; acetaminophen exposure 16687475 8,16
2006 Miura A, Honma R, Togashi T, Yanagisawa Y, Ito E, Imai JI, Isogai T, Goshima N, Watanabe S, Nomura N Differential responses of normal human coronary artery endothelial cells against multiple cytokines comparatively assessed by gene expression profiles. FEBS Lett 580: 6871-6879. Human coronary artery endothelial cell transcripts; cytokines 17157299 7,16
2006 Mochida K, Kawaura K, Shimosaka E, Kawakami N, Shin-I T, Kohara Y, Yamazaki Y, Ogihara Y Tissue expression map of a large number of expressed sequence tags and its application to in silico screening of stress response genes in common wheat. Mol Genet Genomics 276: 304-312. Wheat ESTs 16832693 7
2006 Montaner D|etAl Next station in microarray data analysis: GEPAS. Nucleic Acids Res 34: W486-491. 16845056 7,10
2006 Moore D, Meskauskas A A comprehensive comparative analysis of the occurrence of developmental sequences in fungal, plant and animal genomes. Mycol Res 110: 251-256. 16513334 12,18
2006 Morrison N, Cochrane G, Faruque N, Tatusova T, Tateno Y, Hancock D, Field D Concept of sample in OMICS technology. OMICS a10: 127-137. 16901217 14,15
2006 Morrison RN, Cooper GA, Koop BF, Rise ML, Bridle AR, Adams MB, Nowak BF Transcriptome profiling the gills of amoebic gill disease (AGD)-affected Atlantic salmon (Salmo salar L.) - A role for tumor suppressor p53 in AGD-pathogenesis? Physiol Genomics 26: 15-34. Salmon gill transcripts 16493018 7
2006 Mortazavi A, Thompson EC, Garcia ST, Myers RM, Wold B Comparative genomics modeling of the NRSF/REST repressor network: From single conserved sites to genome-wide repertoire. Genome Res 16: 1208-1221. Human transcripts 16963704 7,17,18
2006 Mracek J|etAl Construction, database integration, and application of an Oenothera EST library. Genomics 88: 372-380. Oenothera ESTs 16829020 5
2006 Mucher E, Jayr L, Rossignol F, Amiot F, Gidrol X, Barrey E Gene expression profiling in equine muscle tissues using mouse cDNA microarrays. Equine Vet J Suppl 1: 97-98. Horse muscle transcripts; mouse arrays 17402448 7
2006 Muro EM, Perez-Iratxeta C, Andrade-Navarro MA Amplification of the Gene Ontology annotation of Affymetrix probe sets. BMC Bioinformatics 7: 159. 16549014 9,10
2006 Myhre S, Tveit H, Mollestad T, Laegreid A Additional Gene Ontology structure for improved biological reasoning. Bioinformatics 22: 2020-2027. 16787968 9,13
2006 Nam D, Kim SB, Kim SK, Yang S, Kim SY, Chu IS ADGO: analysis of differentially expressed gene sets using composite GO annotation. Bioinformatics 22: 2249-2253. 16837524 7,10
2006 Newton JR Linked gene ontology categories are novel and differ from associated gene ontology categories for the bipolar disorders. Psychiatr Genet 17: 29-34. 17167342 13,16
2006 Ng A, Bursteinas B, Gao Q, Mollison E, Zvelebil M pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer. Nucleic Acids Res 34: D527-534. Cancer systems biology 16381926 11,13
2006 Nguyen DQ, Webber C, Ponting CP Bias of selection on human copy-number variants. PLoS Genet 2: e20. 16482228 10.1371/journal.pgen.0020020 18
2006 Nishizawa H, Pryor-Koishi K, Kato T, Kowa H, Kurahashi H, Udagawa Y Microarray analysis of differentially expressed fetal genes in placental tissue derived from early and late onset severe pre-eclampsia. Placenta 28: 487-497. Human placental transcripts; pre-eclampsia 16860862 7,16
2006 Noriega FG, Ribeiro JM, Koener JF, Valenzuela JG, Hernandez-Martinez S, Pham VM, Feyereisen R Comparative genomics of insect juvenile hormone biosynthesis. Insect Biochem Mol Biol 36: 366-374. Cockroach ESTs 16551550 5,18
2006 Numata K, Okada Y, Saito R, Kiyosawa H, Kanai A, Tomita M Comparative analysis of cis-encoded antisense RNAs in eukaryotes. Gene 392: 134-141. 17250976 13,18
2006 O'Donnell SM, Holm GH, Pierce JM, Tian B, Watson MJ, Chari RS, Ballard DW, Brasier AR, Dermody TS Identification of an NF-kappaB-dependent gene network in cells infected by mammalian reovirus. J Virol 80: 1077-1086. HeLa cell transcripts; reovirus infection 16414985 7,17
2006 O'brien EA, Zhang Y, Yang L, Wang E, Marie V, Lang BF, Burger G GOBASE--a database of organelle and bacterial genome information. Nucleic Acids Res 34: D697-699. Organelle and bacterial genomes 16381962 4,11
2006 O'driscoll L|etAl Investigation of the molecular profile of basal cell carcinoma using whole genome microarrays. Mol Cancer 5: 74. Human skin transcripts; basal cell carcinoma 17173689 7,16
2006 Ockenhouse CF|etAl Common and divergent immune response signaling pathways discovered in peripheral blood mononuclear cell gene expression patterns in presymptomatic and clinically apparent malaria. Infect Immun 74: 5561-5573. Human blood cell transcripts; malaria 16988231 7,16,17
2006 Oh JH, Jeon YJ, Jeong SY, Hong SM, Lee JS, Nho SK, Kang SW, Kim NS Gene expression profiling between embryonic and larval stages of the silkworm, Bombyx mori. Biochem Biophys Res Commun 343: 864-872. Silkworm ESTs 16564499 5,7
2006 Ohyama M, Vogel JC, Amagai M Gene ontology analysis of human hair follicle bulge molecular signature. J Dermatol Sci 45: 147-150. Human hair follicle bulge transcripts 17071058 7
2006 Olsson M, Broberg A, Jernas M, Carlsson L, Rudemo M, Suurkula M, Svensson PA, Benson M Increased expression of aquaporin 3 in atopic eczema. Allergy 61: 1132-1137. Human skin transcripts; eczema 16918518 7,16
2006 Onken MD, Ehlers JP, Worley LA, Makita J, Yokota Y, Harbour JW Functional gene expression analysis uncovers phenotypic switch in aggressive uveal melanomas. Cancer Res 66: 4602-4609. Human transcripts; uveal melanoma 16651410 7,16
2006 Orchard S, Hermjakob H, Taylor C, Binz PA, Hoogland C, Julian R, Garavelli JS, Aebersold R, Apweiler R Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005. Proteomics 6: 738-741. 16411267 15
2006 Orre LM, Falt S, Szeles A, Lewensohn R, Wennborg A, Flygare J Rad51-related changes in global gene expression. Biochem Biophys Res Commun 341: 334-342. Human fibrosarcoma cell transcripts 16427610 7
2006 Orru S, Aspesi A, Armiraglio M, Caterino M, Loreni F, Ruoppolo M, Santoro C, Dianzani I Analysis of RPS19's interactome. Mol Cell Proteomics 6: 382-393. 17151020 8
2006 Oster H, Damerow S, Hut RA, Eichele G Transcriptional profiling in the adrenal gland reveals circadian regulation of hormone biosynthesis genes and nucleosome assembly genes. J Biol Rhythms 21: 350-361. Mouse adrenal transcripts 16998155 7
2006 Othman R, Deris S, Illias RM, Alashwal HT, Hassan R, Mohamed F Incorporating Semantic Similarity Measure in Genetic Algorithm: An Approach for Searching the Gene Ontology Terms International Journal of Computational Intelligence 3: 257-266. www.enformatika.org/ijci/v3/v3-3-30.pdf|pdf 10,13
2006 Othman RM, Deris S, Illias RM Computational method for annotation of protein sequence according to Gene Ontology terms International Journal of Biomedical Sciences 1: 186-199. http://www.enformatika.org/ijbs/v1/v1-3-26.pdf|pdf 9,10
2006 Othman RM, Deris S, Illias RM UTMGO: A tool for searching a group of semantically related Gene Ontology terms and application to annotation of anonymous protein International Journal of Biomedical Sciences 1: 111-119. www.enformatika.org/ijbs/v1/v1-2-15.pdf|pdf 10
2006 Othman RM, Deris S, Illias RM, Zakaria Z, Mohamad SM Automatic Clustering of Gene Ontology by Genetic Algorithm International Journal of Information Technology 3: 37-46. http://www.enformatika.org/ijit/v3/v3-1-7.pdf|pdf 13
2006 Packer BR|etAl SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes. Nucleic Acids Res 34: D617-621. 16381944 11
2006 Page TJ, Sikder D, Yang L, Pluta L, Wolfinger RD, Kodadek T, Thomas RS Genome-wide analysis of human HSF1 signaling reveals a transcriptional program linked to cellular adaptation and survival. Mol Biosyst 2: 627-639. Human transcripts; HSF1 signaling 17216044 7,16,17
2006 Pal D On gene ontology and function annotation. Bioinformation 1: 97-98. 17597866 14
2006 Palomero T|etAl Transcriptional regulatory networks downstream of TAL1/SCL in t-cell acute lymphoblastic leukemia. Blood 108: 986-992. Human cell line trancripts; acute lymphoblastic leukemia 16621969 7
2006 Pan H, Zhu L, Deng Y, Pollard JW Microarray analysis of uterine epithelial gene expression during the implantation window in the mouse. Endocrinology 147: 4904-4916. Mouse uterine epithelial genes 16794013 7,16
2006 Parkinson H|etAl ArrayExpress--a public database of microarray experiments and gene expression profiles. Nucleic Acids Res 35: D747-D750. 17132828 11,15
2006 Penkett CJ, Morris JA, Wood V, Bahler J YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms. Nucleic Acids Res 34: W330-334. 16845020 1,10
2006 Perco P, Pleban C, Kainz A, Lukas A, Mayer G, Mayer B, Oberbauer R Protein biomarkers associated with acute renal failure and chronic kidney disease. Eur J Clin Invest 36: 753-763. Kidney proteins; kidney disease 17032342 8,16
2006 Pereira GS, Brandao RM, Giuliatti S, Zago MA, Silva WA Gene Class expression: analysis tool of Gene Ontology terms with gene expression data. Genet Mol Res 5: 108-114. 16755502 7,10
2006 Perocchi F, Jensen LJ, Gagneur J, Ahting U, von Mering C, Bork P, Prokisch H, Steinmetz LM Assessing systems properties of yeast mitochondria through an interaction map of the organelle. PLoS Genet 2: e170. Saccharomyces mitochondrial proteins 17054397 10.1371/journal.pgen.0020170 8,17
2006 Peters B, Moad C, Youn E, Buffington K, Heiland R, Mooney SD Identification of similar regions of protein structures using integrated sequence and structure analysis tools. BMC Struct Biol 6: 4. 16526955 9,10
2006 Pfister KK, Shah PR, Hummerich H, Russ A, Cotton J, Annuar AA, King SM, Fisher EM Genetic analysis of the cytoplasmic dynein subunit families. PLoS Genet 2: e1. 16440056 10.1371/journal.pgen.0020001 18
2006 Phan JH, Quo CF, Wang MD Chapter 4 Functional genomics and proteomics in the clinical neurosciences: data mining and bioinformatics. Prog Brain Res 158: 83-8108. 17027692 14
2006 Plikus MV, Zhang Z, Chuong CM PubFocus: Semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm. BMC Bioinformatics 7: 424. 17014720 15
2006 Plymoth A, Yang Z, Lofdahl CG, Ekberg-Jansson A, Dahlback M, Fehniger TE, Marko-Varga G, Hancock WS Rapid proteome analysis of bronchoalveolar lavage samples of lifelong smokers and never-smokers by micro-scale liquid chromatography and mass spectrometry. Clin Chem 52: 671-679. Human bronchoalveolar proteins 16497942 8,16
2006 Pollard KS|etAl Forces shaping the fastest evolving regions in the human genome. PLoS Genet 2: e168. 17040131 10.1371/journal.pgen.0020168 18
2006 Popescu M, Keller JM, Mitchell JA Fuzzy measures on the Gene Ontology for gene product similarity. IEEE/ACM Trans Comput Biol Bioinform 3: 263-274. 17048464 13
2006 Press WH, Robins H Isochores exhibit evidence of genes interacting with the large-scale genomic environment. Genetics 174: 1029-1040. 16951086 13,18
2006 Price SA, Zeef LA, Wardleworth L, Hayes A, Tomlinson DR Identification of changes in gene expression in dorsal root ganglia in diabetic neuropathy: correlation with functional deficits. J Neuropathol Exp Neurol 65: 722-732. Rat dorsal root ganglion transcripts; diabetic neuropathy 16825959 7,16
2006 Prieto C, De Las Rivas J APID: Agile Protein Interaction DataAnalyzer. Nucleic Acids Res 34: W298-302. 16845013 8,10
2006 Pujar A|etAl Whole plant growth stage ontology for angiosperms and its application in plant biology. Plant Physiol 142: 414-428. 16905665 15
2006 Qian Z, Cai YD, Li Y A novel computational method to predict transcription factor DNA binding preference. Biochem Biophys Res Commun 348: 1034-1037. 16899225 19
2006 Rachlin J, Cohen DD, Cantor C, Kasif S Biological context networks: a mosaic view of the interactome. Mol Syst Biol 2: 66. 17130868 17
2006 Rainer J, Sanchez-Cabo F, Stocker G, Sturn A, Trajanoski Z CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis. Nucleic Acids Res 34: W498-503. 16845058 7,10
2006 Ramos CA, Bowman TA, Boles NC, Merchant AA, Zheng Y, Parra I, Fuqua SA, Shaw CA, Goodell MA Evidence for diversity in transcriptional profiles of single hematopoietic stem cells. PLoS Genet 2: e159. Mouse hematopoietic stem cell genes 17009876 10.1371/journal.pgen.0020159 7,16
2006 Ranjit N, Jones MK, Stenzel DJ, Gasser RB, Loukas A A survey of the intestinal transcriptomes of the hookworms, Necator americanus and Ancylostoma caninum, using tissues isolated by laser microdissection microscopy. Int J Parasitol 36: 701-710. Hookworm ESTs 16545815 5,7
2006 Re A, Cora D, Puliti AM, Caselle M, Sbrana I Correlated fragile site expression allows the identification of candidate fragile genes involved in immunity and associated with carcinogenesis. BMC Bioinformatics 7: 413. Human fragile sites; tumor cell biology 16981993 13,16,17
2006 Rinn JL, Bondre C, Gladstone HB, Brown PO, Chang HY Anatomic demarcation by positional variation in fibroblast gene expression programs. PLoS Genet 2: e119. Human fibroblast transcripts 16895450 10.1371/journal.pgen.0020119 7,16
2006 Risinger JI, Chandramouli GV, Maxwell GL, Litzi T, Berchuck A, Umar A Gene expression analysis of tumor infiltrating lymphocyte markers in endometrial cancers indicates no significant increases in those cases with microsatellite instability. Cancer Biomark 2: 61-68. Human transcripts; endometrial cancer; microsatellite instability 17192060 7,16
2006 Rizzon C, Ponger L, Gaut BS Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice. PLoS Comput Biol 2: e115. 16948529 10.1371/journal.pcbi.0020115 13,18
2006 Roden JC, King BW, Trout D, Mortazavi A, Wold BJ, Hart CE Mining gene expression data by interpreting principal components. BMC Bioinformatics 7: 194. 16600052 7,10,12
2006 Rodriguez-Zas SL, Southey BR, Whitfield CW, Robinson GE Semiparametric approach to characterize unique gene expression trajectories across time. BMC Genomics 7: 233. Honey bee brain transcripts 16970825 7
2006 Rubin DL|etAl National Center for Biomedical Ontology: Advancing biomedicine through structured organization of scientific knowledge. OMICS 10: 185-198. 16901225 1,14,15
2006 Rudnicki M|etAl Gene expression profiles of human proximal tubular epithelial cells in proteinuric nephropathies. Kidney Int 71: 325-335. Human kidney transcripts; kidney disease 17183245 7,16
2006 Ruth MC|etAl Analysis of membrane proteins from human chronic myelogenous leukemia cells: comparison of extraction methods for multidimensional LC-MS/MS. J Proteome Res 5: 709-719. Human membrane proteins 16512687 8,16
2006 Rutherford RB, Foster BL, Bammler T, Beyer RP, Sato S, Somerman MJ Extracellular phosphate alters cementoblast gene expression. J Dent Res 85: 505-509. Mouse cementoblast transcripts 16723645 7,16
2006 Saba L, Bhave SV, Grahame N, Bice P, Lapadat R, Belknap J, Hoffman PL, Tabakoff B Candidate genes and their regulatory elements: alcohol preference and tolerance. Mamm Genome 17: 669-688. Mouse transcripts 16783646 7,13
2006 Saba L, Bhave SV, Grahame N, Bice P, Lapadat R, Belknap J, Hoffman PL, Tabakoff B Candidate genes and their regulatory elements: alcohol preference and tolerance. Mamm Genome 17: 669-688. Mouse transcripts; alcohol 16783646 7,16
2006 Salem M, Kenney PB, Rexroad Iii CE, Yao J Microarray gene expression analysis in atrophying rainbow trout muscle: A unique non-mammalian muscle degradation model. Physiol Genomics 28: 33-45. Trout muscle transcripts 16882886 7
2006 Scheer M|etAl JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information. Nucleic Acids Res 34: W510-515. 16845060 7,10
2006 Schlicker A, Domingues FS, Rahnenfuhrer J, Lengauer T A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics 7: 302. 16776819 13
2006 Schulz M, Uhlendorf J, Klipp E, Liebermeister W SBMLmerge, a system for combining biochemical network models. Genome Inform 17: 62-71. 17503356 10
2006 Sealfon RS, Hibbs MA, Huttenhower C, Myers CL, Troyanskaya OG GOLEM: an interactive graph-based gene-ontology navigation and analysis tool. BMC Bioinformatics 7: 443. 17032457 10
2006 Selengut JD, Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, Nelson WC, Richter AR, White O TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res 35: D260-D264. 17151080 1,9,10
2006 Semeiks JR, Rizki A, Bissell MJ, Mian IS Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological features. BMC Bioinformatics 7: 147. 16542449 12
2006 Semova N, Storms R, John T, Gaudet P, Ulycznyj P, Min XJ, Sun J, Butler G, Tsang A Generation, annotation, and analysis of an extensive Aspergillus niger EST collection. BMC Microbiol 6: 7. Aspergillus niger ESTs 16457709 5
2006 Seo J, Gordish-Dressman H, Hoffman EP An interactive power analysis tool for microarray hypothesis testing and generation. Bioinformatics 22: 808-814 16418236 7,10
2006 Severgnini M|etAl Strategies for comparing gene expression profiles from different microarray platforms: Application to a case-control experiment. Anal Biochem 353: 43-56. 16624241 7
2006 Shafer P, Lin DM, Yona G EST2Prot: Mapping EST sequences to proteins. BMC Genomics 7: 41. 16515706 10,19
2006 Shahi P, Loukianiouk S, Bohne-Lang A, Kenzelmann M, Kuffer S, Maertens S, Eils R, Grone HJ, Gretz N, Brors B Argonaute--a database for gene regulation by mammalian microRNAs. Nucleic Acids Res 34: D115-D118. Human microRNA targets 16381827 3,11
2006 Shames DS|etAl A genome-wide screen for promoter methylation in lung cancer identifies novel methylation markers for multiple malignancies. PLoS Med 3: e486. Human transcripts; lung cancer 17194187 10.1371/journal.pmed.0030486 7,16
2006 Shankar K, Hidestrand M, Liu X, Xiao R, Skinner CM, Simmen FA, Badger TM, Ronis MJ Physiologic and genomic analyses of nutrition-ethanol interactions during gestation: implications for fetal ethanol toxicity. Exp Biol Med (Maywood) 231: 1379-1397. Rat liver genes; nutrition; gestation; ethanol toxicity 16946407 7,16
2006 Shen HB, Chou KC Virus-PLoc: A fusion classifier for predicting the subcellular localization of viral proteins within host and virus-infected cells. Biopolymers 85: 233-240. 17120237 9,10
2006 Shou J|etAl Identification of blood biomarkers of rheumatoid arthritis by transcript profiling of peripheral blood mononuclear cells from the rat collagen-induced arthritis model. Arthritis Res Ther 8: R28. Rat transcripts; arthritis model 16507131 7,16
2006 Sinnett D, Beaulieu P, Belanger H, Lefebvre JF, Langlois S, Theberge MC, Drouin S, Zotti C, Hudson TJ, Labuda D Detection and characterization of DNA variants in the promoter regions of hundreds of human disease candidate genes. Genomics 87: 704-710. Human SNPs; disease genes 16500075 13,16
2006 Siviero F, Rezende-Teixeira P, Andrade A, Machado-Santelli GM, Santelli RV Analysis of expressed sequence tags from Rhynchosciara americana salivary glands. Insect Mol Biol 15: 109-118. Rhynchosciara americana ESTs 16640721 5,7
2006 Sjoblom T|etAl The consensus coding sequences of human breast and colorectal cancers. Science 314: 268-274. Human genes; breast cancer; colorectal cancer 16959974 13,16
2006 Smirnova NA, Romanienko PJ, Khil PP, Camerini-Otero RD Gene expression profiles of Spo11-/- mouse testes with spermatocytes arrested in meiotic prophase I. Reproduction 132: 67-77. Mouse testis transcripts 16816334 7
2006 Snitkin ES, Gustafson AM, Mellor J, Wu J, DeLisi C Comparative assessment of performance and genome dependence among phylogenetic profiling methods. BMC Bioinformatics 7: 420. 17005048 18
2006 Sokolov M, Panyutin IG, Neumann R Genome-wide gene expression changes in normal human fibroblasts in response to low-let gamma-radiation and high-LET-like 125IUdR exposures. Radiat Prot Dosimetry 122: 195-201. Human fibroblast transcripts; ionizing radiation 17145729 7,16
2006 Souza de Oliveira CP|etAl Hepatic gene expression profile associated with non-alcoholic steatohepatitis protection by S-nitroso-N-acetylcysteine in ob/ob mice. J Hepatol 45: 725-733. Mouse liver genes; steatohepatitis 16935387 7,16
2006 Stanley SM, Bailey TL, Mattick JS GONOME: measuring correlations between gene ontology terms and genomic positions. BMC Bioinformatics 7: 94. 16504139 10,13
2006 Sterk P, Kersey PJ, Apweiler R Genome Reviews: Standardizing content and representation of information about complete genomes. OMICS 10: 114-118. 16901215 4
2006 Steuer R, Humburg P, Selbig J Validation and functional annotation of expression-based clusters based on gene ontology. BMC Bioinformatics 7: 380. 16911788 7,17
2006 Stoica E, Hearst M Predicting gene functions from text using a cross-species approach. Pac Symp Biocomput 2006: 88-99. 17094230 9,12
2006 Stover NA, Krieger CJ, Binkley G, Dong Q, Fisk DG, Nash R, Sethuraman A, Weng S, Cherry JM Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena thermophila research. Nucleic Acids Res 34: D500-503. Tetrahymena genomic 16381920 1,4,11
2006 Strizh IG Ontologies for data and knowledge sharing in biology: plant ROS signaling as a case study. Bioessays 28: 199-210. 16435295 14
2006 Su LJ, Hsu SL, Yang JS, Tseng HH, Huang SF, Huang CY Global gene expression profiling of dimethylnitrosamine-induced liver fibrosis: from pathological and biochemical data to microarray analysis. Gene Expr 13: 107-132. Rat liver transcripts; liver fibrosis 17017125 7,16
2006 Su Z, Dong X, Zhang B, Zeng Y, Fu Y, Yu J, Hu S Gene expression profiling in porcine mammary gland during lactation and identification of breed- and developmental-stage-specific genes. Sci China C Life Sci 49: 26-36. Porcine mammary ESTs 16544573 5,7
2006 Sugars RV, Karner E, Petersson U, Ganss B, Wendel M Transcriptome analysis of fetal metatarsal long bones by microarray, as a model for endochondral bone formation. Biochim Biophys Acta 1763: 1031-1039. Mouse embryonic bone transcripts 17005269 7
2006 Sun H, Fang H, Chen T, Perkins R, Tong W GOFFA: Gene Ontology For Functional Analysis - A FDA Gene Ontology tool for analysis of genomic and proteomic data. BMC Bioinformatics 7 Suppl 2: S23. 17118145 10
2006 Sun Y, Li H, Liu Y, Shin S, Mattson MP, Rao MS, Zhan M Cross-species transcriptional profiles establish a functional portrait of embryonic stem cells. Genomics 89: 22-35. Embryonic stem cell transcripts 17055697 7,16,18
2006 Svensson JP, Stalpers LJ, Lange RE, Franken NA, Haveman J, Klein B, Turesson I, Vrieling H, Giphart-Gassler M Analysis of gene expression using gene sets discriminates cancer patients with and without late radiation toxicity. PLoS Med 3: e422. Human lymphocyte transcripts; radiation toxicity 17076557 10.1371/journal.pmed.0030422 7,16
2006 Tabibiazar R|etAl Inflammatory Manifestations of Experimental Lymphatic Insufficiency. PLoS Med 3: e254. Mouse transcripts; lymphedema 16834456 10.1371/journal.pmed.0030254 7,16
2006 Tagari M|etAl E-MSD: improving data deposition and structure quality. Nucleic Acids Res 34: D287-290. Macromolecular Structure Database 16381867 11
2006 Takeuchi T, Tomida S, Yatabe Y, Kosaka T, Osada H, Yanagisawa K, Mitsudomi T, Takahashi T Expression profile-defined classification of lung adenocarcinoma shows close relationship with underlying major genetic changes and clinicopathologic behaviors. J Clin Oncol 24: 1679-1688. Human lung transcripts; lung cancer 16549822 7,16
2006 Taleb S|etAl Microarray profiling of human white adipose tissue after exogenous leptin injection. Eur J Clin Invest 36: 153-163. Human adipose tissue transcripts 16506959 7,16
2006 Tan SH, Reverter A, Wang Y, Byrne KA, McWilliam SM, Lehnert SA Gene expression profiling of bovine in vitro adipogenesis using a cDNA microarray. Funct Integr Genomics 6: 235-249. Bovine transcripts during adipogenesis 16470362 7
2006 Tang S, Zhang Z, Tan SL, Tang MH, Kumar AP, Ramadoss SK, Bajic VB KBERG: KnowledgeBase for Estrogen Responsive Genes. Nucleic Acids Res 35: D732-D736. Mammalian estrogen-responsive genes 17090589 7,11
2006 Tang T, Lu J, Huang J, He J, McCouch SR, Shen Y, Kai Z, Purugganan MD, Shi S, Wu CI Genomic variation in rice: genesis of highly polymorphic linkage blocks during domestication. PLoS Genet 2: e199. 17112320 10.1371/journal.pgen.0020199 18
2006 Taylor CF, Hermjakob H, Julian RK, Garavelli JS, Aebersold R, Apweiler R The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI). OMICS 10: 145-151. 16901219 15
2006 Taylor MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, Semple CA Heterotachy in mammalian promoter evolution. PLoS Genet 2: e30. Human, mouse transcription start sites 16683025 10.1371/journal.pgen.0020030 7,18
2006 Teixeira MC, Monteiro P, Jain P, Tenreiro S, Fernandes AR, Mira NP, Alenquer M, Freitas AT, Oliveira AL, Sa-Correia I The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res 34: D446-451. 16381908 11
2006 Ten Asbroek AL, Van Ruissen F, Ruijter JM, Baas F Comparison of schwann cell and sciatic nerve transcriptomes indicates that mouse is a valid model for the human peripheral nervous system. J Neurosci Res 84: 542-552. Mouse PNS transcripts 16786575 7,16
2006 The Gene Ontology Consortium The Gene Ontology (GO) project in 2006. Nucleic Acids Res 34: D322-D326. 16381878 1,2
2006 Theodosiou T, Angelis L, Vakali A, Thomopoulos GN Gene functional annotation by statistical analysis of biomedical articles. Int J Med Inform 76: 601-613. 16781189 9,12
2006 Tian R, Jiang X, Li X, Jiang X, Feng S, Xu S, Han G, Ye M, Zou H Biological fingerprinting analysis of the interactome of a kinase inhibitor in human plasma by a chemiproteomic approach. J Chromatogr A 1134: 134-142. Human plasma serine proteases 16982065 8
2006 Tomioka H, Morita K, Hasegawa S, Omura K Gene expression analysis by cDNA microarray in oral squamous cell carcinoma. J Oral Pathol Med 35: 206-211. Human transcripts; oral cancer 16519767 7,16
2006 Tompa P, Dosztanyi Z, Simon I Prevalent structural disorder in E. coli and S. cerevisiae proteomes. J Proteome Res 5: 1996-2000. 16889422 13,18
2006 Toyoda T, Mochizuki Y, Player K, Heida N, Sakaki Y OmicBrowse: a browser of multidimensional omics annotations. Bioinformatics 23: 524-526. 17077097 10
2006 Tran TT, Dam P, Su Z, Poole FL, Adams MW, Zhou GT, Xu Y Operon prediction in Pyrococcus furiosus. Nucleic Acids Res 35: 11-20. 17148478 19
2006 Treff NR, Vincent RK, Budde ML, Browning VL, Magliocca JF, Kapur V, Odorico JS Differentiation of embryonic stem cells conditionally expressing neurogenin 3. Stem Cells 24: 2529-2537. Mouse embryonic stem cell transcripts 16809427 7
2006 Tsai JR, Chong IW, Chen CC, Lin SR, Sheu CC, Hwang JJ Mitogen-activated protein kinase pathway was significantly activated in human bronchial epithelial cells by nicotine. DNA Cell Biol 25: 312-322. Human bronchial epithelial transcripts; nicotine 16716121 7,16
2006 Tseng HW, Juan HF, Huang HC, Lin JY, Sinchaikul S, Lai TC, Chen CF, Chen ST, Wang GJ Lipopolysaccharide-stimulated responses in rat aortic endothelial cells by a systems biology approach. Proteomics 6: 5915-5928. Rat aortic endothelial cell transcripts; LPS response 17106915 7,8,16,17
2006 Turecki G, Sequeira A, Klempan T, Canetti L, Gingras Y Global brain expression patterns in suicide. Psychiatr Danub 18 Suppl 1: 101. Human brain transcripts; suicide 16964040 7,16
2006 Twigger SN, Shimoyama M, Bromberg S, Kwitek AE, Jacob HJ The Rat Genome Database, update 2007--Easing the path from disease to data and back again. Nucleic Acids Res 35: D658-D662. Rat genome 17151068 1,4,11
2006 Umar A, Luider TM, Foekens JA, Pasa-Tolic L NanoLC-FT-ICR MS improves proteome coverage attainable for 3000 laser-microdissected breast carcinoma cells. Proteomics 7: 323-329. Human breast cancer cell proteins 17163580 8,16
2006 Usadel B|etAl PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments. BMC Bioinformatics 7: 535. 17176458 7,10
2006 Vartiainen S, Pehkonen P, Lakso M, Nass R, Wong G Identification of gene expression changes in transgenic C. elegans overexpressing human alpha-synuclein. Neurobiol Dis 22: 477-486. Nematode transcripts; human alpha-synuclein 16626960 7,16
2006 Vemuganti R, Kalluri H, Yi JH, Bowen KK, Hazell AS Gene expression changes in thalamus and inferior colliculus associated with inflammation, cellular stress, metabolism and structural damage in thiamine deficiency. Eur J Neurosci 23: 1172-1188. Rat transcripts; thiamine deficiency 16553781 7,16
2006 Vencio RZ, Koide T, Gomes SL, Pereira CA BayGO: Bayesian analysis of ontology term enrichment in microarray data. BMC Bioinformatics 7: 86. 16504085 7,10
2006 Vendelin J|etAl Downstream target genes of the Neuropeptide S--NPSR1 pathway. Hum Mol Genet 15: 2923-2935. Human cell line transcripts; asthma 16926187 7,16
2006 Vermeire JJ, Taft AS, Hoffmann KF, Fitzpatrick JM, Yoshino TP Schistosoma mansoni: DNA microarray gene expression profiling during the miracidium-to-mother sporocyst transformation. Mol Biochem Parasitol 147: 39-47. Schistosoma transcripts 16483678 3,7
2006 Verspoor K, Cohn J, Mniszewski S, Joslyn C A categorization approach to automated ontological function annotation. Protein Sci 15: 1544-1549. 16672243 9
2006 Vinayagam A, Del Val C, Schubert F, Eils R, Glatting KH, Suhai S, Konig R GOPET: A tool for automated predictions of Gene Ontology terms. BMC Bioinformatics 7: 161. 16549020 9,10
2006 Vinogradov AE 'Genome design' model and multicellular complexity: golden middle. Nucleic Acids Res 34: 5906-5914. 17062620 13,17,18
2006 Vizcaino JA|etAl Generation, annotation and analysis of ESTs from Trichoderma harzianum CECT 2413. BMC Genomics 7: 193. Trichoderma harzianum ESTs 16872539 5
2006 Vlachos A, Gasperin C, Lewin I, Briscoe T Bootstrapping the recognition and anaphoric linking of named entities in Drosophila articles. Pac Symp Biocomput 2006: 100-111. 17094231 15
2006 Vogel JP, Gu YQ, Twigg P, Lazo GR, Laudencia-Chingcuanco D, Hayden DM, Donze TJ, Vivian LA, Stamova B, Coleman-Derr D EST sequencing and phylogenetic analysis of the model grass Brachypodium distachyon. Theor Appl Genet 113: 186-195. Brachypodium ESTs 16791686 5
2006 Vogel JP, Gu YQ, Twigg P, Lazo GR, Laudencia-Chingcuanco D, Hayden DM, Donze TJ, Vivian LA, Stamova B, Coleman-Derr D EST sequencing and phylogenetic analysis of the model grass Brachypodium distachyon. Theor Appl Genet 113: 186-195. Brachypodium distachyon ESTs 16791686 5
2006 Voight BF, Kudaravalli S, Wen X, Pritchard JK A map of recent positive selection in the human genome. PLoS Biol 4: e72. 16494531 10.1371/journal.pbio.0040072 13,18
2006 Voy BH, Scharff JA, Perkins AD, Saxton AM, Borate B, Chesler EJ, Branstetter LK, Langston MA Extracting gene networks for low-dose radiation using graph theoretical algorithms. PLoS Comput Biol 2: e89. Mouse transcripts 16854212 10.1371/journal.pcbi.0020089 7,17
2006 Wagstaff SC, Harrison RA Venom gland EST analysis of the saw-scaled viper, Echis ocellatus, reveals novel alpha(9)beta(1) integrin-binding motifs in venom metalloproteinases and a new group of putative toxins, renin-like aspartic proteases. Gene 377: 21-32. Viper ESTs 16713134 5
2006 Walia H, Wilson C, Wahid A, Condamine P, Cui X, Close TJ Expression analysis of barley (Hordeum vulgare L.) during salinity stress. Funct Integr Genomics 6: 143-156. Barley transcripts 16450154 7
2006 Wang D, Amornsiripanitch N, Dong X A genomic approach to identify regulatory nodes in the transcriptional network of systemic acquired resistance in plants. PLoS Pathog 2: e123. Arabidopsis transcripts 17096590 10.1371/journal.ppat.0020123 7,17
2006 Wang D, Amornsiripanitch N, Dong X A genomic approach to identify regulatory nodes in the transcriptional network of systemic acquired resistance in plants. PLoS Pathog 2: e123. Arabidopsis transcripts; systemic acquired resistance 17096590 0.1371/journal.ppat.0020123 7
2006 Wang H|etAl Characterization of the mouse brain proteome using global proteomic analysis complemented with cysteinyl-peptide enrichment. J Proteome Res 5: 361-369. Mouse brain proteins 16457602 8
2006 Wang S|etAl Transcriptional profiling suggests that Barrett's metaplasia is an early intermediate stage in esophageal adenocarcinogenesis. Oncogene 25: 3346-3356. Human transcripts; esophageal cancer 16449976 7,16
2006 Wang X, Grus WE, Zhang J Gene losses during human origins. PLoS Biol 4: e52. 16464126 10.1371/journal.pbio.0040052 18
2006 Wang XD, Wang BE, Soriano R, Zha J, Zhang Z, Modrusan Z, Cunha GR, Gao WQ Expression profiling of the mouse prostate after castration and hormone replacement: implication of H-cadherin in prostate tumorigenesis. Differentiation 75: 219-234. Mouse prostate transcripts; prostate cancer 17288544 7,16
2006 Weeraratna AT|etAl Alterations in immunological and neurological gene expression patterns in Alzheimer's disease tissues. Exp Cell Res 313: 450-461. Human brain transcripts; Alzheimer's disease 17188679 7,16
2006 Wellmer F, Alves-Ferreira M, Dubois A, Riechmann JL, Meyerowitz EM Genome-wide analysis of gene expression during early Arabidopsis flower development. PLoS Genet 2: e117. Arabidopsis transcripts 16789830 10.1371/journal.pgen.0020117 7
2006 Whetzel PL, Parkinson H, Stoeckert CJ [17] Using ontologies to annotate microarray experiments. Methods Enzymol 411: 325-339. 16939798 2,7,15
2006 Whetzel PL|etAl Development of FuGO: An ontology for functional genomics investigations. OMICS 10: 199-204. 16901226 15
2006 Whetzel PL|etAl The MGED Ontology; a resource for semantics-based description of microarray experiments. Bioinformatics 22: 866-873 16428806 15
2006 Wilczynski B, Hvidsten TR, Kryshtafovych A, Tiuryn J, Komorowski J, Fidelis K Using local gene expression similarities to discover regulatory binding site modules. BMC Bioinformatics 7: 505. Saccharomyces genes 17109764 7,13,17
2006 Williams TD, Diab AM, George SG, Godfrey RE, Sabine V, Conesa A, Minchin SD, Watts PC, Chipman JK Development of the GENIPOL European flounder (Platichthys flesus) microarray and determination of temporal transcriptional responses to cadmium at low dose. Environ Sci Technol 40: 6479-6488. Flounder cDNAs 17120584 3,7
2006 Williams TD, Diab AM, George SG, Sabine V, Chipman JK Gene expression responses of European flounder (Platichthys flesus) to 17-beta estradiol. Toxicol Lett 168: 236-248. Flounder transcripts; estradiol 17156945 7
2006 Winnenburg R, Baldwin TK, Urban M, Rawlings C, Kohler J, Hammond-Kosack KE PHI-base: a new database for pathogen host interactions. Nucleic Acids Res 34: D459-464. PHI-base; genes relevant to host-pathogen interactions 16381911 3,11
2006 Winter C, Henschel A, Kim WK, Schroeder M SCOPPI: a structural classification of protein-protein interfaces. Nucleic Acids Res 34: D310-D314. SCOPPI 16381874 6,11
2006 Wiwanitkit V A study on functional similarity between dengue non structural protein 1 and platelet integrin/adhesin protein, CD61. J Ayub Med Coll Abbottabad 18: 13-16. 17348305 9,16
2006 Wiwatwattana N, Landau CM, Cope GJ, Harp GA, Kumar A Organelle DB: an updated resource of eukaryotic protein localization and function. Nucleic Acids Res 35: D810-D814. 17130152 6,11
2006 Wlodarczyk BJ, Cabrera RM, Hill DS, Bozinov D, Zhu H, Finnell RH Arsenic-induced gene expression changes in the neural tube of folate transport defective mouse embryos. Neurotoxicology 27: 547-557. Mouse genes; arsenic 16620997 7,16
2006 Wolstencroft K, Lord P, Tabernero L, Brass A, Stevens R Protein classification using ontology classification. Bioinformatics 22: e530-538. 16873517 6,11,13
2006 Wolting C, McGlade CJ, Tritchler D Cluster analysis of protein array results via similarity of Gene Ontology annotation. BMC Bioinformatics 7: 338. 16836750 8
2006 Wu J, Hu Z, Delisi C Gene annotation and network inference by phylogenetic profiling. BMC Bioinformatics 7: 80. 16503966 9,18
2006 Wu X, Zhu L, Guo J, Fu C, Zhou H, Dong D, Li Z, Zhang DY, Lin K SPIDer: Saccharomyces protein-protein interaction database. BMC Bioinformatics 7 Suppl 5: S16. Saccharomyces proteins 17254300 8,11,17
2006 Wu X, Zhu L, Guo J, Zhang DY, Lin K Prediction of yeast protein-protein interaction network: insights from the Gene Ontology and annotations. Nucleic Acids Res 34: 2137-2150. Saccharomyces protein-protein interactions 16641319 8,17
2006 Xia J, Radford C, Guo X, Magor KE Immune gene discovery by expressed sequence tag analysis of spleen in the duck (Anas platyrhynchos). Dev Comp Immunol 31: 272-285. Duck ESTs 16919729 5
2006 Xia K|etAl Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms. PLoS Comput Biol 2: e145. 17166053 10.1371/journal.pcbi.0020145 7,8,17
2006 Xie Y, Pan W, Jeong KS, Khodursky A Incorporating prior information via shrinkage: a combined analysis of genome-wide location data and gene expression data. Stat Med 26: 2258-2275. 16958153 7,13
2006 Xiong J, Rayner S, Luo K, Li Y, Chen S Genome wide prediction of protein function via a generic knowledge discovery approach based on evidence integration. BMC Bioinformatics 7: 268. 16725034 9
2006 Xu P, Santos RA, Bader M, Alenina N Alterations in gene expression in the testis of angiotensin-(1-7)-receptor Mas-deficient mice. Regul Pept 138: 51-55. Mouse testis transcripts 17196677 7
2006 Xue-Franzen Y, Kjaerulff S, Holmberg C, Wright A, Nielsen O Genomewide identification of pheromone-targeted transcription in fission yeast. BMC Genomics 7: 303. Schizosaccharomyces transcripts 17137508 7
2006 Yang C, Bolotin E, Jiang T, Sladek FM, Martinez E Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters. Gene 389: 52-65. Human and yeast genes 17123746 7,13,18
2006 Yang X, Schadt EE, Wang S, Wang H, Arnold AP, Ingram-Drake L, Drake TA, Lusis AJ Tissue-specific expression and regulation of sexually dimorphic genes in mice. Genome Res 16: 995-991004. Mouse transcripts 16825664 7
2006 Yang Z, Harris LE, Palmer-Toy DE, Hancock WS Multilectin affinity chromatography for characterization of multiple glycoprotein biomarker candidates in serum from breast cancer patients. Clin Chem 52: 1897-1905. Human glycoproteins; breast cancer 16916992 8,16
2006 Ye J|etAl WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34: W293-297. 16845012 10
2006 Yi M, Horton JD, Cohen JC, Hobbs HH, Stephens RM WholePathwayScope: A comprehensive pathway-based analysis tool for high-throughput data. BMC Bioinformatics 7: 30. 16423281 10,13,17
2006 Yu JK, Sun Q, Rota ML, Edwards H, Tefera H, Sorrells ME Expressed sequence tag analysis in tef (Eragrostis tef (Zucc) Trotter). Genome 49: 365-372. Tef ESTs 16699556 5
2006 Yu W, Wang Y, Shaw CA, Qin XF, Rice AP Induction of the HIV-1 Tat co-factor cyclin T1 during monocyte differentiation is required for the regulated expression of a large portion of cellular mRNAs. Retrovirology 3: 32. Human transcripts; HIV-1 Tat 16764723 7,16
2006 Yu X, Griffith WC, Hanspers K, Dillman JF, Ong H, Vredevoogd MA, Faustman EM A system based approach to interpret dose and time-dependent microarray data: quantitative integration of GO ontology analysis for risk assessment. Toxicol Sci 92: 560-577. 16601082 7,10
2006 Zahn JM, Sonu R, Vogel H, Crane E, Mazan-Mamczarz K, Rabkin R, Davis RW, Becker KG, Owen AB, Kim SK Transcriptional profiling of aging in human muscle reveals a common aging signature. PLoS Genet 2: e115. Human muscle transcripts; aging 16789832 10.1371/journal.pgen.0020115 7,16
2006 Zhang C, Liu S, Zhou Y Fast and accurate method for identifying high-quality protein-interaction modules by clique merging and its application to yeast. J Proteome Res 5: 801-807. Yeast proteins 16602686 8,19
2006 Zhang H, Bailey JS, Coss D, Lin B, Tsutsumi R, Lawson MA, Mellon PL, Webster NJ Activin modulates the transcriptional response of L{beta}T2 cells to GnRH and alters cellular proliferation. Mol Endocrinol 20: 2909-2930. Mouse transcripts; activin response 16772531 7,16
2006 Zhang P, Zhang J, Sheng H, Russo JJ, Osborne B, Buetow K Gene functional similarity search tool (GFSST). BMC Bioinformatics 7: 135. 16536867 9,10
2006 Zhang W|etAl SynDB: a Synapse protein DataBase based on synapse ontology. Nucleic Acids Res 17098931 11
2006 Zhang Z|etAl Dynamic changes in subgraph preference profiles of crucial transcription factors. PLoS Comput Biol 2: e47. Saccharomyces transcription networks 16699597 10.1371/journal.pcbi.0020047 7,17
2006 Zhao H, Ljungberg B, Grankvist K, Rasmuson T, Tibshirani R, Brooks JD Gene expression profiling predicts survival in conventional renal cell carcinoma. PLoS Med 3: e13. Human kidney transcripts; renal cell carcinoma 16318415 10.1371/journal.pmed.0030013 7,16
2006 Zheng B, McLean DC, Lu X Identifying biological concepts from a protein-related corpus with a probabilistic topic model. BMC Bioinformatics 7: 58. 16466569 12
2006 Zheng J, Watson AD, Kerr DE Genome-wide expression analysis of lipopolysaccharide-induced mastitis in a mouse model. Infect Immun 74: 1907-1915. Mouse mammary transcripts 16495566 7,16
2006 Zhou GP, Cai YD Predicting protease types by hybridizing gene ontology and pseudo amino acid composition. Proteins 63: 681-684. 16456852 9,10,19
2006 Zhu M, Gao L, Guo Z, Li Y, Wang D, Wang J, Wang C Globally predicting protein functions based on co-expressed protein-protein interaction networks and ontology taxonomy similarities. Gene 391: 113-119. 17289301 9,13,17
2006 Zindy PJ|etAl Upregulation of the tumor suppressor gene menin in hepatocellular carcinomas and its significance in fibrogenesis. Hepatology 44: 1296-1307. Human liver transcripts; cirrhosis; hepatocellular carcinoma 17058241 7,16
2006 van der Pluijm I|etAl Impaired genome maintenance suppresses the growth hormone--insulin-like growth factor 1 axis in mice with Cockayne syndrome. PLoS Biol 5: e2. Mouse liver transcripts; Cockayne syndrome 17326724 7,16
2007 Abernathy JW, Xu P, Li P, Xu DH, Kucuktas H, Klesius P, Arias C, Liu Z Generation and analysis of expressed sequence tags from the ciliate protozoan parasite Ichthyophthirius multifiliis. BMC Genomics 8: 176. Ichthyophthirius ESTs 17577414 5
2007 Abubucker S|etAl The canine hookworm genome: Analysis and classification of Ancylostoma caninum survey sequences. Mol Biochem Parasitol 157: 187-192. Canine hookworm genome 18082904 4
2007 Adzhubei AA, Vlasova AV, Hagen-Larsen H, Ruden TA, Laerdahl JK, Hoyheim B Annotated Expressed Sequence Tags (ESTs) from pre-smolt Atlantic salmon (Salmo salar) in a searchable data resource. BMC Genomics 8: 209. Salmon ESTs 17605782 5
2007 Aerts S, van Helden J, Sand O, Hassan BA Fine-tuning enhancer models to predict transcriptional targets across multiple genomes. PLoS ONE 2: e1115. 17973026 10.1371/journal.pone.0001115 17,19
2007 Aguda BD, Goryachev AB From pathways databases to network models of switching behavior. PLoS Comput Biol 3: 1674-1678. 17907792 10.1371/journal.pcbi.0030152 17
2007 Aidinis V|etAl MUGEN mouse database; Animal models of human immunological diseases. Nucleic Acids Res 36: D1048-1054. 17932065 15
2007 Airoldi EM Getting started in probabilistic graphical models. PLoS Comput Biol 3: e252. 18069887 10.1371/journal.pcbi.0030252 17
2007 Al-Shahrour F, Arbiza L, Dopazo H, Huerta-Cepas J, Minguez P, Montaner D, Dopazo J From genes to functional classes in the study of biological systems. BMC Bioinformatics 8: 114. 17407596 10
2007 Al-Shahrour F, Minguez P, Tarraga J, Medina I, Alloza E, Montaner D, Dopazo J FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res 35: W91-96. 17478504 10
2007 Alibes A, Yankilevich P, Canada A, Diaz-Uriarte R IDconverter and IDClight: Conversion and annotation of gene and protein IDs. BMC Bioinformatics 8: 9. 17214880 10
2007 Almeida PE, Weber PS, Burton JL, Tempelman RJ, Steibel JP, Zanella AJ Gene expression profiling of peripheral mononuclear cells in lame dairy cows with foot lesions. Vet Immunol Immunopathol 120: 234-245. Bovine transcripts; lameness 17675248 7
2007 Alvaro D, Lisby M, Rothstein R Genome-wide analysis of Rad52 foci reveals diverse mechanisms impacting recombination. PLoS Genet 3: e228. 18085829 10.1371/journal.pgen.0030228 13
2007 Andorf C, Dobbs D, Honavar V Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach. BMC Bioinformatics 8: 284. 17683567 3,9
2007 Ao L, Liu JY, Gao LH, Liu SX, Yang MS, Huang MH, Cao J Differential expression of genes associated with cell proliferation and apoptosis induced by okadaic acid during the transformation process of BALB/c 3T3 cells. Toxicol In Vitro 22: 116-127. Mouse cell line transcripts; okadaic acid exposure 17935941 7,16
2007 Apidianakis Y, Mindrinos MN, Xiao W, Tegos GP, Papisov MI, Hamblin MR, Davis RW, Tompkins RG, Rahme LG Involvement of skeletal muscle gene regulatory network in susceptibility to wound infection following trauma. PLoS ONE 2: e1356. Drosophila transcripts; trauma; Pseudomonas aeruginosa infection 18159239 10.1371/journal.pone.0001356 7,16
2007 April CS, Barsh GS Distinct pigmentary and melanocortin 1 receptor-dependent components of cutaneous defense against ultraviolet radiation. PLoS Genet 3: e9. Mouse skin transcripts; UV exposure 17222061 10.1371/journal.pgen.0030009 7,16
2007 Aranguren ME, Bechoffer S, Lord P, Sattler U, Stevens R Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL. BMC Bioinformatics 8: 57. 17311682 13,14,15
2007 Arga KY, Onsan ZI, Kirdar B, Ulgen KO, Nielsen J Understanding signaling in yeast: Insights from network analysis. Biotechnol Bioeng 97: 1246-1258. Saccharomyces proteins 17252576 8,17
2007 Aronica E|etAl Gene expression profile analysis of epilepsy-associated gangliogliomas. Neuroscience 151: 272-292. Human brain transcripts; epilepsy; ganglioglioma 18093740 7,16
2007 Asikainen S, Storvik M, Lakso M, Wong G Whole genome microarray analysis of C. elegans rrf-3 and eri-1 mutants. FEBS Lett 581: 5050-5054. C. elegans transcripts 17919598 7
2007 Badonnel K, Denis JB, Caillol M, Monnerie R, Piumi F, Potier MC, Salesse R, Baly C Transcription profile analysis reveals that OBP-1F mRNA is downregulated in the olfactory mucosa following food deprivation. Chem Senses 13: 982-997. Rat olfactory mucosal transcripts; food deprivation 17584948 7,16
2007 Bao L, Peirce JL, Zhou M, Li H, Goldowitz D, Williams RW, Lu L, Cui Y An integrative genomics strategy for systematic characterization of genetic loci modulating phenotypes. Hum Mol Genet 16: 1381-1390. 17428815 15
2007 Barbe L|etAl Towards a confocal subcellular atlas of the human proteome. Mol Cell Proteomics 7: 499-508. Human proteins 18029348 8,13
2007 Baron D, Montfort J, Houlgatte R, Fostier A, Guiguen Y Androgen-induced masculinization in rainbow trout results in a marked dysregulation of early gonadal gene expression profiles. BMC Genomics 8: 357. Trout gonadal transcripts 17916255 7
2007 Barriot R, Sherman DJ, Dutour I How to decide which are the most pertinent overly-represented features during gene set enrichment analysis. BMC Bioinformatics 8: 332. 17848190 13
2007 Baumbach J CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks. BMC Bioinformatics 8: 429. 17986320 11
2007 Baumgartner WA, Cohen KB, Fox LM, Acquaah-Mensah G, Hunter L Manual curation is not sufficient for annotation of genomic databases. Bioinformatics 23: i41-i48. 17646325 3,13
2007 Begun DJ|etAl Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol 5: e310. 17988176 10.1371/journal.pbio.0050310 18
2007 Beilharz TH, Preiss T Widespread use of poly(A) tail length control to accentuate expression of the yeast transcriptome. RNA 13: 982-997. Saccharomyces transcripts 17586758 7
2007 Beltran S, Angulo M, Pignatelli M, Serras F, Corominas M Functional dissection of the ash2 and ash1 transcriptomes provides insights into the transcriptional basis of wing phenotypes and reveals conserved protein interactions. Genome Biol 8: R67. Drosophila transcripts 17466076 7
2007 Beltrao P, Serrano L Specificity and evolvability in eukaryotic protein interaction networks. PLoS Comput Biol 3: e25. Human proteins 17305419 10.1371/journal.pcbi.0030025 8,17
2007 Bennett KP, Bergeron C, Acar E, Klees RF, Vandenberg SL, Yener B, Plopper GE Proteomics reveals multiple routes to the osteogenic phenotype in mesenchymal stem cells. BMC Genomics 8: 380. Human mesenchymal stem cell proteins; osteogenesis 17949499 8,16
2007 Betel D, Breitkreuz KE, Isserlin R, Dewar-Darch D, Tyers M, Hogue CW Structure-templated predictions of novel protein interactions from sequence information. PLoS Comput Biol 3: 1783-1789. Yeast proteins 17892321 10.1371/journal.pcbi.0030182 8,19
2007 Bhati R, Gokmen-Polar Y, Sledge GW, Fan C, Nakshatri H, Ketelsen D, Borchers CH, Dial MJ, Patterson C, Klauber-Demore N 2-methoxyestradiol inhibits the anaphase-promoting complex and protein translation in human breast cancer cells. Cancer Res 67: 702-708. Human transcripts; breast cancer 17234781 7,16
2007 Blanding CR, Simmons SJ, Casati P, Walbot V, Stapleton AE Coordinated regulation of maize genes during increasing exposure to ultraviolet radiation: identification of ultraviolet-responsive genes, functional processes and associated potential promoter motifs. Plant Biotechnol J 5: 677-695. Maize transcripts; UV exposure 17924934 7
2007 Bomblies K, Lempe J, Epple P, Warthmann N, Lanz C, Dangl JL, Weigel D Autoimmune response as a mechanism for a Dobzhansky-Muller-type incompatibility syndrome in plants. PLoS Biol 5: e236. Arabidopsis transcripts 17803357 10.1371/journal.pbio.0050236 7,18
2007 Bonnet E, Fostier A, Bobe J Microarray-based analysis of fish egg quality after natural or controlled ovulation. BMC Genomics 8: 55. Rainbow trout egg transcripts 17313677 7
2007 Bontempi G A blocking strategy to improve gene selection for classification of gene expression data. IEEE/ACM Trans Comput Biol Bioinform 4: 293-300. 17473321 7
2007 Brown DP, Krishnamurthy N, Sjolander K Automated protein subfamily identification and classification. PLoS Comput Biol 3: e160. 17708678 10.1371/journal.pcbi.0030160 19
2007 Brown KR, Jurisica I Unequal evolutionary conservation of human protein interactions in interologous networks. Genome Biol 8: R95. 17535438 8,17,18
2007 Broz AK, Broeckling CD, He J, Dai X, Zhao PX, Vivanco JM A first step in understanding an invasive weed through its genes: an EST analysis of invasive Centaurea maculosa. BMC Plant Biol 7: 25. Aster ESTs 17524143 5
2007 Buil A, Perera-Lluna A, Souto R, Peralta JM, Almasy L, Vallverdu M, Caminal P, Soria JM Searching for master regulators of transcription in a human gene expression data set. BMC Proc 1 Suppl 1: S81. 18466584 7,17
2007 Bult CJ, Eppig JT, Kadin JA, Richardson JE, Blake JA, The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res 36: D724-728. Mouse genome 18158299 1,4,11,15
2007 Burgoon LD Clearing the standards landscape: the semantics of terminology and their impact on toxicogenomics. Toxicol Sci 99: 403-412. 17483496 15
2007 Bush CR, Havens JM, Necela BM, Su W, Chen L, Yanagisawa M, Anastasiadis PZ, Guerra R, Luxon BA, Thompson EA Functional genomic analysis reveals crosstalk between peroxisome proliferator-activated receptor gamma (PPARgamma) and calcium signaling in human colorectal cancer cells. J Biol Chem 5: 383-405. Human colorectal cancer cell line transcripts; colorectal cancer 17565986 7,16
2007 Butland SL|etAl CAG-encoded polyglutamine length polymorphism in the human genome. BMC Genomics 8: 126. Human genes; CAG trinucleotide repeats 17519034 13,16
2007 Buza TJ, McCarthy FM, Burgess SC Experimental-confirmation and functional-annotation of predicted proteins in the chicken genome. BMC Genomics 8: 425. Chicken genome 18021451 1,4
2007 Cakmak A, Ozsoyoglu G Annotating genes using textual patterns. Pac Symp Biocomput 2007: 221-232. 17990494 9,10,12
2007 Cakmak A, Ozsoyoglu G Mining biological networks for unknown pathways. Bioinformatics 23: 2775-2783. 17766269 17,19
2007 Calsa T, Figueira A Serial analysis of gene expression in sugarcane (Saccharum spp.) leaves revealed alternative C(4) metabolism and putative antisense transcripts. Plant Mol Biol 63: 745-762. Sugar cane SAGE tags 17211512 3
2007 Camargo A, Azuaje F Linking gene expression and functional network data in human heart failure. PLoS ONE 2: e1347. Human proteins; human transcripts; heart failure 18094754 10.1371/journal.pone.0001347 7,8,16,17
2007 Campanaro S, Picelli S, Torregrossa R, Colluto L, Ceol M, Del Prete D, D'Angelo A, Valle G, Anglani F Genes involved in TGFbeta1-driven epithelial-mesenchymal transition of renal epithelial cells are topologically related in the human interactome map. BMC Genomics 8: 383. Human epithelial cell transcripts; differentiation; TGFbeta1 17953753 7,16,17
2007 Campbell PA, Perez-Iratxeta C, Andrade-Navarro MA, Rudnicki MA Oct4 targets regulatory nodes to modulate stem cell function. PLoS ONE 2: e553. Mouse stem cell transcripts 17579724 7,16
2007 Caprera A, Lazzari B, Stella A, Merelli I, Caetano AR, Mariani P GoSh: a web based database for goat and sheep EST sequences. Bioinformatics 23: 1043-1045. Goat ESTs; sheep ESTs 17384426 5,11
2007 Chabalier J, Mosser J, Burgun A A transversal approach to predict gene product networks from ontology-based similarity. BMC Bioinformatics 8: 235. 17605807 7,17
2007 Chambers SM, Shaw CA, Gatza C, Fisk CJ, Donehower LA, Goodell MA Aging hematopoietic stem cells decline in function and exhibit epigenetic dysregulation. PLoS Biol 5: e201. Mouse hematopoietic stem cell transcripts; aging 17676974 10.1371/journal.pbio.0050201 7
2007 Chang MY, Yu YP, Tsai JR, Sheu CC, Chong IW, Lin SR Combined oligonucleotide microarray-bioinformatics and constructed membrane arrays to analyze the biological pathways in the carcinogenesis of human lung adenocarcinoma. Oncol Rep 18: 569-579. Human lung transcripts; adenocarcinoma 17671703 7,16
2007 Chattopadhyay I, Kapur S, Purkayastha J, Phukan R, Kataki A, Mahanta J, Saxena S Gene expression profile of esophageal cancer in North East India by cDNA microarray analysis. World J Gastroenterol 13: 1438-1444. Human esophageal tumor transcripts; esophageal cancer 17457978 7,16
2007 Chelala C, Hahn SA, Whiteman HJ, Barry S, Hariharan D, Radon TP, Lemoine NR, Crnogorac-Jurcevic T Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets. BMC Genomics 8: 439. Human pancreatic transcripts; pancreatic cancer 18045474 7,11,16
2007 Chen C, Fuhrken PG, Huang LT, Apostolidis P, Wang M, Paredes CJ, Miller WM, Papoutsakis ET A systems-biology analysis of isogenic megakaryocytic and granulocytic cultures identifies new molecular components of megakaryocytic apoptosis. BMC Genomics 8: 384. Human hematopoietic cell transcripts; megakaryocyte differentiation; apoptosis 17953764 7,16
2007 Chen H, Ordog T, Chen J, Young DL, Bardsley MR, Redelman D, Ward SM, Sanders KM Differential gene expression in functional classes of interstitial cells of Cajal in murine small intestine. Physiol Genomics 31: 492-509. Mouse intestinal transcripts 17895395 7,16
2007 Chen J, Blackwell TW, Fermin D, Menon R, Chen Y, Gao J, Lee AW, States DJ Evolutionary-conserved gene expression response profiles across mammalian tissues. OMICS 11: 96-9122. Human and mouse transcripts 17411398 7,18
2007 Chen JL, Liu Y, Sam LT, Li J, Lussier YA Evaluation of high-throughput functional categorization of human disease genes. BMC Bioinformatics 8 Suppl 3: S7. 17493290 9,16
2007 Chen JY, Yan Z, Shen C, Fitzpatrick DP, Wang M A systems biology approach to the study of Cisplatin drug resistance in ovarian cancers. J Bioinform Comput Biol 5: 383-405. Human cell line proteins; ovarian cancer; cisplatin resistance 17589967 8,16,17
2007 Chen M, Ying W, Song Y, Liu X, Yang B, Wu S, Jiang Y, Cai Y, He F, Qian X Analysis of human liver proteome using replicate shotgun strategy. Proteomics 7: 2479-2488. Human liver proteins 17623305 8
2007 Chen X, Laudeman TW, Rushton PJ, Spraggins TA, Timko MP CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences. BMC Bioinformatics 8: 129. Cowpea genes 17445272 3,11
2007 Chen Y, Blackwell TW, Chen J, Gao J, Lee AW, States DJ Integration of genome and chromatin structure with gene expression profiles to predict c-MYC recognition site binding and function. PLoS Comput Biol 3: e63. Human c-MYC targets 17411336 10.1371/journal.pcbi.0030063 19
2007 Cheng C, Fabrizio P, Ge H, Wei M, Longo VD, Li LM Significant and systematic expression differentiation in long-lived yeast strains. PLoS ONE 2: e1095. Saccharomyces transcripts; aging 17971858 7
2007 Cheng WY, Hsiang CY, Bau DT, Chen JC, Shen WS, Li CC, Lo HY, Wu SL, Chiang SY, Ho TY Microarray analysis of vanillin-regulated gene expression profile in human hepatocarcinoma cells. Pharmacol Res 56: 474-482. Human hepatocarcinoma cell transcripts; vanillin exposure 17949990 7,16
2007 Cheung F, Town CD A BAC end view of the Musa acuminata genome. BMC Plant Biol 7: 29. Musa acuminata BAC ends 17562019 3
2007 Chitteti BR, Peng Z Proteome and phosphoproteome dynamic change during cell dedifferentiation in Arabidopsis. Proteomics 7: 1473-1500. Arabidopsis proteins 17407188 8
2007 Cho YR, Hwang W, Ramanathan M, Zhang A Semantic integration to identify overlapping functional modules in protein interaction networks. BMC Bioinformatics 8: 265. 17650343 8,17
2007 Choi K, Creighton CJ, Stivers D, Fujimoto N, Kurie JM Transcriptional profiling of non-small cell lung cancer cells with activating EGFR somatic mutations. PLoS ONE 2: e1226. Human lung cancer cell transcripts 18030354 10.1371/journal.pone.0001226 7,16
2007 Choi SC, Hobolth A, Robinson DM, Kishino H, Thorne JL Quantifying the impact of protein tertiary structure on molecular evolution. Mol Biol Evol 24: 1769-1782. 17522088 8,18
2007 Chou JW, Zhou T, Kaufmann WK, Paules RS, Bushel PR Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes. BMC Bioinformatics 8: 427. 17980031 7
2007 Chow KS, Wan KL, Isa MN, Bahari A, Tan SH, Harikrishna K, Yeang HY Insights into rubber biosynthesis from transcriptome analysis of Hevea brasiliensis latex. J Exp Bot 8: R122. Rubber tree ESTs 17545224 5,7
2007 Chua HN, Sung WK, Wong L Using indirect protein interactions for the prediction of Gene Ontology functions. BMC Bioinformatics 8 Suppl 4: S8. 17570151 8,9
2007 Chung WY, Wadhawan S, Szklarczyk R, Pond SK, Nekrutenko A A first look at ARFome: dual-coding genes in mammalian genomes. PLoS Comput Biol 3: e91. Mammalian genes; alternative reading frames 17511511 10.1371/journal.pcbi.0030091 13
2007 Ciaramella A, Cocozza S, Iorio F, Miele G, Napolitano F, Pinelli M, Raiconi G, Tagliaferri R Interactive data analysis and clustering of genomic data. Neural Netw 21: 368-378. 18255261 7,17
2007 Clemente JC, Satou K, Valiente G Phylogenetic reconstruction from non-genomic data. Bioinformatics 23: e110-115. 17237077 10,18,19
2007 Cline MS|etAl Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2: 2366-2382. 17947979 10,17
2007 Cokus S, Mizutani S, Pellegrini M An improved method for identifying functionally linked proteins using phylogenetic profiles. BMC Bioinformatics 8 Suppl 4: S7. 17570150 13,18
2007 Conboy CM|etAl Cell cycle genes are the evolutionarily conserved targets of the E2F4 transcription factor. PLoS ONE 2: e1061. Human genes; mouse genes 17957245 10.1371/journal.pone.0001061 7,13,18
2007 Corsi C, Ferragina P, Marangoni R The BioPrompt-box: an ontology-based clustering tool for searching in biological databases. BMC Bioinformatics 8 Suppl 1: S8. 17430575 10
2007 Crangle CE, Cherry JM, Hong EL, Zbyslaw A Mining experimental evidence of molecular function claims from the literature. Bioinformatics 23: 3232-3240. 17942445 1,9,12
2007 Cromie GA, Hyppa RW, Cam HP, Farah JA, Grewal SI, Smith GR A discrete class of intergenic DNA dictates meiotic DNA break hotspots in fission yeast. PLoS Genet 3: e141. 17722984 10.1371/journal.pgen.0030141 13
2007 Cui GH, Huang LQ, Qiu DY, Yuan Y, Fu GF [Functional genomics studies of Salvia miltiorrhiza II--gene expression profiling of different stage of hairy root] Zhongguo Zhong Yao Za Zhi 32: 1267-1272. Salvia miltiorrhiza cDNAs 17879722 3,7
2007 Cui Y, McBride SJ, Boyd WA, Alper S, Freedman JH Toxicogenomic analysis of Caenorhabditis elegans reveals novel genes and pathways involved in the resistance to cadmium toxicity. Genome Biol 8: R122. Caenorhabditis transcripts; cadmium toxicity 17592649 7,16
2007 Cushion MT, Smulian AG, Slaven BE, Sesterhenn T, Arnold J, Staben C, Porollo A, Adamczak R, Meller J Transcriptome of Pneumocystis carinii during Fulminate Infection: Carbohydrate Metabolism and the Concept of a Compatible Parasite. PLoS ONE 2: e423. Pneumocystis transcripts 17487271 7,16
2007 Cutillas PR, Vanhaesebroeck B Quantitative profile of five murine core proteomes using label-free functional proteomics Mol Cell Proteomics 6: 1560-1573. Mouse proteins 17565973 8
2007 Dai Z, Fan J, Liu Y, Zhou J, Bai D, Tan C, Guo K, Zhang Y, Zhao Y, Yang P Identification and analysis of alpha1,6-fucosylated proteins in human normal liver tissues by a target glycoproteomic approach. Electrophoresis 28: 4382-4391. Human liver proteins 18041034 8,16
2007 Dai ZQ, Wang R, Ling SK, Wan YM, Li YH Simulated microgravity inhibits the proliferation and osteogenesis of rat bone marrow mesenchymal stem cells. Cell Prolif 40: 671-684. Rat bone marrow mesenchymal cell transcripts; microgravity 17877609 7,16
2007 Danley PD, Mullen SP, Liu F, Nene V, Quackenbush J, Shaw KL A cricket Gene Index: A genomic resource for studying neurobiology, speciation, and molecular evolution. BMC Genomics 8: 109. Cricket ESTs 17459168 5,11
2007 Daraselia N, Yuryev A, Egorov S, Mazo I, Ispolatov I Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks. BMC Bioinformatics 8: 243. 17620146 9,12,17
2007 Day-Richter J, Harris MA, Haendel M, Lewis S OBO-Edit - An ontology editor for biologists. Bioinformatics 23: 2198-2200. 17545183 1,10,15
2007 De Bie T, Tranchevent LC, van Oeffelen LM, Moreau Y Kernel-based data fusion for gene prioritization. Bioinformatics 23: i125-i132. 17646288 10,19
2007 De Renzis S, Elemento O, Tavazoie S, Wieschaus EF Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo. PLoS Biol 5: e117. Drosophila embryo transcripts 17456005 10.1371/journal.pbio.0050117 7
2007 Dehan E|etAl Chromosomal aberrations and gene expression profiles in non-small cell lung cancer. Lung Cancer 56: 175-184. Human genes; lung cancer 17258348 7,13,16
2007 Del Bene F, Ettwiller L, Skowronska-Krawczyk D, Baier H, Matter JM, Birney E, Wittbrodt J In vivo validation of a computationally predicted conserved Ath5 target gene set. PLoS Genet 3: 1661-1671. Human genes 17892326 10.1371/journal.pgen.0030159 7,18,19
2007 Derre I, Pypaert M, Dautry-Varsat A, Agaisse H RNAi screen in Drosophila cells reveals the involvement of the Tom complex in Chlamydia infection. PLoS Pathog 3: 1446-1458. Drosophila genes; Chlamydia infection 17967059 10.1371/journal.ppat.0030155 13,16
2007 Diaz-Uriarte R, Alibes A, Morrissey ER, Canada A, Rueda OM, Neves ML Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite. Nucleic Acids Res 35: W75-80. 17488846 10
2007 Diehl AD, Lee JA, Scheuermann RH, Blake JA Ontology development for biological systems: Immunology. Bioinformatics 23: 913-915. 17267433 1,2,3,16
2007 Dihal AA, Tilburgs C, van Erk MJ, Rietjens IM, Woutersen RA, Stierum RH Pathway and single gene analyses of inhibited Caco-2 differentiation by ascorbate-stabilized quercetin suggest enhancement of cellular processes associated with development of colon cancer. Mol Nutr Food Res 51: 1031-1045. Human cell line transcripts; colon cancer 17639512 7,16
2007 Dimmer E, Berardini TZ, Barrell D, Camon E Methods for gene ontology annotation. Methods Mol Biol 406: 495-520. 18287709 1,3
2007 Dixon AL|etAl A genome-wide association study of global gene expression. Nat Genet 39: 1202-1207. Human SNPs; human QTLs; complex diseases 17873877 7,16,18
2007 Domagk D|etAl Expression analysis of pancreatic cancer cell lines reveals association of enhanced gene transcription and genomic amplifications at the 8q22.1 and 8q24.22 loci. Oncol Rep 17: 399-407. Human cell line transcripts; pancreatic cancer 17203180 7,16
2007 Dong C, Qian Z, Jia P, Wang Y, Huang W, Li Y Gene-centric characteristics of genome-wide association studies. PLoS ONE 2: e1262. Human genes 18060058 10.1371/journal.pone.0001262 13,16,18
2007 Dori D, Choder M Conceptual modeling in systems biology fosters empirical findings: the mRNA lifecycle. PLoS ONE 2: e872. 17849002 10.1371/journal.pone.0000872 13
2007 Doss MX|etAl Global transcriptome analysis of murine embryonic stem cell-derived cardiomyocytes. Genome Biol 8: R56. Mouse cardiomyocyte transcripts 17428332 7
2007 Dressman HK, Muramoto GG, Chao NJ, Meadows S, Marshall D, Ginsburg GS, Nevins JR, Chute JP Gene expression signatures that predict radiation exposure in mice and humans. PLoS Med 4: e106. Human and mouse blood cell transcripts; radiation exposure 17407386 10.1371/journal.pmed.0040106 7,16
2007 Duan S, Bleibel WK, Huang RS, Shukla SJ, Wu X, Badner JA, Dolan ME Mapping Genes that Contribute to Daunorubicin-Induced Cytotoxicity. Cancer Res 67: 5425-5433. Human genes; daunorubicin cytotoxicity 17545624 13,16
2007 Edwards RJ, Davey NE, Shields DC SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins. PLoS ONE 2: e967. 10.1371/journal.pone.0000967 17912346 8,10
2007 Eijssen LM, Lindsey PJ, Peeters R, Westra RL, van Eijsden RG, Bolotin-Fukuhara M, Smeets HJ, Vlietinck RF A novel stepwise analysis procedure of genome-wide expression profiles identifies transcript signatures of thiamine genes as classifiers of mitochondrial mutants. Yeast 25: 129-140. Saccharomyces gene expression; Saccharomyces gene knock-outs 18081196 7,13
2007 Emmert-Streib F The chronic fatigue syndrome: a comparative pathway analysis. J Comput Biol 14: 961-972. 17803373 16,17
2007 Eyueboglu B, Pfister K, Haberer G, Chevalier D, Fuchs A, Mayer KF, Schneitz K Molecular characterisation of the STRUBBELIG-RECEPTOR FAMILY of genes encoding putative leucine-rich repeat receptor-like kinases in Arabidopsis thaliana. BMC Plant Biol 7: 16. Arabidopsis transcripts; Strubbelig-receptor family 17397538 7
2007 Fagan A, Culhane AC, Higgins DG A multivariate analysis approach to the integration of proteomic and gene expression data. Proteomics 7: 2162-2171. 17549791 7,8,13
2007 Fair T, Carter F, Park S, Evans AC, Lonergan P Global gene expression analysis during bovine oocyte in vitro maturation. Theriogenology 68 Suppl 1: S91-97. Bovine oocyte transcripts 17512044 7
2007 Feng B, Zhao YP, Chen G, Zhang TP, Wu YD [Selection of genes related to multidrug resistance of pancreatic ductal adenocarcinoma by microarray analysis] Zhonghua Wai Ke Za Zhi 45: 1629-1633. Human pancreatic cell line transcripts; pancreatic cancer 18453221 7,16
2007 Feng Z, Davis DP, Sasik R, Patel HH, Drummond JC, Patel PM Pathway and gene ontology based analysis of gene expression in a rat model of cerebral ischemic tolerance. Brain Res 1177: 103-123. Rat hippocampal transcripts; ischemic tolerance 17916339 7,16
2007 Fernald GH, Knott S, Pachner A, Caillier SJ, Narayan K, Oksenberg JR, Mousavi P, Baranzini SE Genome-wide network analysis reveals the global properties of IFN-beta immediate transcriptional effects in humans. J Immunol 178: 5076-5085. Human lymphocyte transcripts 17404290 7,16,17
2007 Ferrazzi F, Magni P, Sacchi L, Nuzzo A, Petrovic U, Bellazzi R Inferring gene regulatory networks by integrating static and dynamic data. Int J Med Inform 76 Suppl 3: S462-475. Saccharomyces genes 17825607 7,13,17
2007 Field LA, Jordan RM, Hadix JA, Dunn MA, Shriver CD, Ellsworth RE, Ellsworth DL Functional identity of genes detectable in expression profiling assays following globin mRNA reduction of peripheral blood samples. Clin Biochem 40: 499-502. Human blood transcripts 17303101 7,16
2007 Fierro AC|etAl Exploring the nervous system transcriptomes during embryogenesis and metamorphosis in Xenopus tropicalis using EST analysis. BMC Genomics 8: 118. Xenopus ESTs 17506875 5,7
2007 Freeman TC, Goldovsky L, Brosch M, van Dongen S, Maziere P, Grocock RJ, Freilich S, Thornton J, Enright AJ Construction, visualisation, and clustering of transcription networks from microarray expression data. PLoS Comput Biol 3: 2032-2042. Mouse transcripts 17967053 10.1371/journal.pcbi.0030206 7,17
2007 Freudenberg J, Fu YH, Pta Cbreve Ek LJ Enrichment of HapMap recombination hotspot predictions around human nervous system genes: evidence for positive selection ? Eur J Hum Genet 15: 1071-1078. Human genes; recombination hotspots 17568387 13,18
2007 Frijters R, Verhoeven S, Alkema W, van Schaik R, Polman J Literature-based compound profiling: application to toxicogenomics. Pharmacogenomics 8: 1521-1534. 18034617 12
2007 Froehlich H, Speer N, Poustka A, Beissbarth T GOSim - An R-package for computation of information theoretic GO similarities between terms and gene products. BMC Bioinformatics 8: 166. 17519018 10
2007 Fry RC|etAl Activation of inflammation/NF-kappaB signaling in infants born to arsenic-exposed mothers. PLoS Genet 3: e207. Human blood transcripts; prenatal arsenic exposure 18039032 10.1371/journal.pgen.0030207 7,16
2007 Fujishima K, Komasa M, Kitamura S, Suzuki H, Tomita M, Kanai A Proteome-wide prediction of novel DNA/RNA-binding proteins using amino acid composition and periodicity in the hyperthermophilic archaeon Pyrococcus furiosus. DNA Res 14: 91-9102. 17573465 6,9,19
2007 Gahr SA, Rexroad CE, Rise ML, Hunt P, Koop B A survey of expressed sequence tags from the rainbow trout (oncorhynchus mykiss) pituitary. Anim Biotechnol 18: 213-230. Trout pituitary ESTs 17612844 5
2007 Gaj S, van Erk A, van Haaften RI, Evelo CT Linking microarray reporters with protein functions. BMC Bioinformatics 8: 360. 17897448 7,9
2007 Gama-Castro S|etAl RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res 36: D120-124. E. coli transcription 18158297 7,11,17
2007 Gamberoni G, Lamma E, Lodo G, Marchesini J, Mascellani N, Rossi S, Storari S, Tagliavini L, Volinia S Fun&Co: identification of key functional differences in transcriptomes. Bioinformatics 20: 443-452. 17893090 7,10,12
2007 Gao L, Li X, Guo Z, Zhu M, Li Y, Rao S Widely predicting specific protein functions based on protein-protein interaction data and gene expression profile. Sci China C Life Sci 50: 125-134. 17393093 9
2007 Gattiker A, Rischatsch R, Demougin P, Voegeli S, Dietrich FS, Philippsen P, Primig M Ashbya Genome Database 3.0: a cross-species genome and transcriptome browser for yeast biologists. BMC Genomics 8: 9. Ashbya genome 17212814 4,11
2007 Gaulton KJ, Mohlke KL, Vision TJ A computational system to select candidate genes for complex human traits. Bioinformatics 23: 1132-1140. 17237041 10
2007 Georgiev A, Sjostrom M, Wieslander A Binding specificities of the GYF domains from two Saccharomyces cerevisiae Paralogs. Protein Eng Des Sel 20: 443-452. 17804396 13,18
2007 Gerber GK, Dowell RD, Jaakkola TS, Gifford DK Automated discovery of functional generality of human gene expression programs. PLoS Comput Biol 3: e148. Human gene expression 17696603 10.1371/journal.pcbi.0030148 7,19
2007 Gerber GK, Dowell RD, Jaakkola TS, Gifford DK Automated discovery of functional generality of human gene expression programs. PLoS Comput Biol 3: e148. Human genes 17696603 10.1371/journal.pcbi.0030148 7,16,17
2007 Gilbert DG DroSpeGe: rapid access database for new Drosophila species genomes. Nucleic Acids Res 35: D480-485. Drosophila species genomes 17202166 4,11,18
2007 Gnanamani M, Kumar N, Ramachandran S ARC: Automated Resource Classifier for agglomerative functional classification of prokaryotic proteins using annotation texts. J Biosci 32: 937-945. 17914236 9,10
2007 Goeman JJ, Buhlmann P Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics 23: 980-987. 17303618 7
2007 Goertzel B, Pennachin C, Coelho LS, Mudado MA Application of MUTIC to the exploration of gene expression data in prostate cancer. Genet Mol Res 6: 890-900. Human prostate transcripts; prostate cancer 18058710 7,16,17
2007 Goffard N, Weiller G GeneBins: a database for classifying gene expression data, with application to plant genome arrays. BMC Bioinformatics 8: 87. Plant genes; transcripts 17349060 7,11
2007 Gonzalez-Ibeas D|etAl MELOGEN: an EST database for melon functional genomics. BMC Genomics 8: 306. Melon ESTs 17767721 5,11
2007 Gorodkin J|etAl Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 ESTs. Genome Biol 8: R45. Porcine ESTs 17407547 5,7
2007 Gracey AY Interpreting physiological responses to environmental change through gene expression profiling. J Exp Biol 210: 1584-1592. Carp transcripts 17449823 7
2007 Graubert TA|etAl A high-resolution map of segmental DNA copy number variation in the mouse genome. PLoS Genet 3: e3. Mouse genes 17206864 10.1371/journal.pgen.0030003 13,18
2007 Grgurevic L, Macek B, Durdevic D, Vukicevic S Detection of bone and cartilage-related proteins in plasma of patients with a bone fracture using liquid chromatography-mass spectrometry. Int Orthop 7: 24. Human plasma proteins; bone fracture 17602227 8,16
2007 Griffith OL|etAl ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res 36: D107-113. 18006570 15
2007 Grossmann S, Bauer S, Robinson PN, Vingron M Improved detection of overrepresentation of gene-ontology annotations with parent-child analysis. Bioinformatics 23: 3024-3031. 17848398 7,10
2007 Grskovic M, Chaivorapol C, Gaspar-Maia A, Li H, Ramalho-Santos M Systematic identification of cis-regulatory sequences active in mouse and human embryonic stem cells. PLoS Genet 3: e145. Human transcripts; mouse transcripts; embryonic stem cells 17784790 10.1371/journal.pgen.0030145 7,16
2007 Guan Y, Dunham MJ, Troyanskaya OG Functional Analysis of Gene Duplications in Saccharomyces cerevisiae. Genetics 175: 933-943. 17151249 13,18
2007 Gulati AS, Ochsner SA, Henning SJ Molecular properties of side population-sorted cells from mouse small intestine. Am J Physiol Gastrointest Liver Physiol 294: G286-294. Mouse intestinal transcripts 18006601 7
2007 Gunther S|etAl SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Res 36: D919-922. 17942422 11,16
2007 Guo W|etAl A microsatellite-based, gene-rich linkage map reveals genome structure, function, and evolution in Gossypium. Genetics 176: 527-541. Cotton ESTs 17409069 5
2007 Gusev Y, Schmittgen TD, Lerner M, Postier R, Brackett D Computational analysis of biological functions and pathways collectively targeted by co-expressed microRNAs in cancer. BMC Bioinformatics 8 Suppl 7: S16. 18047715 9,12
2007 Gustavsson M, Wilson MA, Mallard C, Rousset C, Johnston MV, Hagberg H Global gene expression in the developing rat brain after hypoxic preconditioning: involvement of apoptotic mechanisms? Pediatr Res 61: 444-450. Rat brain transcripts; hypoxia 17515869 7
2007 Hahn MW, Han MV, Han SG Gene family evolution across 12 Drosophila genomes. PLoS Genet 3: e197. 17997610 10.1371/journal.pgen.0030197 18
2007 Han A, Kim WY, Park SM SNP2NMD: a database of human single nucleotide polymorphisms causing nonsense-mediated mRNA decay. Bioinformatics 23: 397-399. 17121775 11
2007 Hao Y, Sood S, Triadafilopoulos G, Kim JH, Wang Z, Sahbaie P, Omary MB, Lowe AW Gene expression changes associated with Barrett's esophagus and Barrett's-associated adenocarcinoma cell lines after acid or bile salt exposure. BMC Gastroenterol 7: 24. Human transcripts; esophageal cancer 17597535 7,16
2007 Haque T|etAl Gene Expression Profiling from Formalin-Fixed Paraffin-Embedded Tumors of Pediatric Glioblastoma. Clin Cancer Res 13: 6284-6292. Human brain transcripts; pediatric glioblastoma 17975139 7,16
2007 Haroutunian V, Katsel P, Dracheva S, Stewart DG, Davis KL Variations in oligodendrocyte-related gene expression across multiple cortical regions: implications for the pathophysiology of schizophrenia. Int J Neuropsychopharmacol 10: 565-573. Human brain transcripts; schizophrenia 17291370 7,16
2007 Hasegawa Y, Mans JJ, Mao S, Lopez MC, Baker HV, Handfield M, Lamont RJ Gingival epithelial cell transcriptional responses to commensal and opportunistic oral microbial species. Infect Immun 75: 2540-2547. Human gingival epithelial cell transcripts; oral microbes 17307939 7,16
2007 Hashimoto JG, Wiren KM Neurotoxic consequences of chronic alcohol withdrawal: expression profiling reveals importance of gender over withdrawal severity. Neuropsychopharmacology 33: 1084-1096. Mouse brain transcripts; alcohol withdrawal 17593928 7,16
2007 Hassoun H, Grigoryev DN, Lie M, Liu M, Cheadle C, Tuder RM, Rabb H Ischemic acute kidney injury induces a distant organ functional and genomic response distinguishable from bilateral nephrectomy. Am J Physiol Renal Physiol 293: F30-40. Mouse lung transcripts; ischemia 17327501 7,16
2007 Haudry Y, Berube H, Letunic I, Weeber PD, Gagneur J, Girardot C, Kapushesky M, Arendt D, Bork P, Brazma A, Furlong E, Wittbrodt J, Henrich T 4DXpress: a database for cross-species expression pattern comparisons. Nucleic Acids Res 36: D847-853. 17916571 15
2007 Havlioglu N, Wang J, Fushimi K, Vibranovski MD, Kan Z, Gish W, Fedorov A, Long M, Wu JY An intronic signal for alternative splicing in the human genome. PLoS ONE 2: e1246. 18043753 10.1371/journal.pone.0001246 13
2007 He J, Dai X, Zhao X PLAN: A web platform for automating high-throughput BLAST searches and for managing and mining results. BMC Bioinformatics 8: 53. 17291345 10,12
2007 Hermans F, Tsiporkova E Merging microarray cell synchronization experiments through curve alignment. Bioinformatics 23: e64-70. 17237107 7,10
2007 Hernandez P, Sole X, Valls J, Moreno V, Capella G, Urruticoechea A, Pujana MA Integrative analysis of a cancer somatic mutome. Mol Cancer 6: 13. Human genes; mutations; breast cancer 17280605 13,16,17
2007 Hildebrand MS, de Silva MG, Klockars T, Campbell CA, Smith RJ, Dahl HH Gene expression profiling analysis of the inner ear. Hear Res 225: 1-10. 17300888 7,16
2007 Hipp JD, Davies KP, Tar M, Valcic M, Knoll A, Melman A, Christ GJ Using gene chips to identify organ-specific, smooth muscle responses to experimental diabetes: potential applications to urological diseases. BJU Int 99: 418-430. Rat transcripts; diabetes; urological disease 17313427 7,16
2007 Ho CL|etAl Analysis and functional annotation of expressed sequence tags (ESTs) from multiple tissues of oil palm (Elaeis guineensis Jacq.). BMC Genomics 8: 381. Oil palm ESTs 17953740 5
2007 Ho E, Webber R, Wilkins MR Interactive three-dimensional visualization and contextual analysis of protein interaction networks. J Proteome Res 7: 104-112. 18020406 8,17
2007 Hodges A, Hughes G, Brooks S, Elliston L, Holmans P, Dunnett SB, Jones L Brain gene expression correlates with changes in behavior in the R6/1 mouse model of Huntington's disease. Genes Brain Behav 7: 288-299. Mouse brain transcripts; Huntington's disease 17696994 7,16
2007 Hoffman MM, Birney E Estimating the neutral rate of nucleotide substitution using introns. Mol Biol Evol 24: 522-531. 17122369 18
2007 Holloway AK, Lawniczak MK, Mezey JG, Begun DJ, Jones CD Adaptive gene expression divergence inferred from population genomics. PLoS Genet 3: 2007-2013. Drosophila species transcripts 17967066 10.1371/journal.pgen.0030187 7,18
2007 Hong EL|etAl Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res 36: D577-581. Saccharomyces genome 17982175 1,4,11
2007 Hook SE, Skillman AD, Gopalan B, Small JA, Schultz IR Gene expression profiles in rainbow trout, Onchorynchus mykiss, exposed to a simple chemical mixture. Toxicol Sci 102: 42-60. Rainbow trout transcripts 18084045 7
2007 Hornshoj H, Conley LN, Hedegaard J, Sorensen P, Panitz F, Bendixen C Microarray expression profiles of 20.000 genes across 23 healthy porcine tissues. PLoS ONE 2: e1203. Porcine transcripts 18030337 7
2007 Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K WoLF PSORT: protein localization predictor. Nucleic Acids Res 35: W585-587. 17517783 8,10
2007 Horvath MM, Wang X, Resnick MA, Bell DA Divergent evolution of human p53 binding sites: cell cycle versus apoptosis. PLoS Genet 3: e127. Human genes; p53 17677004 10.1371/journal.pgen.0030127 7,18
2007 Hsu CN|etAl Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online). BMC Bioinformatics 8: 66. Human genes; hepatocellular carcinoma 17326819 7,8,10,16,17
2007 Hu Z, Killion PJ, Iyer VR Genetic reconstruction of a functional transcriptional regulatory network. Nat Genet 39: 683-687. Saccharomyces transcripts 17417638 7,17
2007 Hu Z, Killion PJ, Iyer VR Genetic reconstruction of a functional transcriptional regulatory network. Nat Genet 39: 683-687. Saccharomyces transcripts 17417638 7,17
2007 Hu Z, Mellor J, Wu J, Kanehisa M, Stuart JM, Delisi C Towards zoomable multidimensional maps of the cell. Nat Biotechnol 25: 547-554. 17483841 10,13
2007 Huang H, Jedynak BM, Bader JS Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps. PLoS Comput Biol 3: e214. 18039026 10.1371/journal.pcbi.0030214 8,19
2007 Huang JC, Babak T, Corson TW, Chua G, Khan S, Gallie BL, Hughes TR, Blencowe BJ, Frey BJ, Morris QD Using expression profiling data to identify human microRNA targets. Nat Methods 4: 1045-1049. Human microRNA targets 18026111 7
2007 Huang TW, Lin CY, Kao CY Reconstruction of human protein interolog network using evolutionary conserved network. BMC Bioinformatics 8: 152. Human proteins 17493278 8,17,18
2007 Huisinga KL, Pugh BF A TATA Binding Protein regulatory network that governs transcription complex assembly. Genome Biol 8: R46. Saccharomyces genes; TATA binding protein 17407552 7,17
2007 Hunt-Newbury R|etAl High-throughput in vivo analysis of gene expression in Caenorhabditis elegans. PLoS Biol 5: e237. C. elegans proteins 17850180 10.1371/journal.pbio.0050237 7,8
2007 Ingram JL, Antao-Menezes A, Turpin EA, Wallace DG, Mangum JB, Pluta LJ, Thomas RS, Bonner JC Genomic analysis of human lung fibroblasts exposed to vanadium pentoxide to identify candidate genes for occupational bronchitis. Respir Res 8: 34. Human lung fibroblasts; vanadium pentoxide exposure 17459161 7,16
2007 Ishigami T|etAl Genes and molecular pathways related to radioresistance of oral squamous cell carcinoma cells. Int J Cancer 120: 2262-2270. Human transcripts; oral squamous cell carcinoma 17290400 7,16
2007 Itoh T|etAl Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res 17: 175-183. Rice genome 17210932 4
2007 Ivanovski S, Lichanska AM, d'Aniello E, Xiao Y, Waters MJ Gene expression profiling of cells involved in periodontal regeneration. Tissue Eng 13: 393-404. Human periodontal ligament cell transcripts 17518572 7,16
2007 Jaeger J, Koczan D, Thiesen HJ, Ibrahim SM, Gross G, Spang R, Kunz M Gene expression signatures for tumor progression, tumor subtype, and tumor thickness in laser-microdissected melanoma tissues. Clin Cancer Res 13: 806-815. Human transcripts; melanoma 17289871 7,16
2007 Jagalur M, Pal C, Learned-Miller E, Zoeller RT, Kulp D Analyzing in situ gene expression in the mouse brain with image registration, feature extraction and block clustering. BMC Bioinformatics 8 Suppl 10: S5. Mouse brain genes 18269699 7,13
2007 Jain M, Khurana P, Tyagi AK, Khurana JP Genome-wide analysis of intronless genes in rice and Arabidopsis. Funct Integr Genomics 8: 69-78. Arabidopsis genes 17578610 13,18
2007 Jayaraman A, Maguire T, Vemula M, Kwon DW, Vannucci M, Berthiaume F, Yarmush ML Gene expression profiling of long-term changes in rat liver following burn injury. J Surg Res 152: 3-17,17.e1-2. Rat liver transcripts; burn injury 18755477 7,16
2007 Jelier R, Schuemie MJ, Roes PJ, van Mulligen EM, Kors JA Literature-based concept profiles for gene annotation: The issue of weighting. Int J Med Inform 77: 354-362. 17827057 9,12
2007 Jensen K, Paxton E, Waddington D, Talbot R, Darghouth MA, Glass EJ Differences in the transcriptional responses induced by Theileria annulata infection in bovine monocytes derived from resistant and susceptible cattle breeds. Int J Parasitol 38: 313-325. Bovine monocyte transcripts; Theileria infection 17949724 7
2007 Jones CE, Brown AL, Baumann U Estimating the annotation error rate of curated GO database sequence annotations. BMC Bioinformatics 8: 170. 17519041 3,13
2007 Joshi T, Xu D Quantitative assessment of relationship between sequence similarity and function similarity. BMC Genomics 8: 222. 17620139 3,13
2007 Juan HF, Huang HC Bioinformatics: microarray data clustering and functional classification. Methods Mol Biol 382: 405-416. 18220245 7,10
2007 Jung S, Staton M, Lee T, Blenda A, Svancara R, Abbott A, Main D GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. Nucleic Acids Res 36: D1034-1040. Rosaceae ESTs 17932055 5,11
2007 Kaltenbach LS|etAl Huntingtin interacting proteins are genetic modifiers of neurodegeneration. PLoS Genet 3: e82. Human proteins; huntingtin interaction; Huntington's disease 17500595 10.1371/journal.pgen.0030082 8,16
2007 Kaminker JS, Zhang Y, Watanabe C, Zhang Z CanPredict: a computational tool for predicting cancer-associated missense mutations. Nucleic Acids Res 447: 714-719. 17537827 16,19
2007 Kaminker JS|etAl Distinguishing cancer-associated missense mutations from common polymorphisms. Cancer Res 67: 465-473. Human genes; cancer 17234753 13,16
2007 Kamphuis W, Dijk F, Bergen AA Ischemic preconditioning alters the pattern of gene expression changes in response to full retinal ischemia. Mol Vis 13: 1892-1901. Rat retinal transcripts; ischemia 17960128 7,16
2007 Kamphuis W, Dijk F, van Soest S, Bergen AA Global gene expression profiling of ischemic preconditioning in the rat retina. Mol Vis 13: 1020-1030. Rat retinal transcripts; ischemia 17653046 7,16
2007 Kang JS, Wanibuchi H, Murai T, Morimura K, Kinoshita A, Fukushima S Analysis of gene expression in different stages of MeIQx-induced rat hepatocarcinogenesis. Oncol Rep 17: 747-752. Rat liver transcripts; hepatocarcinoma; MelQx 17342310 7,16
2007 Kankel MW, Hurlbut GD, Upadhyay G, Yajnik V, Yedvobnick B, Artavanis-Tsakonas S Investigating the genetic circuitry of mastermind in Drosophila, a notch signal effector. Genetics 177: 2493-2505. 18073442 13,17
2007 Karp PD|etAl Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res 35: 7577-7590. E. coli genome 17940092 4,11
2007 Kasahara M|etAl The medaka draft genome and insights into vertebrate genome evolution. Nature 447: 714-719. Medaka genome 17554307 4
2007 Kelleher ES, Swanson WJ, Markow TA Gene duplication and adaptive evolution of digestive proteases in Drosophila arizonae female reproductive tracts. PLoS Genet 3: e148. Drosophila arizonae ESTs 17784792 10.1371/journal.pgen.0030148 5,18
2007 Keller EF, Harel D Beyond the gene. PLoS ONE 2: e1231. 10.1371/journal.pone.0001231 18043738 15
2007 Keller P, Vollaard N, Babraj J, Ball D, Sewell DA, Timmons JA Using systems biology to define the essential biological networks responsible for adaptation to endurance exercise training. Biochem Soc Trans 35: 1306-1309. Human skeletal muscle transcripts; exercise 17956337 7,16,17
2007 Keurentjes JJ, Fu J, Terpstra IR, Garcia JM, van den Ackerveken G, Snoek LB, Peeters AJ, Vreugdenhil D, Koornneef M, Jansen RC Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci. Proc Natl Acad Sci U S A 104: 1708-1713. Arabidopsis genes 17237218 7,17
2007 Khatri P, Voichita C, Kattan K, Ansari N, Khatri A, Georgescu C, Tarca AL, Draghici S Onto-Tools: new additions and improvements in 2006. Nucleic Acids Res 35: W206-211. 17584796 10
2007 Kikin O, Zappala Z, D'Antonio L, Bagga PS GRSDB2 and GRS_UTRdb: databases of quadruplex forming G-rich sequences in pre-mRNAs and mRNAs. Nucleic Acids Res 36: D141-148. 18045785 11
2007 Kim BH, Cai X, Vaughn JN, von Arnim AG On the functions of the h subunit of eukaryotic initiation factor 3 in late stages of translation initiation. Genome Biol 8: R60. Arabidopsis mRNA translation; eIF3h; uORFs 17439654 7
2007 Kim DS, Huh JW, Kim HS Transposable elements in human cancers by genome-wide EST alignment. Genes Genet Syst 82: 145-156. Human ESTs; cancer 17507780 5,11,16
2007 Kim J, Chung HJ, Jung Y, Kim KK, Kim JH BioLattice: A framework for the biological interpretation of microarray gene expression data using concept lattice analysis. J Biomed Inform 41: 232-241. 18093880 7,10
2007 Kim JH, Moon YR, Kim JS, Oh MH, Lee JW, Chung BY Transcriptomic profile of Arabidopsis rosette leaves during the reproductive stage after exposure to ionizing radiation. Radiat Res 168: 267-280. Arabidopsis rosette leaf transcripts 17705638 7
2007 Kim SB, Yang S, Kim SK, Kim SC, Woo HG, Volsky DJ, Kim SY, Chu IS GAzer: Gene Set Analyzer. Bioinformatics 104: 11334-11339. 17468122 10
2007 Kim SY, Pritchard JK Adaptive evolution of conserved noncoding elements in mammals. PLoS Genet 3: 1572-1586. 17845075 10.1371/journal.pgen.0030147 18
2007 Kimpel MW, Strother WN, McClintick JN, Carr LG, Liang T, Edenberg HJ, McBride WJ Functional gene expression differences between inbred alcohol-preferring and -non-preferring rats in five brain regions. Alcohol 41: 95-9132. Rat brain transcripts; alcohol preference 17517326 7
2007 Kleinberg S, Casey K, Mishra B Systems biology via redescription and ontologies (I): finding phase changes with applications to malaria temporal data. Syst Synth Biol 1: 197-205. Plasmodium falciparum genes 19003444 7,10,16
2007 Klempan TA, Sequeira A, Canetti L, Lalovic A, Ernst C, Ffrench-Mullen J, Turecki G Altered expression of genes involved in ATP biosynthesis and GABAergic neurotransmission in the ventral prefrontal cortex of suicides with and without major depression. Mol Psychiatry 14: 175-189. Human brain transcripts; suicide 17938633 7,16
2007 Kojima K, Nagasaki M, Jeong E, Kato M, Miyano S An efficient grid layout algorithm for biological networks utilizing various biological attributes. BMC Bioinformatics 8: 76. 17338825 10
2007 Kolehmainen M|etAl Weight reduction modulates expression of genes involved in extracellular matrix and cell death: the GENOBIN study. Int J Obes (Lond) 32: 292-303. Human adipose tissue transcripts 17848939 7,16
2007 Kolotilin I, Koltai H, Tadmor Y, Bar-Or C, Reuveni M, Meir A, Nahon S, Shlomo H, Chen L, Levin I Transcriptional profiling of high pigment-2dg tomato mutant links early fruit plastid biogenesis with its overproduction of phytonutrients. Plant Physiol 145: 389-401. Tomato transcripts 17704236 7
2007 Korbel JO|etAl Paired-end mapping reveals extensive structural variation in the human genome. Science 318: 420-426. 17901297 13,18
2007 Kothapalli KS, Anthony JC, Pan BS, Hsieh AT, Nathanielsz PW, Brenna JT Differential cerebral cortex transcriptomes of baboon neonates consuming moderate and high docosahexaenoic acid formulas. PLoS ONE 2: e370. Baboon brain transcripts; infant formula 17426818 7,16
2007 Kourmpetis YA, van der Burgt A, Bink MC, Ter Braak CJ, van Ham RC The use of multiple hierarchically independent gene ontology terms in gene function prediction and genome annotation. In Silico Biol 7: 575-582. 18467770 3
2007 Kourmpetis YAI, van der Burgt A, Bink MCAM, ter Braak CJF, van Ham RCHJ The use of multiple hierarchically independent Gene Ontology terms in gene function prediction and genome annotation. In Silico Biol 7:000-000. http://www.bioinfo.de/isb/2007/07/0050/|full 9
2007 Kramer RW, Slagowski NL, Eze NA, Giddings KS, Morrison MF, Siggers KA, Starnbach MN, Lesser CF Yeast functional genomic screens lead to identification of a role for a bacterial effector in innate immunity regulation. PLoS Pathog 3: e21. Saccharomyces transcripts, proteins 17305427 10.1371/journal.ppat.0030021 7,13
2007 Krig SR, Jin VX, Bieda MC, O'geen H, Yaswen P, Green R, Farnham PJ Identification of genes directly regulated by the oncogene ZNF217 using ChIP-chip assays. J Biol Chem 282: 9703-9712. Human tumor cell line genes; oncogene regulatory targets 17259635 13,16
2007 Kultz D, Fiol D, Valkova N, Gomez-Jimenez S, Chan SY, Lee J Functional genomics and proteomics of the cellular osmotic stress response in ;non-model' organisms. J Exp Biol 210: 1593-1601. Euryhaline fish genes 17449824 3,7
2007 Kumar S, Chaudhary K, Foster JM, Novelli JF, Zhang Y, Wang S, Spiro D, Ghedin E, Carlow CK Mining predicted essential genes of Brugia malayi for nematode drug targets. PLoS ONE 2: e1189. Nematode predicted genes 18000556 12,13,16
2007 Kusnierczyk W Taxonomy-based partitioning of the Gene Ontology. J Biomed Inform 41: 282-292. 17921072 13
2007 Laayouni H, Garcia-Franco F, Chavez-Sandoval BE, Trotta V, Beltran S, Corominas M, Santos M Thermal evolution of gene expression profiles in Drosophila subobscura. BMC Evol Biol 7: 42. Drosophila subobscura transcripts; thermotolerance 17371595 7,18
2007 Langille MG, Clark DV Parent genes of retrotransposition-generated gene duplicates in Drosophila melanogaster have distinct expression profiles. Genomics 90: 334-343. 17628393 13,18
2007 Larkin P, Villeneuve DL, Knoebl I, Miracle AL, Carter BJ, Liu L, Denslow ND, Ankley GT Development and validation of a 2,000-gene microarray for the fathead minnow (Pimephales promelas). Environ Toxicol Chem 26: 1497-1506. Minnow transcripts 17665692 7
2007 Larmande P|etAl Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library. Nucleic Acids Res 36: D1022-1027. 17947330 15
2007 Larsen P, Almasri E, Chen G, Dai Y A statistical method to incorporate biological knowledge for generating testable novel gene regulatory interactions from microarray experiments. BMC Bioinformatics 8: 317. 17727721 7,17
2007 Lazzari B, Caprera A, Cosentino C, Stella A, Milanesi L, Viotti A ESTuber db: an online database for Tuber borchii EST sequences. BMC Bioinformatics 8 Suppl 1: S13. Truffle ESTs 17430557 5,11
2007 Lee H, Lee HK, An G, Lee YK Analysis of expressed sequence tags from the red alga Griffithsia okiensis. J Microbiol 45: 541-546. Griffithsia okiensis ESTs 18176538 5,7
2007 Lee J, Garrett WM, Cooper B Shotgun proteomic analysis of Arabidopsis thaliana leaves. J Sep Sci 30: 2225-2230. Arabidopsis leaf proteins 17654619 8
2007 Lee JM, Ivanova EV, Seong IS, Cashorali T, Kohane I, Gusella JF, Macdonald ME Unbiased gene expression analysis implicates the huntingtin polyglutamine tract in extra-mitochondrial energy metabolism. PLoS Genet 3: e135. Human transcripts; Huntington's disease 17708681 10.1371/journal.pgen.0030135 7,16
2007 Lee SH|etAl Identification of differentially expressed genes related to intramuscular fat development in the early and late fattening stages of hanwoo steers. J Biochem Mol Biol 40: 757-764. Bovine transcripts 17927910 7
2007 Lemay DG, Neville MC, Rudolph MC, Pollard KS, German JB Gene regulatory networks in lactation: identification of global principles using bioinformatics. BMC Syst Biol 1: 56. Mouse transcripts; mouse proteins; lactation 18039394 7,8,16,17
2007 Lenk GM, Tromp G, Weinsheimer S, Gatalica Z, Berguer R, Kuivaniemi H Whole genome expression profiling reveals a significant role for immune function in human abdominal aortic aneurysms. BMC Genomics 8: 237. Human aortic transcripts; aneurysm 17634102 7,16
2007 Lerman G, Shakhnovich BE Defining functional distance using manifold embeddings of gene ontology annotations. Proc Natl Acad Sci U S A 104: 11334-11339. 17595300 13
2007 Leu JH, Chang CC, Wu JL, Hsu CW, Hirono I, Aoki T, Juan HF, Lo CF, Kou GH, Huang HC Comparative analysis of differentially expressed genes in normal and white spot syndrome virus infected Penaeus monodon. BMC Genomics 8: 120. Shrimp ESTs 17506900 5,7
2007 Levy S|etAl The diploid genome sequence of an individual human. PLoS Biol 5: e254. Human genome 17803354 10.1371/journal.pbio.0050254 4
2007 Li M, Xu W, Yang W, Kong Z, Xue Y Genome-wide gene expression profiling reveals conserved and novel molecular functions of the stigma in rice (Oryza sativa L.). Plant Physiol 144: 1797-1812. Rice transcripts 17556504 7
2007 Li N, Wu B, Wei P, Xie B, Xie Y, Xiao G, Pan W Functional group-based linkage analysis of gene expression trait loci. BMC Proc 1 Suppl 1: S117. 18466458 7
2007 Lin H, Doddapaneni H, Takahashi Y, Walker MA Comparative analysis of ESTs involved in grape responses to Xylella fastidiosa infection. BMC Plant Biol 7: 8. Grape ESTs 17316447 5,7
2007 Lin H, Gupta V, Vermilyea MD, Falciani F, Lee JT, O'Neill LP, Turner BM Dosage compensation in the mouse balances up-regulation and silencing of x-linked genes. PLoS Biol 5: e326. Mouse transcripts 18076287 10.1371/journal.pbio.0050326 7
2007 Lin HM, Chatterjee A, Lin YH, Anjomshoaa A, Fukuzawa R, McCall JL, Reeve AE Genome wide expression profiling identifies genes associated with colorectal liver metastasis. Oncol Rep 17: 1541-1549. Human transcripts; colorectal cancer; liver metastasis 17487416 7,16
2007 Liu H, Adler AS, Segal E, Chang HY A transcriptional program mediating entry into cellular quiescence. PLoS Genet 3: e91. Human transcripts; serum deprivation; cancer 17559306 10.1371/journal.pgen.0030091 7,16
2007 Liu J, Hughes-Oliver JM, Menius JA Domain enhanced analysis of microarray data using GO annotations. Bioinformatics 23: 1225-1234. 17379692 7,10
2007 Liu M, Liberzon A, Kong SW, Lai WR, Park PJ, Kohane IS, Kasif S Network-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet 3: e96. Human genes; human proteins; diabetes 17571924 10.1371/journal.pgen.0030096 7,8,16,17
2007 Liu RH, Cheng SL, Ueng KC, Wu DJ, Chen ST, Sinchaikul S, Lee TH Gene expression analysis in LLC-PK1 renal tubular cells by atrial natriuretic peptide (ANP): correlation of homologous human genes with renal response. J Biomed Sci 14: 383-393. Porcine kidney cell transcripts; human homologs; ANP response 17334945 7,16
2007 Liu ZP, Wu LY, Wang Y, Chen L, Zhang XS Predicting gene ontology functions from protein's regional surface structures. BMC Bioinformatics 8: 475. 18070366 9
2007 Lobley A, Swindells MB, Orengo CA, Jones DT Inferring function using patterns of native disorder in proteins. PLoS Comput Biol 3: e162. Human proteins; disordered proteins 17722973 10.1371/journal.pcbi.0030162 8,9
2007 Loganantharaj R, Atwi M Towards validating the hypothesis of phylogenetic profiling. BMC Bioinformatics 8 Suppl 7: S25. Human microRNAs; cancer 18047725 7,16,17
2007 Lopez G, Rojas A, Tress M, Valencia A Assessment of predictions submitted for the CASP7 function prediction category. Proteins 69: 165-174. 17654548 9
2007 Lovegrove FE, Gharib SA, Patel SN, Hawkes CA, Kain KC, Liles WC Expression microarray analysis implicates apoptosis and interferon-responsive mechanisms in susceptibility to experimental cerebral malaria. Am J Pathol 171: 1894-1903. Mouse brain transcripts; malaria 17991715 7,16
2007 Lu J, Xie L, Sylvester J, Wang J, Bai J, Baybutt R, Wang W Different gene expression of skin tissues between mice with weight controlled by either calorie restriction or physical exercise. Exp Biol Med (Maywood) 232: 473-480. Mouse skin transcripts; caloric restriction; exercise 17392482 7,16
2007 Lu X, Jain VV, Finn PW, Perkins DL Hubs in biological interaction networks exhibit low changes in expression in experimental asthma. Mol Syst Biol 3: 98. Mouse transcripts; asthma 17437023 7,16,17
2007 Lu Y, Yi Y, Liu P, Wen W, James M, Wang D, You M Common human cancer genes discovered by integrated gene-expression analysis. PLoS ONE 2: e1149. Human transcripts; cancer 17989776 10.1371/journal.pone.0001149 7,16
2007 Ma S, Bohnert HJ Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression. Genome Biol 8: R49. Arabidopsis transcripts 17408486 7
2007 Ma'ayan A, Jenkins SL, Goldfarb J, Iyengar R Network analysis of FDA approved drugs and their targets. Mt Sinai J Med 74: 27-32. Drug targets 17516560 13,17
2007 Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, Westerfield M Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J Exp Zoolog B Mol Dev Evol 308B: 655-668. 17599725 11,15,18
2007 Madoui MA, Gaulin E, Mathe C, San Clemente H, Couloux A, Wincker P, Dumas B AphanoDB: a genomic resource for Aphanomyces pathogens. BMC Genomics 8: 471. Aphanomyces ESTs 18096036 5,10
2007 Maekawa S, Matsumoto A, Takenaka Y, Matsuda H Tissue-specific functions based on information content of gene ontology using cap analysis gene expression. Med Biol Eng Comput 45: 1029-1036. Human transcripts; mouse transcripts; CAGE 17968606 7
2007 Magalhaes TR, Palmer J, Tomancak P, Pollard KS Transcriptional control in embryonic Drosophila midline guidance assessed through a whole genome approach. BMC Neurosci 8: 59. Drosophila embryonic transcripts; axon guidance 17672901 7
2007 Maglietta R, Piepoli A, Catalano D, Licciulli F, Carella M, Liuni S, Pesole G, Perri F, Ancona N Statistical assessment of functional categories of genes deregulated in pathological conditions by using microarray data. Bioinformatics 23: 2063-2072. 17540679 7,16,19
2007 Mahdavi MA, Lin YH False positive reduction in protein-protein interaction predictions using gene ontology annotations. BMC Bioinformatics 8: 262. 17645798 12,19
2007 Mallard C, Hagberg H Inflammation-induced preconditioning in the immature brain. Semin Fetal Neonatal Med 12: 280-286. Rat brain transcripts; inflammation 17327146 7,16
2007 Malmstrom L, Riffle M, Strauss CE, Chivian D, Davis TN, Bonneau R, Baker D Superfamily assignments for the yeast proteome through integration of structure prediction with the Gene Ontology. PLoS Biol 5: e76. Saccharomyces proteins 17373854 10.1371/journal.pbio.0050076 8,19
2007 Mandal S, Davie J An integrated analysis of genes and pathways exhibiting metabolic differences between estrogen receptor positive breast cancer cells. BMC Cancer 7: 181. Human breast transcripts; breast cancer 17883861 7,16,17
2007 Mao L|etAl Proteomic shifts in embryonic stem cells with gene dose modifications suggest the presence of balancer proteins in protein regulatory networks. PLoS ONE 2: e1218. Mouse embryonic stem cell proteins 18043732 10.1371/journal.pone.0001218 8,17
2007 Marquez-Quinones A, Paris A, Roussel B, Perez-Carreon J, Le Berre V, Francois JM, Villa-Trevino S, Gueraud F Proteasome activity deregulation in LEC rat hepatitis: following the insights of transcriptomic analysis. OMICS 11: 367-384. Rat liver transcripts; hepatitis 18092909 7,16
2007 Marti-Renom MA, Rossi A, Al-Shahrour F, Davis FP, Pieper U, Dopazo J, Sali A The AnnoLite and AnnoLyze programs for comparative annotation of protein structures. BMC Bioinformatics 8 Suppl 4: S4. 17570147 9,10
2007 Martinez-Morales JR, Henrich T, Ramialison M, Wittbrodt J New genes in the evolution of the neural crest differentiation program. Genome Biol 8: R36. 17352807 15,18
2007 Martyniuk CJ, Gerrie ER, Popesku JT, Ekker M, Trudeau VL Microarray analysis in the zebrafish (Danio rerio) liver and telencephalon after exposure to low concentration of 17alpha-ethinylestradiol. Aquat Toxicol 84: 38-49. Zebrafish transcripts; 17alpha-ethinylestradiol exposure 17606305 7
2007 Mash DC, ffrench-Mullen J, Adi N, Qin Y, Buck A, Pablo J Gene expression in human hippocampus from cocaine abusers identifies genes which regulate extracellular matrix remodeling. PLoS ONE 2: e1187. Human brain transcripts; cocaine abuse 18000554 10.1371/journal.pone.0001187 7,16
2007 Masseroli M Management and analysis of genomic functional and phenotypic controlled annotations to support biomedical investigation and practice. IEEE Trans Inf Technol Biomed 11: 376-385. 17674620 10
2007 Masuya H, Yoshikawa S, Heida N, Toyoda T, Wakana S, Shiroishi T Phenosite: a web database integrating the mouse phenotyping platform and the experimental procedures in mice. J Bioinform Comput Biol 5: 1173-1191. 18172924 11,15
2007 Matarasso N, Bar-Shira A, Rozovski U, Rosner S, Orr-Urtreger A Functional analysis of the Aurora Kinase A Ile31 allelic variant in human prostate. Neoplasia 9: 707-715. Human prostate transcripts; Aurora kinase 17898866 7,16
2007 Mathew JP, Taylor BS, Bader GD, Pyarajan S, Antoniotti M, Chinnaiyan AM, Sander C, Burakoff SJ, Mishra B From bytes to bedside: data integration and computational biology for translational cancer research. PLoS Comput Biol 3: e12. 17319736 10.1371/journal.pcbi.0030012 14
2007 Matigian N, Windus L, Smith H, Filippich C, Pantelis C, McGrath J, Mowry B, Hayward N Expression profiling in monozygotic twins discordant for bipolar disorder reveals dysregulation of the WNT signalling pathway. Mol Psychiatry 12: 815-825. Human lymphoblastoid cell line transcripts; bipolar disorder 17440432 7,16
2007 Matsunaga T, Muramatsu M Disease-related concept mining by knowledge-based two-dimensional gene mapping. J Bioinform Comput Biol 5: 1047-1067. 17933010 13,16
2007 McCarthy FM, Bridges SM, Burgess SC GOing from functional genomics to biological significance. Cytogenet Genome Res 117: 278-287. Chicken genome 17675869 1,4,11
2007 McDougal JN, Garrett CM Gene expression and target tissue dose in the rat epidermis after brief JP-8 and JP-8 aromatic and aliphatic component exposures. Toxicol Sci 97: 569-581. Rat skin transcripts; jet fuel component exposure 17337753 7,16
2007 McNair K, Broad J, Riedel G, Davies CH, Cobb SR Global changes in the hippocampal proteome following exposure to an enriched environment. Neuroscience 145: 413-422. Rat hippocampal proteins 17261355 8
2007 McQuillin A, Rizig M, Gurling HM A microarray gene expression study of the molecular pharmacology of lithium carbonate on mouse brain mRNA to understand the neurobiology of mood stabilization and treatment of bipolar affective disorder. Pharmacogenet Genomics 17: 605-617. Mouse brain transcripts; bipolar affective disorder; lithium treatment 17622937 7,16
2007 Mehta JP, O'Driscoll L, Barron N, Clynes M, Doolan P A microarray approach to translational medicine in breast cancer: how representative are cell line models of clinical conditions? Anticancer Res 27: 1295-1300. Human cell line transcripts; breast cancer 17593622 7,16
2007 Meynard D, Le Morvan V, Bonnet J, Robert J Functional analysis of the gene expression profiles of colorectal cancer cell lines in relation to oxaliplatin and cisplatin cytotoxicity. Oncol Rep 17: 1213-1221. Human colorectal cancer cell line transcripts; colon cancer; cisplatin; oxaliplatin 17390068 7,16
2007 Michel C, Desdouets C, Slaoui M, Isaacs KR, Roberts RA, Eric B Diethylnitrosamine initiation does not alter clofibric acid-induced hepatocarcinogenesis in the rat. Toxicol Sci 99: 58-69. Rat liver transcripts; liver cancer 17602206 7,16
2007 Mikkelsen TS|etAl Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447: 167-177. Opossum genome 17495919 4
2007 Miller DL, Myers C, Rickards B, Coller H, Flint J Adenovirus type 5 exerts genome-wide control over cellular programs governing proliferation, quiescence and survival. Genome Biol 8: R58. Human fibroblast transcripts; adenovirus infection 17430596 7,16
2007 Miller WR|etAl Aromatase inhibitors-Gene discovery. J Steroid Biochem Mol Biol 106: 130-142. Human transcripts; breast tumors 17616392 7,16
2007 Miller WR|etAl Changes in breast cancer transcriptional profiles after treatment with the aromatase inhibitor, letrozole. Pharmacogenet Genomics 17: 813-826. Human breast transcripts; breast cancer; letrozole treatment 17885619 7,16
2007 Minguez P, Al-Shahrour F, Montaner D, Dopazo J Functional profiling of microarray experiments using text-mining derived bioentities. Bioinformatics 23: 3098-3099. 17855415 7,10,12
2007 Montenegro D|etAl Differential expression of microRNAs with progression of gestation and inflammation in the human chorioamniotic membranes. Am J Obstet Gynecol 197: 289.e1-6. Human miRNA; gestation; chorioamnionitis 17826424 7,16
2007 Moreira D, Shah N, Musen M Interpretation Errors related to the GO Annotation File Format. AMIA Annu Symp Proc 2007: 538-542. 18693894 3
2007 Moreira DA, Musen MA OBO to OWL: A Protege OWL tab to read/save OBO ontologies. Bioinformatics 23: 1868-1870. 17496317 10,15
2007 Morton CO, Hayes A, Wilson M, Rash BM, Oliver SG, Coote P Global phenotype screening and transcript analysis outlines the inhibitory mode(s) of action of two amphibian-derived, {alpha}-helical, cationic peptides on Saccharomyces cerevisiae. Antimicrob Agents Chemother 51: 3948-3959. Saccharomyces genes 17846143 7,13
2007 Muller V, Viemann D, Schmidt M, Endres N, Ludwig S, Leverkus M, Roth J, Goebeler M Candida albicans triggers activation of distinct signaling pathways to establish a proinflammatory gene expression program in primary human endothelial cells. J Immunol 179: 8435-8445. Human transcripts; Candida albicans infection; sepsis 18056390 7,16
2007 Murphy EF, Hooiveld GJ, Muller M, Calogero RA, Cashman KD Conjugated linoleic acid alters global gene expression in human intestinal-like Caco-2 cells in an isomer-specific manner. J Nutr 137: 2359-2365. Human intestinal cell line transcripts; conjugated linoleic acid exposure 17951470 7,16
2007 Murray KD, Choudary PV, Jones EG Nucleus- and cell-specific gene expression in monkey thalamus. Proc Natl Acad Sci U S A 104: 1989-1994. Monkey brain transcripts 17261798 7
2007 Naciff JM, Overmann GJ, Torontali SM, Carr GJ, Khambatta ZS, Tiesman JP, Richardson BD, Daston GP Uterine temporal response to acute exposure to 17 {alpha}-ethynyl estradiol in the immature rat. Toxicol Sci 97: 467-490. Rat uterine transcripts; ethinyl estradiol exposure 17351261 7
2007 Nam S, Kim B, Shin S, Lee S miRGator: an integrated system for functional annotation of microRNAs. Nucleic Acids Res 36: D159-164. 17942429 11
2007 Nariai N, Kolaczyk ED, Kasif S Probabilistic protein function prediction from heterogeneous genome-wide data. PLoS ONE 2: e337. 17396164 9
2007 Natale DA, Arighi CN, Barker WC, Blake J, Chang TC, Hu Z, Liu H, Smith B, Wu CH Framework for a protein ontology. BMC Bioinformatics 8 Suppl 9: S1. 18047702 9
2007 Natarajan J, Ganapathy J Functional gene clustering via gene annotation sentences, MeSH and GO keywords from biomedical literature. Bioinformation 2: 185-193. 18305827 9,12
2007 Nelson GM, Ahlborn GJ, Delker DA, Kitchin KT, O'brien TG, Chen Y, Kohan MJ, Roop BC, Ward WO, Allen JW Folate deficiency enhances arsenic effects on expression of genes involved in epidermal differentiation in transgenic K6/ODC mouse skin. Toxicology 241: 134-145. Mouse skin transcripts; arsenic exposure 17928125 7,16
2007 Neuweger H|etAl CoryneCenter - An online resource for the integrated analysis of corynebacterial genome and transcriptome data. BMC Syst Biol 1: 55. 18034885 11
2007 Newbold RR, Jefferson WN, Grissom SF, Padilla-Banks E, Snyder RJ, Lobenhofer EK Developmental exposure to diethylstilbestrol alters uterine gene expression that may be associated with uterine neoplasia later in life. Mol Carcinog 46: 783-796. Mouse uterine transcripts; diethylstilbestrol (DES) 17394237 7,16
2007 Newrzella D|etAl The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia. BMC Genomics 8: 370. Mouse hippocampal transcripts; ischemia 17937787 7,16
2007 Nickel GC, Tefft D, Adams MD Human PAML browser: a database of positive selection on human genes using phylogenetic methods. Nucleic Acids Res 36: D800-808. 17962310 10,18
2007 Niculescu MD, da Costa KA, Fischer LM, Zeisel SH Lymphocyte gene expression in subjects fed a low-choline diet differs between those who develop organ dysfunction and those who do not. Am J Clin Nutr 86: 230-239. Human lymphocyte transcripts; choline; organ dysfunction 17616785 7,16
2007 Nierhoff D, Levoci L, Schulte S, Goeser T, Rogler LE, Shafritz DA New cell surface markers for murine fetal hepatic stem cells identified through high density complementary DNA microarrays. Hepatology 46: 535-547. Mouse fetal stem cell transcripts 17508344 7
2007 Noel S, Sharma S, Shanker R, Rath SK Primaquine-induced differential gene expression analysis in mice liver using DNA microarrays. Toxicology 239: 96-9107. Mouse liver transcripts 17686563 7,16
2007 Nogami S, Ohya Y, Yvert G Genetic complexity and quantitative trait loci mapping of yeast morphological traits. PLoS Genet 3: e31. Saccharomyces strains, genes, transcripts 17319748 10.1371/journal.pgen.0030031 7,13,18
2007 Norden-Krichmar TM, Holtz J, Pasquinelli AE, Gaasterland T Computational prediction and experimental validation of Ciona intestinalis microRNA genes. BMC Genomics 8: 445. Ciona microRNAs 18047675 3
2007 Nymark P, Lindholm PM, Korpela MV, Lahti L, Ruosaari S, Kaski S, Hollmen J, Anttila S, Kinnula VL, Knuutila S Gene expression profiles in asbestos-exposed epithelial and mesothelial lung cell lines. BMC Genomics 8: 62. Human lung cell line transcripts; asbestos exposure 17331233 7,16
2007 O'Geen H, Squazzo SL, Iyengar S, Blahnik K, Rinn JL, Chang HY, Green R, Farnham PJ Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs. PLoS Genet 3: e89. Human genes; histone methylation 17542650 10.1371/journal.pgen.0030089 7,13
2007 Ochs MF, Peterson AJ, Kossenkov A, Bidaut G Incorporation of gene ontology annotations to enhance microarray data analysis. Methods Mol Biol 377: 243-254. 17634621 7,10,12
2007 Ochsner S, Strick-Marchand H, Qiu Q, Venable S, Dean A, Wilde M, Weiss M, Darlington G Transcriptional profiling of bipotential embryonic liver cells to identify liver progenitor cell surface markers. Stem Cells 25: 2476-2487. Arabidopsis genes; rice genes 17641245 7,18
2007 Ohr H, Bui AQ, Le BH, Fischer RL, Choi Y Identification of putative Arabidopsis DEMETER target genes by GeneChip analysis. Biochem Biophys Res Commun 364: 856-860. Arabidopsis transcripts 17964287 7,17
2007 Okoli AS, Wadstrom T, Mendz GL MiniReview: Bioinformatic study of bile responses in Campylobacterales. FEMS Immunol Med Microbiol 49: 101-123. 17266717 13,18
2007 Olsen CM, Huang Y, Goodwin S, Ciobanu DC, Lu L, Sutter TR, Winder DG Microarray Analysis Reveals Distinctive Signaling Between the Bed Nucleus of the Stria Terminalis, Nucleus Accumbens, and Dorsal Striatum. Physiol Genomics 32: 283-298. Mouse brain transcripts 17911379 7
2007 Omura K, Kiyosawa N, Uehara T, Hirode M, Shimizu T, Miyagishima T, Ono A, Nagao T, Urushidani T Gene expression profiling of rat liver treated with serum triglyceride-decreasing compounds. J Toxicol Sci 32: 387-399. Rat liver transcripts; plasma triglycerides 17965553 7,16
2007 Ortutay C, Vihinen M Immunome: A reference set of genes and proteins for systems biology of the human immune system. Cell Immunol 244: 87-89. Human immune system genes and proteins 17434156 3,11
2007 Osborne JD, Zhu LJ, Lin SM, Kibbe WA Interpreting microarray results with gene ontology and MeSH. Methods Mol Biol 377: 223-242. 17634620 7,10,12
2007 Othman RM, Deris S, Illias RM A genetic similarity algorithm for searching the Gene Ontology terms and annotating anonymous protein sequences. J Biomed Inform 41: 65-81. 17681495 10,12
2007 Oti M, Brunner H The modular nature of genetic diseases. Clin Genet 71: 1-11. 17204041 16,17
2007 Otu HH, Naxerova K, Ho K, Can H, Nesbitt N, Libermann TA, Karp SJ Global gene expression patterns reveal restoration of liver mass after injury as hepatocyte hyperplasia, not true regeneration. J Biol Chem 282: 11197-11204. Mouse liver transcripts; hepatectomy 17227769 7,16
2007 Pan S, Zhu D, Quinn JF, Peskind ER, Montine TJ, Lin B, Goodlett DR, Taylor G, Eng J, Zhang J A combined dataset of human cerebrospinal fluid proteins identified by multi-dimensional chromatography and tandem mass spectrometry. Proteomics 7: 469-473. human cerebrospinal fluid proteins; neurodegenerative disease 17211832 8,16
2007 Pandey J, Koyuturk M, Kim Y, Szpankowski W, Subramaniam S, Grama A Functional annotation of regulatory pathways. Bioinformatics 23: i377-i386. 17646320 3,10,17
2007 Papanicolaou A, Gebauer-Jung S, Blaxter ML, Owen McMillan W, Jiggins CD ButterflyBase: a platform for lepidopteran genomics. Nucleic Acids Res 36: D582-587. Butterfly ESTs 17933781 5,11
2007 Papapanou PN, Sedaghatfar MH, Demmer RT, Wolf DL, Yang J, Roth GA, Celenti R, Belusko PB, Lalla E, Pavlidis P Periodontal therapy alters gene expression of peripheral blood monocytes. J Clin Periodontol 34: 736-747. Human blood cell transcripts; periodontal therapy 17716309 7,16
2007 Park T, Kim Y, Bekiranov S, Lee JK Error-pooling-based statistical methods for identifying novel temporal replication profiles of human chromosomes observed by DNA tiling arrays. Nucleic Acids Res 35: e69. 17430969 13
2007 Patel BB|etAl Searchable High-Resolution 2D Gel Proteome of the Human Colon Crypt. J Proteome Res 6: 2232-2238. Human colonic crypt transcripts; colon cancer 17444668 8,16
2007 Patel OV, Bettegowda A, Ireland JJ, Coussens PM, Lonergan P, Smith GW Functional genomics studies of oocyte competence: evidence that reduced transcript abundance for follistatin is associated with poor developmental competence of bovine oocytes. Reproduction 133: 95-9106. Bovine oocyte transcriipts 17244736 7
2007 Peirson SN, Oster H, Jones SL, Leitges M, Hankins MW, Foster RG Microarray analysis and functional genomics identify novel components of melanopsin signaling. Curr Biol 17: 1363-1372. Mouse eye transcripts 17702581 7
2007 Peng FY, Reid KE, Liao N, Schlosser J, Lijavetzky D, Holt R, Martinez Zapater JM, Jones S, Marra M, Bohlmann J, Lund ST Generation of ESTs in Vitis vinifera wine grape (Cabernet Sauvignon) and table grape (Muscat Hamburg) and discovery of new candidate genes with potential roles in berry development. Gene 402: 40-50. Grape ESTs 17761391 5
2007 Peng H, Long F, Zhou J, Leung G, Eisen MB, Myers EW Automatic image analysis for gene expression patterns of fly embryos. BMC Cell Biol 8 Suppl 1: S7. 17634097 13
2007 Perrin RM, Fedorova ND, Bok JW, Cramer RA, Wortman JR, Kim HS, Nierman WC, Keller NP Transcriptional regulation of chemical diversity in Aspergillus fumigatus by LaeA. PLoS Pathog 3: e50. Aspergillus transcripts 17432932 10.1371/journal.ppat.0030050 7
2007 Pilati S|etAl Genome-wide transcriptional analysis of grapevine berry ripening reveals a set of genes similarly modulated during three seasons and the occurrence of an oxidative burst at veraison. BMC Genomics 8: 428. Grape transcripts 18034875 7
2007 Pineles BL|etAl Distinct subsets of microRNAs are expressed differentially in the human placentas of patients with preeclampsia. Am J Obstet Gynecol 196: 261.e1-6. Human placental miRNAs; preeclampsia 17346547 7,16
2007 Pirooznia M, Gong P, Guan X, Inouye LS, Yang K, Perkins EJ, Deng Y Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida. BMC Bioinformatics 8 Suppl 7: S7. 18047730 9,18
2007 Polanski A, Polanska J, Jarzab M, Wiench M, Jarzab B Application of Bayesian networks for inferring cause-effect relations from gene expression profiles of cancer versus normal cells. Math Biosci 209: 528-546. 17467015 7,16
2007 Pollanen E, Ronkainen PH, Suominen H, Takala T, Koskinen S, Puolakka J, Sipila S, Kovanen V Muscular transcriptome in postmenopausal women with or without hormone replacement. Rejuvenation Res 10: 485-500. Human muscle transcripts; hormone replacement therapy 17985945 7,16
2007 Prufer K, Muetzel B, Do HH, Weiss G, Khaitovich P, Rahm E, Paabo S, Lachmann M, Enard W FUNC: a package for detecting significant associations between gene sets and ontological annotations. BMC Bioinformatics 8: 41. 17284313 10
2007 Pulliam L, Sun B, Rempel H, Martinez PM, Hoekman JD, Rao RJ, Frey WH, Hanson LR Intranasal tat alters gene expression in the mouse brain. J Neuroimmune Pharmacol 2: 87-92. Mouse brain transcripts; HIV 18040830 7,16
2007 Qin X, Ahn S, Speed TP, Rubin GM Global analyses of mRNA translational control during early Drosophila embryogenesis. Genome Biol 8: R63. Drosophila mRNA translation 17448252 7
2007 Qiu J, Hue M, Ben-Hur A, Vert JP, Noble WS A structural alignment kernel for protein structures. Bioinformatics 23: 1090-1098. 17234638 9
2007 Quilang J|etAl Generation and analysis of ESTs from the eastern oyster, Crassostrea virginica Gmelin and identification of microsatellite and SNP markers. BMC Genomics 8: 157. Oyster ESTs 17559679 5
2007 Ramirez F, Schlicker A, Assenov Y, Lengauer T, Albrecht M Computational analysis of human protein interaction networks. Proteomics 7: 2541-2552. 17647236 8,17
2007 Ramlawi B, Otu H, Rudolph JL, Mieno S, Kohane IS, Can H, Libermann TA, Marcantonio ER, Bianchi C, Sellke FW Genomic expression pathways associated with brain injury after cardiopulmonary bypass. J Thorac Cardiovasc Surg 134: 996-991005. Human blood transcripts; cardiopulmonary bypass 17903520 7,16
2007 Ranea JA, Yeats C, Grant A, Orengo CA Predicting protein function with hierarchical phylogenetic profiles: the Gene3D Phylo-Tuner method applied to eukaryotic genomes. PLoS Comput Biol 3: e237. 18052542 10.1371/journal.pcbi.0030237 9,18
2007 Rannikko K, Ortutay C, Vihinen M Immunity genes and their orthologs: a multi-species database. Int Immunol 19: 1361-1370. Metazoan immune genes 17965450 3,18
2007 Rao SQ|etAl Familial aggregation analysis of gene expressions. BMC Proc 1 Suppl 1: S49. Human genes 18466548 13,16
2007 Razvi MH, Peng D, Dar AA, Powell SM, Frierson HF, Moskaluk CA, Washington K, El-Rifai W Transcriptional oncogenomic hot spots in Barrett's adenocarcinomas: Serial analysis of gene expression. Genes Chromosomes Cancer 46: 914-928. Human transcripts; Barrett's adenocarcinoma 17636545 7,16
2007 Rebholz-Schuhmann D, Arregui M, Gaudan S, Kirsch H, Jimeno A Text processing through Web services: Calling Whatizit. Bioinformatics 24: 296-298. 18006544 10,12
2007 Rebholz-Schuhmann D, Kirsch H, Arregui M, Gaudan S, Riethoven M, Stoehr P EBIMed--text crunching to gather facts for proteins from Medline. Bioinformatics 23: e237-244. 17237098 10,12
2007 Reimand J, Kull M, Peterson H, Hansen J, Vilo J g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Res 35: W193-200. 17478515 10
2007 Ren XY, Stiekema WJ, Nap JP Local coexpression domains in the genome of rice show no microsynteny with Arabidopsis domains. Plant Mol Biol 65: 205-217. Mouse embryonic liver transcripts 17641976 7,16
2007 Rensing SA, Ick J, Fawcett JA, Lang D, Zimmer A, Van de Peer Y, Reski R An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens. BMC Evol Biol 7: 130. Physcomitrella patens ESTs 17683536 5,18
2007 Reuveni E, Ramensky VE, Gross C Mouse SNP Miner: An annotated database of mouse functional single nucleotide polymorphisms. BMC Genomics 8: 24. 17239255 11
2007 Richardt S, Lang D, Reski R, Frank W, Rensing SA PlanTAPDB, a Phylogeny-Based Resource of Plant Transcription-Associated Proteins. Plant Physiol 143: 1452-1466. 17337525 11
2007 Riechelmann H, Deutschle T, Grabow A, Heinzow B, Butte W, Reiter R Differential response of Mono Mac 6, BEAS-2B, and Jurkat cells to indoor dust. Environ Health Perspect 115: 1325-1332. Human cell line transcripts; indoor dust 17805423 7,16
2007 Rinkevich Y, Douek J, Haber O, Rinkevich B, Reshef R Urochordate whole body regeneration inaugurates a diverse innate immune signaling profile. Dev Biol 312: 131-146. Ascidian ESTs 17964563 5,7
2007 Rizzolo LJ, Chen X, Weitzman M, Sun R, Zhang H Analysis of the RPE transcriptome reveals dynamic changes during the development of the outer blood-retinal barrier. Mol Vis 13: 1259-1273. Chicken retinal transcripts 17679949 7
2007 Robb SM, Ross E, Sanchez Alvarado A SmedGD: the Schmidtea mediterranea genome database. Nucleic Acids Res 36: D599-606. Planarian genome 17881371 11
2007 Roberts ES, Soucy NV, Bonner AM, Page TJ, Thomas RS, Dorman DC Basal gene expression in male and female Sprague-Dawley rat nasal respiratory and olfactory epithelium. Inhal Toxicol 19: 941-949. Rat epithelial transcripts 17849278 7,16
2007 Roger J, Goureau O, Sahel JA, Guillonneau X Use of suppression subtractive hybridization to identify genes regulated by ciliary neurotrophic factor in postnatal retinal explants. Mol Vis 13: 206-219. Rat retinal transcripts 17327826 7
2007 Rokhlenko O, Shlomi T, Sharan R, Ruppin E, Pinter RY Constraint-based functional similarity of metabolic genes: going beyond network topology. Bioinformatics 23: 2139-2146. 17586548 13,17
2007 Rustici G, van Bakel H, Lackner DH, Holstege F, Wijmenga C, Bahler J, Brazma A Global transcriptional responses of fission and budding yeast to changes in copper and iron levels: a comparative study. Genome Biol 8: R73. Saccharomyces transcripts; Schizosaccharomyces transcripts 17477863 7,18
2007 Rusyn I, Fry RC, Begley TJ, Klapacz J, Svensson JP, Ambrose M, Samson LD Transcriptional networks in S. cerevisiae linked to an accumulation of base excision repair intermediates. PLoS ONE 2: e1252. Saccharomyces transcripts 18043759 10.1371/journal.pone.0001252 7,17
2007 Ryan JC, Bottein Dechraoui MY, Morey JS, Rezvani A, Levin ED, Gordon CJ, Ramsdell JS, Van Dolah FM Transcriptional profiling of whole blood and serum protein analysis of mice exposed to the neurotoxin Pacific Ciguatoxin-1. Neurotoxicology 28: 1099-1109. Mouse blood cell transcripts; ciguatoxin exposure 17868886 7,16
2007 Ryu T, Jung J, Lee S, Nam HJ, Hong SW, Yoo JW, Lee DK, Lee D bZIPDB : A database of regulatory information for human bZIP transcription factors. BMC Genomics 8: 136. 17535445 6,11
2007 Saban R, D'Andrea MR, Andrade-Gordon P, Derian CK, Dozmorov I, Ihnat MA, Hurst RE, Simpson C, Saban MR Regulatory network of inflammation downstream of proteinase-activated receptors. BMC Physiol 7: 3. Mouse urinary bladder transcripts; inflammation 17397547 7,16,17
2007 Sagiv E, Rozovski U, Kazanov D, Liberman E, Arber N Gene expression analysis proposes alternative pathways for the mechanism by which celecoxib selectively inhibits the growth of transformed but not normal enterocytes. Clin Cancer Res 13: 6807-6815. Rat enterocyte transcripts 18006783 7,16
2007 Sahoo D, Dill DL, Tibshirani R, Plevritis SK Extracting binary signals from microarray time-course data. Nucleic Acids Res 35: 3705-3712. 17517782 7,10
2007 Sahoo SS, Zeng K, Bodenreider O, Sheth A From "glycosyltransferase" to "congenital muscular dystrophy": integrating knowledge from NCBI Entrez Gene and the Gene Ontology. Stud Health Technol Inform 129: 1260-1264. 17911917 13
2007 Salati S, Bianchi E, Zini R, Tenedini E, Quaglino D, Manfredini R, Ferrari S Eosinophils, but not neutrophils, exhibit an efficient DNA repair machinery and high nucleolar activity. Haematologica 92: 1311-1318. Human blood cell transcripts 17768116 7,16
2007 Sam L, Liu Y, Li J, Friedman C, Lussier YA Discovery of protein interaction networks shared by diseases. Pac Symp Biocomput 2007: 76-87. 17992746 8,16,17
2007 Samsonova AA, Niranjan M, Russell S, Brazma A Prediction of gene expression in embryonic structures of Drosophila melanogaster. PLoS Comput Biol 3: e144. 17658945 7,19
2007 Sanfilippo A, Posse C, Gopalan B, Riensche R, Beagley N, Baddeley B, Tratz S, Gregory M Combining hierarchical and associative gene ontology relations with textual evidence in estimating gene and gene product similarity. IEEE Trans Nanobioscience 6: 51-59. 17393850 12,13
2007 Sangar V, Blankenberg DJ, Altman N, Lesk AM Quantitative sequence-function relationships in proteins based on gene ontology. BMC Bioinformatics 8: 294. 17686158 3,13
2007 Schindler J, Lewandrowski U, Sickmann A, Friauf E Aqueous polymer two-phase systems for the proteomic analysis of plasma membranes from minute brain samples. J Proteome Res 7: 432-442. Rat brain proteins 17997518 8
2007 Schlenke TA, Morales J, Govind S, Clark AG Contrasting infection strategies in generalist and specialist wasp parasitoids of Drosophila melanogaster. PLoS Pathog 3: 1486-1501. Drosophila transcripts 17967061 10.1371/journal.ppat.0030158 7
2007 Schlicker A, Albrecht M FunSimMat: a comprehensive functional similarity database. Nucleic Acids Res 36: D434-439. 17932054 11,13
2007 Schlicker A, Huthmacher C, Ramirez F, Lengauer T, Albrecht M Functional evaluation of domain-domain interactions and human protein interaction networks. Bioinformatics 23: 859-865. Human proteins 17456608 8,17
2007 Schlicker A, Rahnenfuhrer J, Albrecht M, Lengauer T, Domingues FS GOTax: investigating biological processes and biochemical activities along the taxonomic tree. Genome Biol 8: R33. 17346342 10,11
2007 Schmidt CJ, Romanov M, Ryder O, Magrini V, Hickenbotham M, Glasscock J, McGrath S, Mardis E, Stein LD Gallus GBrowse: a unified genomic database for the chicken. Nucleic Acids Res 36: D719-723. Chicken genome 17933775 4,11
2007 Schmitt AO, Al-Hasani H, Cheverud JM, Pomp D, Bunger L, Brockmann GA Fine mapping of mouse QTLs for fatness using SNP data. OMICS 11: 341-350. Mouse QTLs 18092907 13,16
2007 Schulz WA|etAl Factor interaction analysis for chromosome 8 and DNA methylation alterations highlights innate immune response suppression and cytoskeletal changes in prostate cancer. Mol Cancer 6: 14. Human genes and transcripts; prostate cancer 17280610 7,13,16
2007 Schwartz EF, Diego-Garcia E, Rodriguez de la Vega RC, Possani LD Transcriptome analysis of the venom gland of the Mexican scorpion Hadrurus gertschi (Arachnida: Scorpiones). BMC Genomics 8: 119. Scorpion venom gland ESTs 17506894 5,7
2007 Schwarz DF, Hadicke O, Erdmann J, Ziegler A, Bayer D, Moller S SNPtoGO: Characterising SNPs by Enriched GO Terms. Bioinformatics 24: 146-148. 18024970 10,13
2007 Sequeira A, Klempan T, Canetti L, Ffrench-Mullen J, Benkelfat C, Rouleau GA, Turecki G Patterns of gene expression in the limbic system of suicides with and without major depression. Mol Psychiatry 12: 640-655. Human brain transcripts; depression; suicide 17353912 7,16
2007 Seshi B Proteomics strategy based on liquid-phase IEF and 2-D DIGE: Application to bone marrow mesenchymal progenitor cells. Proteomics 7: 1984-1999. Human bone marrow proteins; leukemia 17516591 8,16
2007 Severino P|etAl Comparative transcriptome analysis of Listeria monocytogenes strains of the two major lineages reveals differences in virulence, cell wall and stress response. Appl Environ Microbiol 73: 6078-6088. Listeria transcripts 17704270 7,16
2007 Shalgi R, Lieber D, Oren M, Pilpel Y Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Comput Biol 3: e131. Mammalian miRNAs 17630826 10.1371/journal.pcbi.0030131 7,17
2007 Shankavaram UT|etAl Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray study. Mol Cancer Ther 6: 820-832. NCI-60 cancer cell transcripts 17339364 7,16
2007 Shaw WM, Luo S, Landis J, Ashraf J, Murphy CT The C. elegans TGF-beta dauer pathway regulates longevity via insulin signaling. Curr Biol 17: 1635-1645. C. elegans dauer transcripts 17900898 7
2007 Shen HB, Chou KC Gpos-PLoc: an ensemble classifier for predicting subcellular localization of Gram-positive bacterial proteins. Protein Eng Des Sel 20: 39-46. 17244638 9,10
2007 Shen HB, Yang J, Chou KC Euk-PLoc: an ensemble classifier for large-scale eukaryotic protein subcellular location prediction. Amino Acids 33: 57-67. 17235453 9,10
2007 Shen L, Kondo Y, Guo Y, Zhang J, Zhang L, Ahmed S, Shu J, Chen X, Waterland RA, Issa JP Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters. PLoS Genet 3: 2023-2036. Human genes; CpG methylation 17967063 10.1371/journal.pgen.0030181 7,16
2007 Shi W, Zhou W, Xu D Identifying cis-regulatory elements by statistical analysis and phylogenetic footprinting and analysing their coexistence and related Gene Ontology. Physiol Genomics 31: 374-384. Human; mouse; Drosophila; promoters 17848606 7,17,18
2007 Shimanuki M, Chung SY, Chikashige Y, Kawasaki Y, Uehara L, Tsutsumi C, Hatanaka M, Hiraoka Y, Nagao K, Yanagida M Two-step, extensive alterations in the transcriptome from G0 arrest to cell division in Schizosaccharomyces pombe. Genes Cells 12: 677-692. Schizosaccharomyces transcripts 17535257 7
2007 Shlomi T, Herrgard M, Portnoy V, Naim E, Palsson BO, Sharan R, Ruppin E Systematic condition-dependent annotation of metabolic genes. Genome Res 17: 1626-1633. 17895423 13
2007 Sluimer JC, Kisters N, Cleutjens KB, Volger OL, Horrevoets AJ, van den Akker LH, Bijnens AP, Daemen MJ Dead or Alive: Gene expression profiles of advanced atherosclerotic plaques from autopsy and surgery. Physiol Genomics 30: 335-341. Human blood vessel genes; atherosclerotic plaques 17519360 7,16
2007 Smith B|etAl The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 25: 1251-1255. 17989687 15
2007 Smith TJ|etAl Analysis of the neurotoxin complex genes in Clostridium botulinum A1-A4 and B1 strains: BoNT/A3, /Ba4 and /B1 clusters are located within plasmids. PLoS ONE 2: e1271. Clostridium botulinum genome 18060065 10.1371/journal.pone.0001271 4,13,16
2007 So AY, Chaivorapol C, Bolton EC, Li H, Yamamoto KR Determinants of cell- and gene-specific transcriptional regulation by the glucocorticoid receptor. PLoS Genet 3: e94. Human lung cell line transcripts 17559307 10.1371/journal.pgen.0030094 7,16
2007 Song YC, Kawas E, Good BM, Wilkinson MD, Tebbutt SJ DataBiNS: Data mining tool for biological pathways and non-synonymous SNPs. Bioinformatics 23: 780-782. 17237074 10,12
2007 Sorensen P|etAl Analysis of the real EADGENE data set: Multivariate approaches and post analysis (Open Access publication). Genet Sel Evol 39: 651-668. 18053574 7
2007 Sperandeo MP|etAl Slc7a7 disruption causes fetal growth retardation by down-regulating Igf1 in the mouse model of lysinuric protein intolerance. Am J Physiol Cell Physiol 293: C191-198. Mouse transcripts; lysinuric protein intolerance 17376816 7,16
2007 Sprague J|etAl The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res 36: D768-772. Zebrafish genome 17991680 1,4,11,15
2007 Srinivasan P Adaptive classifiers, topic drifts and GO annotations. AMIA Annu Symp Proc 2007: 681-685. 18693923 3,13
2007 Srinivasan P, Qiu XY GO for gene documents. BMC Bioinformatics 8 Suppl 9: S3. 18047704 15
2007 Staab CA, Ceder R, Jagerbrink T, Nilsson JA, Roberg K, Jornvall H, Hoog JO, Grafstrom RC Bioinformatics processing of protein and transcript profiles of normal and transformed cell lines indicates functional impairment of transcriptional regulators in buccal carcinoma. J Proteome Res 6: 3705-3717. Human buccal keratinocyte cell line transcripts and proteins; buccal carcinoma 17696463 7,8,16
2007 Stein T, Salomonis N, Gusterson BA Mammary gland involution as a multi-step process. J Mammary Gland Biol Neoplasia 12: 25-35. Mouse mammary gland transcripts 17431797 7
2007 Strand AD, Aragaki AK, Baquet ZC, Hodges A, Cunningham P, Holmans P, Jones KR, Jones L, Kooperberg C, Olson JM Conservation of regional gene expression in mouse and human brain. PLoS Genet 3: e59. Mouse and human brain transcripts 17447843 10.1371/journal.pgen.0030059 7,16,18
2007 Su Z, Huang Y, Gu X Tissue-driven Hypothesis with Gene Ontology (GO) Analysis. Ann Biomed Eng 35: 1088-1094. Human and mouse genes and transcripts 17372837 7,18
2007 Suarez MB, Vizcaino JA, Llobell A, Monte E Characterization of genes encoding novel peptidases in the biocontrol fungus Trichoderma harzianum CECT 2413 using the TrichoEST functional genomics approach. Curr Genet 51: 331-342. Trichoderma ESTs 17415567 5
2007 Sugaya N|etAl An integrative in silico approach for discovering candidates for drug-targetable protein-protein interactions in interactome data. BMC Pharmacol 7: 10. Human protein-protein interactions 17705877 8,19
2007 Suhr ML, Dysvik B, Bruland O, Warnakulasuriya S, Amaratunga AN, Jonassen I, Vasstrand EN, Ibrahim SO Gene expression profile of oral squamous cell carcinomas from Sri Lankan betel quid users. Oncol Rep 18: 1061-1075. Human transcripts; oral cancer; betel nut 17914555 7,16
2007 Sun J, Tuncay K, Haidar AA, Ensman L, Stanley F, Trelinski M, Ortoleva P Transcriptional regulatory network discovery via multiple method integration: application to e.coli K12. Algorithms Mol Biol 2: 2. E. coli transcripts 17397539 7,17
2007 Sun Q, Wang Y, Zhang Y, Liu F, Cheng X, Hou N, Zhao X, Yang X Expression profiling reveals dysregulation of cellular cytoskeletal genes in HBx-induced hepatocarcinogenesis. Cancer Biol Ther 6: 668-674. Mouse transcripts; hepatitis B; tumorigenesis 17873514 7,16
2007 Sun Q, Zhang Y, Liu F, Zhao X, Yang X Identification of candidate biomarkers for hepatocellular carcinoma through pre-cancerous expression analysis in an HBx transgenic mouse. Cancer Biol Ther 6: 1532-1538. Mouse liver transcripts; liver cancer 18245957 7,16
2007 Sun W, Yu T, Li KC Detection of eQTL modules mediated by activity levels of transcription factors. Bioinformatics 23: 2290-2297. Saccharomyces expression QTLs 17599927 7,13
2007 Tabach Y, Brosh R, Buganim Y, Reiner A, Zuk O, Yitzhaky A, Koudritsky M, Rotter V, Domany E Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site. PLoS ONE 2: e807. Human promoters 17726537 10.1371/journal.pone.0000807 7,17
2007 Tadros W, Goldman AL, Babak T, Menzies F, Vardy L, Orr-Weaver T, Hughes TR, Westwood JT, Smibert CA, Lipshitz HD SMAUG is a major regulator of maternal mRNA destabilization in Drosophila and its translation is activated by the PAN GU kinase. Dev Cell 12: 143-155. Drosophila transcripts 17199047 7
2007 Takenaka Y, Matsumoto A, Matsuda H GO based tissue specific functions of mouse using countable gene expression profiles. Genome Inform 19: 154-165. Mouse transcripts 18546513 ,
2007 Talavera D, Vogel C, Orozco M, Teichmann SA, de la Cruz X The (in)dependence of alternative splicing and gene duplication. PLoS Comput Biol 3: e33. 17335345 10.1371/journal.pcbi.0030033 13,18
2007 Tamura T, Akutsu T Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition. BMC Bioinformatics 8: 466. 18047679 9
2007 Tan MP, Broach JR, Floudas CA Evaluation of normalization and pre-clustering issues in a novel clustering approach: global optimum search with enhanced positioning. J Bioinform Comput Biol 5: 895-913. 17787062 7
2007 Tang A, Yu Z, Gui Y, Zhu H, Zhang L, Zhang J, Cai Z Characteristics of 292 testis-specific genes in human. Biol Pharm Bull 30: 865-872. Human testis-specific genes 17473427 7,16
2007 Tang K, Thornton KR, Stoneking M A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biol 5: e171. Human genome; polymorphisms 17579516 18
2007 Tang Z, Li Y, Wan P, Li X, Zhao S, Liu B, Fan B, Zhu M, Yu M, Li K LongSAGE analysis of skeletal muscle at three prenatal stages in Tongcheng and Landrace pigs. Genome Biol 8: R115. Fetal pig muscle transcripts 17573972 7
2007 Tao Y, Sam L, Li J, Friedman C, Lussier YA Information theory applied to the sparse gene ontology annotation network to predict novel gene function. Bioinformatics 23: i529-i538. 17646340 9,10
2007 Tatematsu K, Nakabayashi K, Kamiya Y, Nambara E Transcription factor AtTCP14 regulates embryonic growth potential during seed germination in Arabidopsis thaliana. Plant J 53: 42-52. Arabidopsis transcripts; seed germination 17953649 7
2007 Te Pas MF, Hulsegge I, Coster A, Pool MH, Heuven HH, Janss LL Biochemical pathways analysis of microarray results: regulation of myogenesis in pigs. BMC Dev Biol 7: 66. Pig muscle transcripts 17567520 7,17
2007 Thalmeier A, Dickmann M, Giegling I, Schneider B, M Hartmann A, Maurer K, Schnabel A, Kauert G, Moller HJ, Rujescu D Gene expression profiling of post-mortem orbitofrontal cortex in violent suicide victims. Int J Neuropsychopharmacol 11: 217-228. Human brain transcripts; suicide 17608962 7,16
2007 The Gene Ontology Consortium The Gene Ontology project in 2008. Nucleic Acids Res 36: D440-444. 17984083 1,2
2007 Theodosiou T, Angelis L, Vakali A Non-linear correlation of content and metadata information extracted from biomedical article datasets. J Biomed Inform 41: 202-216. 17643352 12
2007 Thimon V, Koukoui O, Calvo E, Sullivan R Region-specific gene expression profiling along the human epididymis. Mol Hum Reprod 13: 691-704. Human epididymal transcripts 17881722 7,16
2007 Thomas BC, Rapaka L, Lyons E, Pedersen B, Freeling M Arabidopsis intragenomic conserved noncoding sequence. Proc Natl Acad Sci U S A 104: 3348-3353. 17301222 13
2007 Thomas PD, Mi H, Lewis S Ontology annotation: mapping genomic regions to biological function. Curr Opin Chem Biol 11: 4-11. 17208035 1,3,14
2007 Thomas RS, Allen BC, Nong A, Yang L, Bermudez E, Clewell HJ, Andersen ME A method to integrate benchmark dose estimates with genomic data to assess the functional effects of chemical exposure. Toxicol Sci 98: 240-248. Rat nasal epithelial transcripts; formaldehyde exposure 17449896 7,16
2007 Thorne T, Stumpf MP Generating confidence intervals on biological networks. BMC Bioinformatics 8: 467. 18053130 17
2007 Tilton RG, Haidacher SJ, Lejeune WS, Zhang X, Zhao Y, Kurosky A, Brasier AR, Denner L Diabetes-induced changes in the renal cortical proteome assessed with two-dimensional gel electrophoresis and mass spectrometry. Proteomics 7: 1729-1742. Human kidney proteins; diabetes 17436268 8,16
2007 Timmermans MJ, de Boer ME, Nota B, de Boer TE, Marien J, Klein-Lankhorst RM, van Straalen NM, Roelofs D Collembase: a repository for springtail genomics and soil quality assessment. BMC Genomics 8: 341. Springtail ESTs 17900339 5,10
2007 Tirosh I, Barkai N Comparative analysis indicates regulatory neofunctionalization of yeast duplicates. Genome Biol 8: R50. Saccharomyces duplicated genes 17411427 7,13,18
2007 Tochigi M, Iwamoto K, Bundo M, Sasaki T, Kato N, Kato T Gene expression profiling of major depression and suicide in the prefrontal cortex of postmortem brains. Neurosci Res 60: 184-191. Human brain transcripts; depression; suicide 18068248 7,16
2007 Tomida S, Yanagisawa K, Koshikawa K, Yatabe Y, Mitsudomi T, Osada H, Takahashi T Identification of a metastasis signature and the DLX4 homeobox protein as a regulator of metastasis by combined transcriptome approach. Oncogene 26: 4600-4608. Human lung cancer cell line transcripts; metastasis 17260014 7,16
2007 Torres A, Storey L, Anders M, Miller RL, Bulbulian BJ, Jin J, Raghavan S, Lee J, Slade HB, Birmachu W Immune-mediated changes in actinic keratosis following topical treatment with imiquimod 5% cream. J Transl Med 5: 7. Human skin transcripts; actinic keratosis; imiquimod treatment 17257431 7,16
2007 Toussaint A, Lima-Mendez G, Leplae R PhiGO, a phage ontology associated with the ACLAME database. Res Microbiol 158: 567-571. Phage genomes, phage ontology 17614261 4,13
2007 Trajkovski I, Lavrac N, Tolar J SEGS: Search for enriched gene sets in microarray data. J Biomed Inform 41: 588-601. 18234563 7,10
2007 Tripathi A|etAl Gene expression abnormalities in histologically normal breast epithelium of breast cancer patients. Int J Cancer 122: 1557-1566. Human breast transcripts; breast cancer 18058819 7,16
2007 Tu LL|etAl Genes expression analyses of sea-island cotton (Gossypium barbadense L.) during fiber development. Plant Cell Rep 196: 384-393. Cotton cDNAs 17377794 5,7
2007 Tulipano A, Donvito G, Licciulli F, Maggi G, Gisel A Gene analogue finder: a GRID solution for finding functionally analogous gene products. BMC Bioinformatics 8: 329. 17767718 9,10
2007 Tuller T, Kupiec M, Ruppin E Determinants of protein abundance and translation efficiency in S. cerevisiae. PLoS Comput Biol 3: e248. Saccharomyces transcripts; Saccharomyces proteins 18159940 10.1371/journal.pcbi.0030248 7,8,19
2007 Tuncay K, Ensman L, Sun J, Haidar AA, Stanley F, Trelinski M, Ortoleva P Transcriptional regulatory networks via gene ontology and expression data. In Silico Biol 7: 21-34. 17688426 7,17
2007 Turck F, Roudier F, Farrona S, Martin-Magniette ML, Guillaume E, Buisine N, Gagnot S, Martienssen RA, Coupland G, Colot V Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genet 3: e86. Arabidopsis genes; histone methylation 17542647 10.1371/journal.pgen.0030086 7,13
2007 Ueno Y, Fukushima K, Nakagome Y, Kido O, Shimosegawa T Bioinformatic approach for cholangiocyte pathophysiology. Hepatol Res 37 Suppl 3: S444-448. Cholangiocyte cell line transcripts 17931200 7
2007 Vahey MT, Ockenhouse CF, Wang Z, Yalley-Ogunro J, Greenhouse J, Nau ME, Lewis MG Impact of antiretroviral treatment on gene expression in peripheral blood mononuclear cells from SIVmac251-infected macaques. J Infect Dis 196: 384-393. Macaque blood cell transcripts; SIV; antiretroviral treatment 17597453 7,16
2007 Van Vooren S, Thienpont B, Menten B, Speleman F, Moor BD, Vermeesch J, Moreau Y Mapping biomedical concepts onto the human genome by mining literature on chromosomal aberrations. Nucleic Acids Res 35: 2533-2543. Human cytogenetic bands 17403693 3,10,12
2007 Velasco R|etAl A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE 2: e1326. Grape genome 18094749 10.1371/journal.pone.0001326 4
2007 Vencio RZ, Shmulevich I ProbCD: enrichment analysis accounting for categorization uncertainty. BMC Bioinformatics 8: 383. 17935624 10
2007 Venkataraman S, Stevenson P, Yang Y, Richardson L, Burton N, Perry TP, Smith P, Baldock RA, Davidson DR, Christiansen JH EMAGE Edinburgh Mouse Atlas of Gene Expression: 2008 update. Nucleic Acids Res 36: D860-865. 18077470 15
2007 Visel A, Carson J, Oldekamp J, Warnecke M, Jakubcakova V, Zhou X, Shaw CA, Alvarez-Bolado G, Eichele G Regulatory pathway analysis by high-throughput in situ hybridization. PLoS Genet 3: 1867-1883. Mouse embryonic transcripts 17953485 10.1371/journal.pgen.0030178 7,17
2007 Vissers JP, Langridge JI, Aerts JM Analysis and quantification of diagnostic serum markers and protein signatures for Gaucher disease. Mol Cell Proteomics 6: 755-766. Human serum proteins; Gaucher disease 17293593 8,16
2007 Vizcaino JA, Redondo J, Suarez MB, Cardoza RE, Hermosa R, Gonzalez FJ, Rey M, Monte E Generation, annotation, and analysis of ESTs from four different Trichoderma strains grown under conditions related to biocontrol. Appl Microbiol Biotechnol 75: 853-862. Trichoderma ESTs 17333173 5
2007 Vogel H, Kroymann J, Mitchell-Olds T Different transcript patterns in response to specialist and generalist herbivores in the wild Arabidopsis relative Boechera divaricarpa. PLoS ONE 2: e1081. Boechera divaricarpa transcripts 17957263 10.1371/journal.pone.0001081 7
2007 Vroling AB, Jonker MJ, Luiten S, Breit TM, Fokkens WJ, van Drunen CM Primary nasal epithelium exposed to house dust mite extract shows activated expression in allergics. Am J Respir Cell Mol Biol 38: 293-299. Human nasal epithelial transcripts; dust mites 17901406 7,16
2007 Walley JW, Coughlan S, Hudson ME, Covington MF, Kaspi R, Banu G, Harmer SL, Dehesh K Mechanical stress induces biotic and abiotic stress responses via a novel cis-element. PLoS Genet 3: 1800-1812. Arabidopsis transcripts 17953483 10.1371/journal.pgen.0030172 7
2007 Walther D, Brunnemann R, Selbig J The regulatory code for transcriptional response diversity and its relation to genome structural properties in A. thaliana. PLoS Genet 3: e11. Arabidopsis transcripts 17291162 10.1371/journal.pgen.0030011 7,13
2007 Wang J, Gutala R, Hwang YY, Kim JM, Konu O, Ma JZ, Li MD Strain- and region-specific gene expression profiles in mouse brain in response to chronic nicotine treatment. Genes Brain Behav 7: 78-87. Mouse brain transcripts; nicotine exposure 17504244 7
2007 Wang J, Li YH, Guo Z, Zhu J, Ma WC, Peng CF, Liu Q [Finding finer functions for proteins related to breast cancer based on protein interaction networkPCR] Yi Chuan 29: 1061-1066. 17855254 9,17
2007 Wang J, Xu Z, Fang H, Duhart HM, Patterson TA, Ali SF Gene expression profiling of MPP(+)-treated MN9D cells: A mechanism of toxicity study. Neurotoxicology 28: 979-987. Mouse MN9D cell transcripts; MPP(+) treatment; Parkinson's disease 17475336 7,16
2007 Wang JZ, Du Z, Payattakool R, Yu PS, Chen CF A new method to measure the semantic similarity of GO terms. Bioinformatics 23: 1274-1281. 17344234 10,13
2007 Wang X, Pal R, Chen XW, Kumar KN, Kim OJ, Michaelis EK Genome-wide transcriptome profiling of region-specific vulnerability to oxidative stress in the hippocampus. Genomics 99: 201-205. Hippocampal transcripts; oxidative stress 17553663 7,16
2007 Wang Z, Lin S, Popesco M, Rotter A Modeling and Analysis of Multi-Library, Multi-Group SAGE Data with Application to a Study of Mouse Cerebellum. Biometrics 63: 777-786. Mouse cerebellar transcripts 17825009 7
2007 Waters KM, Tan R, Genetos DC, Verma S, Yellowley CE, Karin NJ DNA microarray analysis reveals a role for lysophosphatidic acid in the regulation of anti-inflammatory genes in MC3T3-E1 cells. Bone 41: 833-841. Mouse cell line transcripts; lysophosphatidic acid; bone healing 17719864 7,16
2007 Watson JD, Sanderson S, Ezersky A, Savchenko A, Edwards A, Orengo C, Joachimiak A, Laskowski RA, Thornton JM Towards fully automated structure-based function prediction in structural genomics: A case study. J Mol Biol 367: 1511-1522. 17316683 9,10
2007 Wei Y, Ringe D, Wilson MA, Ondrechen MJ Identification of functional subclasses in the DJ-1 superfamily proteins. PLoS Comput Biol 3: e10. 17257049 10.1371/journal.pcbi.0030010 9,19
2007 Williamson AJ|etAl Quantitative proteomic analysis demonstrates post-transcriptional regulation of embryonic stem cell differentiation to hematopoiesis. Mol Cell Proteomics 7: 459-472. Mouse cell line proteins 18045800 8
2007 Winnenburg R, Urban M, Beacham A, Baldwin TK, Holland S, Lindeberg M, Hansen H, Rawlings C, Hammond-Kosack KE, Kohler J PHI-base update: additions to the pathogen host interaction database. Nucleic Acids Res 36: D572-576. 17942425 11
2007 Wiwanitkit V Endothelin-1 and protein kinase C co-expression in the pathogenesis of diabetic retinopathy. J Diabetes Complications 21: 359-362. 17967707 16
2007 Wiwanitkit V Functions of AAV-CMV-F.IX and AAV-EF1alpha-F.IX in gene therapy for hemophilia B. Hum Gene Ther 18: 89-92. 17266422 13,16
2007 Wiwanitkit V I/D genetic polymorphism of angiotensin-converting enzyme: pathogenesis evaluation for erectile dysfunction by gene ontology. Fertil Steril 89: 1095-1097. 17889866 16
2007 Wiwanitkit V Interaction between leptin and leptin receptor in gastric carcinoma: Gene ontology analysis. Rev Esp Enferm Dig 99: 201-205. 17590101 16
2007 Wiwanitkit V Interleukin-18 gene polymorphism - 607 genotype and susceptibility to chronic hepatitis B virus infection: functional analysis by gene ontology. J Gastrointestin Liver Dis 16: 468-469. 18193135 16
2007 Wiwanitkit V Plasmodium and host lactate dehydrogenase molecular function and biological pathways: implication for antimalarial drug discovery. Chem Biol Drug Des 69: 280-283. 17461976 9,16
2007 Wolf Y, Madej T, Babenko V, Shoemaker B, Panchenko AR Long-term trends in evolution of indels in protein sequences. BMC Evol Biol 7: 19. 17298668 18
2007 Wu J, Liu W, Bemis A, Wang E, Qiu Y, Morris EA, Flannery CR, Yang Z Comparative proteomic characterization of articular cartilage tissue from normal donors and patients with osteoarthritis. Arthritis Rheum 56: 3675-3684. Human cartilage proteins; osteoarthritis 17968891 8,16
2007 Xu J|etAl Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol 5: e156. Bacteroides genomes 17579514 10.1371/journal.pbio.0050156 4,16,18
2007 Xu Y, Ikegami M, Wang Y, Matsuzaki Y, Whitsett JA Gene expression and biological processes influenced by deletion of Stat3 in pulmonary type II epithelial cells. BMC Genomics 8: 455. Mouse lung transcripts 18070348 7,16
2007 Yamaguchi R, Yamamoto M, Imoto S, Nagasaki M, Yoshida R, Tsuiji K, Ishige A, Asou H, Watanabe K, Miyano S Identification of activated transcription factors from microarray gene expression data of kampo medicine-treated mice. Genome Inform 18: 119-129. 18546480 7
2007 Yan B, Yang X, Lee TL, Friedman J, Tong J, Van Waes C, Chen Z Genome-wide identification of novel expression signatures reveal distinct patterns and prevalence of binding motifs for p53, NF-kappaB and other signal transcription factors in head and neck squamous cell carcinoma. Genome Biol 8: R78. Human cell line transcripts; squamous cell carcinoma 17498291 7,16
2007 Yang JO, Charny P, Lee B, Kim S, Bhak J, Woo HG GS2PATH: A web-based integrated analysis tool for finding functional relationships using gene ontology and biochemical pathway data. Bioinformation 2: 194-196. 18305828 10
2007 Yang L, Allen BC, Thomas RS BMDExpress: a software tool for the benchmark dose analyses of genomic data. BMC Genomics 8: 387. 17961223 7,10
2007 Yang MQ, Koehly LM, Elnitski LL Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes. PLoS Comput Biol 3: e72. Human transcripts; ovarian cancer 17447839 10.1371/journal.pcbi.0030072 7,16
2007 Yang S, Wang K, Valladares O, Hannenhalli S, Bucan M Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex. Genome Biol 8: R247. Mouse brain transcripts 18028544 7
2007 Yeo GW, Nostrand EL, Liang TY Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements. PLoS Genet 3: e85. Mammalian genes; intronic splicing regulatory elements 17530930 10.1371/journal.pgen.0030085 13
2007 Yeo GW, Xu X, Liang TY, Muotri AR, Carson CT, Coufal NG, Gage FH Alternative splicing events identified in human embryonic stem cells and neural progenitors. PLoS Comput Biol 3: 1951-1967. Human transcripts 17967047 10.1371/journal.pcbi.0030196 7,13,16
2007 Yi G, Sze SH, Thon MR Identifying clusters of functionally related genes in genomes. Bioinformatics 23: 1053-1060. 17237058 10,13,18
2007 Yin L, Dale BA Activation of protective responses in oral epithelial cells by Fusobacterium nucleatum and human {beta}-defensin-2. J Med Microbiol 56: 976-987. Human oral epithelial cells; commensal bacterium 17577065 7,16
2007 Yoo JH, Shin SW, Kim JS, Kim CB, Kim JS, Koh SC Identification of potential biomarkers for diazinon exposure to Japanese Medaka (Oryzias latipes) using annealing control primers. J Environ Sci Health B 42: 373-379. Medaka genes; diazinon exposure 17474016 7
2007 Yooseph S|etAl The Sorcerer II Global Ocean Sampling Expedition: Expanding the universe of protein families. PLoS Biol 5: e16. Global Ocean Sampling Expedition 17355171 3
2007 Yu H, Jansen R, Gerstein M Developing a similarity measure in biological function space. Bioinformatics 23: 2163-2173. 17540677 13
2007 Yu H, Kim PM, Sprecher E, Trifonov V, Gerstein M The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol 3: e59. Yeast genes and proteins 17447836 10.1371/journal.pcbi.0030059 7,8,17
2007 Yu JX, Sieuwerts AM, Zhang Y, Martens JW, Smid M, Klijn JG, Wang Y, Foekens JA Pathway analysis of gene signatures predicting metastasis of node-negative primary breast cancer. BMC Cancer 7: 182. Human breast tumor transcripts; breast cancer 17894856 7,16,17
2007 Zahn JM|etAl AGEMAP: a gene expression database for aging in mice. PLoS Genet 3: e201. Mouse transcripts; aging 18081424 10.1371/journal.pgen.0030201 7,11,16
2007 Zakrzewska A, Boorsma A, Delneri D, Brul S, Oliver SG, Klis FM Identification of cellular processes and pathways that protect yeast cells against the plasma membrane-perturbing compound chitosan. Eukaryot Cell 6: 600-608. 17259547 13
2007 Zanivan S, Cascone I, Peyron C, Molineris I, Marchio S, Caselle M, Bussolino F A new computational approach to analyze human protein complexes and predict novel protein interactions. Genome Biol 8: R256. 18053208 8,19
2007 Zeitouni B, Senatore S, Severac D, Aknin C, Semeriva M, Perrin L Signalling pathways involved in adult heart formation revealed by gene expression profiling in Drosophila. PLoS Genet 3: 1907-1921. Drosophila transcripts; heart development 17937502 10.1371/journal.pgen.0030174 7
2007 Zelinkova Z, van Beelen AJ, de Kort F, Moerland PD, van Themaat EV, Velde AA, van Deventer SJ, de Jong EC, Hommes DW Muramyl dipeptide-induced differential gene expression in NOD2 mutant and wild-type crohn's disease patient-derived dendritic cells. Inflamm Bowel Dis 14: 186-194. Human dendritic cell transcripts; Crohn's disease 17941075 7,16
2007 Zhang J, He Q, Liu QY, Guo W, Deng XM, Zhang WW, Hu XX, Li N Differential gene expression profile in pig adipose tissue treated with/without clenbuterol. BMC Genomics 8: 433. Porcine adipose tissue transcripts; clenbuterol treatment 18039366 7
2007 Zhang W, Bleibel WK, Roe CA, Cox NJ, Eileen Dolan M Gender-specific differences in expression in human lymphoblastoid cell lines. Pharmacogenet Genomics 17: 447-450. Human cell line transcripts 17502836 7,16
2007 Zhang W, Li L, Li X, Jiang W, Huo J, Wang Y, Lin M, Rao S Unravelling the hidden heterogeneities of diffuse large B-cell lymphoma based on coupled two-way clustering. BMC Genomics 8: 332. Human transcripts; diffuse large B-cell lymphoma 17888167 7,13,16
2007 Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, Goodrich J, Jacobsen SE Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol 5: e129. Arabidopsis transcripts 17439305 10.1371/journal.pbio.0050129 7
2007 Zhao YP, Chen G, Feng B, Zhang TP, Ma EL, Wu YD Microarray analysis of gene expression profile of multidrug resistance in pancreatic cancer. Chin Med J (Engl) 120: 1743-1752. Human pancreatic cell line transcripts; pancreatic cancer 18028764 7,16
2007 Zheng B, Lu X Using protein-semantic network metrics to evaluate functional coherence of protein groups. AMIA Annu Symp Proc 2007: 1174. 18694270 6,12
2007 Zheng Z, Zheng H, Yan W Fank1 is a testis-specific gene encoding a nuclear protein exclusively expressed during the transition from the meiotic to the haploid phase of spermatogenesis. Gene Expr Patterns 7: 777-783. Human, mouse genes; FANK1 regulation 17604233 7,16
2007 Zhong S, Xie D Gene Ontology analysis in multiple gene clusters under multiple hypothesis testing framework. Artif Intell Med 41: 105-115. 17913480 10
2007 Zhong W, Sternberg PW Automated data integration for developmental biological research. Development 134: 3227-3238. Zebrafish genome 17686968 1,4,11,15
2007 Zhou T, Chou J, Zhou Y, Simpson DA, Cao F, Bushel PR, Paules RS, Kaufmann WK Ataxia telangiectasia-mutated dependent DNA damage checkpoint functions regulate gene expression in human fibroblasts. Mol Cancer Res 5: 813-822. Human fibroblast cell line transcripts; ataxia telangiectasia 17699107 7,16
2007 Zhou X, Su Z EasyGO: Gene Ontology-based annotation and functional enrichment analysis tool for agronomical species. BMC Genomics 8: 246. 17645808 3,10
2007 Zhu H, Cabrera R, Wlodarczyk BJ, Bozinov D, Wang D, Schwartz RJ, Finnell RH Differentially expressed genes in embryonic cardiac tissues of mice lacking Folr1 gene activity. BMC Dev Biol 7: 128. Mouse embryonic heart transcripts 18028541 7,16
2007 Zhu J, Wang J, Guo Z, Zhang M, Yang D, Li Y, Wang D, Xiao G GO-2D: identifying 2-dimensional cellular-localized functional modules in Gene Ontology. BMC Genomics 8: 30. 17250772 7,10,13
2007 Zilliox MJ, Moss WJ, Griffin DE Gene expression changes in peripheral blood mononuclear cells during measles. Clin Vaccine Immunol 14: 918-923. Human blood cell transcripts; measles 17538120 7,16
2007 de Bivort B, Huang S, Bar-Yam Y Empirical multiscale networks of cellular regulation. PLoS Comput Biol 3: e207. 17953478 10.1371/journal.pcbi.0030207 17
2007 de Sa SV|etAl Serpin Peptidase Inhibitor Clade A Member 1 as a Potential Marker for Malignancy in Insulinomas. Clin Cancer Res 13: 5322-5330. Human transcripts; endocrinoma 17855650 7,16
2007 van Gassen KL, de Wit M, Groot Koerkamp MJ, Rensen MG, van Rijen PC, Holstege FC, Lindhout D, de Graan PN Possible role of the innate immunity in temporal lobe epilepsy. Epilepsia 49: 1055-1065. Human hippocampal transcripts; temporal lobe epilepsy 18076643 7,16
2007 van Lunteren E, Moyer M Oxidoreductase, morphogenesis, extracellular matrix and calcium ion binding gene expression in streptozotocin-induced diabetic rat heart. Am J Physiol Endocrinol Metab 293: E759-768. Rat heart transcripts; diabetes 17566115 7,16
2007 van Lunteren E, Spiegler S, Moyer M Contrast between cardiac left ventricle and diaphragm muscle in expression of genes involved in carbohydrate and lipid metabolism. Respir Physiol Neurobiol 161: 41-53. Rat muscle transcripts 18207466 7,16
2007 van den Berg BH, Harris T, McCarthy FM, Lamont SJ, Burgess SC Non-electrophoretic differential detergent fractionation proteomics using frozen whole organs. Rapid Commun Mass Spectrom 21: 3905-3909. Frozen tissue proteomes 17990261 8
2007 van der Pouw Kraan TC, van Baarsen LG, Wijbrandts CA, Voskuyl AE, Rustenburg F, Baggen JM, Dijkmans BA, Tak PP, Verweij CL Expression of a pathogen-response program in peripheral blood cells defines a subgroup of Rheumatoid Arthritis patients. Genes Immun 9: 16-22. Human blood cell transcripts; rheumatoid arthritis 17928867 7,16
2007 van der Pouw Kraan TC|etAl Rheumatoid arthritis subtypes identified by genomic profiling of peripheral blood cells: Assignment of a type I interferon signature in a subpopulation of patients. Ann Rheum Dis 66: 1008-1014. Human blood cell transcripts; rheumatoid arthritis 17223656 7,16
2008 Abdel-Aziz HO|etAl Targeted disruption of the galectin-3 gene results in decreased susceptibility to NNK-induced lung tumorigenesis: an oligonucleotide microarray study. J Cancer Res Clin Oncol 134: 777-788. Mouse transcripts; lung cancer 18204863 7,16
2008 Abdeltawab NF|etAl An unbiased systems genetics approach to mapping genetic loci modulating susceptibility to severe streptococcal sepsis. PLoS Pathog 4: e1000042. 18421376 10.1371/journal.ppat.1000042 13,16,18
2008 Adams HA, Southey BR, Robinson GE, Rodriguez-Zas SL Meta-analysis of genome-wide expression patterns associated with behavioral maturation in honey bees. BMC Genomics 9: 503. Honey bee transcripts 18950506 7
2008 Agudelo-Romero P, Carbonell P, Perez-Amador MA, Elena SF Virus adaptation by manipulation of host's gene expression. PLoS ONE 3: e2397. Tobacco etch potyvirus transcripts 18545680 10.1371/journal.pone.0002397 7,18
2008 Ahmad Y, Boisvert FM, Gregor P, Cobley A, Lamond AI NOPdb: Nucleolar Proteome Database--2008 update. Nucleic Acids Res 37: D181-184. 18984612 8,11
2008 Ala U, Piro RM, Grassi E, Damasco C, Silengo L, Oti M, Provero P, Di Cunto F Prediction of human disease genes by human-mouse conserved coexpression analysis. PLoS Comput Biol 4: e1000043. Human transcripts; mouse transcripts 18369433 10.1371/journal.pcbi.1000043 7,16,18
2008 Alcorn JF, Guala AS, van der Velden J, McElhinney B, Irvin CG, Davis RJ, Janssen-Heininger YM Jun N-terminal kinase 1 regulates epithelial-to-mesenchymal transition induced by TGF-{beta}1. J Cell Sci 121: 1036-1045. Mouse tracheal epithelial cell transcripts 18334556 7,16
2008 Alibes A, Canada A, Diaz-Uriarte R PaLS: filtering common literature, biological terms and pathway information. Nucleic Acids Res 36: W364-367. 18467422 10,12
2008 Alonso S, Lopez S, Izagirre N, de la Rua C Title: Overdominance in the human genome and olfactory receptor activity. Mol Biol Evol 25: 997-991001. 18296703 18
2008 Alten JA, Moran A, Tsimelzon AI, Mastrangelo MA, Hilsenbeck SG, Poli V, Tweardy DJ Prevention of hypovolemic circulatory collapse by IL-6 activated Stat3. PLoS ONE 3: e1605. Rat heart transcripts 18270592 10.1371/journal.pone.0001605 7,16
2008 Alvesalo J, Greco D, Leinonen M, Raitila T, Vuorela P, Auvinen P Microarray analysis of a Chlamydia pneumoniae-infected human epithelial cell line by use of Gene Ontology hierarchy. J Infect Dis 197: 156-162. Human epithelial cell transcripts; Chlamydia infection 18171299 7,16
2008 Andersen MC, Engstrom PG, Lithwick S, Arenillas D, Eriksson P, Lenhard B, Wasserman WW, Odeberg J In silico detection of sequence variations modifying transcriptional regulation. PLoS Comput Biol 4: e5. 18208319 10.1371/journal.pcbi.0040005 7,10
2008 Andersen ME, Clewell HJ, Bermudez E, Willson GA, Thomas RS Genomic signatures and dose dependent transitions in nasal epithelial responses to inhaled formaldehyde in the rat. Toxicol Sci 105: 368-383. Rat nasal epithelial transcripts; formaldehyde exposure 18499655 7,16
2008 Andersson A, Isaksson M, Wefer J, Norling A, Flores-Morales A, Rorsman F, Kampe O, Harris RA, Lobell A Impaired autoimmune T helper 17 cell responses following DNA vaccination against rat experimental autoimmune encephalomyelitis. PLoS ONE 3: e3682. Rat spleen transcripts 18997868 10.1371/journal.pone.0003682 7,16
2008 Antonov AV, Schmidt T, Wang Y, Mewes HW ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data. Nucleic Acids Res 36: W347-351. 18460543 10
2008 Argout X|etAl Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao generated from various tissues and under various conditions. BMC Genomics 9: 512. Theobroma cacao ESTs 18973681 5,11
2008 Arunkumar KP, Tomar A, Daimon T, Shimada T, Nagaraju J WildSilkbase: an EST database of wild silkmoths. BMC Genomics 9: 338. Silkworm ESTs 18637161 5,11
2008 Asikainen S, Heikkinen L, Wong G, Storvik M Functional characterization of endogenous siRNA target genes in Caenorhabditis elegans. BMC Genomics 9: 270. C. elegans siRNA target genes 18522735 7
2008 Aubry M, Monnier A, Chicault C, Galibert MD, Burgun A, Mosser J Iron-related transcriptomic variations in Caco-2 cells: In silico perspectives. Biochimie 90: 669-678. Human cell line transcripts; iron overload 18226600 7,16
2008 Avraham S|etAl The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Res 36: D449-454. 18194960 15
2008 Baek JM, Han P, Iandolino A, Cook DR Characterization and comparison of intron structure and alternative splicing between Medicago truncatula, Populus trichocarpa, Arabidopsis and rice. Plant Mol Biol 67: 499-510. Plant introns 18438730 13,18
2008 Bandapalli OR, Kahlert C, Hellstern V, Galindo L, Schirmacher P, Weitz J, Brand K Cross-species comparison of biological themes and underlying genes on a global gene expression scale in a mouse model of colorectal liver metastasis and in clinical specimens. BMC Genomics 9: 448. Mouse liver transcripts; human liver transcripts; colorectal cancer; metastasis 18823562 7,16
2008 Bandhakavi S, Xie H, O'Callaghan B, Sakurai H, Kim DH, Griffin TJ Hsf1 activation inhibits rapamycin resistance and TOR signaling in yeast revealed by combined proteomic and genetic analysis. PLoS ONE 3: e1598. Saccharomyces proteins 18270585 10.1371/journal.pone.0001598 8,13,17
2008 Bandyopadhyay S, Kelley R, Krogan NJ, Ideker T Functional maps of protein complexes from quantitative genetic interaction data. PLoS Comput Biol 4: e1000065. 18421374 10.1371/journal.pcbi.1000065 8,13,17
2008 Banks E, Nabieva E, Chazelle B, Singh M Organization of physical interactomes as uncovered by network schemas. PLoS Comput Biol 4: e1000203. 18949022 10.1371/journal.pcbi.1000203 8,17
2008 Baranzini SE|etAl Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. Hum Mol Genet 18: 767-778. Human genes; multiple sclerosis 19010793 13,16
2008 Barger JL|etAl A low dose of dietary resveratrol partially mimics caloric restriction and retards aging parameters in mice. PLoS ONE 3: e2264. Mouse transcripts 18523577 10.1371/journal.pone.0002264 7,16
2008 Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R The GOA database in 2009--an integrated Gene Ontology Annotation resource. Nucleic Acids Res 37: D396-403. 18957448 1,6,10,11
2008 Barthold JS, McCahan SM, Singh AV, Knudsen TB, Si X, Campion L, Akins RE Altered expression of muscle- and cytoskeleton-related genes in a rat strain with inherited cryptorchidism. J Androl 29: 352-366. Rat transcripts; cryptorchidism 18222913 7,16
2008 Battilana J, Costantini L, Emanuelli F, Sevini F, Segala C, Moser S, Velasco R, Versini G, Grando MS The 1-deoxy-D: -xylulose 5-phosphate synthase gene co-localizes with a major QTL affecting monoterpene content in grapevine. Theor Appl Genet 118: 653-669. 19037624 13
2008 Bauer S, Grossmann S, Vingron M, Robinson PN Ontologizer 2.0 - A multifunctional tool for GO term enrichment analysis and data exploration. Bioinformatics 24: 1650-1651. 18511468 10
2008 Baye TM, Perry RT, Wiener HW, Chen Z, Harrell LE, Go RC Candidate gene discovery procedure after follow-up confirmatory analyses of candidate regions of interests for Alzheimer's disease in the NIMH sibling dataset. Dis Markers 24: 293-309. Human loci; Alzheimer's disease 18688078 13,16
2008 Befort K|etAl Mu-opioid receptor activation induces transcriptional plasticity in the central extended amygdala. Eur J Neurosci 27: 2973-2984. Mouse brain transcripts 18588537 7,16
2008 Beisswanger E, Lee V, Kim JJ, Rebholz-Schuhmann D, Splendiani A, Dameron O, Schulz S, Hahn U Gene Regulation Ontology (GRO): Design Principles and Use Cases. Stud Health Technol Inform 136: 9-14. 18487700 15
2008 Belleau F, Nolin MA, Tourigny N, Rigault P, Morissette J Bio2RDF: Towards a mashup to build bioinformatics knowledge systems. J Biomed Inform 41: 706-716. 18472304 10,15
2008 Berchtold NC|etAl Gene expression changes in the course of normal brain aging are sexually dimorphic. Proc Natl Acad Sci U S A 105: 15605-15610. Human brain transcripts; aging 18832152 7,16
2008 Bhasin JM, Chakrabarti E, Peng DQ, Kulkarni A, Chen X, Smith JD Sex specific gene regulation and expression QTLs in mouse macrophages from a strain intercross. PLoS ONE 3: e1435. Mouse transcripts 18197246 10.1371/journal.pone.0001435 7,13
2008 Bhati R|etAl Molecular characterization of human breast tumor vascular cells. Am J Pathol 172: 1381-1390. Human breast transcripts; breast cancer 18403594 7,16
2008 Biswas S, Storey JD, Akey JM Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis. BMC Bioinformatics 9: 244. 18492285 7,13
2008 Blake JA, Harris MA The Gene Ontology (GO) project: structured vocabularies for molecular biology and their application to genome and expression analysis. Curr Protoc Bioinformatics Chapter 7: Unit 7.2. 18819077 1,2
2008 Blauw HM|etAl Copy-number variation in sporadic amyotrophic lateral sclerosis: a genome-wide screen. Lancet Neurol 7: 319-326. Human genes; copy-number variants; amyotrophic lateral sclerosis 18313986 13,16,18
2008 Bluhm BH, Dhillon B, Lindquist EA, Kema GH, Goodwin SB, Dunkle LD Analyses of expressed sequence tags from the maize foliar pathogen Cercospora zeae-maydis identify novel genes expressed during vegetative, infectious, and reproductive growth. BMC Genomics 9: 523. Cercospora zeae-maydis ESTs 18983654 7
2008 Boden M, Bailey TL Associating transcription factor-binding site motifs with target GO terms and target genes. Nucleic Acids Res 36: 4108-4117. 18544606 7,19
2008 Bodenreider O Biomedical ontologies in action: role in knowledge management, data integration and decision support. Yearb Med Inform 2008: 67-79. 18660879 14
2008 Bogan RL, Murphy MJ, Hennebold JD Dynamic changes in gene expression that occur during the period of spontaneous functional regression in the rhesus macaque corpus luteum. Endocrinology 150: 1521-1529. Rhesus macaque corpus luteum transcripts 18948396 7,16
2008 Bogan RL, Murphy MJ, Stouffer RL, Hennebold JD Systematic determination of differential gene expression in the primate corpus luteum during the luteal phase of the menstrual cycle. Mol Endocrinol 22: 1260-1273. Rhesus macaque corpus luteum transcripts; menstrual cycle 18258683 7,16
2008 Bonifaci N, Berenguer A, Diez J, Reina O, Medina I, Dopazo J, Moreno V, Pujana MA Biological processes, properties and molecular wiring diagrams of candidate low-penetrance breast cancer susceptibility genes. BMC Med Genomics 1: 62. Human genes; breast cancer 19094230 13,16
2008 Bonow RH, Aid S, Zhang Y, Becker KG, Bosetti F The brain expression of genes involved in inflammatory response, the ribosome, and learning and memory is altered by centrally injected lipopolysaccharide in mice. Pharmacogenomics J 9: 116-126. Mouse brain transcripts; neuroinflammation 18957951 7,16
2008 Borges F, Gomes G, Gardner R, Moreno N, McCormick S, Feijo JA, Becker JD Comparative transcriptomics of Arabidopsis thaliana sperm cells. Plant Physiol 148: 1168-1181. Arabidopsis sperm cell transcripts 18667720 7
2008 Borkamo ED, Dahl O, Bruland O, Fluge O Global gene expression analyses reveal changes in biological processes after hyperthermia in a rat glioma model. Int J Hyperthermia 24: 425-441. Rat tumor transcripts; hyperthermia 18608572 7,16
2008 Boswell MG, Wells MC, Kirk LM, Ju Z, Zhang Z, Booth RE, Walter RB Comparison of gene expression responses to hypoxia in viviparous (Xiphophorus) and oviparous (Oryzias) fishes using a medaka microarray. Comp Biochem Physiol C Toxicol Pharmacol 149: 258-265. Medaka transcripts; Xiphophorus transcripts 19049829 7
2008 Botton A, Galla G, Conesa A, Bachem C, Ramina A, Barcaccia G Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology. BMC Genomics 9: 347. Plant ESTs 18652646 5
2008 Brehelin L, Dufayard JF, Gascuel O PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data. BMC Bioinformatics 9: 440. Plasmodium falciparum genes 18925948 3,9,11
2008 Brinkmeier ML, Davis SW, Carninci P, Macdonald JW, Kawai J, Ghosh D, Hayashizaki Y, Lyons RH, Camper SA Discovery of transcriptional regulators and signaling pathways in the developing pituitary gland by bioinformatic and genomic approaches. Genomics 93: 449-460. Human proteins; schizophrenia 19121383 8,16,17
2008 Bungay A, Selden C, Brown D, Malik R, Hubank M, Hodgson H Microarray analysis of mitogenic effects of T3 on the rat liver. J Gastroenterol Hepatol 23: 1926-1933. Rat liver transcripts; tri-iodothyronine treatment 18717759 7,16
2008 Burgio G|etAl Genetic identification of a network of factors that functionally interact with the nucleosome remodeling ATPase ISWI. PLoS Genet 4: e1000089. 10.1371/journal.pgen.1000089 18535655 13,17
2008 Burgoon LD, Zacharewski TR Automated quantitative dose response modeling and point of departure determination for large toxicogenomic and high throughput screening datasets. Toxicol Sci 104: 412-418. 18441342 7,10,13
2008 Burgoon LD, Zacharewski TR Bioinformatics: Databasing and gene annotation. Methods Mol Biol 460: 145-157. 18449486 11,14
2008 Buttner F, Cordes C, Gerlach F, Heimann A, Alessandri B, Luxemburger U, Tureci O, Hankeln T, Kempski O, Burmester T Genomic response of the rat brain to global ischemia and reperfusion. Brain Res 1252: 1-14. Rat brain transcripts; ischemia 19071098 7,16
2008 Buza TJ, McCarthy FM, Wang N, Bridges SM, Burgess SC Gene Ontology annotation quality analysis in model eukaryotes. Nucleic Acids Res 36: e12. 18187504 1,3,11
2008 Bye A, Hoydal MA, Catalucci D, Langaas M, Kemi OJ, Beisvag V, Koch LG, Britton SL, Ellingsen O, Wisloff U Gene expression profiling of skeletal muscle in exercise-trained and sedentary rats with inborn high and low VO2max. Physiol Genomics 35: 213-221. Rat muscle transcripts; oxygen uptake 18780757 7,16
2008 Bye A, Langaas M, Hoydal MA, Kemi OJ, Heinrich G, Koch LG, Britton SL, Najjar SM, Ellingsen O, Wisloff U Aerobic capacity-dependent differences in cardiac gene expression. Physiol Genomics 33: 100-109. Rat heart transcripts 18171719 7,16
2008 Cai S, Lashbrook CC Stamen abscission zone transcriptome profiling reveals new candidates for abscission control. Enhanced retention of floral organs in transgenic plants overexpressing Arabidopsis Zinc Finger Protein 2. Plant Physiol 146: 1305-1321. Arabidopsis stamen transcripts 18192438 7
2008 Cakmak A, Ozsoyoglu G Discovering gene annotations in biomedical text databases. BMC Bioinformatics 9: 143. 18325104 9,10,12
2008 Calin GA|etAl MiR-15a and miR-16-1 cluster functions in human leukemia. Proc Natl Acad Sci U S A 105: 5166-5171. Human microRNA; leukemia 18362358 7,16
2008 Calvanese V|etAl Cancer genes hypermethylated in human embryonic stem cells. PLoS ONE 3: e3294. Human genes; methylation; cancer 18820729 10.1371/journal.pone.0003294 7,13,16
2008 Cantacessi C, Loukas A, Campbell BE, Mulvenna J, Ong EK, Zhong W, Sternberg PW, Otranto D, Gasser RB Exploring transcriptional conservation between Ancylostoma caninum and Haemonchus contortus by oligonucleotide microarray and bioinformatic analyses. Mol Cell Probes 23: 1-9. Nematode transcripts 18977290 7,18
2008 Cao F|etAl Transcriptional and functional profiling of human embryonic stem cell-derived cardiomyocytes. PLoS ONE 3: e3474. Human cardiomyocyte transcripts 18941512 10.1371/journal.pone.0003474 7,16
2008 Cao R, He Q, Zhou J, He Q, Liu Z, Wang X, Chen P, Xie J, Liang S High-throughput analysis of rat liver plasma membrane proteome by a nonelectrophoretic in-gel tryptic digestion coupled with mass spectrometry identification. J Proteome Res 7: 535-545. Rat liver proteins 18166008 8
2008 Cervigni GD|etAl Expressed sequence tag analysis and development of gene associated markers in a near-isogenic plant system of Eragrostis curvula. Plant Mol Biol 67: 1-10. Eragrostis curvula ESTs 18196464 5
2008 Ceusters W Applying evolutionary terminology auditing to the Gene Ontology. J Biomed Inform 42: 518-529. 19162233 13
2008 Chan G, Bivins-Smith ER, Smith MS, Smith PM, Yurochko AD Transcriptome analysis reveals human cytomegalovirus reprograms monocyte differentiation toward an M1 macrophage. J Immunol 181: 698-711. Human monocyte transcripts; cytomegalovirus 18566437 7,16
2008 Chang DW|etAl Proteomic analysis of sequential lung lavage proteins during the acute respiratory distress syndrome. Am J Respir Crit Care Med 178: 701-709. Human lung proteins; acute respiratory distress syndrome 18658106 8,16
2008 Chang ML|etAl Altered expression patterns of lipid metabolism genes in an animal model of HCV core-related, nonobese, modest hepatic steatosis. BMC Genomics 9: 109. Mouse liver transcripts; nonobese hepatic steatosis 18307821 7,16
2008 Charoenphandhu N, Wongdee K, Teerapornpuntakit J, Thongchote K, Krishnamra N Transcriptome responses of duodenal epithelial cells to prolactin in pituitary-grafted rats. Mol Cell Endocrinol 296: 41-52. Rat duodenal epithelial transcripts 18951951 7
2008 Chen EI, McClatchy D, Park SK, Yates Iii JR Comparisons of mass spectrometry compatible surfactants for global analysis of the mammalian brain proteome. Anal Chem 80: 8694-8701. Rat brain proteins 18937422 8,16
2008 Chen H, Liu B, Lukas TJ, Neufeld AH The aged retinal pigment epithelium/choroid: a potential substratum for the pathogenesis of age-related macular degeneration. PLoS ONE 3: e2339. Mouse retinal transcripts 18523633 10.1371/journal.pone.0002339 7,16
2008 Chen J, Ryu S, Gharib SA, Goodlett DR, Schnapp LM Exploration of the normal human bronchoalveolar lavage fluid proteome. Proteomics Clin Appl 2: 585-595. 21136857 8,16
2008 Chen L, Zheng S Identify alternative splicing events based on position-specific evolutionary conservation. PLoS ONE 3: e2806. 18665247 10.1371/journal.pone.0002806 13,18
2008 Chen PY, Deane CM, Reinert G Predicting and validating protein interactions using network structure. PLoS Comput Biol 4: e1000118. 18654616 10.1371/journal.pcbi.1000118 8,17
2008 Chen SL, Sun YQ, Song JY, Li Y, Li CJ, Hu SN, Li XW, Yao H, Zhang XW [Analysis of expressed sequence tags (EST) from Panax quinquefolium root] Yao Xue Xue Bao 43: 657-663. Ginseng ESTs 18822972 7
2008 Chen X, Wang L, Smith JD, Zhang B Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes. Bioinformatics 24: 2474-2481. 18753155 7,10
2008 Chen XW, Liu M, Ward R Protein function assignment through mining cross-species protein-protein interactions. PLoS ONE 3: e1562. 18253506 10.1371/journal.pone.0001562 9,12
2008 Chen YH, Liu CK, Chang SC, Lin YJ, Tsai MF, Chen YT, Yao A GenoWatch: a disease gene mining browser for association study. Nucleic Acids Res 36: W336-340. 18440974 10
2008 Cheng KC, Stromvik MV SoyXpress: a database for exploring the soybean transcriptome. BMC Genomics 9: 368. Soybean ESTs 18671881 5,11
2008 Cheng KO, Law NF, Siu WC, Liew AW Identification of coherent patterns in gene expression data using an efficient biclustering algorithm and parallel coordinate visualization. BMC Bioinformatics 9: 210. 18433478 7,17
2008 Cheung F, Win J, Lang JM, Hamilton J, Vuong H, Leach JE, Kamoun S, Levesque CA, Tisserat N, Buell CR Analysis of the Pythium ultimum transcriptome using Sanger and Pyrosequencing approaches. BMC Genomics 9: 542. Pythium ultimum ESTs 19014603 5
2008 Cheviron ZA, Whitehead A, Brumfield RT Transcriptomic variation and plasticity in rufous-collared sparrows (Zonotrichia capensis) along an altitudinal gradient. Mol Ecol 17: 4556-4569. Sparrow muscle transcripts 18986500 7,18
2008 Cho H, Dhillon IS Coclustering of human cancer microarrays using Minimum Sum-Squared Residue coclustering. IEEE/ACM Trans Comput Biol Bioinform 5: 385-400. Human transcripts; cancer 18670042 7,16
2008 Cho YR, Shi L, Ramanathan M, Zhang A A probabilistic framework to predict protein function from interaction data integrated with semantic knowledge. BMC Bioinformatics 9: 382. 18801191 9
2008 Choi JK, Hwang S, Kim YJ Stochastic and regulatory role of chromatin silencing in genomic response to environmental changes. PLoS ONE 3: e3002. Yeast genes 18714342 7
2008 Choke E, Cockerill GW, Laing K, Dawson J, Wilson WR, Loftus IM, Thompson MM Whole genome-expression profiling reveals a role for immune and inflammatory response in abdominal aortic aneurysm rupture. Eur J Vasc Endovasc Surg 37: 305-310. Human transcripts; aortic aneurysm 19111481 7,16
2008 Christinat Y, Wachmann B, Zhang L Gene expression data analysis using a novel approach to biclustering combining discrete and continuous data. IEEE/ACM Trans Comput Biol Bioinform 5: 583-593. 18989045 7
2008 Cimino JJ, Hayamizu TF, Bodenreider O, Davis B, Stafford GA, Ringwald M The caBIG terminology review process. J Biomed Inform 42: 571-580. 19154797 14
2008 Cohen CD|etAl Improved elucidation of biological processes linked to diabetic nephropathy by single probe-based microarray data analysis. PLoS ONE 3: e2937. Human renal transcripts; diabetic nephropathy 18698414 7,16
2008 Cohen KB, Hunter L Getting started in text mining. PLoS Comput Biol 4: e20. 18225946 10.1371/journal.pcbi.0040020 12
2008 Collins JF, Hu Z, Ranganathan PN, Feng D, Garrick LM, Garrick MD, Browne RW Induction of arachidonate 12-lipoxygenase (Alox15) in intestine of iron-deficient rats correlates with production of biologically active lipid mediators. Am J Physiol Gastrointest Liver Physiol 294: G948-962. Rat intestinal transcripts; iron deficiency 18258795 7,16
2008 Conesa A, Goetz S Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics. Int J Plant Genomics 2008: 619832. 18483572 10
2008 Cook MA, Chan CK, Jorgensen P, Ketela T, So D, Tyers M, Ho CY Systematic validation and atomic force microscopy of non-covalent short oligonucleotide barcode microarrays. PLoS ONE 3: e1546. 18253494 10.1371/journal.pone.0001546 13
2008 Coulibaly I, Page GP Bioinformatic tools for inferring functional information from plant microarray data II: Analysis beyond single gene. Int J Plant Genomics 2008: 893941. 18615189 7,10
2008 Coussens M, Maresh JG, Yanagimachi R, Maeda G, Allsopp R Sirt1 deficiency attenuates spermatogenesis and germ cell function. PLoS ONE 3: e1571. Mouse germ line transcripts 18270565 10.1371/journal.pone.0001571 7,16
2008 Dail MB, Shack LA, Chambers JE, Burgess SC Global liver proteomics of rats exposed for five days to phenobarbital identifies changes associated with cancer and with Cyp metabolism. Toxicol Sci 106: 556-569. 18796496 1,3
2008 Danaher RJ, McGarrell BS, Stromberg AJ, Miller CS Herpes simplex virus type 1 modulates cellular gene expression during quiescent infection of neuronal cells. Arch Virol 153: 1335-1345. Rat neuronal cell line transcripts; HSV-i infection 18548318 7,16
2008 Datu BJ, Gasser RB, Nagaraj SH, Ong EK, O'Donoghue P, McInnes R, Ranganathan S, Loukas A Transcriptional changes in the hookworm, Ancylostoma caninum, during the transition from a free-living to a parasitic larva. PLoS Negl Trop Dis 2: e130. Canine hookworm ESTs 18235850 10.1371/journal.pntd.0000130 7
2008 Davis AP, Murphy CG, Rosenstein MC, Wiegers TC, Mattingly CJ The Comparative Toxicogenomics Database facilitates identification and understanding of chemical-gene-disease associations: arsenic as a case study. BMC Med Genomics 1: 48. 18845002 11,13,16,17
2008 Davis AP, Murphy CG, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Mattingly CJ Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks. Nucleic Acids Res 37: D786-792. 18782832 11
2008 Day RC, Herridge RP, Ambrose BA, Macknight RC Transcriptome analysis of proliferating arabidopsis endosperm reveals biological implications for the control of syncytial division, cytokinin signalling, and gene expression regulation. Plant Physiol 148: 1964-1984. Arabidopsis endosperm transcripts 18923020 7
2008 De Michele R|etAl Transcriptome analysis of Medicago truncatula leaf senescence: similarities and differences in metabolic and transcriptional regulations as compared with Arabidopsis, nodule senescence and nitric oxide signalling. New Phytol 181: 563-575. Medicago truncatula transcripts 19021865 7
2008 De Pitta C, Bertolucci C, Mazzotta GM, Bernante F, Rizzo G, De Nardi B, Pallavicini A, Lanfranchi G, Costa R Systematic sequencing of mRNA from the Antarctic krill (Euphausia superba) and first tissue specific transcriptional signature. BMC Genomics 9: 45. Krill ESTs 18226200 5,7
2008 De Preter K, Barriot R, Speleman F, Vandesompele J, Moreau Y Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions. Nucleic Acids Res 36: e43. 18346969 13
2008 De S, Lopez-Bigas N, Teichmann SA Patterns of evolutionary constraints on genes in humans. BMC Evol Biol 8: 275. 18840274 10,18
2008 Del Pozo A, Pazos F, Valencia A Defining functional distances over Gene Ontology. BMC Bioinformatics 9: 50. 18221506 12,13
2008 Demmer RT, Behle JH, Wolf DL, Handfield M, Kebschull M, Celenti R, Pavlidis P, Papapanou PN Transcriptomes in healthy and diseased gingival tissues. J Periodontol 79: 2112-2124. Human gingival transcripts; periodontitis 18980520 7,16
2008 Denaxas SC, Tjortjis C Scoring and summarising gene product clusters using the Gene Ontology. Int J Data Min Bioinform 2: 216-235. 19024495 12
2008 Depuydt S, Trenkamp S, Fernie AR, Elftieh S, Renou JP, Vuylsteke M, Holsters M, Vereecke D An integrated genomics approach to define niche establishment by Rhodococcus fascians. Plant Physiol 149: 1366-1386. Rhodococcus fascians transcripts 19118125 7
2008 Derambure C|etAl Genome-wide differences in hepatitis C- vs alcoholism-associated hepatocellular carcinoma. World J Gastroenterol 14: 1749-1758. Human liver transcripts; hepatitis C; hepatocellular carcinoma 18350606 7,16
2008 Desert C|etAl Transcriptome profiling of the feeding-to-fasting transition in chicken liver. BMC Genomics 9: 611. Chicken liver transcripts; starvation 19091074 7
2008 Devarajan K Nonnegative matrix factorization: an analytical and interpretive tool in computational biology. PLoS Comput Biol 4: e1000029. 18654623 10.1371/journal.pcbi.1000029 13
2008 Dezso Z|etAl A comprehensive functional analysis of tissue specificity of human gene expression. BMC Biol 6: 49. Human genes 19014478 7,16,17
2008 Diehl AD, Camon EB, Lovering RC Immunology on the GO Immunology News May 2008: 15-21. 1,3,16
2008 Dillon GP, Feltwell T, Skelton J, Coulson PS, Wilson RA, Ivens AC Altered patterns of gene expression underlying the enhanced immunogenicity of radiation-attenuated schistosomes. PLoS Negl Trop Dis 2: e240. 10.1371/journal.pntd.0000240 Schistosome cercariae transcripts 18493602 7,16
2008 Dimmer EC, Huntley RP, Barrell DG, Binns D, Draghici S, Camon EB, Hubank M, Talmud PJ, Apweiler R, Lovering RC The Gene Ontology - providing a functional role in proteomic studies. Proteomics epub 18634107 1,8
2008 Dinov ID|etAl iTools: a framework for classification, categorization and integration of computational biology resources. PLoS ONE 3: e2265. 18509477 10.1371/journal.pone.0002265 15
2008 Dinsdale EA|etAl Microbial ecology of four coral atolls in the Northern Line Islands. PLoS ONE 3: e1584. Microbial metagenomes 18301735 10.1371/journal.pone.0001584 13
2008 Diz AP, Dudley E, Macdonald BW, Pina B, Kenchington EL, Zouros E, Skibinski DO Genetic variation underlying protein expression in eggs of the marine mussel Mytilus edulis. Mol Cell Proteomics 8: 132-144. 18794572 8,17
2008 Doddapaneni H, Lin H, Walker MA, Yao J, Civerolo EL VitisExpDB: A database resource for grape functional genomics. BMC Plant Biol 8: 23. Grape ESTs 18307813 5,11
2008 Dolinay T, Wu W, Kaminski N, Ifedigbo E, Kaynar AM, Szilasi M, Watkins SC, Ryter SW, Hoetzel A, Choi AM Mitogen-activated protein kinases regulate susceptibility to ventilator-induced lung injury. PLoS ONE 3: e1601. Mouse lung transcripts 18270588 10.1371/journal.pone.0001601 7,16
2008 Dominguez F, Gadea B, Esteban FJ, Horcajadas JA, Pellicer A, Simon C Comparative protein-profile analysis of implanted versus non-implanted human blastocysts. Hum Reprod 23: 1993-2000. Human blasocyst proteins 18556682 8,16
2008 Dragin N, Shi Z, Madan R, Karp CL, Sartor MA, Chen C, Gonzalez FJ, Nebert D Phenotype of the Cyp1a1/1a2/1b1(-/-) Triple-Knockout Mouse. Mol Pharmacol 73: 1844-1856. Mouse transcripts 18372398 7,13
2008 Dudek P, Picard D Genomics of signaling crosstalk of estrogen receptor alpha in breast cancer cells. PLoS ONE 3: e1859. Human breast cancer cell transcripts 18365014 10.1371/journal.pone.0001859 7,16
2008 Durrens P, Nikolski M, Sherman D Fusion and fission of genes define a metric between fungal genomes. PLoS Comput Biol 4: e1000200. 18949021 10.1371/journal.pcbi.1000200 13,18
2008 Dusek JA, Otu HH, Wohlhueter AL, Bhasin M, Zerbini LF, Joseph MG, Benson H, Libermann TA Genomic counter-stress changes induced by the relaxation response. PLoS ONE 3: e2576. Human blood cell transcripts; relaxation response 18596974 10.1371/journal.pone.0002576 7,16
2008 Dyer MD, Murali TM, Sobral BW The landscape of human proteins interacting with viruses and other pathogens. PLoS Pathog 4: e32. Human proteins; host-pathogen interaction 18282095 10.1371/journal.ppat.0040032 8,13,16,17
2008 Edelman EJ, Guinney J, Chi JT, Febbo PG, Mukherjee S Modeling cancer progression via pathway dependencies. PLoS Comput Biol 4: e28. 18282083 10.1371/journal.pcbi.0040028 16,17
2008 Edelman EJ, Guinney J, Chi JT, Febbo PG, Mukherjee S Modeling cancer progression via pathway dependencies. PLoS Comput Biol 4: e28. Human genes; human pathways; cancer 18282083 10.1371/journal.pcbi.0040028 16,17
2008 Edwards YJ, Bryson K, Jones DT A meta-analysis of microarray gene expression in mouse stem cells: redefining stemness. PLoS ONE 3: e2712. Mouse stem cell transcripts 18628962 10.1371/journal.pone.0002712 7
2008 Ehlting J, Chowrira SG, Mattheus N, Aeschliman DS, Arimura GI, Bohlmann J Comparative transcriptome analysis of Arabidopsis thaliana infested by diamond back moth (Plutella xylostella) larvae reveals signatures of stress response, secondary metabolism, and signaling. BMC Genomics 9: 154. Arabidopsis transcripts 18400103 7
2008 Eilon T, Barash I Different gene-expression profiles for the poorly differentiated carcinoma and the highly differentiated papillary adenocarcinoma in mammary glands support distinct metabolic pathways. BMC Cancer 8: 270. Mouse mammary tumor transcripts 18811984 7,16
2008 Emes RD, Yang Z Duplicated paralogous genes subject to positive selection in the genome of Trypanosoma brucei. PLoS ONE 3: e2295. Trypanosoma brucei genes 18509460 10.1371/journal.pone.0002295 16,18
2008 Emmons J, Townley-Tilson WH, Deleault KM, Skinner SJ, Gross RH, Whitfield ML, Brooks SA Identification of TTP mRNA targets in human dendritic cells reveals TTP as a critical regulator of dendritic cell maturation. RNA 14: 888-902. Human dendritic cell transcripts 18367721 7,16
2008 Enomoto Y, Ushijima M, Miyata S, Matsuura M, Ohtaki M Inference on biological mechanisms using an integrated phenotype prediction model. Hiroshima J Med Sci 57: 7-15. 18578362 16,19
2008 Ericson E, Gebbia M, Heisler LE, Wildenhain J, Tyers M, Giaever G, Nislow C Off-target effects of psychoactive drugs revealed by genome-wide assays in yeast. PLoS Genet 4: e1000151. 18688276 10.1371/journal.pgen.1000151 13,16
2008 Ernst J, Beg QK, Kay KA, Balazsi G, Oltvai ZN, Bar-Joseph Z A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli. PLoS Comput Biol 4: e1000044. 18369434 10.1371/journal.pcbi.1000044 19
2008 Esteves E|etAl Cellular and molecular characterization of an embryonic cell line (BME26) from the tick Rhipicephalus (Boophilus) microplus. Insect Biochem Mol Biol 38: 568-580. Cattle tick mRNAs 18405834 3
2008 Ettinger NA, Wilson ME Macrophage and T-cell gene expression in a model of early infection with the protozoan Leishmania chagasi. PLoS Negl Trop Dis 2: e252. Human macrophage transcripts; leishmaniasis 18575603 10.1371/journal.pntd.0000252 7,16
2008 Evans H, Mello LV, Fang Y, Wit E, Thompson FJ, Viney ME, Paterson S Microarray analysis of gender- and parasite-specific gene transcription in Strongyloides ratti. Int J Parasitol 38: 1329-1341. Strongyloides ratti transcripts 18455172 7
2008 Farthing CR, Ficz G, Ng RK, Chan CF, Andrews S, Dean W, Hemberger M, Reik W Global mapping of DNA methylation in mouse promoters reveals epigenetic reprogramming of pluripotency genes. PLoS Genet 4: e1000116. Mouse genes; promoter methylation 18584034 10.1371/journal.pgen.1000116 7,13
2008 Fatima N, Yi M, Ajaz S, Stephens RM, Stauffer S, Greenwald P, Munroe DJ, Ali IU Altered gene expression profiles define pathways in colorectal cancer cell lines affected by celecoxib. Cancer Epidemiol Biomarkers Prev 17: 3051-3061. Human colorectal cancer cell transcripts; celecoxib treatment 18957522 7,16
2008 Faustino RS, Behfar A, Perez-Terzic C, Terzic A Genomic chart guiding embryonic stem cell cardiopoiesis. Genome Biol 9: R6. Mouse embryonic stem cell transcripts 18184438 7,16,17
2008 Fedorova ND|etAl Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genet 4: e1000046. Aspergillus clavatus; Aspergillus fumigatus; Neosartorya fischeri 18404212 10.1371/journal.pgen.1000046 4,18
2008 Fehrmann RS|etAl A new perspective on transcriptional system regulation (TSR): towards TSR profiling. PLoS ONE 3: e1656. 18297136 10.1371/journal.pone.0001656 7,17
2008 Fermin DR|etAl Sex and age dimorphism of myocardial gene expression in nonischemic human heart failure. Circ Cardiovasc Genet 1: 117-125. Human heart transcripts 20031553 7,16
2008 Fernandez-Suarez XM, Birney E Advanced genomic data mining. PLoS Comput Biol 4: e1000121. 18818719 10.1371/journal.pcbi.1000121 11,12
2008 Ferrada E, Wagner A Protein robustness promotes evolutionary innovations on large evolutionary time-scales. Proc Biol Sci 275: 1595-1602. 18430649 18
2008 Ferraz AL, Ojeda A, Lopez-Bejar M, Fernandes LT, Castello A, Folch JM, Perez-Enciso M Transcriptome architecture across tissues in the pig. BMC Genomics 9: 173. Pig transcripts 18416811 7,18
2008 Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, Lubling Y, Widom J, Segal E Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput Biol 4: e1000216. Saccharomyces genes 18989395 10.1371/journal.pcbi.1000216 7
2008 Finucane KA, McFadden TB, Bond JP, Kennelly JJ, Zhao FQ Onset of lactation in the bovine mammary gland: gene expression profiling indicates a strong inhibition of gene expression in cell proliferation. Funct Integr Genomics 8: 251-264. Bovine mammary transcripts; lactation 18259788 7,16
2008 Fitzpatrick JM, Protasio AV, McArdle AJ, Williams GA, Johnston DA, Hoffmann KF Use of genomic DNA as an indirect reference for identifying gender-associated transcripts in morphologically identical, but chromosomally distinct, Schistosoma mansoni cercariae. PLoS Negl Trop Dis 2: e323. Schistosoma mansoni transcripts 18941520 7,13
2008 Flores C, Pino-Yanes MD, Villar J A quality assessment of genetic association studies supporting susceptibility and outcome in acute lung injury. Crit Care 12: R130. 18950526 13,16
2008 Foley JW, Katagiri F Unsupervised reduction of random noise in complex data by a row-specific, sorted principal component-guided method. BMC Bioinformatics 9: 508. 19040754 7
2008 Forslund K, Sonnhammer EL Predicting protein function from domain content. Bioinformatics 24: 1681-1687. 18591194 9,10
2008 Forsyth NR, Kay A, Hampson K, Downing A, Talbot R, McWhir J Transcriptome alterations due to physiological normoxic (2% O2) culture of human embryonic stem cells. Regen Med 3: 817-833. Human embryonic stem cell transcripts; oxygen levels 18947306 7,16
2008 Forte A|etAl Injury to rat carotids causes time-dependent changes in gene expression in contralateral uninjured arteries. Clin Sci (Lond) 116: 125-136. Rat artery transcripts 18522534 7,16
2008 Francesconi M, Remondini D, Neretti N, Sedivy JM, Cooper LN, Verondini E, Milanesi L, Castellani G Reconstructing networks of pathways via significance analysis of their intersections. BMC Bioinformatics 9 Suppl 4: S9. 18460182 17
2008 Franssen EH, De Bree FM, Essing AH, Ramon-Cueto A, Verhaagen J Comparative gene expression profiling of olfactory ensheathing glia and Schwann cells indicates distinct tissue repair characteristics of olfactory ensheathing glia. Glia 56: 1285-1298. Rat brain transcripts; spinal cord injury 18615567 7,16
2008 Fredriksson K, Tjader I, Keller P, Petrovic N, Ahlman B, Scheele C, Wernerman J, Timmons JA, Rooyackers O Dysregulation of mitochondrial dynamics and the muscle transcriptome in ICU patients suffering from sepsis induced multiple organ failure. PLoS ONE 3: e3686. Human transcripts 18997871 10.1371/journal.pone.0003686 7,16
2008 Fu S|etAl Peripheral arterial occlusive disease: global gene expression analyses suggest a major role for immune and inflammatory responses. BMC Genomics 9: 369. Human artery transcripts; peripheral arterial disease 18673543 7,16
2008 Fuhrken PG, Chen C, Apostolidis PA, Wang M, Miller WM, Papoutsakis ET Gene-Ontology driven transcriptional analysis of CD34+-cell initiated megakaryocytic cultures identifies new transcriptional regulators of megakaryopoiesis. Physiol Genomics 33: 159-169. Human blood cell transcripts; megakaryopoiesis 18252802 7,16
2008 Fushimi K|etAl Susceptible genes and molecular pathways related to heavy ion irradiation in oral squamous cell carcinoma cells. Radiother Oncol 89: 237-244. Human oral squamous cell carcinoma cell transcripts 18514338 7,16
2008 Fyshe A, Liu Y, Szafron D, Greiner R, Lu P Improving subcellular localization prediction using text classification and the Gene Ontology. Bioinformatics 24: 2512-2517. 18728042 9,12
2008 Galamb O, Sipos F, Dinya E, Spisak S, Somoracz A, Molnar B, Tulassay Z [Functional mRNA expression analysis and classification of colonic biopsy samples using overall cDNA microarray technique.] Orv Hetil 149: 219-232. Human colon biopsy transcripts 18218589 7,16
2008 Galea CA|etAl Large-scale analysis of thermostable, mammalian proteins provides insights into the intrinsically disordered proteome. J Proteome Res 8: 211-226. Mouse fibroblast proteins 19067583 8
2008 Galgano A, Forrer M, Jaskiewicz L, Kanitz A, Zavolan M, Gerber AP Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system. PLoS ONE 3: e3164. Human genes 18776931 10.1371/journal.pone.0003164 7
2008 Gamalielsson J, Olsson B GOSAP: Gene Ontology-based semantic alignment of biological pathways. Int J Bioinform Res Appl 4: 274-294. 18640904 17
2008 Gamalielsson J, Olsson B Gene ontology-based semantic alignment of biological pathways by evolutionary search. J Bioinform Comput Biol 6: 825-842. 18763745 17,18
2008 Gao Z, Barth AS, Disilvestre D, Akar FG, Tian Y, Tanskanen A, Kass DA, Winslow RL, Tomaselli GF Key pathways associated with heart failure development revealed by gene networks correlated with cardiac remodeling. Physiol Genomics 35: 222-230. Canine heart transcripts; heart failure 18780759 7,16
2008 Gaudan S, Jimeno Yepes A, Lee V, Rebholz-Schuhmann D Combining evidence, specificity, and proximity towards the normalization of Gene Ontology terms in text. EURASIP J Bioinform Syst Biol 2008: 342746 18437221 12
2008 Gaudet P, Williams JG, Fey P, Chisholm RL An anatomy ontology to represent biological knowledge in Dictyostelium discoideum. BMC Genomics 9: 130. 18366659 1,15
2008 Gelineau-van Waes J, Maddox JR, Smith LM, van Waes M, Wilberding J, Eudy JD, Bauer LK, Finnell RH Microarray analysis of E9.5 reduced folate carrier (RFC1; Slc19a1) knockout embryos reveals altered expression of genes in the cubilin-megalin multiligand endocytic receptor complex. BMC Genomics 9: 156. Mouse embryonic transcripts 18400109 7
2008 Genini S, Malinverni R, Delputte PL, Fiorentini S, Stella A, Botti S, Nauwynck HJ, Giuffra E Gene expression profiling of porcine alveolar macrophages after antibody-mediated cross-linking of sialoadhesin (sn, siglec-1). J Recept Signal Transduct Res 28: 185-243. Porcine macrophage transcripts 18569525 7
2008 Gennarino VA, Sardiello M, Avellino R, Meola N, Maselli V, Anand S, Cutillo L, Ballabio A, Banfi S MicroRNA target prediction by expression analysis of host genes. Genome Res 19: 481-490. Human miRNA targets 19088304 7,19
2008 Gerecke DR, Chen M, Isukapalli SS, Gordon MK, Chang YC, Tong W, Androulakis IP, Georgopoulos PG Differential gene expression profiling of mouse skin after sulfur mustard exposure: Extended time response and inhibitor effect. Toxicol Appl Pharmacol 234: 156-165. Mouse skin transcripts; sulfur mustard exposure 18955075 7,16
2008 Ghandhi SA, Yaghoubian B, Amundson SA Global gene expression analyses of bystander and alpha particle irradiated normal human lung fibroblasts: Synchronous and differential responses. BMC Med Genomics 1: 63. Human lung transcripts; radiation exposure 19108712 7,16
2008 Ghouila A, Yahia SB, Malouche D, Jmel H, Laouini D, Guerfali FZ, Abdelhak S Application of Multi-SOM clustering approach to macrophage gene expression analysis. Infect Genet Evol 9: 328-336. Human macrophage transcripts 18992849 7,16
2008 Giefing M|etAl Identification of candidate tumour suppressor gene loci for Hodgkin and Reed-Sternberg cells by characterisation of homozygous deletions in classical Hodgkin lymphoma cell lines. Br J Haematol 142: 916-924. Human tumor suppressor genes; Hodgkin lymphoma 18671701 13,16
2008 Glazov EA, McWilliam S, Barris WC, Dalrymple BP Origin, evolution and biological role of miRNA cluster in DLK-DIO3 genomic region in placental mammals. Mol Biol Evol 25: 939-948. 18281269 18
2008 Gmeiner WH, Hellmann GM, Shen P Tissue-dependent and -independent gene expression changes in metastatic colon cancer. Oncol Rep 19: 245-251. Human colon transcripts; colon cancer 18097602 7,16
2008 Gnad F, Oroshi M, Birney E, Mann M MAPU 2.0: high-accuracy proteomes mapped to genomes. Nucleic Acids Res 37: D902-906. 18948283 8,11
2008 Gobeill J, Tbahriti I, Ehrler F, Mottaz A, Veuthey AL, Ruch P Gene Ontology density estimation and discourse analysis for automatic GeneRiF extraction. BMC Bioinformatics 9 Suppl 3: S9. 18426554 12
2008 Goeman JJ, Mansmann U Multiple testing on the directed acyclic graph of gene ontology. Bioinformatics 24: 537-544. 18203773 7,10
2008 Goetz S, Garcia-Gomez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talon M, Dopazo J, Conesa A High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36: 3420-3435. 18445632 3,10
2008 Gong Y, Wang N, Wu F, Cass CE, Damaraju S, Mackey JR, Li L Proteome profile of human breast cancer tissue generated by LC-ESI-MS/MS combined with sequential protein precipitation and solubilization. J Proteome Res 7: 3583-3590. Human breast proteins; breast cancer 18576677 8,16
2008 Gonzales JM, Patel JJ, Ponmee N, Jiang L, Tan A, Maher SP, Wuchty S, Rathod PK, Ferdig MT Regulatory hotspots in the malaria parasite genome dictate transcriptional variation. PLoS Biol 6: e238. Plasmodium falciparum transcripts 18828674 10.1371/journal.pbio.0060238 7
2008 Gonzalez J, Lenkov K, Lipatov M, Macpherson JM, Petrov DA High rate of recent transposable element-induced adaptation in Drosophila melanogaster. PLoS Biol 6: e251. 18942889 10.1371/journal.pbio.0060251 18
2008 Goo YA, Liu AY, Ryu S, Shaffer SA, Malmstrom L, Page L, Nguyen LT, Doneanu CE, Goodlett DR Identification of secreted glycoproteins of human prostate and bladder stromal cells by comparative quantitative proteomics. Prostate 69: 49-61. Human secreted proteins 18792917 8,16
2008 Greco D, Somervuo P, Di Lieto A, Raitila T, Nitsch L, Castren E, Auvinen P Physiology, pathology and relatedness of human tissues from gene expression meta-analysis. PLoS ONE 3: e1880. Human transcripts 18382664 10.1371/journal.pone.0001880 7,13,16
2008 Grigoryev DN|etAl Identification of candidate genes in scleroderma-related pulmonary arterial hypertension. Transl Res 151: 197-207. Human blood cell transcripts; hypertension 18355767 7,16
2008 Groth P, Weiss B, Pohlenz HD, Leser U Mining phenotypes for gene function prediction. BMC Bioinformatics 9: 136. 18315868 9,12
2008 Guan Y, Myers CL, Hess DC, Barutcuoglu Z, Caudy AA, Troyanskaya OG Predicting gene function in a hierarchical context with an ensemble of classifiers. Genome Biol 9 Suppl 1: S3. 18613947 9,12,17
2008 Guan Y, Myers CL, Lu R, Lemischka IR, Bult CJ, Troyanskaya OG A genomewide functional network for the laboratory mouse. PLoS Comput Biol 4: e1000165. 18818725 10.1371/journal.pcbi.1000165 17,18,19
2008 Guerrero FD, Wang M, Nene VM, Dowd SE, Saldivar L EST-based gene indices for the cattle fever tick, the horn fly, and the screwworm fly. Dev Biol (Basel) 132: 115-120. Cattle pest ESTs 18817293 5
2008 Guimaraes PE|etAl DNA polymorphisms as tools for spinal cord injury research. Spinal Cord 47: 171-175. 18504448 13,16,17
2008 Guo Y|etAl How is mRNA expression predictive for protein expression? A correlation study on human circulating monocytes. Acta Biochim Biophys Sin (Shanghai) 40: 426-436. Human monocyte transcripts and proteins 18465028 7,8,16,19
2008 Gusev Y Computational methods for analysis of cellular functions and pathways collectively targeted by differentially expressed microRNA. Methods 44: 61-72. 18158134 9,13
2008 Gustin MP, Paultre CZ, Randon J, Bricca G, Cerutti C Functional meta-analysis of double connectivity in gene co-expression networks in mammals. Physiol Genomics 34: 34-41. Mammalian transcripts 18430810 7,17
2008 Haddad R, Romero R, Gould BR, Tromp G, Gotsch F, Edwin SS, Zingg HH Angiogenesis gene expression in mouse uterus during the common pathway of parturition. Am J Obstet Gynecol 198: 539.e1-8. Mouse uterine transcripts 18455529 7
2008 Han S, Kim D Inference of protein complex activities from chemical-genetic profile and its applications: predicting drug-target pathways. PLoS Comput Biol 4: e1000162. 18769708 10.1371/journal.pcbi.1000162 8,17,19
2008 Hanada K, Zou C, Lehti-Shiu MD, Shinozaki K, Shiu SH Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol 148: 993-991003. Arabidopsis duplicated genes 18715958 7,18
2008 Harris MA Developing an ontology. Methods Mol Biol 452: 111-124. 18563371 1,14
2008 Harris MA, Feltrin E Browsing and searching Gene Ontology resources using AmiGO. EMBnet News 14: 17-21. 1,2
2008 Hawkins T, Chitale M, Luban S, Kihara D PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data. Proteins 74: 566-582. 18655063 9
2008 Hegde A|etAl Genomewide expression analysis in zebrafish mind bomb alleles with pancreas defects of different severity identifies putative Notch responsive genes. PLoS ONE 3: e1479. Zebrafish transcripts 18213387 10.1371/journal.pone.0001479 7
2008 Hendrickson DG, Hogan DJ, Herschlag D, Ferrell JE, Brown PO Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance. PLoS ONE 3: e2126. Human kidney cell line transcripts 18461144 10.1371/journal.pone.0002126 7,16
2008 Hendrickson EL, Lamont RJ, Hackett M Tools for interpreting large-scale protein profiling in microbiology. J Dent Res 87: 1004-1015. 18946006 8,10,14
2008 Herve C, Dabos P, Bardet C, Jauneau A, Auriac MC, Ramboer A, Lacout F, Tremousaygue D In vivo interference with AtTCP20 function induces severe plant growth alterations and deregulates the expression of many genes important for development. Plant Physiol 149: 1462-1477. Arabidopsis transcripts 19091878 7
2008 Hill DP, Smith B, McAndrews-Hill MS, Blake JA Gene Ontology annotations: what they mean and where they come from. BMC Bioinformatics 9 Suppl 5: S2. 18460184 1,3
2008 Hipp JA, Hipp JD, Yoo JJ, Atala A, Andersson KE Microarray analysis of bladder smooth muscle from patients with myelomeningocele. BJU Int 102: 741-746. Human bladder transcripts; myelomeningocele 18336610 7,16
2008 Hirschman L, Clark C, Cohen KB, Mardis S, Luciano J, Kottmann R, Cole J, Markowitz V, Kyrpides N, Field D Habitat-Lite: A GSC Case Study Based on Free Text Terms for Environmental Metadata. OMICS 12: 129-136. 18416669 15
2008 Hobo T|etAl Various spatiotemporal expression profiles of anther-expressed genes in rice. Plant Cell Physiol 49: 1417-1428. Rice anther transcripts 18776202 7
2008 Hogan DJ, Riordan DP, Gerber AP, Herschlag D, Brown PO Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol 6: e255. Saccharomyces genes 18959479 10.1371/journal.pbio.0060255 7
2008 Hong MG, Myers AJ, Magnusson PK, Prince JA Transcriptome-wide assessment of human brain and lymphocyte senescence. PLoS ONE 3: e3024. 10.1371/journal.pone.0003024 Human brain transcripts; human lymphocyte transcripts 18714388 7,16
2008 Horan K, Jang C, Bailey-Serres J, Mittler R, Shelton C, Harper JF, Zhu JK, Cushman JJ, Gollery M, Girke T Annotating genes of known and unknown function by large-scale co-expression analysis. Plant Physiol 147: 41-57. Arabidopsis genes 18354039 7,9,11
2008 Horvath DP, Chao WS, Suttle JC, Thimmapuram J, Anderson JV Transcriptome analysis identifies novel responses and potential regulatory genes involved in seasonal dormancy transitions of leafy spurge (Euphorbia esula L.). BMC Genomics 9: 536. Leafy spurge transcripts 19014493 7
2008 Horvath S, Dong J Geometric interpretation of gene coexpression network analysis. PLoS Comput Biol 4: e1000117. 17 18704157 7
2008 Hosgood HD|etAl Pathway-based evaluation of 380 candidate genes and lung cancer susceptibility suggests the importance of the cell cycle pathway. Carcinogenesis 29: 1938-1943. Human SNPs; lung cancer 18676680 13,16,17
2008 Hovav R, Udall JA, Chaudhary B, Hovav E, Flagel L, Hu G, Wendel JF The evolution of spinnable cotton fiber entailed prolonged development and a novel metabolism. PLoS Genet 4: e25. Cotton transcripts 18248099 10.1371/journal.pgen.0040025 7,17
2008 Hsing M, Byler KG, Cherkasov A The use of Gene Ontology terms for predicting highly-connected 'hub' nodes in protein-protein interaction networks. BMC Syst Biol 2: 80. 18796161 9,10
2008 Hsu PC, Yang UC, Shih KH, Liu CM, Liu YL, Hwu HG A protein interaction based model for schizophrenia study. BMC Bioinformatics 9 Suppl 12: S23. 19091023 8,16,17
2008 Hu J, Barlet X, Deslandes L, Hirsch J, Feng DX, Somssich I, Marco Y Transcriptional responses of Arabidopsis thaliana during wilt disease caused by the soil-borne phytopathogenic bacterium, Ralstonia solanacearum. PLoS ONE 3: e2589. 3002 Arabidopsis transcripts 18596930 7
2008 Hu Y, Jian X, Peng J, Jiang X, Li N, Zhou S Gene expression profiling of oral submucous fibrosis using oligonucleotide microarray. Oncol Rep 20: 287-294. Human oral tissue transcripts; oral submucous fibrosis 18636188 7,16
2008 Hu YJ, Jian XC, Liu BJ, Peng JY [Application of bioinformatics tools in analysis of differentially expressed genes in oral submucosal fibrosis] Zhonghua Kou Qiang Yi Xue Za Zhi 43: 168-171. Human genes; oral submucous fibrosis 18788553 7,16
2008 Huang CQ|etAl Genomic-bioinformatic analysis of transcripts enriched in the third-stage larva of the parasitic nematode Ascaris suum. PLoS Negl Trop Dis 2: e246. Ascaris ESTs 18560474 5,7
2008 Huang JC, Frey BJ, Morris QD Comparing sequence and expression for predicting microRNA targets using GenMiR3. Pac Symp Biocomput 2008: 52-63. 18229676 19
2008 Huang WL, Tung CW, Ho SW, Hwang SF, Ho SY ProLoc-GO: Utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization. BMC Bioinformatics 9: 80. 18241343 9,10,19
2008 Huang X, Wang JY, Lu X Systems analysis of quantitative shRNA-library screens identifies regulators of cell adhesion. BMC Syst Biol 2: 49. 18549508 13
2008 Hunter L, Lu Z, Firby J, Baumgartner WA, Johnson HL, Ogren PV, Cohen KB OpenDMAP: An open-source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-specific gene expression. BMC Bioinformatics 9: 78. 18237434 10,12,15
2008 Hunter MP|etAl Detection of microRNA expression in human peripheral blood microvesicles. PLoS ONE 3: e3694. Human blood miRNAs 19002258 10.1371/journal.pone.0003694 7,16
2008 Idaghdour Y, Storey JD, Jadallah SJ, Gibson G A genome-wide gene expression signature of environmental geography in leukocytes of Moroccan Amazighs. PLoS Genet 4: e1000052. Human leukocyte transcripts 18404217 10.1371/journal.pgen.1000052 7,18
2008 Illingworth R|etAl A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol 6: e22. Human genes; CpG islands 18232738 7,13
2008 Inamura K, Togashi Y, Ninomiya H, Shimoji T, Noda T, Ishikawa Y HOXB2, an adverse prognostic indicator for stage I lung adenocarcinomas, promotes invasion by transcriptional regulation of metastasis-related genes in HOP-62 non-small cell lung cancer cells. Anticancer Res 28: 2121-2127. Human lung cancer cell transcripts; lung adenocarcinoma 18751384 7,13,16
2008 Irmler M, Hartl D, Schmidt T, Schuchhardt J, Lach C, Meyer HE, Hrabe de Angelis M, Klose J, Beckers J An approach to handling and interpretation of ambiguous data in transcriptome and proteome comparisons. Proteomics 8: 1165-1169. Mouse brain transcripts; mouse brain proteins 18283664 7,8
2008 Ishikawa S|etAl Abnormal expression of the genes involved in cytokine networks and mitochondrial function in systemic juvenile idiopathic arthritis identified by DNA maicroarray analysis. Ann Rheum Dis 68: 264-272. Human leukocyte transcripts; arthritis 18388159 7,16
2008 Izadpanah R, Kaushal D, Kriedt C, Tsien F, Patel B, Dufour J, Bunnell BA Long-term in vitro expansion alters the biology of adult mesenchymal stem cells. Cancer Res 68: 4229-4238. Human stem cell transcripts; rhesus macaque stem cell transcripts 18519682 7,16
2008 Jancek S, Gourbiere S, Moreau H, Piganeau G Clues about the genetic basis of adaptation emerge from comparing the proteomes of two Ostreococcus ecotypes (Chlorophyta, Prasinophyceae). Mol Biol Evol 25: 2293-2300. 18678753 8,18
2008 Jarvinen AP, Hiissa J, Elo LL, Aittokallio T Predicting quantitative genetic interactions by means of sequential matrix approximation. PLoS ONE 3: e3284. 18818762 10.1371/journal.pone.0003284 13,19
2008 Jaulent MC, Grabar N, Hamon T Combination of endogenous clues for profiling inferred semantic relations: experiments with Gene Ontology. AMIA Annu Symp Proc 2008: 252-256. 18999042 12,13
2008 Jelier R, 't Hoen PA, Sterrenburg E, den Dunnen JT, van Ommen GJ, Kors JA, Mons B Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease. BMC Bioinformatics 9: 291. 18577208 7,12
2008 Jelier R, Schuemie MJ, Veldhoven A, Dorssers LC, Jenster G, Kors JA Anni 2.0: a multipurpose text-mining tool for the life sciences. Genome Biol 9: R96. 18549479 10,12
2008 Jia SQ, Niu ZJ, Zhang LH, Zhong XY, Shi T, Du H, Zhang GG, Hu Y, Su XL, Ji JF Identification of prognosis-related proteins in advanced gastric cancer by mass spectrometry-based comparative proteomics. J Cancer Res Clin Oncol 135: 403-411. Human gastric proteins; stomach cancer 18830628 8,16
2008 Jiang H, Patel JJ, Yi M, Mu J, Ding J, Stephens R, Cooper RA, Ferdig MT, Su XZ Genome-wide compensatory changes accompany drug- selected mutations in the Plasmodium falciparum crt gene. PLoS ONE 3: e2484. Plasmodium falciparum transcripts 18575593 10.1371/journal.pone.0002484 7,16
2008 Jiang W, Li X, Rao S, Wang L, Du L, Li C, Wu C, Wang H, Wang Y, Yang B Constructing disease-specific gene networks using pair-wise relevance metric: application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements. BMC Syst Biol 2: 72. Human disease genes 18691435 7,16,17
2008 Jiang X, Nariai N, Steffen M, Kasif S, Kolaczyk ED Integration of relational and hierarchical network information for protein function prediction. BMC Bioinformatics 9: 350. 18721473 9
2008 Jimeno A, Jimenez-Ruiz E, Lee V, Gaudan S, Berlanga R, Rebholz-Schuhmann D Assessment of disease named entity recognition on a corpus of annotated sentences. BMC Bioinformatics 9 Suppl 3: S3. 18426548 12
2008 Jin B, Muller B, Zhai C, Lu X Multi-label literature classification based on the Gene Ontology graph. BMC Bioinformatics 9: 525. 19063730 10,12
2008 Jin H, Vacic V, Girke T, Lonardi S, Zhu JK Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis. BMC Mol Biol 9: 6. Arabidopsis antisense transcripts 18194570 7,13
2008 Jin R, Si L, Chan C A Bayesian framework for knowledge driven regression model in micro-array data analysis. Int J Data Min Bioinform 2: 250-267. 19024497 7
2008 Jin YH, Dunlap PE, McBride SJ, Al-Refai H, Bushel PR, Freedman JH Global transcriptome and deletome profiles of yeast exposed to transition metals. PLoS Genet 4: e1000053. Saccharomyces genes; Saccharomyces transcripts 18437200 7,13
2008 Johannessen TC, Wang J, Skaftnesmo KO, Sakariassen PO, Enger PO, Petersen K, Oyan AM, Kalland KH, Bjerkvig R, Tysnes BB Highly infiltrative brain tumours show reduced chemosensitivity associated with a stem cell-like phenotype. Neuropathol Appl Neurobiol 35: 380-393. Human brain tumor transcripts 19508445 7,16
2008 Johnson R|etAl REST regulates distinct transcriptional networks in embryonic and neural stem cells. PLoS Biol 6: e256. Mouse embryonic stem cell genes 18959480 10.1371/journal.pbio.0060256 7
2008 Jones CE, Schwerdt J, Bretag TA, Baumann U, Brown AL GOSLING: a rule-based protein annotator using BLAST and GO. Bioinformatics 24: 2628-2629. Rat liver proteins; phenobarbital exposure 18796479 8,16
2008 Jung KH|etAl Identification and functional analysis of light-responsive unique genes and gene family members in rice. PLoS Genet 4: e1000164. Rice genes; rice transcripts 18725934 10.1371/journal.pgen.1000164 7,13,17
2008 Jung KH|etAl Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy. PLoS ONE 3: e3337. Rice transcripts; rice ESTs 18836531 10.1371/journal.pone.0003337 7,11,18
2008 Jupiter DC, VanBuren V A visual data mining tool that facilitates reconstruction of transcription regulatory networks. PLoS ONE 3: e1717. 18320038 10.1371/journal.pone.0001717 7,10,17
2008 Kaiser P|etAl Integrated immunogenomics in the chicken: deciphering the immune response to identify disease resistance genes. Dev Biol (Basel) 132: 57-66. Chicken SNPs; chicken QTLs; immune system 18817286 13,16,18
2008 Kanistanon D|etAl A Francisella mutant in lipid A carbohydrate modification elicits protective immunity. PLoS Pathog 4: e24. Francisella genes; tularemia 18266468 10.1371/journal.ppat.0040024 13,16
2008 Karuppasamy M, Pal D, Suryanarayanarao R, Brener NE, Iyengar SS, Seetharaman G Functionally important segments in proteins dissected using Gene Ontology and geometric clustering of peptide fragments. Genome Biol 9: R52. 18331637 13
2008 Kasabov N, Jain V, Benuskova L Integrating evolving brain-gene ontology and connectionist-based system for modeling and knowledge discovery. Neural Netw 21: 266-275. 18343308 13
2008 Kausch U, Alberti M, Haindl S, Budczies J, Hock B Biomarkers for exposure to estrogenic compounds: Gene expression analysis in zebrafish (Danio rerio). Environ Toxicol 23: 15-24. Zebrafish liver transcripts; estrogen exposure 18214933 7
2008 Kawaura K, Mochida K, Ogihara Y Genome-wide analysis for identification of salt-responsive genes in common wheat. Funct Integr Genomics 8: 277-286. Wheat transcripts 18320247 7
2008 Kemmer D, Podowski RM, Yusuf D, Brumm J, Cheung W, Wahlestedt C, Lenhard B, Wasserman WW Gene characterization index: assessing the depth of gene annotation. PLoS ONE 3: e1440. 18213364 10.1371/journal.pone.0001440 13
2008 Keseler IM|etAl EcoCyc: A comprehensive view of Escherichia coli biology. Nucleic Acids Res 37: D464-470. E. coli genome; metabolic pathways 18974181 3,11,17
2008 Kestler HA, Muller A, Kraus JM, Buchholz M, Gress TM, Liu H, Kane DW, Zeeberg BR, Weinstein JN VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays. BMC Bioinformatics 9: 67. 18230172 7,10
2008 Khaladkar M, Liu J, Wen D, Wang JT, Tian B Mining small RNA structure elements in untranslated regions of human and mouse mRNAs using structure-based alignment. BMC Genomics 9: 189. Human mRNAs; mouse mRNAs 18439287 12,13
2008 Khan RL, Vadigepalli R, McDonald MK, Rogers RF, Gao GR, Schwaber JS Dynamic transcriptomic response to acute hypertension in the nucleus tractus solitarius. Am J Physiol Regul Integr Comp Physiol 295: R15-27. Rat brain genes; acute hypertension 18434436 7,16
2008 Killion PJ, Iyer VR ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets. Genome Biol 9: R159. 19014503 10
2008 Kim CH, Lillehoj HS, Hong YH, Keeler CL Comparison of transcriptional changes associated with E. acervulina and E. maxima infections using cDNA microarray technology. Dev Biol (Basel) 132: 121-130. Avian lymphocyte transcripts; Eimeria infection 18817294 7
2008 Kim CS Self-Organizing Maps with Statistical Phase Synchronization (SOMPS) for analyzing cell cycle-specific gene expression data. Stat Appl Genet Mol Biol 7: Article1. Saccharomyces genes; cell cycle 18241191 7,17
2008 Kim CS, Bae CS, Tcha HJ A phase synchronization clustering algorithm for identifying interesting groups of genes from cell cycle expression data. BMC Bioinformatics 9: 56. 18221564 7,17
2008 Kim HJ, Baek KH, Lee SW, Kim J, Lee BW, Cho HS, Kim WT, Choi D, Hur CG Pepper EST database: comprehensive in silico tool for analyzing the chili pepper (Capsicum annuum) transcriptome. BMC Plant Biol 8: 101. Chili pepper ESTs 18844979 5,11
2008 Kim SY, Kim YS A gene sets approach for identifying prognostic gene signatures for outcome prediction. BMC Genomics 9: 177. Human transcripts; breast cancer 18416850 7,16,19
2008 Kim WK, Krumpelman C, Marcotte EM Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy. Genome Biol 9 Suppl 1: S5. 18613949 9,12,17
2008 Kitamura H, Ito M, Yuasa T, Kikuguchi C, Hijikata A, Takayama M, Kimura Y, Yokoyama R, Kaji T, Ohara O Genome-wide identification and characterization of transcripts translationally regulated by bacterial lipopolysaccharide in macrophage-like J774.1 cells. Physiol Genomics 33: 121-132. Mouse cell line transcripts; E. coli LPS 18230670 7,16
2008 Kitsou E|etAl Identification of proteins in human substantia nigra. Proteomics Clin Appl 2: 776-782. 21136874 8,16
2008 Kliebenstein DJ A role for gene duplication and natural variation of gene expression in the evolution of metabolism. PLoS ONE 3: e1838. 18350173 10.1371/journal.pone.0001838 18
2008 Kloosterman B|etAl Genes driving potato tuber initiation and growth: identification based on transcriptional changes using the POCI array. Funct Integr Genomics 8: 329-340. Potato ESTs; potato transcripts 18504629 5,7
2008 Koehn J|etAl Potential involvement of MYC- and p53-related pathways in tumorigenesis in human oral squamous cell carcinoma revealed by proteomic analysis. J Proteome Res 7: 3818-3829. Human oral tissue transcripts; oral squamous cell carcinoma 18700792 7,16
2008 Kolmakov NN, Kube M, Reinhardt R, Canario AV Analysis of the goldfish Carassius auratus olfactory epithelium transcriptome reveals the presence of numerous non-olfactory GPCR and putative receptors for progestin pheromones. BMC Genomics 9: 429. Goldfish ESTs 18803863 5,7
2008 Kosiol C, Vinar T, da Fonseca RR, Hubisz MJ, Bustamante CD, Nielsen R, Siepel A Patterns of positive selection in six Mammalian genomes. PLoS Genet 4: e1000144. 18670650 10.1371/journal.pgen.1000144 18
2008 Koudritsky M, Domany E Positional distribution of human transcription factor binding sites. Nucleic Acids Res 36: 6795-6805. 18953043 7,13
2008 Krens SF, Corredor-Adamez M, He S, Snaar-Jagalska BE, Spaink HP ERK1 and ERK2 MAPK are key regulators of distinct gene sets in zebrafish embryogenesis. BMC Genomics 9: 196. Zebrafish transcripts 18442396 7
2008 Krischek B|etAl Network-based gene expression analysis of intracranial aneurysm tissue reveals role of antigen presenting cells. Neuroscience 154: 1398-1407. Human artery transcripts; intracranial aneurysm 18538937 7,16
2008 Krishnan K, Salomonis N, Guo S Identification of Spt5 target genes in zebrafish development reveals its dual activity in vivo. PLoS ONE 3: e3621. Zebrafish genes 18978947 10.1371/journal.pone.0003621 7
2008 Krom N, Ramakrishna W Comparative analysis of divergent and convergent gene pairs and their expression patterns in rice, Arabidopsis, and Populus. Plant Physiol 147: 1763-1773. Plant genes 18515639 7,18
2008 Ku M|etAl Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet 4: e1000242. Human embryonic stem cell genes; mouse embryonic stem cell genes 18974828 10.1371/journal.pgen.1000242 7,16
2008 Kundaje A, Xin X, Lan C, Lianoglou S, Zhou M, Zhang L, Leslie C A predictive model of the oxygen and heme regulatory network in yeast. PLoS Comput Biol 4: e1000224. Saccharomyces genes 19008939 10.1371/journal.pcbi.1000224 7,17
2008 Kuper CF, Heijne WH, Dansen M, Verhoeckx KC, Boorsma A, Radonjic M, Bruijntjes J, Stierum R, Muijser H, Arts JH Molecular characterization of trimellitic anhydride-induced respiratory allergy in Brown Norway rats. Toxicol Pathol 36: 985-998. Ant ESTs 19126793 5,11
2008 Kwong C, Adryan B, Bell I, Meadows L, Russell S, Manak JR, White R Stability and dynamics of polycomb target sites in Drosophila development. PLoS Genet 4: e1000178. Drosophila genes 18773083 10.1371/journal.pgen.1000178 7
2008 Lalonde J, Lachance PE, Chaudhuri A Developmental and activity-dependent genomic occupancy profiles of CREB in monkey area V1. Genes Brain Behav 8: 149-160. Monkey brain genes 19016891 7,16
2008 Lam HY, Khurana E, Fang G, Cayting P, Carriero N, Cheung KH, Gerstein MB Pseudofam: the pseudogene families database. Nucleic Acids Res 37: D738-743. 18957444 15
2008 Landi MT|etAl Gene expression signature of cigarette smoking and its role in lung adenocarcinoma development and survival. PLoS ONE 3: e1651. Human lung transcripts; lung cancer; cigarette smoke 18297132 10.1371/journal.pone.0001651 7,16
2008 Landi MT|etAl Gene expression signature of cigarette smoking and its role in lung adenocarcinoma development and survival. PLoS ONE 3: e1651. Human lung transcripts; smoking; adenocarcinoma 18297132 10.1371/journal.pone.0001651 7,16
2008 Landry J|etAl Essential role of chromatin remodeling protein Bptf in early mouse embryos and embryonic stem cells. PLoS Genet 4: e1000241. Mouse embryonic transcripts 18974875 10.1371/journal.pgen.1000241 7
2008 Langlais D, Couture C, Balsalobre A, Drouin J Regulatory network analyses reveal genome-wide potentiation of LIF signaling by glucocorticoids and define an innate cell defense response. PLoS Genet 4: e1000224. Mouse pituitary transcripts 18927629 10.1371/journal.pgen.1000224 7,13,17
2008 Larsson O, Diebold D, Fan D, Peterson M, Nho RS, Bitterman PB, Henke CA Fibrotic myofibroblasts manifest genome-wide derangements of translational control. PLoS ONE 3: e3220. Human myofibroblast transcript translation 18795102 10.1371/journal.pone.0003220 7,16
2008 Lasonder E|etAl Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity. PLoS Pathog 4: e1000195. Plasmodium proteins 18974882 10.1371/journal.ppat.1000195 8,16
2008 Law PJ, Claudel-Renard C, Joubert F, Louw AI, Berger DK MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters. BMC Genomics 9: 105. 18307768 7,10,11
2008 Le Bechec A, Zindy P, Sierocinski T, Petritis D, Bihouee A, Le Meur N, Leger J, Theret N M@IA: A modular open-source application for microarray workflow and integrative datamining. In Silico Biol 8: 63-69. 18430991 7,10
2008 Le Roch KG|etAl A systematic approach to understand the mechanism of action of the bisthiazolium compound T4 on the human malaria parasite, Plasmodium falciparum. BMC Genomics 9: 513. Plasmodium falciparum transcripts 18973684 7,16
2008 Lee B, Brown K, Hathout Y, Seo J GOTreePlus: An Interactive Gene Ontology Browser for Proteomics Projects. Bioinformatics 24: 1026-1028. 18292113 8,10
2008 Lee KH, Yu DH, Lee YS Gene expression profiling of rat cerebral cortex development using cDNA microarrays. Neurochem Res 34: 1030-1038. Rat brain transcripts 18987971 7
2008 Lee S, Sayin A, Grice S, Burdett H, Baban D, van den Heuvel M Genome-wide expression analysis of a spinal muscular atrophy model: towards discovery of new drug targets. PLoS ONE 3: e1404. Drosophila transcripts 18167563 10.1371/journal.pone.0001404 7,16
2008 Lee T, Desai VG, Velasco C, Reis RJ, Delongchamp RR Testing for treatment effects on gene ontology. BMC Bioinformatics 9 Suppl 9: S20. Human transcripts; breast cancer; bevacizumab treatment 18793466 7,16
2008 Lemieux C, Cloutier I, Tanguay JF Estrogen-induced gene expression in bone marrow c-kit+ stem cells and stromal cells: identification of specific biological processes involved in the functional organization of the stem cell niche. Stem Cells Dev 17: 1153-1163. 19006456 7,16
2008 Leng W, Liu T, Li R, Yang J, Wei C, Zhang W, Jin Q Proteomic profile of dormant Trichophyton rubrum conidia. BMC Genomics 9: 303. Trichophyton rubrum proteins 18578874 8,16
2008 Lenka SK, Lohia B, Kumar A, Chinnusamy V, Bansal KC Genome-wide targeted prediction of ABA responsive genes in rice based on over-represented cis-motif in co-expressed genes. Plant Mol Biol 69: 261-271. Rice genes 18998058 7,17
2008 Lesnick TG, Sorenson EJ, Ahlskog JE, Henley JR, Shehadeh L, Papapetropoulos S, Maraganore DM Beyond Parkinson disease: amyotrophic lateral sclerosis and the axon guidance pathway. PLoS ONE 3: e1449. 18197259 10.1371/journal.pone.0001449 13,16
2008 Levy SF, Siegal ML Network hubs buffer environmental variation in Saccharomyces cerevisiae. PLoS Biol 6: e264. 18986213 10.1371/journal.pbio.0060264 13,17
2008 Li CY, Liu QR, Zhang PW, Li XM, Wei L, Uhl GR OKCAM: an ontology-based, human-centered knowledgebase for cell adhesion molecules. Nucleic Acids Res 37: D251-260. 18790807 11
2008 Li CY, Mao X, Wei L Genes and (common) pathways underlying drug addiction. PLoS Comput Biol 4: e2. Human genes; human pathways; drug addiction 18179280 10.1371/journal.pcbi.0040002 11,16,17
2008 Li JZ, Pan HY, Zheng JW, Zhou XJ, Zhang P, Chen WT, Zhang ZY Benzo (a) pyrene induced tumorigenesity of human immortalized oral epithelial cells: transcription profiling. Chin Med J (Engl) 121: 1882-1890. Human epithelial cell line transcripts; benzo(a)pyrene exposure 19080118 7,16
2008 Li L, Wu C, Huang H, Zhang K, Gan J, Li SS Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach. Nucleic Acids Res 36: 3263-3273. 18424801 10,17,19
2008 Li Q, Li YL, Li W, Yang XY, Wang YM, Li YL [Analysis of human normal prostate cells membrane proteins by shotgun-MS coupled with laser capture microdissection] Zhonghua Yi Xue Za Zhi 88: 158-161. Human prostate proteins 18361810 8,16
2008 Li SJ, Peng M, Li H, Liu BS, Wang C, Wu JR, Li YX, Zeng R Sys-BodyFluid: a systematical database for human body fluid proteome research. Nucleic Acids Res 37: D907-912. Human proteins 18978022 8,11
2008 Li S|etAl Assessment of diet-induced obese rats as an obesity model by comparative functional genomics. Obesity (Silver Spring) 16: 811-818. Rat fat tissue transcripts; obesity 18239588 7,16
2008 Li XY|etAl Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol 6: e27. Drosophila blastoderm promoters 18271625 10.1371/journal.pbio.0060027 7
2008 Li Y, Guo Z, Peng C, Liu Q, Ma W, Wang J, Yao C, Zhang M, Zhu J Identifying cancer genes from cancer mutation profiles by cancer functions. Sci China C Life Sci 51: 569-574. 18488178 16,19
2008 Li Y, Zhu Y, Liu Y, Shu Y, Meng F, Lu Y, Bai X, Liu B, Guo D Genome-wide identification of osmotic stress response gene in Arabidopsis thaliana. Genomics 92: 488-493. Arabidopsis transcripts; osmotic stress 18804526 7,17
2008 Liang H, Plazonic KR, Chen J, Li WH, Fernandez A Protein under-wrapping causes dosage sensitivity and decreases gene duplicability. PLoS Genet 4: e11. 18208334 0.1371/journal.pgen.0040011 18
2008 Liang Y An expression meta-analysis of predicted microRNA targets identifies a diagnostic signature for lung cancer. BMC Med Genomics 1: 61. Human lung genes; miRNA targets; lung cancer 19087325 7,16
2008 Liao ZJ, Ma WL, Meng W, Liang S, Meng FY, Zheng WL [Effect of Velcade on the gene expression profiles of K562 cells: study of its molecular mechanism.] Nan Fang Yi Ke Da Xue Xue Bao 28: 373-376. Human cell line transcripts; bortezomib treatment 18359694 7,16
2008 Lildballe DL, Pedersen DS, Kalamajka R, Emmersen J, Houben A, Grasser KD The expression level of the chromatin-associated HMGB1 protein influences growth, stress tolerance, and transcriptome in Arabidopsis. J Mol Biol 384: 9-21. Arabidopsis transcripts; HMGB1 18822296 7
2008 Lin H, Ouyang S, Egan A, Nobuta K, Haas B, Zhu W, Gu X, Silva JC, Meyers BC, Buell CR Characterization of paralogous protein families in rice. BMC Plant Biol 8: 18. 18284697 18
2008 Lin MF, Deoras AN, Rasmussen MD, Kellis M Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes. PLoS Comput Biol 4: e1000067. Drosophila genes 18421375 10.1371/journal.pcbi.1000067 13
2008 Lin MK, Lee YJ, Lough TJ, Phinney BS, Lucas WJ Analysis of the pumpkin phloem proteome provides functional insights into angiosperm sieve tube function. Mol Cell Proteomics 8: 343-356. Pumpkin phloem proteins 18936055 8
2008 Liu B, Pop M ARDB--Antibiotic Resistance Genes Database. Nucleic Acids Res 37: D443-447. 18832362 15
2008 Liu F, Chen P, Cui SJ, Wang ZQ, Han ZG SjTPdb: integrated transcriptome and proteome database and analysis platform for Schistosoma japonicum. BMC Genomics 9: 304. 18578888 7,8,11
2008 Liu H, Li X, Yoon V, Clarke R Annotating breast cancer microarray samples using ontologies. AMIA Annu Symp Proc 2008: 414-418. 18999108 15
2008 Liu MG, Li H, Xu X, Barnstable CJ, Zhang SS Comparison of gene expression during in vivo and in vitro postnatal retina development. J Ocul Biol Dis Infor 1: 59-72. Mouse retinal transcripts 20072636 7
2008 Lo L, Zhang Z, Hong N, Peng J, Hong Y 3640 Unique EST clusters from the medaka testis and their potential use for identifying conserved testicular gene expression in fish and mammals. PLoS ONE 3: e3915. Medaka testis ESTs 19104663 5,7,18
2008 Lobley AE, Nugent T, Orengo CA, Jones DT FFPred: an integrated feature-based function prediction server for vertebrate proteomes. Nucleic Acids Res 36: W297-302. 18463141 3,10
2008 Lockyer AE, Spinks J, Kane RA, Hoffmann KF, Fitzpatrick JM, Rollinson D, Noble LR, Jones CS Biomphalaria glabrata transcriptome: cDNA microarray profiling identifies resistant- and susceptible-specific gene expression in haemocytes from snail strains exposed to Schistosoma mansoni. BMC Genomics 9: 634. Biomphalaria glabrata transcripts 19114004 7,16
2008 Loerch PM, Lu T, Dakin KA, Vann JM, Isaacs A, Geula C, Wang J, Pan Y, Gabuzda DH, Li C, Prolla TA, Yankner BA Evolution of the aging brain transcriptome and synaptic regulation. PLoS ONE 3: e3329. Mammalian brain transcipts; aging 18830410 7,16
2008 Loire E, Praz F, Higuet D, Netter P, Achaz G Hypermutability of genes in Homo sapiens due to the hosting of long mono-SSR. Mol Biol Evol 26: 111-121. 18845548 18
2008 Lotito L, Russo A, Bueno S, Chillemi G, Fogli MV, Capranico G A specific transcriptional response of yeast cells to camptothecin dependent on the Swi4 and Mbp1 factors. Eur J Pharmacol 603: 29-36. Saccharomyces transcripts 19094980 7
2008 Lovas A, Radke D, Albrecht D, Yilmaz BZ, Moeller U, Habenicht AJ, Weih F Differential RelA- and RelB-dependent gene transcription in LTbetaR-stimulated mouse embryonic fibroblasts. BMC Genomics 9: 606. Mouse fibroblast transcripts 19087315 7
2008 Lovegrove FE, Gharib SA, Pena-Castillo L, Patel SN, Ruzinski JT, Hughes TR, Liles WC, Kain KC Parasite burden and CD36-mediated sequestration are determinants of acute lung injury in an experimental malaria model. PLoS Pathog 4: e1000068. Mouse lung transcripts; malaria 18483551 10.1371/journal.ppat.1000068 7,16
2008 Lovell PV, Clayton DF, Replogle KL, Mello CV Birdsong "transcriptomics": neurochemical specializations of the oscine song system. PLoS ONE 3: e3440. Zebra finch transcripts 18941504 10.1371/journal.pone.0003440 7
2008 Lovering RC, Camon EB, Blake JA, Diehl AD Access to immunology through the Gene Ontology. Immunology 125: 154-160. Mouse liver genes; acrylamide exposure 18798919 7,16
2008 Lovering RC, Dimmer E, Khodiyar VK, Barrell DG, Scambler P, Hubank M, Apweiler R, Talmud PJ Cardiovascular GO annotation initiative year 1 report: why cardiovascular GO? Proteomics 8: 1950-1953. 18491309 1,3,16
2008 Lovering RC, Dimmer EC, Talmud PJ Improvements to cardiovascular Gene Ontology. Atherosclerosis 205: 9-14. 19046747 1,3,16
2008 Low ET, Alias H, Boon SH, Shariff EM, Tan CY, Ooi LC, Cheah SC, Raha AR, Wan KL, Singh R Oil palm (Elaeis guineensis Jacq.) tissue culture ESTs: Identifying genes associated with callogenesis and embryogenesis. BMC Plant Biol 8: 62. Oil palm ESTs 18507865 5,7
2008 Lu D|etAl IPEP: An in silico tool to examine proteolytic peptides for mass spectrometry. Bioinformatics 24: 2801-2802. 18842605 8,10
2008 Lu X, Bao X, Huang Y, Qu Y, Lu H, Lu Z Mechanisms of cytotoxicity of nickel ions based on gene expression profiles. Biomaterials 30: 141-148. Mouse fibroblast transcripts; nickel exposure 18922574 7,16
2008 Lu Y, Rosenfeld R, Simon I, Nau GJ, Bar-Joseph Z A probabilistic generative model for GO enrichment analysis. Nucleic Acids Res 36: e109. 18676451 7,13
2008 Lukas TJ, Miao H, Chen L, Riordan SM, Li W, Crabb AM, Wise A, Du P, Lin SM, Hernandez MR Susceptibility to glaucoma: differential comparison of the astrocyte transcriptome from glaucomatous African American and Caucasian American donors. Genome Biol 9: R111. Human astrocyte transcripts; glaucoma 18613964 7,16
2008 Luo D, Hu W, Chen S, Xiao Y, Sun Y, Zhu Z Identification of differentially expressed genes between cloned and zygote-developing zebrafish (Danio rerio) embryos at the dome stage using suppression subtractive hybridization. Biol Reprod 80: 674-684. Zebrafish embryonic genes 19092113 7
2008 Ma J, Skibbe DS, Fernandes J, Walbot V Male reproductive development: gene expression profiling of maize anther and pollen ontogeny. Genome Biol 9: R181. Maize anther transcripts; maize pollen transcripts 19099579 7
2008 Ma LJ, Tian YQ, Xiao JY, Li W, Zhang H, Zhang X, Huang DH [Global gene expression profiling of laryngeal squamous cell carcinoma by laser capture microdissection and complementary DNA microarrays] Zhonghua Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 43: 696-700. Human transcripts; laryngeal cancer 19035265 7,16
2008 Ma X, Tarone AM, Li W Mapping genetically compensatory pathways from synthetic lethal interactions in yeast. PLoS ONE 3: e1922. 18398455 10.1371/journal.pone.0001922 17
2008 Ma XJ, Yin HJ, Chen KJ [Investigation of gene expression profiles in patients with blood stasis syndrome.] Zhong Xi Yi Jie He Xue Bao 6: 355-360. Human blood cell transcripts; blood stasis syndrome 18405601 7,16
2008 Mahller YY, Sakthivel B, Baird WH, Aronow BJ, Hsu YH, Cripe TP, Mehrian-Shai R Molecular analysis of human cancer cells infected by an oncolytic HSV-1 reveals multiple upregulated cellular genes and a role for SOCS1 in virus replication. Cancer Gene Ther 15: 733-741. Human cancer cell transcripts 18551144 7,16
2008 Malaspina A, Jokic N, Huang WL, Priestley JV Comparative analysis of the time-dependent functional and molecular changes in spinal cord degeneration induced by the G93A SOD1 gene mutation and by mechanical compression. BMC Genomics 9: 500. Rat spinal cord transcripts; cortico-spinal degeneration 18947433 7,16
2008 Malik MR, Wang F, Dirpaul JM, Zhou N, Hammerlindl J, Keller W, Abrams SR, Ferrie AM, Krochko JE Isolation of an embryogenic line from non-embryogenic Brassica napus cv. Westar through microspore embryogenesis. J Exp Bot 59: 2857-2873. Brassica napus transcripts 18552352 7
2008 Maluf DG, Mas VR, Archer KJ, Yanek K, Gibney EM, King AL, Cotterell A, Fisher RA, Posner MP Molecular pathways involved in loss of kidney graft function with tubular atrophy and interstitial fibrosis. Mol Med 14: 276-285. Human kidney transcripts 18286166 7,16
2008 Maningat PD, Sen P, Rijnkels M, Sunehag AL, Hadsell DL, Bray MS, Haymond MW Gene expression in the human mammary epithelium during lactation: the milk fat globule transcriptome. Physiol Genomics 37: 12-22. Human milk transcripts 19018045 7,16
2008 Mank JE, Hultin-Rosenberg L, Webster MT, Ellegren H The unique genomic properties of sex-biased genes: Insights from avian microarray data. BMC Genomics 9: 148. Chicken transcripts 18377635 7,13
2008 Maouche S, Poirier O, Godefroy T, Olaso R, Gut I, Collet JP, Montalescot G, Cambien F Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells. BMC Genomics 9: 302. 18578872 7,16
2008 Marko NF, Toms SA, Barnett GH, Weil R Genomic expression patterns distinguish long-term from short-term glioblastoma survivors: A preliminary feasibility study. Genomics 91: 395-406. Human brain transcripts; glioblastoma 18343632 7,16
2008 Marshall AM, Pai VP, Sartor MA, Horseman ND In vitro multipotent differentiation and barrier function of a human mammary epithelium. Cell Tissue Res 335: 383-395. Human mammary epithelial cell transcripts 19005683 7,16
2008 Martin J, Abubucker S, Wylie T, Yin Y, Wang Z, Mitreva M Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics. Nucleic Acids Res 37: D571-578. 18940860 5,11
2008 Martinez-Godoy MA, Mauri N, Juarez J, Marques MC, Santiago J, Forment J, Gadea J A genome-wide 20K citrus microarray for gene expression analysis. BMC Genomics 9: 318. Citrus genes 18598343 3,7,11
2008 Martinovic D, Villeneuve DL, Kahl MD, Blake LS, Brodin JD, Ankley GT Hypoxia alters gene expression in the gonads of zebrafish (Danio rerio). Aquat Toxicol 95: 258-272. Zebrafish gonad transcripts 18977541 7
2008 Mas VR|etAl Gene expression patterns in deceased donor kidneys developing delayed graft function after kidney transplantation. Transplantation 85: 626-635. Human kidney transcripts; kidney transplant 18347543 7,16
2008 McDonagh A|etAl Sub-telomere directed gene expression during initiation of invasive aspergillosis. PLoS Pathog 4: e1000154. Aspergillus transcripts 18787699 10.1371/journal.ppat.1000154 7,16,18
2008 McDunn JE|etAl Plasticity of the systemic inflammatory response to acute infection during critical illness: development of the riboleukogram. PLoS ONE 3: e1564. Mouse leukocyte transcripts; intratracheal bacterial infection 18270561 10.1371/journal.pone.0001564 7,16
2008 McKellar CE, Shatz CJ Synaptogenesis in purified cortical subplate neurons. Cereb Cortex 19: 1723-1737. Rat neuron transcripts 19029062 7
2008 Mei N, Guo L, Tseng J, Dial SL, Liao W, Manjanatha MG Gene expression changes associated with xenobiotic metabolism pathways in mice exposed to acrylamide. Environ Mol Mutagen 49: 741-745. Mouse liver transcripts; acrylamide exposure 18800343 7,16
2008 Meier S, Bastian R, Donaldson L, Murray S, Bajic V, Gehring C Co-expression and promoter content analyses assign a role in biotic and abiotic stress responses to plant natriuretic peptides. BMC Plant Biol 8: 24. Arabidopsis transcripts; natriuretic peptides 18307823 7
2008 Meier S, Gehring C A guide to the integrated application of on-line data mining tools for the inference of gene functions at the systems level. Biotechnol J 3: 1375-1387. 18830970 7,12,17
2008 Menges M, Doczi R, Okresz L, Morandini P, Mizzi L, Soloviev M, Murray JA, Bogre L Comprehensive gene expression atlas for the Arabidopsis MAP kinase signalling pathways. New Phytol 179: 643-662. Arabidopsis transcripts 18715324 7
2008 Miao H|etAl Gene expression and functional studies of the optic nerve head astrocyte transcriptome from normal african americans and caucasian americans donors. PLoS ONE 3: e2847. Human astrocyte transcripts; glaucoma 18716680 10.1371/journal.pone.0002847 7,16
2008 Michael S, Trave G, Ramu C, Chica C, Gibson TJ Discovery of candidate KEN box motifs using Cell Cycle keyword enrichment combined with native disorder prediction and motif conservation. Bioinformatics 24: 453-457. 18184688 12,13
2008 Michael TP|etAl Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules. PLoS Genet 4: e14. Arabidopsis transcripts; circadian regulation 18248097 10.1371/journal.pgen.0040014 7
2008 Milano A, Pendergrass SA, Sargent JL, George LK, McCalmont TH, Connolly MK, Whitfield ML Molecular subsets in the gene expression signatures of scleroderma skin. PLoS ONE 3: e2696. Human skin transcripts 18648520 10.1371/journal.pone.0002696 7,16
2008 Mill J|etAl Epigenomic profiling reveals DNA-methylation changes associated with major psychosis. Am J Hum Genet 82: 696-711. Human genes; methylation; major psychosis 18319075 7,13,16
2008 Miller RA, Christoforou N, Pevsner J, McCallion AS, Gearhart JD Efficient array-based identification of novel cardiac genes through differentiation of mouse ESCs. PLoS ONE 3: e2176. Mouse transcripts 18478100 10.1371/journal.pone.0002176 7,16
2008 Miozzi L, Piro RM, Rosa F, Ala U, Silengo L, Di Cunto F, Provero P Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data. PLoS ONE 3: e2439. Human transcripts 18560577 10.1371/journal.pone.0002439 7,9,16,19
2008 Mistry M, Pavlidis P Gene Ontology term overlap as a measure of gene functional similarity. BMC Bioinformatics 9: 327. 18680592 13,19
2008 Mitko K, Ulbrich SE, Wenigerkind H, Sinowatz F, Blum H, Wolf E, Bauersachs S Dynamic changes in messenger RNA profiles of bovine endometrium during the oestrous cycle: Focus on Mammalian Embryogenomics. Reproduction 135: 225-240. Bovine endometrial transcripts 18239051 7
2008 Miyama M, Tada Y Transcriptional and physiological study of the response of Burma mangrove (Bruguiera gymnorhiza) to salt and osmotic stress. Plant Mol Biol 68: 119-129. Mangrove transcripts; osmotic stress 18568404 7
2008 Miyazaki K|etAl Gene expression profiling of diffuse large B-cell lymphoma supervised by CD21 expression. Br J Haematol 142: 562-570. Human B cell transcripts; diffuse large B-cell lymphoma 18537973 7,16
2008 Monaci P|etAl Differential screening of phage-ab libraries by oligonucleotide microarray technology. PLoS ONE 3: e1508. 18231595 10.1371/journal.pone.0001508 13,16
2008 Monsellier E, Ramazzotti M, Taddei N, Chiti F Aggregation propensity of the human proteome. PLoS Comput Biol 4: e1000199. Human proteins 18927604 10.1371/journal.pcbi.1000199 8,16
2008 Moore NH, Costa LG, Shaffer SA, Goodlett DR, Guizzetti M Shotgun proteomics implicates extracellular matrix proteins and protease systems in neuronal development induced by astrocyte cholinergic stimulation. J Neurochem 108: 891-908. Rat astrocyte proteins 19077055 8
2008 Moreno Y, Geary TG Stage- and gender-specific proteomic analysis of Brugia malayi excretory-secretory products. PLoS Negl Trop Dis 2: e326. Brugia malayi proteins 18958170 8,16
2008 Mori R, Xiong S, Wang Q, Tarabolous C, Shimada H, Panteris E, Danenberg KD, Danenberg PV, Pinski JK Gene profiling and pathway analysis of neuroendocrine transdifferentiated prostate cancer cells. Prostate 69: 12-23. Neuroendocrine cell line transcripts; prostate cancer 18814146 7,16,17
2008 Morozova O, Morozov V, Hoffman BG, Helgason CD, Marra MA A seriation approach for visualization-driven discovery of co-expression patterns in Serial Analysis of Gene Expression (SAGE) data. PLoS ONE 3: e3205. 18787709 10.1371/journal.pone.0003205 7
2008 Morris RT, O'Connor TR, Wyrick JJ Osiris: an integrated promoter database for Oryza sativa L. Bioinformatics 24: 2915-2917. Rice transcription factors 18922805 7,11,17
2008 Motoyama K|etAl Isolation stress for 30 days alters hepatic gene expression profiles, especially with reference to lipid metabolism in mice. Physiol Genomics 37: 79-87. Mouse liver transcripts; isolation stress 19106182 7,16
2008 Moustafa A, Reyes-Prieto A, Bhattacharya D Chlamydiae has contributed at least 55 genes to Plantae with predominantly plastid functions. PLoS ONE 3: e2205. 18493612 10.1371/journal.pone.0002205 18
2008 Musen M, Shah N, Noy N, Dai B, Dorf M, Griffith N, Buntrock JD, Jonquet C, Montegut MJ, Rubin DL BioPortal: Ontologies and data resources with the click of a mouse. AMIA Annu Symp Proc 2008: 1223-1224. 18999306 15
2008 Musgrove EA|etAl Identification of functional networks of estrogen- and c-Myc-responsive genes and their relationship to response to tamoxifen therapy in breast cancer. PLoS ONE 3: e2987. Human breast cancer cell line transcripts 18714337 10.1371/journal.pone.0002987 7,16
2008 Nagaraj SH, Gasser RB, Ranganathan S Needles in the EST haystack: Large-scale identification and analysis of excretory-secretory (ES) proteins in parasitic nematodes using expressed sequence tags (ESTs). PLoS Negl Trop Dis 2: e301. Parasitic nematode ESTs 18820748 5,13
2008 Nakai Y, Hashida H, Kadota K, Minami M, Shimizu K, Matsumoto I, Kato H, Abe K Up-regulation of genes related to the ubiquitin-proteasome system in the brown adipose tissue of 24-h-fasted rats. Biosci Biotechnol Biochem 72: 139-148. Rat adipose tissue transcripts; rat liver transcripts 18175912 7,16
2008 Nakazato T, Takinaka T, Mizuguchi H, Matsuda H, Bono H, Asogawa M BioCompass: A novel functional inference tool that utilizes MeSH hierarchy to analyze groups of genes. In Silico Biol 8: 53-61. 18430990 10
2008 Nan Y, Yang S, Tian Y, Zhang W, Zhou B, Bu L, Huo S Analysis of the expression protein profiles of lung squamous carcinoma cell using shot-gun proteomics strategy. Med Oncol 26: 215-221. Human lung proteins; lung cancer 18988000 8,16
2008 Nanni L, Lumini A Combing ontologies and dipeptide composition for predicting DNA-binding proteins. Amino Acids 34: 635-641. 18175049 19
2008 Newman JC, Bailey AD, Fan HY, Pavelitz T, Weiner AM An abundant evolutionarily conserved CSB-PiggyBac fusion protein expressed in Cockayne syndrome. PLoS Genet 4: e1000031. Primate genes; Cockayne syndrome 18369450 10.1371/journal.pgen.1000031 13,16,18
2008 Ngoka LC Dramatic down-regulation of oxidoreductases in human hepatocellular carcinoma hepG2 cells: proteomics and gene ontology unveiling new frontiers in cancer enzymology. Proteome Sci 6: 29. Human hepatocellular carcinoma cell proteins; liver cancer 18950483 8,16
2008 Ngoka LC Sample prep for proteomics of breast cancer: proteomics and gene ontology reveal dramatic differences in protein solubilization preferences of radioimmunoprecipitation assay and urea lysis buffers. Proteome Sci 6: 30. Human breast proteins 18950484 8,16
2008 Nguyen C, Mannino M, Gardiner K, Cios KJ ClusFCM: An algorithm for predicting protein functions using homologies and protein interactions. J Bioinform Comput Biol 6: 203-222. 18324753 9,10
2008 Niu H, Zhang Y, Jiang H, Cheng B, Sun G, Wang Y, E Y, Pang D, Chang J Differences in shotgun protein expression profile between superficial bladder transitional cell carcinoma and normal urothelium. Urol Oncol 27: 400-406. Human bladder proteins; bladder cancer 18818109 8,16
2008 Niu W, Li Z, Zhan W, Iyer VR, Marcotte EM Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in S. cerevisiae. PLoS Genet 4: e1000120. Saccharomyces genes 18617996 10.1371/journal.pgen.1000120 13,17
2008 Noel S, Sharma S, Shankar R, Rath SK Identification of differentially expressed genes after acute exposure to bulaquine (CDRI 80/53) in mice liver. Basic Clin Pharmacol Toxicol 103: 522-529. Mouse liver transcripts; plasmodium infection; bulaquine treatment 18684221 7,16
2008 Nota B, Timmermans MJ, Franken O, Montagne-Wajer K, Marien J, De Boer ME, De Boer TE, Ylstra B, Van Straalen NM, Roelofs D Gene expression analysis of collembola in cadmium containing soil. Environ Sci Technol 42: 8152-8157. Folsomia candida transcripts 19031917 7
2008 Nygren JM, Bryder D A novel assay to trace proliferation history in vivo reveals that enhanced divisional kinetics accompany loss of hematopoietic stem cell self-renewal. PLoS ONE 3: e3710. Mouse hematopoietic cell transcripts 19002266 10.1371/journal.pone.0003710 7,16
2008 O'Neill K, Garcia A, Schwegmann A, Jimenez R, Jacobson D, Hermjakob H OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology. BMC Bioinformatics 9: 437. 18925933 10
2008 Obozinski G, Lanckriet G, Grant C, Jordan MI, Noble WS Consistent probabilistic outputs for protein function prediction. Genome Biol 9 Suppl 1: S6. 18613950 9,12,17
2008 Oh SJ|etAl Cell cycle and immune-related processes are significantly altered in chronic GVHD. Bone Marrow Transplant 41: 1047-1057. Human mononuclear cell transcripts; GVHD 18332912 7,16
2008 Okada A, Yasui T, Hamamoto S, Hirose M, Kubota Y, Itoh Y, Tozawa K, Hayashi Y, Kohri K Genome-wide analysis of genes related to kidney stone formation and elimination in the calcium oxalate nephrolithiasis model mouse: detection of stone-preventive factors and involvement of macrophage activity. J Bone Miner Res 24: 908-924. Mouse kidney transcripts; kidney stones 19113933 7,16
2008 Okada H, Tajima A, Shichiri K, Tanaka A, Tanaka K, Inoue I Genome-wide expression of azoospermia testes demonstrates a specific profile and implicates ART3 in genetic susceptibility. PLoS Genet 4: e26. Human testis transcripts; azoospermia 18266473 10.1371/journal.pgen.0040026 7,16
2008 Ongenaert M, Wisman GB, Volders HH, Koning AJ, Zee AG, van Criekinge W, Schuuring E Discovery of DNA methylation markers in cervical cancer using relaxation ranking. BMC Med Genomics 1: 57. Human genes; cancer; methylation 19025626 7,13
2008 Oren M, Escande ML, Paz G, Fishelson Z, Rinkevich B Urochordate histoincompatible interactions activate vertebrate-like coagulation system components. PLoS ONE 3: e3123. Botryllus schlosseri ESTs 18769590 10.1371/journal.pone.0003123 7
2008 Ortutay C, Vihinen M Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: case study of primary immunodeficiencies. Nucleic Acids Res 37: 622-628. Human protein interactions 19073697 16,17
2008 Ovaska K, Laakso M, Hautaniemi S Fast Gene Ontology based clustering for microarray experiments. BioData Min 1: 11. 19025591 7,10
2008 Ovcharenko I Widespread ultraconservation divergence in primates. Mol Biol Evol 25: 1668-1676. 18492662 18
2008 Owen J|etAl Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus. BMC Genomics 9: 266. Lumbricus rubellus ESTs; Lumbricus rubellus transcripts 18522720 5,7
2008 Paakkonen V, Bleicher F, Carrouel F, Vuoristo JT, Salo T, Wappler I, Couble ML, Magloire H, Peters H, Tjaderhane L General expression profiles of human native odontoblasts and pulp-derived cultured odontoblast-like cells are similar but reveal differential neuropeptide expression levels. Arch Oral Biol 54: 55-62. Human odontoblast transcripts 18951121 7,16
2008 Park D, Kim BC, Cho SW, Park SJ, Choi JS, Kim SI, Bhak J, Lee S MassNet: a functional annotation service for protein mass spectrometry data. Nucleic Acids Res 36: W491-495. 18448467 8,10
2008 Park JC, Kim TE, Park J Monitoring the evolutionary aspect of the Gene Ontology to enhance predictability and usability. BMC Bioinformatics 9 Suppl 3: S7. 18426552 10
2008 Park JY|etAl Homeostatic imbalance between apoptosis and cell renewal in the liver of premature aging Xpd mice. PLoS ONE 3: e2346. Mouse liver transcripts 18545656 10.1371/journal.pone.0002346 7,16
2008 Pearl EJ, Barker D, Day RC, Beck CW Identification of genes associated with regenerative success of Xenopus laevis hindlimbs. BMC Dev Biol 8: 66. Xenopus genes; limb regeneration 18570684 13
2008 Pena-Castillo L|etAl A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol 9 Suppl 1: S2. 18613946 9,12,17
2008 Pennings JL, Kimman TG, Janssen R Identification of a common gene expression response in different lung inflammatory diseases in rodents and macaques. PLoS ONE 3: e2596. Mammalian lung transcripts 18612392 10.1371/journal.pone.0002596 7,16
2008 Perco P, Wilflingseder J, Bernthaler A, Wiesinger M, Rudnicki M, Wimmer B, Mayer B, Oberbauer R Biomarker candidates for cardiovascular disease and bone metabolism disorders in chronic kidney disease: A systems biology perspective. J Cell Mol Med 12: 1177-1187. 18266955 16,17
2008 Pesquita C, Faria D, Bastos H, Ferreira AE, Falcao AO, Couto FM Metrics for GO based protein semantic similarity: a systematic evaluation. BMC Bioinformatics 9 Suppl 5: S4. 18460186 13
2008 Peterson DB, Sander T, Kaul S, Wakim BT, Halligan B, Twigger S, Pritchard KA, Oldham KT, Ou JS Comparative proteomic analysis of PAI-1 and TNF-alpha-derived endothelial microparticles. Proteomics 8: 2430-2446. Human umbilical endothelial cell proteins 18563738 8,16
2008 Pico AR, Smirnov IV, Chang JS, Yeh RF, Wiemels JL, Wiencke JK, Tihan T, Conklin BR, Wrensch M SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system. Nucleic Acids Res 37: D803-809. 18984625 10
2008 Piersma SR, Broxterman HJ, Kapci M, de Haas RR, Hoekman K, Verheul HM, Jimenez CR Proteomics of the TRAP-induced platelet releasate. J Proteomics 72: 91-9109. Human blood proteins 19049909 8,16
2008 Pietilainen KH|etAl Global transcript profiles of fat in monozygotic twins discordant for BMI: pathways behind acquired obesity. PLoS Med 5: e51. Human adipose tissue transcripts; monozygotic twins; acquired obesity 18336063 7,16
2008 Pirooznia M, Habib T, Perkins EJ, Deng Y GOfetcher: A database with complex searching facility for Gene Ontology. Bioinformatics 24: 2561-2563. 18728045 10
2008 Ponsuksili S, Murani E, Wimmers K Porcine genome-wide gene expression in response to tetanus toxoid vaccine. Dev Biol (Basel) 132: 185-195. Porcine leukocyte transcripts; tetanus toxoid exposure 18817301 7
2008 Pottier N|etAl The SWI/SNF chromatin-remodeling complex and glucocorticoid resistance in acute lymphoblastic leukemia. J Natl Cancer Inst 100: 1792-1803. 19066270 13,16
2008 Poussin C, Hall D, Minehira K, Galzin AM, Tarussio D, Thorens B Different transcriptional control of metabolism and extracellular matrix in visceral and subcutaneous fat of obese and rimonabant treated mice. PLoS ONE 3: e3385. Mouse adipose tissue transcripts; rimonabant treatment 19030233 10.1371/journal.pone.0003385 7,16
2008 Prasher B|etAl Whole genome expression and biochemical correlates of extreme constitutional types defined in Ayurveda. J Transl Med 6: 48. Human blood cell transcripts; Ayurvedic medicine 18782426 7,16
2008 Proto-Siqueira R|etAl SAGE analysis demonstrates increased expression of TOSO contributing to Fas mediated resistance in CLL. Blood 112: 394-397. Human blood cell transcripts; chronic lymphocytic leukemia 18434611 7,16
2008 Provenzano PP, Inman DR, Eliceiri KW, Beggs HE, Keely PJ Mammary epithelial-specific disruption of focal adhesion kinase retards tumor formation and metastasis in a transgenic mouse model of human breast cancer. Am J Pathol 173: 1551-1565. Mouse mammary transcripts; focal adhesion kinase disruption; breast cancer 18845837 7,16
2008 Prudencio M|etAl Kinome-wide RNAi screen implicates at least 5 host hepatocyte kinases in Plasmodium sporozoite infection. PLoS Pathog 4: e1000201. Human kinases; Plasmodium infection 18989463 10.1371/journal.ppat.1000201 8,16
2008 Punta M, Ofran Y The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function. PLoS Comput Biol 4: e1000160. 18974821 10.1371/journal.pcbi.1000160 9
2008 Putnam EA, Smartt A, Groves A, Schwanke C, Brezinski M, Pershouse MA Gene expression changes after exposure to six-mix in a mouse model. J Immunotoxicol 5: 139-144. Mouse lung transcripts; asbestos exposure 18569383 7,16
2008 Qin QM, Pei J, Ancona V, Shaw BD, Ficht TA, de Figueiredo P RNAi screen of endoplasmic reticulum-associated host factors reveals a role for IRE1alpha in supporting Brucella replication. PLoS Pathog 4: e1000110. Drosophila cell genes; Brucella infection 18654626 10.1371/journal.ppat.1000110 13
2008 Qiu J, Noble WS Predicting co-complexed protein pairs from heterogeneous data. PLoS Comput Biol 4: e1000054. 18421371 10.1371/journal.pcbi.1000054 19
2008 Radauer C, Bublin M, Wagner S, Mari A, Breiteneder H Allergens are distributed into few protein families and possess a restricted number of biochemical functions. J Allergy Clin Immunol 121: 847-852.e7. Allergens 18395549 11,16
2008 Radivojac P, Peng K, Clark WT, Peters BJ, Mohan A, Boyle SM, Mooney SD An integrated approach to inferring gene-disease associations in humans. Proteins 72: 1030-1037. Human disease genes 18300252 15,16
2008 Rai M, Soragni E, Jenssen K, Burnett R, Herman D, Coppola G, Geschwind DH, Gottesfeld JM, Pandolfo M HDAC inhibitors correct frataxin deficiency in a Friedreich ataxia mouse model. PLoS ONE 3: e1958. Mouse transcripts 18463734 10.1371/journal.pone.0001958 7,16
2008 Rakyan V|etAl An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res 18: 1518-1529. Human genes; methylation profile 18577705 11,13,16
2008 Ramanathan P, Martin IC, Gardiner-Garden M, Thomson PC, Taylor RM, Ormandy CJ, Moran C, Williamson P Transcriptome analysis identifies pathways associated with enhanced maternal performance in QSi5 mice. BMC Genomics 9: 197. Mouse transcripts 18442417 7
2008 Ramsey SA|etAl Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics. PLoS Comput Biol 4: e1000021. Mouse macrophage transcripts 18369420 10.1371/journal.pcbi.1000021 7,16
2008 Ranheim T, Mattingsdal M, Lindvall JM, Holla OL, Berge KE, Kulseth MA, Leren TP Genome-wide expression analysis of cells expressing gain of function mutant D374Y-PCSK9. J Cell Physiol 217: 459-467. Human cell line transcripts 18570182 7,16
2008 Reed BD, Charos AE, Szekely AM, Weissman SM, Snyder M Genome-wide occupancy of SREBP1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes. PLoS Genet 4: e1000133. 18654640 10.1371/journal.pgen.1000133 7,13
2008 Reimand J, Tooming L, Peterson H, Adler P, Vilo J GraphWeb: mining heterogeneous biological networks for gene modules with functional significance. Nucleic Acids Res 36: W452-459. 18460544 10,17
2008 Reinius B, Saetre P, Leonard JA, Blekhman R, Merino-Martinez R, Gilad Y, Jazin E An evolutionarily conserved sexual signature in the primate brain. PLoS Genet 4: e1000100. Primate brain transcripts 18566661 10.1371/journal.pgen.1000100 7,18
2008 Renn SC, Aubin-Horth N, Hofmann HA Fish and chips: functional genomics of social plasticity in an African cichlid fish. J Exp Biol 211: 3041-3056. Astatotilapia burtoni neural genes 18775941 7
2008 Reyal F|etAl A comprehensive analysis of prognostic signatures reveals the high predictive capacity of the Proliferation, Immune response and RNA splicing modules in breast cancer. Breast Cancer Res 10: R93. Human breast transcripts; breast cancer 19014521 7,16
2008 Rhee SY, Wood V, Dolinski K, Draghici S Use and misuse of the gene ontology annotations. Nat Rev Genet 9: 509-515. 18475267 1,3
2008 Rines DR|etAl Whole genome functional analysis identifies novel components required for mitotic spindle integrity in human cells. Genome Biol 9: R44. Human genes; mitotic spindle 18302737 13,16
2008 Ritchie W, Granjeaud S, Puthier D, Gautheret D Entropy measures quantify global splicing disorders in cancer. PLoS Comput Biol 4: e1000011. 18369415 10.1371/journal.pcbi.1000011 13,16
2008 Roberg K, Ceder R, Farnebo L, Norberg-Spaak L, Grafstrom RC Multiple genotypic aberrances associate to terminal differentiation-deficiency of an oral squamous cell carcinoma in serum-free culture. Differentiation 76: 868-880. Human cell line transcripts; oral squamous cell carcinoma 18452551 7,16
2008 Roberts ES, Thomas RS, Dorman DC Gene expression changes following acute hydrogen sulfide (H2S)-induced nasal respiratory epithelial injury. Toxicol Pathol 36: 560-567. Rat nasal epithelial cell transcripts; hydrogen sulfide exposure 18467678 7,16
2008 Robinson JF, Yu X, Hong S, Griffith WC, Beyer R, Kim E, Faustman EM Cadmium-induced differential toxicogenomic response in resistant and sensitive mouse strains undergoing neurulation. Toxicol Sci 107: 206-219. Mouse embryonic transcripts; teratogen exposure 18974090 7,13,16
2008 Rodd ZA, Kimpel MW, Edenberg HJ, Bell RL, Strother WN, McClintick JN, Carr LG, Liang T, McBride WJ Differential gene expression in the nucleus accumbens with ethanol self-administration in inbred alcohol-preferring rats. Pharmacol Biochem Behav 89: 481-498. Rat brain transcripts; ethanol self-administration 18405950 7,16
2008 Rodriguez-Ortega MJ, Luque I, Tarradas C, Barcena JA Overcoming function annotation errors in the Gram-positive pathogen Streptococcus suis by a proteomics-driven approach. BMC Genomics 9: 588. Streptococcus suis proteins 19061494 5,8,9
2008 Rogers S, Girolami M, Kolch W, Waters KM, Liu T, Thrall B, Wiley HS Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models. Bioinformatics 24: 2894-2900. 18974169 7,8
2008 Romaschin AD, Youssef Y, Chow TF, Siu KW, Desouza LV, Honey RJ, Stewart R, Pace KT, Yousef GM Exploring the pathogenesis of renal cell carcinoma: pathway and bioinformatics analysis of dysregulated genes and proteins. Biol Chem 390: 125-135. Human kidney proteins; kidney cancer 19090715 8,16
2008 Rome S, Lecomte V, Meugnier E, Rieusset J, Debard C, Euthine V, Vidal H, Lefai E Microarrays analysis of SREBP-1a and SREBP-1c target genes identify new regulatory pathways in muscle. Physiol Genomics 34: 327-337. Human skeletal muscle transcripts 18559965 7,16
2008 Romero-Zaliz R, Del Val C, Cobb JP, Zwir I Onto-CC: a web server for identifying Gene Ontology conceptual clusters. Nucleic Acids Res 36: W352-357. 18544607 10
2008 Rooney JP, George AD, Patil A, Begley U, Bessette E, Zappala MR, Huang X, Conklin DA, Cunningham RP, Begley TJ Systems based mapping demonstrates that recovery from alkylation damage requires DNA repair, RNA processing, and translation associated networks. Genomics 93: 42-51. E. coli genes; DNA damage 18824089 13
2008 Rosenfeld JA, DeSalle R, Lee EK, O'Grady P Using whole genome presence/absence data to untangle function in 12 Drosophila genomes. Fly (Austin) 2: 291-299. Drosophila genes 19139635 13,18
2008 Ross-Ibarra J, Wright SI, Foxe JP, Kawabe A, DeRose-Wilson L, Gos G, Charlesworth D, Gaut BS Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata. PLoS ONE 3: e2411. 18545707 10.1371/journal.pone.0002411 18
2008 Royer L, Reimann M, Andreopoulos B, Schroeder M Unraveling protein networks with power graph analysis. PLoS Comput Biol 4: e1000108. 18617988 10.1371/journal.pcbi.1000108 8,17
2008 Ruike Y, Ichimura A, Tsuchiya S, Shimizu K, Kunimoto R, Okuno Y, Tsujimoto G Global correlation analysis for micro-RNA and mRNA expression profiles in human cell lines. J Hum Genet 53: 515-523. Human miRNAs 18465083 7,13
2008 Ruosaari S, Hienonen-Kempas T, Puustinen A, Sarhadi VK, Hollmen J, Knuutila S, Saharinen J, Wikman H, Anttila S Pathways affected by asbestos exposure in normal and tumour tissue of lung cancer patients. BMC Med Genomics 1: 55. Human lung transcripts; human lung proteins; asbestos; lung cancer 19014429 7,8,16,17
2008 Rustici G, Kapushesky M, Kolesnikov N, Parkinson H, Sarkans U, Brazma A Data storage and analysis in ArrayExpress and Expression Profiler. Curr Protoc Bioinformatics Chapter 7: Unit 7.13. 18819076 10,11
2008 Saba R, Goodman CD, Huzarewich RL, Robertson C, Booth SA A miRNA signature of prion induced neurodegeneration. PLoS ONE 3: e3652. Mouse brain miRNAs; scrapie 18987751 10.1371/journal.pone.0003652 7,16
2008 Saha S, Harrison SH, Chen JY Dissecting the human plasma proteome and inflammatory response biomarkers. Proteomics 9: 470-484. Human plasma proteins 19105179 8,16
2008 Salter KH|etAl An integrated approach to the prediction of chemotherapeutic response in patients with breast cancer. PLoS ONE 3: e1908. Human transcripts 18382681 10.1371/journal.pone.0001908 7,16
2008 Salzburger W, Renn SC, Steinke D, Braasch I, Hofmann HA, Meyer A Annotation of expressed sequence tags for the East African cichlid fish Astatotilapia burtoni and evolutionary analyses of cichlid ORFs. BMC Genomics 9: 96. Cichlid ESTs 18298844 5,18
2008 Samper E, Morgado L, Estrada JC, Bernad A, Hubbard A, Cadenas S, Melov S Increase in mitochondrial biogenesis, oxidative stress, and glycolysis in murine lymphomas. Free Radic Biol Med 46: 387-396. Mouse thymic lymphoma transcripts 19038329 7,16
2008 Sancho M, Diani E, Beato M, Jordan A Depletion of human histone H1 variants uncovers specific roles in gene expression and cell growth. PLoS Genet 4: e1000227. Human cancer cell line transcripts 18927631 10.1371/journal.pgen.1000227 7,16,17
2008 Sander TL, Ou JS, Densmore JC, Kaul S, Matus I, Twigger S, Halligan B, Greene AS, Pritchard KA, Oldham KT Protein composition of plasminogen activator inhibitor type 1-derived endothelial microparticles. Shock 29: 504-511. Human endothelial cell transcripts 18598005 8,16
2008 Sanderson LM, de Groot PJ, Hooiveld GJ, Koppen A, Kalkhoven E, Muller M, Kersten S Effect of synthetic dietary triglycerides: a novel research paradigm for nutrigenomics. PLoS ONE 3: e1681. Mouse liver transcripts 18301758 10.1371/journal.pone.0001681 7,16
2008 Sarmento L, Afonso CL, Estevez C, Wasilenko J, Pantin-Jackwood M Differential host gene expression in cells infected with highly pathogenic H5N1 avian influenza viruses. Vet Immunol Immunopathol 125: 291-302. Chicken fibroblast transcripts; influenza virus infection 18617273 7,16
2008 Sasahara A, Kasuya H, Krischek B, Tajima A, Onda H, Sasaki T, Akagawa H, Hori T, Inoue I Gene expression in a canine basilar artery vasospasm model: a genome-wide network-based analysis. Neurosurg Rev 31: 283-290. Dog artery transcripts; vasospasm 18463908 7,16
2008 Sato A, Sekine Y, Saruta C, Nishibe H, Morita N, Sato Y, Sadakata T, Shinoda Y, Kojima T, Furuichi T Cerebellar development transcriptome database (CDT-DB): Profiling of spatio-temporal gene expression during the postnatal development of mouse cerebellum. Neural Netw 21: 1056-1069. Mouse cerebellar transcripts 18603407 7,11
2008 Schirra HJ, Anderson CG, Wilson WJ, Kerr L, Craik DJ, Waters MJ, Lichanska AM Altered metabolism of growth hormone receptor mutant mice: a combined NMR metabonomics and microarray study. PLoS ONE 3: e2764. Mouse liver transcripts; mouse metabolites 18648510 7,16
2008 Scholz B|etAl Striatal proteomic analysis suggests that first L-dopa dose equates to chronic exposure. PLoS ONE 3: e1589. Macaque brain transcripts; L-DOPA treatment 18270577 10.1371/journal.pone.0001589 8,16
2008 Schumacher B|etAl Delayed and accelerated aging share common longevity assurance mechanisms. PLoS Genet 4: e1000161. Mouse liver transcripts; aging 18704162 10.1371/journal.pgen.1000161 7,16
2008 Sebastiani P|etAl A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples. BMC Genet 9: 6. 18194558 13
2008 Segerdell E, Bowes JB, Pollet N, Vize PD An ontology for Xenopus anatomy and development. BMC Dev Biol 8: 92. 18817563 15
2008 Seko Y, Azuma N, Takahashi Y, Makino H, Morito T, Muneta T, Matsumoto K, Saito H, Sekiya I, Umezawa A Human sclera maintains common characteristics with cartilage throughout evolution. PLoS ONE 3: e3709. Human scleral cell transcripts 19002264 10.1371/journal.pone.0003709 7,16
2008 Sepulveda DE, Andrews BA, Asenjo JA, Papoutsakis ET Comparative transcriptional analysis of embryoid body versus two-dimensional differentiation of murine embryonic stem cells. Tissue Eng Part A 14: 1603-1614. Mouse embryonic stem cell transcripts 18433312 7
2008 Shack LA, Buza JJ, Burgess SC The neoplastically transformed (CD30(hi)) Marek's disease lymphoma cell phenotype most closely resembles T-regulatory cells. Cancer Immunol Immunother 57: 1253-1262. Chicken transcripts; Marek's disease; lymphoma 18256827 7,16
2008 Shalchian-Tabrizi K, Minge MA, Espelund M, Orr R, Ruden T, Jakobsen KS, Cavalier-Smith T Multigene phylogeny of choanozoa and the origin of animals. PLoS ONE 3: e2098. Ministeria vibrans genes 18461162 10.1371/journal.pone.0002098 3,18
2008 Sharma SK, Millam S, Hedley PE, McNicol J, Bryan GJ Molecular regulation of somatic embryogenesis in potato: an auxin led perspective. Plant Mol Biol 68: 185-201. Potato transcripts 18553172 7
2008 Shazman S, Mandel-Gutfreund Y Classifying RNA-binding proteins based on electrostatic properties. PLoS Comput Biol 4: e1000146. 18716674 10.1371/journal.pcbi.1000146 19
2008 Sheehan B, Quigley A, Gaudin B, Dobson S A relation based measure of semantic similarity for Gene Ontology annotations. BMC Bioinformatics 9: 468. 18983678 3,13
2008 Shen HB, Chou KC Identification of proteases and their types. Anal Biochem 385: 153-160. 19007742 19
2008 Shi M, Jin J, Wang Y, Beyer RP, Kitsou E, Albin RL, Gearing M, Pan C, Zhang J Mortalin: A protein associated with progression of Parkinson disease? J Neuropathol Exp Neurol 67: 117-124. Human brain proteins; Parkinson's disease 18219256 8,16
2008 Shriner D, Baye TM, Padilla MA, Zhang S, Vaughan LK, Loraine AE Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies. Nucleic Acids Res 36: e26. 18263617 13,16
2008 Singh S, Wall DP Testing the accuracy of eukaryotic phylogenetic profiles for prediction of biological function. Evol Bioinform Online 4: 217-223. 19204819 18
2008 Skov V, Glintborg D, Knudsen S, Tan Q, Jensen T, Kruse TA, Beck-Nielsen H, Hojlund K Pioglitazone enhances mitochondrial biogenesis and ribosomal protein biosynthesis in skeletal muscle in polycystic ovary syndrome. PLoS ONE 3: e2466. Human muscle transcripts 18560589 10.1371/journal.pone.0002466 7,16
2008 Smith SL|etAl Gene expression profiling of single bovine embryos uncovers significant effects of in vitro maturation, fertilization and culture. Mol Reprod Dev 76: 38-47. Bovine embryo transcripts 18449896 7
2008 Somel M, Creely H, Franz H, Mueller U, Lachmann M, Khaitovich P, Paabo S Human and chimpanzee gene expression differences replicated in mice fed different diets. PLoS ONE 3: e1504. Mouse transcripts; diet 18231591 10.1371/journal.pone.0001504 7,16
2008 Song N, Joseph JM, Davis GB, Durand D Sequence similarity network reveals common ancestry of multidomain proteins. PLoS Comput Biol 4: e1000063. 18475320 10.1371/journal.pcbi.1000063 18
2008 Soong TT, Wrzeszczynski KO, Rost B Physical protein-protein interactions predicted from microarrays. Bioinformatics 24: 2608-2614. 18829707 7,8,19
2008 Sorensen G, Medina S, Parchaliuk D, Phillipson C, Robertson C, Booth SA Comprehensive transcriptional profiling of prion infection in mouse models reveals networks of responsive genes. BMC Genomics 9: 114. Mouse brain transcripts; prion disease 18315872 7,16
2008 Soreq L, Gilboa-Geffen A, Berrih-Aknin S, Lacoste P, Darvasi A, Soreq E, Bergman H, Soreq H Identifying alternative hyper-splicing signatures in MG-thymoma by exon arrays. PLoS ONE 3: e2392. Human hyper-spliced transcripts 18545673 13,16
2008 Soreq L, Israel Z, Bergman H, Soreq H Advanced microarray analysis highlights modified neuro-immune signaling in nucleated blood cells from Parkinson's disease patients. J Neuroimmunol 201-202: 227-236. Human blood cell transcripts; Parkinson's disease 18692253 7,16
2008 Sousa JF, Espreafico EM Suppression subtractive hybridization profiles of radial growth phase and metastatic melanoma cell lines reveal novel potential targets. BMC Cancer 8: 19. Human cell line cDNAs; melanoma 18211678 7,16
2008 Srivastava S, Zhang L, Jin R, Chan C A novel method incorporating gene ontology information for unsupervised clustering and feature selection. PLoS ONE 3: e3860. 19052637 7,17
2008 Stapleton AR, Chan VT Subtoxic chlorpyrifos treatment resulted in differential expression of genes implicated in neurological functions and development. Arch Toxicol 83: 319-333. Rat brain transcripts; chlorpyrifos exposure 18668222 7,16
2008 Steinert S, Kroll TC, Taubert I, Pusch L, Hortschansky P, Hoeffken K, Woelfl S, Clement JH Differential expression of cancer-related genes by single and permanent exposure to bone morphogenetic protein 2. J Cancer Res Clin Oncol 134: 1237-1245. Human breast cancer cell line transcripts; BMP2 18446370 7,16
2008 Stevens SM, Duncan RS, Koulen P, Prokai L Proteomic analysis of mouse brain microsomes: identification and bioinformatic characterization of endoplasmic reticulum proteins in the mammalian central nervous system. J Proteome Res 7: 1046-1054. Mouse brain proteins 18271522 8,16
2008 Sun CJ, Zhang WY, Yu S, Cui MH [Microarray analysis of differentially expressed genes in peripheral leucocytes derived from severe preeclampsia and normotensive pregnancies.] Zhonghua Fu Chan Ke Za Zhi 43: 651-656. Human blood transcripts; preeclampsia 19087513 7,16
2008 Sun H, Skogerbo G, Wang Z, Liu W, Li Y Structural relationships between highly conserved elements and genes in vertebrate genomes. PLoS ONE 3: e3727. Vertebrate genes 19008958 10.1371/journal.pone.0003727 18
2008 Sun Y, Li H, Liu Y, Mattson MP, Rao MS, Zhan M Evolutionarily conserved transcriptional co-expression guiding embryonic stem cell differentiation. PLoS ONE 3: e3406. Mammalian stem cell transcripts 18923680 10.1371/journal.pone.0003406 7,18
2008 Suzuki S, Takeshita K, Asamoto M, Takahashi S, Kandori H, Tsujimura K, Saito F, Masuko K, Shirai T High mobility group box associated with cell proliferation appears to play an important role in hepatocellular carcinogenesis in rats and humans. Toxicology 255: 160-170. Rat liver transcripts; human liver transcripts 19041683 7,16
2008 Synnergren J, Akesson K, Dahlenborg K, Vidarsson H, Ameen C, Steel D, Lindahl A, Olsson B, Sartipy P Molecular signature of cardiomyocyte clusters derived from human embryonic stem cells. Stem Cells 26: 1831-1840. Human embryonic stem cell transcripts 18436862 7,16
2008 Szakasits D, Heinen P, Wieczorek K, Hofmann J, Wagner F, Kreil DP, Sykacek P, Grundler FM, Bohlmann H The transcriptome of syncytia induced by the cyst nematode Heterodera schachtii in Arabidopsis roots. Plant J 57: 771-784. Arabidopsis root transcripts 18980640 7
2008 Tailleux L|etAl Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages. PLoS ONE 3: e1403. Human monocyte transcripts; Mycobacterium tuberculosis transcripts 18167562 10.1371/journal.pone.0001403 7,16
2008 Taji T|etAl Large-scale collection and annotation of full-length enriched cDNAs from a model halophyte, Thellungiella halophila. BMC Plant Biol 8: 115. Thellungiella halophila cDNAs 19014467 3
2008 Takamura T, Misu H, Yamashita T, Kaneko S SAGE application in the study of diabetes. Curr Pharm Biotechnol 9: 392-399. Human liver transcripts; diabetes 18855692 7,16
2008 Tam NN, Szeto CY, Sartor MA, Medvedovic M, Ho SM Gene expression profiling identifies lobe-specific and common disruptions of multiple gene networks in testosterone-supported, 17beta-estradiol- or diethylstilbestrol-induced prostate dysplasia in Noble rats. Neoplasia 10: 20-40. Rat prostate transcripts; DES exposure 18231636 7,16
2008 Tari L, Baral C, Kim S Fuzzy c-means clustering with prior biological knowledge. J Biomed Inform 42: 74-81. 18595779 10
2008 Tasan M, Tian W, Hill DP, Gibbons FD, Blake JA, Roth FP An en masse phenotype and function prediction system for Mus musculus. Genome Biol 9 Suppl 1: S8. 18613952 9
2008 Taubert S, Hansen M, Van Gilst MR, Cooper SB, Yamamoto KR The Mediator subunit MDT-15 confers metabolic adaptation to ingested material. PLoS Genet 4: e1000021. Caenorhabditis transcripts 18454197 10.1371/journal.pgen.1000021 7
2008 Taylor RC, Acquaah-Mensah G, Singhal M, Malhotra D, Biswal S Network inference algorithms elucidate Nrf2 regulation of mouse lung oxidative stress. PLoS Comput Biol 4: e1000166. 18769717 10.1371/journal.pcbi.1000166 7,16,17
2008 Thongjuea S, Ruanjaichon V, Bruskiewich R, Vanavichit A RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome. Nucleic Acids Res 37: D996-991000. 18820292 10,11
2008 Tian R, Li L, Tang W, Liu H, Ye M, Zhao ZK, Zou H Chemical proteomic study of isoprenoid chain interactome with a synthetic photoaffinity probe. Proteomics 8: 3094-3104. Saccharomyces proteins 18615431 8
2008 Tian W, Zhang LV, Tasan M, Gibbons FD, King OD, Park J, Wunderlich Z, Cherry JM, Roth FP Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. Genome Biol 9 Suppl 1: S7. 18613951 9
2008 Timko MP, Rushton PJ, Laudeman TW, Bokoviec MT, Chipumuro E, Cheung F, Town CD, Chen X Sequencing and analysis of the gene-rich space of cowpea. BMC Genomics 9: 103. Cowpea genes 18304330 3
2008 Tonikian R|etAl A specificity map for the PDZ domain family. PLoS Biol 6: e239. C. elegans proteins 18828675 10.1371/journal.pbio.0060239 8
2008 Trehanpati N, Geffers R, Sukriti, Hissar S, Riese P, Toepfer T, Buer J, Kumar M, Guzman CA, Sarin SK Gene expression signatures of peripheral CD4+ T cells clearly discriminate between patients with acute and chronic hepatitis B infection. Hepatology 49: 781-790. Human T cell transcripts; hepatitis 19185001 7,16
2008 Trummer E, Ernst W, Hesse F, Schriebl K, Lattenmayer C, Kunert R, Vorauer-Uhl K, Katinger H, Muller D Transcriptional profiling of phenotypically different Epo-Fc expressing CHO clones by cross-species microarray analysis. Biotechnol J 3: 924-937. CHO cell transcripts 18481264 7,13
2008 Tuch BB, Galgoczy DJ, Hernday AD, Li H, Johnson AD The evolution of combinatorial gene regulation in fungi. PLoS Biol 6: e38. Fungal genes 18303948 10.1371/journal.pbio.0060038 7,17
2008 Tuggle CK, Wang YF, Couture OP, Qu L, Uthe JJ, Kuhar D, Lunney JK, Nettleton D, Dekkers JC, Bearson SM Computational integration of structural and functional genomics data across species to develop information on the porcine inflammatory gene regulatory pathway. Dev Biol (Basel) 132: 105-113. Porcine gut transcripts; immune response 18817292 7
2008 Turner DP, Findlay VJ, Kirven AD, Moussa O, Watson DK Global gene expression analysis identifies PDEF transcriptional networks regulating cell migration during cancer progression. Mol Biol Cell 19: 3745-3757. Human cancer cell line transcripts 18579687 7,16,17
2008 Turner TL, von Wettberg EJ, Nuzhdin SV Genomic analysis of differentiation between soil types reveals candidate genes for local adaptation in Arabidopsis lyrata. PLoS ONE 3: e3183. 18784841 10.1371/journal.pone.0003183 13,18
2008 Tweedie S|etAl FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res 37: D555-559. Drosophila genome 18948289 1,4,11
2008 Uriarte SM, Powell DW, Luerman GC, Merchant ML, Cummins TD, Jog NR, Ward RA, McLeish KR Comparison of proteins expressed on secretory vesicle membranes and plasma membranes of human neutrophils. J Immunol 180: 5575-5581. Human proteins 18390742 8
2008 Uriguen L, Arteta D, Diez-Alarcia R, Ferrer-Alcon M, Diaz A, Pazos A, Meana JJ Gene expression patterns in brain cortex of three different animal models of depression. Genes Brain Behav 7: 3879-3889. Rat brain transcripts; depression 18363858 7,16
2008 Valentini G, Cesa-Bianchi N HCGene: a software tool to support the hierarchical classification of genes. Bioinformatics 24: 729-731. 18204060 10
2008 Vallee M, Aiba K, Piao Y, Palin MF, Ko MS, Sirard MA Comparative analysis of oocyte transcript profiles reveals a high degree of conservation among species. Reproduction 135: 439-448. Oocyte transcripts 18367505 7,18
2008 Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods 5: 829-834. 19160518 7,13
2008 Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods 7: 3879-3889. 18711362 7,12,17
2008 Vanselow J, Nurnberg G, Koczan D, Langhammer M, Thiesen HJ, Reinsch N Expression profiling of a high-fertility mouse line by microarray analysis and qPCR. BMC Genomics 9: 307. Mouse ovarian transcripts 18588666 7
2008 Varshavsky R, Horn D, Linial M Global considerations in hierarchical clustering reveal meaningful patterns in data. PLoS ONE 3: e2247. 18493326 10.1371/journal.pone.0002247 7,10
2008 Verstraelen S, Nelissen I, Hooyberghs J, Witters H, Schoeters G, Van Cauwenberge P, Van Den Heuvel R Gene profiles of a human alveolar epithelial cell line after in vitro exposure to respiratory (non-)sensitizing chemicals: Identification of discriminating genetic markers and pathway analysis. Toxicol Lett 185: 16-22. Human epithelial cell line transcripts; chemical exposure 19110044 7,16
2008 Villa-Diaz LG, Pacut C, Slawny NA, Ding J, O'Shea KS, Smith GD Analysis of the factors that limit the ability of feeder-cells to maintain the undifferentiated state of human embryonic stem cells. Stem Cells Dev 7: 3879-3889. Human embryonic stem cell transcripts 18764735 7,16
2008 Vinogradov AE Modularity of cellular networks shows general center-periphery polarization. Bioinformatics 24: 2814-2817. 18953046 8,17
2008 Viswanathan GA, Seto J, Patil S, Nudelman G, Sealfon SC Getting started in biological pathway construction and analysis. PLoS Comput Biol 4: e16. 18463709 10.1371/journal.pcbi.0040016 17
2008 Viti F, Merelli I, Caprera A, Lazzari B, Stella A, Milanesi L Ontology-based, Tissue MicroArray oriented, image centered tissue bank. BMC Bioinformatics 9 Suppl 4: S4. 18460177 7,11,15
2008 Volinia S, Mascellani N, Marchesini J, Veronese A, Ormondroyd E, Alder H, Palatini J, Negrini M, Croce CM Genome wide identification of recessive cancer genes by combinatorial mutation analysis. PLoS ONE 3: e3380. Human genes; cancer 18846217 10.1371/journal.pone.0003380 13,16
2008 Wahls WP, Siegel ER, Davidson MK Meiotic recombination hotspots of fission yeast are directed to loci that express non-coding RNA. PLoS ONE 3: e2887. 18682829 10.1371/journal.pone.0002887 13
2008 Wakabayashi T, Natsume A, Hashizume Y, Fujii M, Mizuno M, Yoshida J A phase I clinical trial of interferon-beta gene therapy for high-grade glioma: novel findings from gene expression profiling and autopsy. J Gene Med 10: 329-339. Human brain transcript; high-grade glioma; gene therapy 18220319 7,16
2008 Wang F|etAl Environmental adaptation: genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium Shewanella piezotolerans WP3. PLoS ONE 3: e1937. Shewanella piezotolerans genome 18398463 10.1371/journal.pone.0001937 4,18
2008 Wang J, Han DM, Kang HW, Ma LJ, Ye JY, Xiao Y [Primary study on glycan structure in pathopoiesis mechanism of recurrent respiratory papillomatosis] Zhonghua Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 43: 355-359. Human larynx transcripts; recurrent respiratory papillomatosis 18717311 7,16
2008 Wang J, Ross KG, Keller L Genome-wide expression patterns and the genetic architecture of a fundamental social trait. PLoS Genet 4: e1000127. Fire ant transcripts 18636101 10.1371/journal.pgen.1000127 7,18
2008 Wang J, Yuan Y, Zhou Y, Guo L, Zhang L, Kuai X, Deng B, Pan Z, Li D, He F Protein interaction data set highlighted with human Ras-MAPK/PI3K signaling pathways. J Proteome Res 7: 3879-3889. Human proteins 18624398 8
2008 Wang KJ, Ren HL, Xu DD, Cai L, Yang M Identification of the up-regulated expression genes in hemocytes of variously colored abalone (Haliotis diversicolor Reeve, 1846) challenged with bacteria. Dev Comp Immunol 32: 1326-1347. Abalone cDNAs 18538840 7
2008 Wang L, Zhang B, Wolfinger RD, Chen X An integrated approach for the analysis of biological pathways using mixed models. PLoS Genet 4: e1000115. 18852846 17
2008 Wang M, Windgassen D, Papoutsakis ET A global transcriptional view of apoptosis in human T-cell activation. BMC Med Genomics 1: 53. Human T cell transcripts 18947405 7,16
2008 Wang M, Windgassen D, Papoutsakis ET Comparative analysis of transcriptional profiling of CD3+, CD4+ and CD8+ T cells identifies novel immune response players in T-Cell activation. BMC Genomics 9: 225. Human T cell transcripts 18485203 7,16
2008 Wang Z, Neuberg D, Su L, Kim JY, Chen JC, Christiani DC Prospective study of metal fume-induced responses of global gene expression profiling in whole blood. Inhal Toxicol 20: 1233-1244. Human blood transcripts; metal particulate exposure 18951227 7,16
2008 Ward RM, Erdin S, Tran TA, Kristensen DM, Lisewski AM, Lichtarge O De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features. PLoS ONE 3: e2136. 18461181 10.1371/journal.pone.0002136 8,18
2008 Warden CD, Kim SH, Yi SV Predicted functional RNAs within coding regions constrain evolutionary rates of yeast proteins. PLoS ONE 3: e1559. 18270559 10.1371/journal.pone.0001559 13,18
2008 Wasmuth J, Schmid R, Hedley A, Blaxter M On the extent and origins of genic novelty in the phylum nematoda. PLoS Negl Trop Dis 2: e258. Nematode genes 18596977 10.1371/journal.pntd.0000258 18
2008 Wass MN, Sternberg MJ ConFunc - Functional Annotation in the Twilight Zone. Bioinformatics 24: 798-806. 18263643 9,10
2008 Wegmann D, Dupanloup I, Excoffier L Width of gene expression profile drives alternative splicing. PLoS ONE 3: e3587. 18974852 10.1371/journal.pone.0003587 7,18
2008 Wei L, Yu J Bioinformatics in China: a personal perspective. PLoS Comput Biol 4: e1000020. 18437216 10.1371/journal.pcbi.1000020 3,10
2008 Wei P, Pan W Incorporating gene functions into regression analysis of DNA-protein binding data and gene expression data to construct transcriptional networks. IEEE/ACM Trans Comput Biol Bioinform 5: 401-415. 18670043 7,17
2008 Weinhold N, Sander O, Domingues FS, Lengauer T, Sommer I Local function conservation in sequence and structure space. PLoS Comput Biol 4: e1000105. 18604264 10.1371/journal.pcbi.1000105 9,10
2008 Welle S, Tawil R, Thornton CA Sex-related differences in gene expression in human skeletal muscle. PLoS ONE 3: e1385. Human skeletal muscle transcripts 18167544 10.1371/journal.pone.0001385 7,16
2008 Wellensiek BP, Ramakrishnan R, Sundaravaradan V, Mehta R, Harris DT, Ahmad N Differential HIV-1 integration targets more actively transcribed host genes in neonatal than adult blood mononuclear cells. Virology 385: 28-38. Human blood cells; HIV-1 integration sites 19100594 13,16
2008 Werner T Bioinformatics applications for pathway analysis of microarray data. Curr Opin Biotechnol 19: 50-54. 18207385 7,10
2008 West J, Cogan J, Geraci M, Robinson L, Newman J, Phillips JA, Lane K, Meyrick B, Loyd J Gene expression in BMPR2 mutation carriers with and without evidence of Pulmonary Arterial Hypertension suggests pathways relevant to disease penetrance. BMC Med Genomics 1: 45. Human B cell transcripts; hypertension 18823550 7,16
2008 Weston Glenn JL, Chen CF, Lewandowski A, Cheng CH, Ramsdell CM, Bullard-Dillard R, Chen J, Dewey MJ, Glenn TC Expressed sequence tags from Peromyscus testis and placenta tissue: analysis, annotation, and utility for mapping. BMC Genomics 9: 300. Peromyscus testis ESTs; Peromyscus placenta ESTs 18577228 5,7
2008 Whittle CM, McClinic KN, Ercan S, Zhang X, Green RD, Kelly WG, Lieb JD The genomic distribution and function of histone variant HTZ-1 during C. elegans embryogenesis. PLoS Genet 4: e1000187. 18787694 10.1371/journal.pgen.1000187 13
2008 Wilding Crawford L, Tweedie Ables E, Oh YA, Boone B, Levy S, Gannon M Gene expression profiling of a mouse model of pancreatic islet dysmorphogenesis. PLoS ONE 3: e1611. Mouse pancreatic transcripts 18297134 10.1371/journal.pone.0001611 7,16
2008 Wilflingseder J, Kainz A, Perco P, Korbely R, Mayer B, Oberbauer R Molecular predictors for anaemia after kidney transplantation. Nephrol Dial Transplant 24: 1015-1023. Human kidney transcripts 19096080 7,16,17
2008 Williams TD, Diab A, Ortega F, Sabine VS, Godfrey RE, Falciani F, Chipman JK, George SG Transcriptomic responses of European flounder (Platichthys flesus) to model toxicants. Aquat Toxicol 90: 83-91. Flounder transcripts 18804290 7
2008 Wilson KD|etAl Transcriptome alteration in the diabetic heart by rosiglitazone: implications for cardiovascular mortality. PLoS ONE 3: e2609. Mouse heart transcripts 18648539 10.1371/journal.pone.0002609 7,16
2008 Witt H|etAl Sex-specific pathways in early cardiac response to pressure overload in mice. J Mol Med 86: 1013-1024. Mouse genes; cardiac hypertrophy 18665344 7,16
2008 Wiwanitkit V CAG repeat polymorphism in the androgen receptor: a study on the effect of different numbers of repeats using Gene Ontology technique. Fertil Steril 91: e5-6. 18222439 16,19
2008 Wiwanitkit V Effect of interleukin-2 and tumor necrosis factor-alpha on osteopontin: molecular function and biological process. Pediatr Int 50: 213-215. 18353062 9,16
2008 Wiwanitkit V Interaction between BCL2 and JUNB in primary cutaneous lymphoma: a gene ontology approach. Int J Dermatol 47: 867-869. 18717876 16
2008 Wiwanitkit V Single amino acid substitution in important hemoglobinopathies does not disturb molecular function and biological process. Int J Nanomedicine 3: 225-227. 18686781 16
2008 Wiwanitkit V Synergistic interaction between semicarbazide-sensitive amine oxidase and angiotensin-converting enzyme in diabetes: functional analysis by gene ontology. J Diabetes Complications 22: 413-419. 18413170 16
2008 Wongdee K, Teerapornpuntakit J, Riengrojpitak S, Krishnamra N, Charoenphandhu N Gene expression profile of duodenal epithelial cells in response to chronic metabolic acidosis. Mol Cell Biochem 321: 173-188. Rat duodenal epithelial transcripts 18979233 7,16
2008 Wu CH, Sahoo D, Arvanitis C, Bradon N, Dill DL, Felsher DW Combined analysis of murine and human microarrays and ChIP analysis reveals genes associated with the ability of MYC to maintain tumorigenesis. PLoS Genet 4: e1000090. Human lymphoma transcripts; mouse tumor transcripts 18535662 10.1371/journal.pgen.1000090 7,13,16
2008 Wu C|etAl Gene set enrichment in eQTL data identifies novel annotations and pathway regulators. PLoS Genet 4: e1000070. Mouse QTLs 18464898 10.1371/journal.pgen.1000070 7,17
2008 Xi Z, Ramirez JL, Dimopoulos G The Aedes aegypti toll pathway controls dengue virus infection. PLoS Pathog 4: e1000098. Aedes aegypti genes; dengue virus 18604274 10.1371/journal.ppat.1000098 7,16
2008 Xiao P, Tang A, Yu Z, Gui Y, Cai Z Gene expression profile of 2058 spermatogenesis-related genes in mice. Biol Pharm Bull 31: 201-206. Mouse testis transcripts 18239273 7
2008 Xu J, Deng X, Demetriou AA, Farkas DL, Hui T, Wang C Factors released from cholestatic rat livers possibly involved in inducing bone marrow hepatic stem cell priming. Stem Cells Dev 17: 143-156. Rat liver transcripts; stem cell priming 18225978 7,16
2008 Xu J, Wang W, Ludeman M, Cheng K, Hayami T, Lotz JC, Kapila S Chondrogenic differentiation of human mesenchymal stem cells in three-dimensional alginate gels. Tissue Eng Part A 14: 667-680. Human mesenchymal stem cell transcripts 18377198 7,16
2008 Xu Q, Shi Y, Lu Q, Zhang G, Luo Q, Li Y GORouter: an RDF model for providing semantic query and inference services for Gene Ontology and its associations. BMC Bioinformatics 9 Suppl 1: S6. 18315859 10
2008 Xu T, Du L, Zhou Y Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data. BMC Bioinformatics 9: 472. Saccharomyces transcripts; Saccharomyces proteins 18986551 7,8,13
2008 Xu X, Wu J, Xiao J, Tan Y, Bao Q, Zhao F, Li X PlasmoGF: an integrated system for comparative genomics and phylogenetic analysis of Plasmodium gene families. Bioinformatics 24: 1217-1220. 18337260 11,18
2008 Xun Z, Kaufman TC, Clemmer DE Proteome response to the panneural expression of human wild-type alpha-synuclein: A Drosophila model of Parkinson's disease. J Proteome Res 7: 3911-3921. Drosophila proteins; Parkinson's disease 18683964 8,16
2008 Xun Z, Sowell RA, Kaufman TC, Clemmer DE Quantitative proteomics of a presymptomatic A53T a-synuclein Drosophila model of Parkinson's disease. Mol Cell Proteomics 7: 1191-1203. Drosophila proteins; Parkinson's disease 18353766 8,16,17
2008 Yakabe S, Soejima H, Yatsuki H, Tominaga H, Zhao W, Higashimoto K, Joh K, Kudo S, Miyazaki K, Mukai T MeCP2 knockdown reveals DNA methylation-independent gene repression of target genes in living cells and a bias in the cellular location of target gene products. Genes Genet Syst 83: 199-208. Human lung genes; DNA methylation 18506103 7,16
2008 Yamaguchi-Kabata Y, Shimada MK, Hayakawa Y, Minoshima S, Chakraborty R, Gojobori T, Imanishi T Distribution and effects of nonsense polymorphisms in human genes. PLoS ONE 3: e3393. Human SNPs 18852891 10.1371/journal.pone.0003393 7
2008 Yamano Y, Uzawa K, Shinozuka K, Fushimi K, Ishigami T, Nomura H, Ogawara K, Shiiba M, Yokoe H, Tanzawa H Hyaluronan-mediated motility: a target in oral squamous cell carcinoma. Int J Oncol 32: 1001-1009. Human oral cell transcripts; oral squamous cell carcinoma 18425326 7,16
2008 Yan J, Wang H, Liu Y, Shao C Analysis of gene regulatory networks in the mammalian circadian rhythm. PLoS Comput Biol 4: e1000193. Mouse transcripts 17 18846204 7
2008 Yang CC, Lin YS, Hsu CC, Wu SC, Lin EC, Cheng WT Identification and sequencing of remnant messenger RNAs found in domestic swine (Sus scrofa) fresh ejaculated spermatozoa. Anim Reprod Sci 113: 143-155. Swine spermatozoal mRNAs 18786788 7
2008 Yang CY|etAl PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database. Bioinformatics 24: i14-20. Human phosphoproteins 18689816 8,11,17
2008 Yang H, Nenadic G, Keane JA Identification of transcription factor contexts in literature using machine learning approaches. BMC Bioinformatics 9 Suppl 3: S11. 18426546 12
2008 Yang J, Zhao JJ, Zhu Y, Xiong W, Lin JY, Ma X Identification of candidate cancer genes involved in human retinoblastoma by data mining. Childs Nerv Syst 24: 893-900. Human retinal transcripts; retinoblastoma 18350306 7,16
2008 Yang SX, Steinberg SM, Nguyen D, Wu TD, Modrusan Z, Swain SM Gene expression profile and angiogenic marker correlates with response to neoadjuvant bevacizumab followed by bevacizumab plus chemotherapy in breast cancer. Clin Cancer Res 14: 5893-5899. Mussel egg proteins 18794102 8
2008 Yang Y, Iyer LK, Adelstein SJ, Kassis AI Integrative genomic data mining for discovery of potential blood-borne biomarkers for early diagnosis of cancer. PLoS ONE 3: e3661. Human trancripts; cancer 18987750 7,12,16
2008 Yang Y, Iyer LK, Adelstein SJ, Kassis AI Integrative genomic data mining for discovery of potential blood-borne biomarkers for early diagnosis of cancer. PLoS ONE 3: e3661. Human transcripts; cancer 18987750 10.1371/journal.pone.0003661 7,12,16
2008 Yatsu J, Hayashi M, Mukai M, Arita K, Shigenobu S, Kobayashi S Maternal RNAs encoding transcription factors for germline-specific gene expression in Drosophila embryos. Int J Dev Biol 52: 913-923. Drosophila germ plasm transcripts 18956321 7
2008 Ye H, Yu T, Temam S, Ziober BL, Wang J, Schwartz JL, Mao L, Wong DT, Zhou X Transcriptomic dissection of tongue squamous cell carcinoma. BMC Genomics 9: 69. Human oral tissue transcripts; squamous cell carcinoma 18254958 7,16
2008 Yeh CS, Wang JY, Chung FY, Lee SC, Huang MY, Kuo CW, Yang MJ, Lin SR Significance of the glycolytic pathway and glycolysis related-genes in tumorigenesis of human colorectal cancers. Oncol Rep 19: 81-91. Human colon transcripts; colorectal cancer 18097579 7,16
2008 Yellaboina S, Dudekula DB, Ko MS Prediction of evolutionarily conserved interologs in Mus musculus. BMC Genomics 9: 465. Mouse proteins 18842131 8,11,18
2008 Yener B, Acar E, Agius P, Bennett K, Vandenberg SL, Plopper GE Multiway modeling and analysis in stem cell systems biology. BMC Syst Biol 2: 63. 18625054 7,8,17
2008 Yi M, Stephens RM SLEPR: a sample-level enrichment-based pathway ranking method -- seeking biological themes through pathway-level consistency. PLoS ONE 3: e3288. 10.1371/journal.pone.0003288 18818771 7,17
2008 Yi Z|etAl Global relationship between the proteome and transcriptome of human skeletal muscle. J Proteome Res 7: 3230-3241. Human muscle transcripts; human muscle proteins 18613714 7,8,16
2008 Yin LM, Jiang GH, Wang Y, Wang Y, Liu YY, Jin WR, Zhang Z, Xu YD, Yang YQ Serial analysis of gene expression in a rat lung model of asthma. Respirology 13: 972-982. Rat lung transcripts; asthma 18922145 7,16
2008 Yin Y, Martin J, Abubucker S, Scott AL, McCarter JP, Wilson RK, Jasmer DP, Mitreva M Intestinal transcriptomes of nematodes: Comparison of the parasites Ascaris suum and Haemonchus contortus with the free-living Caenorhabditis elegans. PLoS Negl Trop Dis 2: e269. Nematode intestinal transcripts 18682827 10.1371/journal.pntd.0000269 7,16,18
2008 Young JA, Johnson JR, Benner C, Yan SF, Chen K, Le Roch KG, Zhou Y, Winzeler EA In silico discovery of transcription regulatory elements in Plasmodium falciparum. BMC Genomics 9: 70. Plasmodium transcripts 18257930 7,17
2008 Young ND, Cooper GA, Nowak BF, Koop BF, Morrison RN Coordinated down-regulation of the antigen processing machinery in the gills of amoebic gill disease-affected Atlantic salmon (Salmo salar L.). Mol Immunol 45: 2581-2597. Salmon transcripts 18282602 7
2008 Yu C, Zavaljevski N, Desai V, Johnson S, Stevens FJ, Reifman J The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation. BMC Bioinformatics 9: 52. 18221520 9,10
2008 Yu M, Zloty D, Cowan B, Shapiro J, Haegert A, Bell RH, Warshawski L, Carr N, McElwee KJ Superficial, nodular, and morpheiform basal-cell carcinomas exhibit distinct gene expression profiles. J Invest Dermatol 128: 1797-1805. Human skin transcripts; basal cell carcinoma 18200053 7,16
2008 Yu RX, Liu J, True N, Wang W Identification of direct target genes using joint sequence and expression likelihood with application to DAF-16. PLoS ONE 3: e1821. 18350157 10.1371/journal.pone.0001821 7,17
2008 Yu S, Van Vooren S, Tranchevent LC, De Moor B, Moreau Y Comparison of vocabularies, representations and ranking algorithms for gene prioritization by text mining. Bioinformatics 24: i119-125. 18689812 12
2008 Yu W, Ramakrishnan R, Wang Y, Chiang K, Sung TL, Rice AP Cyclin T1-dependent genes in activated CD4 T and macrophage cell lines appear enriched in HIV-1 co-factors. PLoS ONE 3: e3146. Human monocytic cell line transcripts; HIV-1 replication 18773076 10.1371/journal.pone.0003146 7,16
2008 Yuan Y, Li CT, Wilson R Partial mixture model for tight clustering of gene expression time-course. BMC Bioinformatics 9: 287. 18564420 7
2008 Yukhananov R, Kissin I Persistent changes in spinal cord gene expression after recovery from inflammatory hyperalgesia: a preliminary study on pain memory. BMC Neurosci 9: 32. Rat spinal cord transcripts; hyperalgesia 18366630 7,16
2008 Zagorski J, Sanapareddy N, Gellar MA, Kline JA, Watts JA Transcriptional profile of right ventricular tissue during acute pulmonary embolism in rats. Physiol Genomics 34: 101-111. Rat heart transcripts; acute pulmonary embolism 18430806 7,16
2008 Zhang B, Park BH, Karpinets T, Samatova NF From pull-down data to protein interaction networks and com-plexes with biological relevance. Bioinformatics 24: 979-986. 18304937 8
2008 Zhang J, Burridge KA, Friedman MH In vivo differences between endothelial transcriptional profiles of coronary and iliac arteries revealed by microarray analysis. Am J Physiol Heart Circ Physiol 295: H1556-1561. Porcine artery transcripts; atherosclerosis 18689496 7,16
2008 Zhang W, Dolan ME Exploring the evolutionary history of the differentially expressed genes between human populations: action of recent positive selection. Evol Bioinform Online 4: 171-179. Human genes 19030115 7,18
2008 Zhang W, Liu W, Poradosu E, Ratain MJ Genome-wide identification of genetic determinants for the cytotoxicity of perifosine. Hum Genomics 3: 53-70. 19129090 10
2008 Zhang W, Zou S, Song J Term-tissue specific models for prediction of gene ontology biological processes using transcriptional profiles of aging in drosophila melanogaster. BMC Bioinformatics 9: 129. Drosophila transcripts; aging 18307794 7,9
2008 Zhang X, Shiu S, Cal A, Borevitz JO Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana using whole genome tiling arrays. PLoS Genet 4: e1000032. Arabidopsis genes; Arabidopsis transcripts 18369451 10.1371/journal.pgen.1000032 7,13
2008 Zhang Y, Lai J, Sun S, Li Y, Liu Y, Liang L, Chen M, Xie Q Comparison analysis of transcripts from the halophyte Thellungiella halophila. J Integr Plant Biol 50: 1327-1335. Thellungiella halophila ESTs 19017120 7
2008 Zhang Y, Liu T, Yan P, Huang T, Dewille J Identification and characterization of CCAAT/Enhancer Binding proteindelta (C/EBPdelta) target genes in G0 growth arrested mammary epithelial cells. BMC Mol Biol 9: 83. Human mammary cell line genes; C/EBPdelta 18828910 7,16
2008 Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data. BMC Bioinformatics 9: 203. 18426580 7,17
2008 Zhao WJ, Zhang H, Bo X, Li Y, Fu X Generation and analysis of expressed sequence tags from a cDNA library of Moniezia expansa. Mol Biochem Parasitol 164: 80-85. Moniezia expansa ESTs 19118581 5
2008 Zhao Z, Zhang W, Stanley BA, Assmann SM Functional proteomics of Arabidopsis thaliana guard cells uncovers new stomatal signaling pathways. Plant Cell 20: 3210-3226. Arabidopsis guard cell proteins 19114538 8
2008 Zheng H, Wang H, Glass DH Integration of genomic data for inferring protein complexes from global protein-protein interaction networks. IEEE Trans Syst Man Cybern B Cybern 38: 5-16. Saccharomyces proteins 18270078 8,17
2008 Zheng Q, Wang XJ GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res 36: W358-363. 18487275 10
2008 Zhou D, Xue J, Lai JC, Schork NJ, White KP, Haddad GG Mechanisms underlying hypoxia tolerance in Drosophila melanogaster: hairy as a metabolic switch. PLoS Genet 4: e1000221. Drosophila transcripts 18927626 10.1371/journal.pgen.1000221 7
2008 Zhou Y, Li L, Liu Q, Xing G, Kuai X, Sun J, Yin X, Wang J, Zhang L, He F E3 ubiquitin ligase SIAH1 mediates ubiquitination and degradation of TRB3. Cell Signal 20: 942-948. 18276110 8
2008 Zhou Y|etAl Evidence-based annotation of the malaria parasite's genome using comparative expression profiling. PLoS ONE 3: e1570. Plasmodium falciparum genome 18270564 10.1371/journal.pone.0001570 4,7
2008 Zhu H, Casselman A, Reppert SM Chasing migration genes: A brain expressed sequence tag resource for summer and migratory monarch butterflies (Danaus plexippus). PLoS ONE 3: e1345. Monarch butterfly ESTs 18183285 5,7
2008 de Godoy LM, Olsen JV, Cox J, Nielsen ML, Hubner NC, Frohlich F, Walther TC, Mann M Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455: 1251-1254. Yeast proteins 18820680 8
2008 de Wit E, Braunschweig U, Greil F, Bussemaker HJ, van Steensel B Global chromatin domain organization of the Drosophila genome. PLoS Genet 4: e1000045. 18369463 10.1371/journal.pgen.1000045 13
2008 dos Santos CC|etAl Differential gene profiling in acute lung injury identifies injury-specific gene expression. Crit Care Med 36: 855-865. Rat lung transcripts; acute lung injury 18431273 7,16
2008 van der Pouw Kraan TC, Zwiers A, Mulder CJ, Kraal G, Bouma G Acute experimental colitis and human chronic inflammatory diseases share expression of inflammation-related genes with conserved Ets2 binding sites. Inflamm Bowel Dis 15: 224-235. Human colon transcripts; inflammatory disease 18942749 7,16
2008 van der Stoop P, Boutsma EA, Hulsman D, Noback S, Heimerikx M, Kerkhoven RM, Voncken JW, Wessels LF, van Lohuizen M Ubiquitin E3 ligase Ring1b/Rnf2 of polycomb repressive complex 1 contributes to stable maintenance of mouse embryonic stem cells. PLoS ONE 3: e2235. Mouse embryonic stem cell transcripts 18493325 10.1371/journal.pone.0002235 7
2009 In this issue: Proteomics 3/2009. Proteomics epub 19180626 8
2009 The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. PLoS Comput Biol 5: e1000431. GO Reference Genomes 19578431 1,4
2009 Jing L, Ng M, Liu Y. Construction of gene networks with hybrid approach from expression profile and Gene Ontology. IEEE Trans Inf Technol Biomed 14: 107-118. 19789116 7,17
2009 The Gene Ontology Consortium The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res 38: D331-335. 19920128 1,2
2009 [No authors listed] SVM-RFE With MRMR Filter for Gene Selection. IEEE Trans Nanobioscience 9: 31-37. 19884101 13
2009 Abe N, Almenar-Queralt A, Lillo C, Shen Z, Lozach J, Briggs SP, Williams DS, Goldstein LS, Cavalli V Sunday Driver interacts with two distinct classes of axonal organelles. J Biol Chem 284: 34628-34639. Xenopus laevis transcripts 19801628 7
2009 Adema CM, Hanington PC, Lun CM, Rosenberg GH, Aragon AD, Stout BA, Lennard Richard ML, Gross PS, Loker ES Differential transcriptomic responses of Biomphalaria glabrata (Gastropoda, Mollusca) to bacteria and metazoan parasites, Schistosoma mansoni and Echinostoma paraensei (Digenea, Platyhelminthes). Mol Immunol 47: 849-860. Biomphalaria glabrata transcripts 19962194 7
2009 Adhikari BN, Wall DH, Adams BJ Desiccation survival in an Antarctic nematode: Molecular analysis using expressed sequenced tags. BMC Genomics 10: 69. Plectus murrayi ESTs 19203352 5,7
2009 Agarwal SM, Srivastava PK Human intronless disease associated genes are slowly evolving. BMB Rep 42: 356-360. 19558794 16,18
2009 Alekseev OM, Richardson RT, Alekseev O, O'Rand MG Analysis of gene expression profiles in HeLa cells in response to overexpression or siRNA-mediated depletion of NASP. Reprod Biol Endocrinol 7: 45. HeLa cell transcripts; NASP 19439102 7,16,17
2009 Alexopoulou D, Andreopoulos B, Dietze H, Doms A, Gandon F, Hakenberg J, Khelif K, Schroeder M, Wachter T Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy. BMC Bioinformatics 10: 28. 19159460 12
2009 Alttoa A, Koiv K, Hinsley TA, Brass A, Harro J Differential gene expression in a rat model of depression based on persistent differences in exploratory activity. Eur Neuropsychopharmacol 20: 288-300. Rat brain transcripts; depression 19854624 7,16
2009 An L, Xie H, Chin MH, Obradovic Z, Smith DJ, Megalooikonomou V Analysis of multiplex gene expression maps obtained by voxelation. BMC Bioinformatics 10 Suppl 4: S10. Mouse brain genes 19426449 7
2009 Andreassen R, Lunner S, Hoyheim B Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon (Salmo salar). BMC Genomics 10: 502. Atlantic salmon cDNAs 19878547 3
2009 Ansell A, Jerhammar F, Ceder R, Grafstrom R, Grenman R, Roberg K Matrix metalloproteinase-7 and -13 expression associate to cisplatin resistance in head and neck cancer cell lines. Oral Oncol 45: 866-871. Human cell line transcripts; squamous cell carcinoma 19442568 7,16
2009 Aranda B|etAl The IntAct molecular interaction database in 2010. Nucleic Acids Res 38: D525-531. 19850723 11,15
2009 Arighi CN, Liu H, Natale DA, Barker WC, Drabkin H, Blake JA, Smith B, Wu CH TGF-beta signaling proteins and the Protein Ontology. BMC Bioinformatics 10 Suppl 5: S3. 19426460 1,15
2009 Arnaud MB, Costanzo MC, Shah P, Skrzypek MS, Sherlock G Gene Ontology and the annotation of pathogen genomes: the case of Candida albicans. Trends Microbiol 17: 295-303. Candida albicans genome 19577928 1,4,16
2009 Arnaud MB|etAl The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community. Nucleic Acids Res 38: D420-427. 19773420 1,11
2009 Arpanahi A, Brinkworth M, Iles D, Krawetz SA, Paradowska A, Platts AE, Saida M, Steger K, Tedder P, Miller D Endonuclease-sensitive regions of human spermatozoal chromatin are highly enriched in promoter and CTCF binding sequences. Genome Res 19: 1338-1349. Human sperm DNA 19584098 13,16
2009 Aslett M|etAl TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic Acids Res 38: D457-462. 19843604 11
2009 Atias O, Chor B, Chamovitz DA Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network. BMC Syst Biol 3: 86. Arabidopsis transcripts 19728874 7
2009 Ayroles JF|etAl Systems genetics of complex traits in Drosophila melanogaster. Nat Genet 41: 299-307. Drosophila transcripts 19234471 7,13,18
2009 Baek JH, Woo TH, Kim CB, Park JH, Kim H, Lee S, Lee SH Differential gene expression profiles in the venom gland/sac of Orancistrocerus drewseni (Hymenoptera: Eumenidae). Arch Insect Biochem Physiol 71: 205-222. Orancistrocerus drewsen ESTs 19479740 5,7
2009 Bai X, Adams BJ, Ciche TA, Clifton S, Gaugler R, Hogenhout SA, Spieth J, Sternberg PW, Wilson RK, Grewal PS Transcriptomic analysis of the entomopathogenic nematode, Heterorhabditis bacteriophora TTO1. BMC Genomics 10: 205. Heterorhabditis bacteriophora ESTs 19405965 5,7
2009 Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37: W202-208. 19458158 10
2009 Bakheet TM, Doig AJ Properties and identification of human protein drug targets. Bioinformatics 25: 451-457. 19164304 8,13,16
2009 Bannon DI, Dillman JF, Hable MA, Phillips CS, Perkins EJ Global gene expression in rat brain and liver after oral exposure to the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). Chem Res Toxicol 22: 620-625. Rat brain transcripts; rat liver transcripts; RDX exposure 19239275 7,16
2009 Barrenas F, Chavali S, Holme P, Mobini R, Benson M Network properties of complex human disease genes identified through genome-wide association studies. PLoS One 4: e8090. 19956617 10.1371/journal.pone.0008090 13,16,17
2009 Baumer D, Lee S, Nicholson G, Davies JL, Parkinson NJ, Murray LM, Gillingwater TH, Ansorge O, Davies KE, Talbot K Alternative splicing events are a late feature of pathology in a mouse model of spinal muscular atrophy. PLoS Genet 5: e1000773. Mouse neuronal transcripts 20019802 7,16
2009 Baye TM, Wilke RA, Olivier M Genomic and geographic distribution of private SNPs and pathways in human populations. Per Med 6: 623-641. 20352079 13,18
2009 Bell RL|etAl Gene expression changes in the nucleus accumbens of alcohol-preferring rats following chronic ethanol consumption. Pharmacol Biochem Behav 94: 131-147. Rat brain transcripts; alcohol; binge drinking 19666046 7,16
2009 Benardete EA, Bergold PJ Genomic analysis of ischemic preconditioning in adult rat hippocampal slice cultures. Brain Res 1292: 107-122. Rat brain transcripts; ischemia 19631194 7,16
2009 Bhatia VN, Perlman DH, Costello CE, McComb ME Software Tool for Researching Annotations of Proteins: Open-Source Protein Annotation Software with Data Visualization. Anal Chem 81: 9819-9823. 19839595 3,8,10
2009 Bilder RM, Sabb FW, Parker DS, Kalar D, Chu WW, Fox J, Freimer NB, Poldrack RA Cognitive ontologies for neuropsychiatric phenomics research. Cogn Neuropsychiatry 14: 419-450. 19634038 14
2009 Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pages F, Trajanoski Z, Galon J ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25: 1091-1093. 19237447 10,17
2009 Binns D, Dimmer E, Huntley R, Barrell D, O'Donovan C, Apweiler R QuickGO: a web-based tool for Gene Ontology searching. Bioinformatics 25: 3045-3046. 19744993 1,10
2009 Blake A|etAl MouseBook: an integrated portal of mouse resources. Nucleic Acids Res 38: D593-599. 19854936 15
2009 Blake JA, Bult CJ, Eppig JT, Kadin JA, Richardson JE, The Mouse Genome Database genotypes::phenotypes. Nucleic Acids Res 37: D712-719. Mouse genome 18981050 1,4,11
2009 Blomster HA, Hietakangas V, Wu J, Kouvonen P, Hautaniemi S, Sistonen L Novel proteomics strategy brings insight into the prevalence of SUMO-2 target sites. Mol Cell Proteomics 8: 1382-1390. Mammalian SUMO proteins 19240082 8
2009 Blum T, Briesemeister S, Kohlbacher O MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction. BMC Bioinformatics 10: 274. 19723330 9,10,18
2009 Bluthgen N|etAl A systems biological approach suggests that transcriptional feedback regulation by dual-specificity phosphatase 6 shapes extracellular signal-related kinase activity in RAS-transformed fibroblasts. FEBS J 276: 1024-1035. 19154344 13,17
2009 Bollopragada S, Youssef R, Jordan F, Greer I, Norman J, Nelson S Term labor is associated with a core inflammatory response in human fetal membranes, myometrium, and cervix. Am J Obstet Gynecol 200: 104.e1-11. Mouse embryonic pituitary gland transcripts 19121663 7
2009 Bolognani F, Contente-Cuomo T, Perrone-Bizzozero NI Novel recognition motifs and biological functions of the RNA-binding protein HuD revealed by genome-wide identification of its targets. Nucleic Acids Res 38: 117-130. Mouse brain transcripts 19846595 7
2009 Borate BR, Chesler EJ, Langston MA, Saxton AM, Voy BH Comparison of threshold selection methods for microarray gene co-expression matrices. BMC Res Notes 2: 240. 19954523 7,17
2009 Bos CL|etAl Molecular subtypes of systemic sclerosis in association with anti-centromere antibodies and digital ulcers. Genes Immun 10: 210-218. 19129850 9,10
2009 Bousette N, Kislinger T, Fong V, Isserlin R, Hewel JA, Emil A, Gramolini AO Large-scale characterization and analysis of the murine cardiac proteome. J Proteome Res 8: 1887-1901. Mouse heart proteins 19714876 8
2009 Bowen NJ, Walker LD, Matyunina LV, Logani S, Totten KA, Benigno BB, McDonald JF Gene expression profiling supports the hypothesis that human ovarian surface epithelia are multipotent and capable of serving as ovarian cancer initiating cells. BMC Med Genomics 2: 71. Human ovarian epithelial transcripts 20040092 7,16
2009 Bowes JB, Snyder KA, Segerdell E, Jarabek CJ, Azam K, Zorn AM, Vize PD Xenbase: gene expression and improved integration. Nucleic Acids Res 38: D607-612. 19884130 15
2009 Boyd M, Bressendorff S, Moller J, Olsen J, Troelsen JT Mapping of HNF4alpha target genes in intestinal epithelial cells. BMC Gastroenterol 9: 68. Human intestinal epithelial cell line promoters 19761587 7,13,16
2009 Bradford JR, Needham CJ, Tedder P, Care MA, Bulpitt AJ, Westhead DR GO-At: In silico prediction of gene function in Arabidopsis thaliana by combining heterogeneous data. Plant J 61: 713-721. 19947983 9,10
2009 Bridges SM, Burgess SC, McCarthy FM Introduction to the proceedings of the Avian Genomics and Gene Ontology Annotation Workshop. BMC Genomics 10 Suppl 2: I1. 19607650 1,3
2009 Briesemeister S, Blum T, Brady S, Lam Y, Kohlbacher O, Shatkay H SherLoc2: a high-accuracy hybrid method for predicting subcellular localization of proteins. J Proteome Res 8: 5363-5366. 19764776 9,10
2009 Bright LA, Burgess SC, Chowdhary B, Swiderski CE, McCarthy FM Structural and functional-annotation of an equine whole genome oligoarray. BMC Bioinformatics 10 Suppl 11: S8. Horse genome array 19811692 1,4,7
2009 Brinkac LM|etAl Pathema: a clade-specific bioinformatics resource center for pathogen research. Nucleic Acids Res 38: D408-414. 19843611 11
2009 Bruheim S, Xi Y, Ju J, Fodstad O Gene expression profiles classify human osteosarcoma xenografts according to sensitivity to doxorubicin, cisplatin, and ifosfamide. Clin Cancer Res 15: 7161-7169. Human osteosarcoma transcripts 19920113 7,16
2009 Brustolini OJ, Fietto LG, Cruz CD, Passos FM Computational analysis of the interaction between transcription factors and the predicted secreted proteome of the yeast Kluyveromyces lactis. BMC Bioinformatics 10: 194. Kluyveromyces secreted proteins 19555482 7,8,19
2009 Bult CJ, Kadin JA, Richardson JE, Blake JA, Eppig JT, The Mouse Genome Database: enhancements and updates. Nucleic Acids Res 38: D586-592. Mouse genome 19864252 1,4,11,15
2009 Busacca S, Germano S, De Cecco L, Rinaldi M, Comoglio F, Favero F, Murer B, Mutti L, Pierotti M, Gaudino G MicroRNA signature of malignant mesothelioma with potential diagnostic and prognostic implications. Am J Respir Cell Mol Biol 42: 312-319. Human mesothelial cell miRNAs; mesothelioma 19502386 7,16
2009 Buza TJ, Kumar R, Gresham CR, Burgess SC, McCarthy FM Facilitating functional annotation of chicken microarray data. BMC Bioinformatics 10 Suppl 11: S2. Chicken genome array 19811685 1,4,7
2009 Calabrese R, Capriotti E, Fariselli P, Martelli PL, Casadio R Functional annotations improve the predictive score of human disease-related mutations in proteins. Hum Mutat 30: 1237-1244. 19514061 10,16,19
2009 Calligaris R, Bellarosa C, Foti R, Roncaglia P, Giraudi P, Krmac H, Tiribelli C, Gustincich S A transcriptome analysis identifies molecular effectors of unconjugated bilirubin in human neuroblastoma SH-SY5Y cells. BMC Genomics 10: 543. Human neuroblastoma cell transcripts 19925663 7,16
2009 Cameron TL, Belluoccio D, Farlie PG, Brachvogel B, Bateman JF Global comparative transcriptome analysis of cartilage formation in vivo. BMC Dev Biol 9: 20. Mouse fetal cartilage transcripts 19272164 7
2009 Capoccia BJ, Huh WJ, Mills JC How form follows functional genomics: Gene expression profiling gastric epithelial cells with a particular discourse on the parietal cell. Physiol Genomics 37: 67-78. Human transcripts (various tissues) 19208773 7,16
2009 Capomaccio S, Barone P, Reale L, Veronesi F, Rosellini D Isolation of genes from female sterile flowers in Medicago sativa. Sex Plant Reprod 22: 97-9107. Medicago sativa transcripts 20033460 7
2009 Cappuzzello C|etAl Gene expression profiles in peripheral blood mononuclear cells of chronic heart failure patients. Physiol Genomics 38: 233-240. Human blood cell transcripts; heart disease 19336532 7,16
2009 Capulli M, Rufo A, Teti A, Rucci N Global transcriptome analysis in mouse calvarial osteoblasts highlights sets of genes regulated by modeled microgravity and identifies a "mechanoresponsive osteoblast gene signature". J Cell Biochem 107: 240-252. Mouse osteoblast transcripts; microgravity 19288527 7,16
2009 Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, AmiGO Hub, Web Presence Working Group AmiGO: online access to ontology and annotation data. Bioinformatics 25: 288-289. 19033274 1,10
2009 Carneiro Pdos S, Peters LC, Vorraro F, Borrego A, Ribeiro OG, Starobinas N, Jensen JR, Cabrera WH, Ibanez OM, De Franco M Gene expression profiles of bone marrow cells from mice phenotype-selected for maximal or minimal acute inflammations: searching for genes in acute inflammation modifier loci. Immunology 128: e562-571. Mouse bone marrow transcripts 19740317 7,16
2009 Carvalho PC, Fischer JS, Chen EI, Domont GB, Carvalho MG, Degrave WM, Yates JR, Barbosa VC GO Explorer: A gene-ontology tool to aid in the interpretation of spectral counting data in shotgun proteomics. Proteome Sci 7: 6. 19239707 8,10
2009 Casel P, Moreews F, Lagarrigue S, Klopp C sigReannot: an oligo-set re-annotation pipeline based on similarities with the Ensembl transcripts and Unigene clusters. BMC Proc 3 Suppl 4: S3. 19615116 10
2009 Caspi R|etAl The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 38: D473-479. 19850718 11
2009 Castellanos-Rubio A, Santin I, Martin-Pagola A, Irastorza I, Castano L, Vitoria JC, Bilbao JR Long-term and acute effects of gliadin on small intestine of patients on potentially pathogenic networks in celiac disease. Autoimmunity 43: 131-139. Human intestinal transcripts; celiac disease 19814655 7,16
2009 Caye-Thomasen P, Borup R, Stangerup SE, Thomsen J, Nielsen FC Deregulated genes in sporadic vestibular schwannomas. Otol Neurotol 31: 256-266. Human nerve transcripts; vestibular schwannoma 19816230 7,16
2009 Chacko E, Ranganathan S Genome-wide analysis of alternative splicing in cow: implications in bovine as a model for human diseases. BMC Genomics 10 Suppl 3: S11. Bovine genes 19958474 13,18
2009 Chagoyen M, Pazos F Quantifying the biological significance of Gene Ontology bio-logical processes - implications for the analysis of systems-wide data. Bioinformatics 26: 378-384. 19965879 13
2009 Chambers KF, Bacon JR, Kemsley EK, Mills RD, Ball RY, Mithen RF, Traka MH Gene expression profile of primary prostate epithelial and stromal cells in response to sulforaphane or iberin exposure. Prostate 69: 1411-1421. Human prostate transcripts; prostate cancer 19489030 7,16
2009 Chang KO The role of cholesterol pathways in norovirus replication. J Virol 83: 8587-8595. Mammalian cell line transcripts; Norwalk virus infection 19515767 7,16
2009 Chen CC, Lin CY, Lo YS, Yang JM PPISearch: a web server for searching homologous protein-protein interactions across multiple species. Nucleic Acids Res 37: W369-375. 19417070 8,10,19
2009 Chen FC, Chen YZ, Chuang TJ CNVVdb: a database of copy number variations across vertebrate genomes. Bioinformatics 25: 1419-1421. 19321736 11
2009 Chen FY, Liu HP, Bo J, Ren HL, Wang KJ Identification of genes differentially expressed in hemocytes of Scylla paramamosain in response to lipopolysaccharide. Fish Shellfish Immunol 28: 167-177. Scylla paramamosain cDNAs 19854276 3,7
2009 Chen GQ, Zhao ZW, Zhou HY, Liu YJ, Yang HJ Systematic analysis of microRNA involved in resistance of the MCF-7 human breast cancer cell to doxorubicin. Med Oncol 27: 406-415. Human breast cancer cell transcripts; multidrug resistance 19412672 7,16
2009 Chen H, Ding L, Wu Z, Yu T, Dhanapalan L, Chen JY Semantic web for integrated network analysis in biomedicine. Brief Bioinform 10: 177-192. 19304873 17
2009 Chen H, Li C, Fang M, Zhu M, Li X, Zhou R, Li K, Zhao S Understanding Haemophilus parasuis infection in porcine spleen through a transcriptomics approach. BMC Genomics 10: 64. Porcine spleen transcripts 19196461 7
2009 Chen L, Qian Z, Fen K, Cai Y Prediction of interactiveness between small molecules and enzymes by combining gene ontology and compound similarity. J Comput Chem 31: 1766-1776. 20033913 13,19
2009 Chen X, Wang L Integrating biological knowledge with gene expression profiles for survival prediction of cancer. J Comput Biol 16: 265-278. Human transcripts; cancer 19183004 7,16
2009 Cheng JS, Ding MZ, Tian HC, Yuan YJ Inoculation-density-dependent responses and pathway shifts in Saccharomyces cerevisiae. Proteomics 9: 4704-4713. Saccharomyces proteins 19743421 8,17
2009 Chibucos MC, Collmer CW, Torto-Alalibo T, Gwinn-Giglio M, Lindeberg M, Li D, Tyler BM Programmed cell death in host-symbiont associations, viewed through the Gene Ontology. BMC Microbiol 9 Suppl 1: S5. 19278553 1,3,13,18
2009 Chibucos MC, Tseng TT, Setubal JC Describing commonalities in microbial effector delivery using the Gene Ontology. Trends Microbiol 17: 312-319. Microbial genomes 19576779 1,4,18
2009 Chibucos MC, Tyler BM Common themes in nutrient acquisition by plant symbiotic microbes, described by the Gene Ontology. BMC Microbiol 9 Suppl 1: S6. 19278554 1,3,13,18
2009 Cho YR, Zhang A, Xu X Semantic similarity based feature extraction from microarray expression data. Int J Data Min Bioinform 3: 333-345. 19623774 7,12
2009 Choi KH, Zepp ME, Higgs BW, Weickert CS, Webster MJ Expression profiles of schizophrenia susceptibility genes during human prefrontal cortical development. J Psychiatry Neurosci 34: 450-458. Human brain transcripts 19949721 7,16
2009 Choi Y, Tee JB, Gallegos TF, Shah MM, Oishi H, Sakurai H, Kitamura S, Wu W, Bush KT, Nigam SK Neuropeptide Y functions as a facilitator of GDNF-induced budding of the Wolffian duct. Development 136: 4213-4224. Rat Wolffian duct transcripts 19934016 7,16
2009 Christie KR, Hong EL, Cherry JM Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns. Trends Microbiol 17: 286-294. Saccharomyces cerevisiae genome 19577472 1,4
2009 Cibrian-Jaramillo A, Martienssen RA Darwin's "Abominable Mystery": the role of RNA interference in the evolution of flowering plants. Cold Spring Harb Symp Quant Biol 74: 267-273. 20508061 7,18
2009 Cochrane GR, Galperin MY The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources. Nucleic Acids Res 38: D1-4. 19965766 11
2009 Colak D, Kaya N, Al-Zahrani J, Al Bakheet A, Muiya P, Andres E, Quackenbush J, Dzimiri N Left ventricular global transcriptional profiling in human end-stage dilated cardiomyopathy. Genomics 94: 20-31. Human heart transcripts; idiopathic dilated cardiomyopathy 19332114 7,16
2009 Conde-Pueyo N, Munteanu A, Sole RV, Rodriguez-Caso C Human synthetic lethal inference as potential anti-cancer target gene detection. BMC Syst Biol 3: 116. 20015360 13,16
2009 Coram TE, Settles ML, Chen X Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array. BMC Genomics 10: 253. Wheat antisense transcripts 19480707 7
2009 Corradi L, Mirisola V, Porro I, Torterolo L, Fato M, Romano P, Pfeffer U Survival Online: a web-based service for the analysis of correlations between gene expression and clinical and follow-up data. BMC Bioinformatics 10 Suppl 12: S10. 19828070 7,10,16
2009 Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM; the Saccharomyces Genome Database Project New mutant phenotype data curation system in the Saccharomyces Genome Database. Database (Oxford) 2009: bap001. 20157474 1,4,11
2009 Costello JC, Dalkilic MM, Beason SM, Gehlhausen JR, Patwardhan R, Middha S, Eads BD, Andrews JR Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function. Genome Biol 10: R97. 19758432 7,8,17
2009 Costello JC, Schrider D, Gehlhausen J, Dalkilic M Data-driven ontologies. Pac Symp Biocomput 2008: 15-26. 19213131 14
2009 Covert J, Mathison AJ, Eskra L, Banai M, Splitter G Brucella melitensis, B. neotomae and B. ovis elicit common and distinctive macrophage defense transcriptional responses. Exp Biol Med (Maywood) 234: 1450-1467. Macrophage transcripts 19934366 7
2009 Cox J, Matic I, Hilger M, Nagaraj N, Selbach M, Olsen JV, Mann M A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics. Nat Protoc 4: 698-705. 19373234 8,10
2009 Crack PJ, Gould J, Bye N, Ross S, Ali U, Habgood MD, Morganti-Kossman C, Saunders NR, Hertzog PJ, The genomic profile of the cerebral cortex after closed head injury in mice: effects of minocycline. J Neural Transm 116: 1-12. Mouse brain transcripts; head injury 19018450 7,16
2009 Cuervo P, De Jesus JB, Saboia-Vahia L, Mendonca-Lima L, Domont GB, Cupolillo E Proteomic characterization of the released/secreted proteins of Leishmania (Viannia) braziliensis promastigotes. J Proteomics 73: 79-92. Leishmania (Viannia) braziliensis promastigote proteins 19703603 8
2009 Culhane AC|etAl GeneSigDB--a curated database of gene expression signatures. Nucleic Acids Res 38: D716-725. 19934259 11
2009 Dai X, Wang G, Yang DS, Tang Y, Broun P, Marks MD, Sumner LW, Dixon RA, Zhao PX TrichOME: A comparative omics database for plant trichomes. Plant Physiol 152: 44-54. Plant trichome ESTs 19939948 5,11
2009 Dakhova O, Ozen M, Creighton CJ, Li R, Ayala G, Rowley D, Ittmann M Global gene expression analysis of reactive stroma in prostate cancer. Clin Cancer Res 15: 3979-3989. Human prostate transcripts; prostate cancer 19509179 7,16
2009 Dal Cin V, Barbaro E, Danesin M, Murayama H, Velasco R, Ramina A Fruitlet abscission: A cDNA-AFLP approach to study genes differentially expressed during shedding of immature fruits reveals the involvement of a putative auxin hydrogen symporter in apple (Malus domestica L. Borkh). Gene 442: 26-36. Apple cDNAs 19393302 7
2009 Dan A, Ofran Y, Kliger Y Large-scale analysis of secondary structure changes in proteins suggests a role for disorder-to-order transitions in nucleotide binding proteins. Proteins 78: 236-248. 19676113 8,13
2009 Danko CG, Pertsov AM Identification of gene co-regulatory modules and associated cis-elements involved in degenerative heart disease. BMC Med Genomics 2: 31. Human heart transcripts; cardiomyopathy 19476647 7,16
2009 Das B, Heimeier RA, Buchholz DR, Shi YB Identification of direct thyroid hormone response genes reveals the earliest gene regulation programs during frog metamorphosis. J Biol Chem 284: 34167-34178. 19801647 11,13
2009 Dassanayake M, Haas JS, Bohnert HJ, Cheeseman JM Shedding light on an extremophile lifestyle through transcriptomics. New Phytol 183: 764-775. Mangrove transcripts 19549131 7
2009 Davidsen T, Beck E, Ganapathy A, Montgomery R, Zafar N, Yang Q, Madupu R, Goetz P, Galinsky K, White O, Sutton G The comprehensive microbial resource. Nucleic Acids Res 38: D340-345. 19892825 11
2009 Davidson ME, Kerepesi LA, Soto A, Chan VT D: -Serine exposure resulted in gene expression changes implicated in neurodegenerative disorders and neuronal dysfunction in male Fischer 344 rats. Arch Toxicol 83: 747-762. Rat brain transcripts 19212759 7,16
2009 De Bodt S, Proost S, Vandepoele K, Rouze P, Van de Peer Y Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. BMC Genomics 10: 288. Arabidopsis proteins 19563678 8,17,19
2009 Dean MD, Clark NL, Findlay GD, Karn RC, Yi X, Swanson WJ, Maccoss MJ, Nachman MW Proteomics and comparative genomic investigations reveal heterogeneity in evolutionary rate of male reproductive proteins in mice (Mus domesticus). Mol Biol Evol 26: 1733-1743. Mouse reproductive tract proteins 19420050 8,16
2009 Dehal PS|etAl MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res 38: D396-400. 19906701 11
2009 Dejeans N, Auclair S, Chauvet S, Milenkovic D, Mazur A Transcriptomic analysis of aorta from a short-term high-fat diet fed mouse reveals changes in the expression of vessel structure genes. J Physiol Pharmacol 60 Suppl 1: 37-45. Mouse blood vessel transcripts; atherogenesis 19609012 7,16
2009 Deng L, Zhang D, Richards E, Tang X, Fang J, Long F, Wang Y Constructing an initial map of transmission distortion based on high density HapMap SNPs across the human autosomes. J Genet Genomics 36: 703-709. 20129397 13,18
2009 Diella F, Chabanis S, Luck K, Chica C, Ramu C, Nerlov C, Gibson TJ KEPE--a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors. Bioinformatics 25: 1-5. 19033273 8,18
2009 Dillman JF, Phillips CS, Kniffin DM, Tompkins CP, Hamilton TA, Kan RK Gene expression profiling of rat hippocampus following exposure to the acetylcholinesterase inhibitor soman. Chem Res Toxicol 22: 633-638. Rat brain transcripts; soman exposure 19281266 7,16
2009 Donate C, Balasch JC, Callol A, Bobe J, Tort L, Mackenzie S The effects of immunostimulation through dietary manipulation in the rainbow trout; evaluation of mucosal immunity. Mar Biotechnol (NY) 12: 88-99. Rainbow trout transcripts 19609615 7
2009 Dondrup M|etAl EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data. BMC Bioinformatics 10: 50. 19200358 15
2009 Dong Q, Zhou S, Deng L, Guan J Gene Ontology-based protein function prediction by using sequence composition information. Protein Pept Lett 17: 789-795. 19995340 9
2009 Donson AM, Birks DK, Barton VN, Wei Q, Kleinschmidt-Demasters BK, Handler MH, Waziri AE, Wang M, Foreman NK Immune gene and cell enrichment is associated with a good prognosis in ependymoma. J Immunol 183: 7428-7440. Human genes; ependymoma 19917695 7,16
2009 Dotan-Cohen D, Kasif S, Melkman AA Seeing the forest for the trees: Using the Gene Ontology to re-structure hierarchical clustering. Bioinformatics 25: 1789-1795. 19497934 7,17
2009 Dotan-Cohen D, Letovsky S, Melkman AA, Kasif S Biological process linkage networks. PLoS ONE 4: e5313. 19390589 9,17
2009 Dowell J, Johnson J, Li L Identification of Astrocyte Secreted Proteins with a Combination of Shotgun Proteomics and Bioinfomatics. J Proteome Res 8: 4135-4143. Astrocyte proteome 19469553 8
2009 Dowell KG, McAndrews-Hill MS, Hill DP, Drabkin HJ, Blake JA Integrating text mining into the MGI biocuration workflow. Database (Oxford) 2009: bap019. 20157492 1,11,12
2009 Du J, Xu H, Wei N, Wakim B, Halligan B, Pritchard KA, Shi Y Identification of proteins interacting with GTP cyclohydrolase I. Biochem Biophys Res Commun 385: 143-147. Human kidney cell line proteins 19442649 8
2009 Du P, Feng G, Flatow J, Song J, Holko M, Kibbe WA, Lin SM From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations. Bioinformatics 25: i63-68. 19478018 15
2009 Du Z, Li L, Chen CF, Yu PS, Wang JZ G-SESAME: web tools for GO-term-based gene similarity analysis and knowledge discovery. Nucleic Acids Res 37: W345-349. 19491312 10,12
2009 Du Z, Zhou X, Li L, Su Z plantsUPS: a database of plants' Ubiquitin Proteasome System. BMC Genomics 10: 227. Plant ubiquitin systems 19445698 3,11
2009 Duan J, Li R, Cheng D, Fan W, Zha X, Cheng T, Wu Y, Wang J, Mita K, Xiang Z, Xia Q SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology. Nucleic Acids Res 38: D453-456. 19793867 11
2009 Dumas E, Desvaux M, Chambon C, Hebraud M Insight into the core and variant exoproteomes of Listeria monocytogenes species by comparative subproteomic analysis. Proteomics 9: 3136-3155. Listeria monocytogenes proteins 19526548 8,16
2009 Elam MB|etAl Hepatic gene expression in morbidly obese women: implications for disease susceptibility. Obesity (Silver Spring) 17: 1563-1573. Human liver transcripts; obesity 19265796 7,16
2009 Ema M, Ise R, Kato H, Oneda S, Hirose A, Hirata-Koizumi M, Singh AV, Knudsen TB, Ihara T Fetal malformations and early embryonic gene expression response in cynomolgus monkeys maternally exposed to thalidomide. Reprod Toxicol 29: 49-56. Cynomolgus monkey embryonic transcripts; thalidomide exposure 19751816 7,16
2009 Endo T, Uzawa K, Suzuki H, Tanzawa H, Ichikawa T Characteristic gene expression profiles of benign prostatic hypertrophy and prostate cancer. Int J Oncol 35: 499-509. Human prostate transcripts 19639170 7,16
2009 Erdin S, Ward RM, Venner E, Lichtarge O Evolutionary trace annotation of protein function in the structural proteome. J Mol Biol 396: 1451-1473. 20036248 8,9
2009 Evans P, Dampier W, Ungar L, Tozeren A Prediction of HIV-1 virus-host protein interactions using virus and host sequence motifs. BMC Med Genomics 2: 27. Human proteins, HIV-1 proteins 19450270 8,16
2009 Fang H, Harris SC, Su Z, Chen M, Qian F, Shi L, Perkins R, Tong W ArrayTrack: An FDA and public genomic tool. Methods Mol Biol 563: 379-398. 19597796 10,11
2009 Fasanaro P|etAl An integrated approach for experimental target identification of hypoxia-induced miR-210. J Biol Chem 284: 35134-35143. Human miRNA targets 19826008 7,16
2009 Fedorov VB|etAl Elevated expression of protein biosynthesis genes in liver and muscle of hibernating black bears (Ursus americanus). Physiol Genomics 37: 108-118. Bear liver transcripts; bear muscle transcripts; hibernation 19240299 7
2009 Feltrin E|etAl Muscle research and Gene Ontology: New standards for improved data integration. BMC Med Genomics 2: 6. 19178689 1,3,14
2009 Feng ZP|etAl Transcriptome analysis of the central nervous system of the mollusc Lymnaea stagnalis. BMC Genomics 10: 451. Lymnaea stagnalis ESTs 19775440 5,7
2009 Finigan JH|etAl Activated protein C protects against ventilator-induced pulmonary capillary leak. Am J Physiol Lung Cell Mol Physiol 296: L1002-1011. Mouse lung transcripts; acute lung injury 19363121 7,16
2009 Fitzpatrick JM, Peak E, Perally S, Chalmers IW, Barrett J, Yoshino TP, Ivens AC, Hoffmann KF Anti-schistosomal intervention targets identified by lifecycle transcriptomic analyses. PLoS Negl Trop Dis 3: e543. Schistosoma mansoni transcripts 19885392 7,16
2009 Fleury E|etAl Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase. BMC Genomics 10: 341. Pacific oyster ESTs 19640306 5
2009 Flicek P|etAl Ensembl's 10th year. Nucleic Acids Res 38: D557-562. 19906699 11
2009 Floyd HS, Chen LC, Vallanat B, Dreher K Fine ambient air particulate matter exposure induces molecular alterations associated with vascular disease progression within plaques of atherosclerotic susceptible mice. Inhal Toxicol 21: 394-403. Mouse vascular tissue transcripts; particulate exposure 19496694 7,16
2009 Foley ME, Anderson JV, Chao WS, Dogramacı M, Horvath DP Initial changes in the transcriptome of Euphorbia esula seeds induced to germinate with a combination of constant and diurnal alternating temperatures. Plant Mol Biol 73: 131-142. Euphorbia esula transcripts 19916049 7
2009 Fontana P, Cestaro A, Velasco R, Formentin E, Toppo S Rapid annotation of anonymous sequences from genome projects using semantic similarities and a weighting scheme in gene ontology. PLoS ONE 4: e4619. 19247487 9,10
2009 Fujikane T|etAl Genomic screening for genes upregulated by demethylation revealed novel targets of epigenetic silencing in breast cancer. Breast Cancer Res Treat 122: 699-710. Human genes; breast cancer 19859801 7,16
2009 Fukuchi S, Homma K, Sakamoto S, Sugawara H, Tateno Y, Gojobori T, Nishikawa K The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions. Nucleic Acids Res 37: D333-337. 18987007 6,11
2009 Gai Y|etAl The construction of an immune genes enriched cDNA library and the analysis of 7535 ESTs from Chinese mitten crab Eriocheir sinensis. Fish Shellfish Immunol 27: 684-694. Chinese mitten crab ESTs 19748587 5
2009 Galla G, Barcaccia G, Ramina A, Collani S, Alagna F, Baldoni L, Cultrera NG, Martinelli F, Sebastiani L, Tonutti P Computational annotation of genes differentially expressed along olive fruit development. BMC Plant Biol 9: 128. Olive genes 19852839 3,7
2009 Gao C, Dang X, Chen Y, Wilkins D Graph ranking for exploratory gene data analysis. BMC Bioinformatics 10 Suppl 11: S19. 19811684 7
2009 Gao H, Wang S, Li H, Meng H [Screening of sexual differentially expressed genes in the chicken early embryonic gonads using DNA microarray] Sheng Wu Gong Cheng Xue Bao 25: 230-234. Chicken gonad transcripts 19459328 7
2009 Gao M, Skolnick J A threading-based method for the prediction of DNA-binding proteins with application to the human genome. PLoS Comput Biol 5: e1000567. 19911048 19
2009 Garcia-Marcos A, Pacheco R, Martianez J, Gonzalez-Jara P, Diaz-Ruiz JR, Tenllado F Transcriptional changes and oxidative stress associated with the synergistic interaction between potato virus X and potato virus Y and their relationship with symptom expression. Mol Plant Microbe Interact 22: 1431-1444. Nicotiana benthamiana transcripts 19810812 7
2009 Garcia-Reyero N, Kroll KJ, Liu L, Orlando EF, Watanabe KH, Sepulveda MS, Villeneuve DL, Perkins EJ, Ankley GT, Denslow ND Gene expression responses in male fathead minnows exposed to binary mixtures of an estrogen and antiestrogen. BMC Genomics 10: 308. Minnow gonad transcripts 19594897 7
2009 Gattiker A, Dessimoz C, Schneider A, Xenarios I, Pagni M, Rougemont J The Microbe browser for comparative genomics. Nucleic Acids Res 37: W296-299. 19406928 10,18
2009 Gharib S, Vaisar T, Aitken ML, Park DR, Heinecke JW, Fu X Mapping the lung proteome in cystic fibrosis. J Proteome Res 8: 3020-3028. Human lung proteins; cystic fibrosis 19354268 8,16
2009 Giglio MG, Collmer CW, Lomax J, Ireland A Applying the Gene Ontology in microbial annotation. Trends Microbiol 17: 262-268. Microbial genomes 19577473 1,4
2009 Gillis J, Pavlidis P A methodology for the analysis of differential coexpression across the human lifespan. BMC Bioinformatics 10: 306. Human transcripts 19772654 7,16,17
2009 Giusti B, Rossi L, Lapini I, Magi A, Pratesi G, Lavitrano M, Biasi GM, Pulli R, Pratesi C, Abbate R Gene expression profiling of peripheral blood in patients with abdominal aortic aneurysm. Eur J Vasc Endovasc Surg 38: 104-112. Human blood transcripts; aortic aneurysm 19233690 7,16
2009 Gkoutos GV, Mungall C, Dolken S, Ashburner M, Lewis S, Hancock J, Schofield P, Kohler S, Robinson PN Entity/quality-based logical definitions for the human skeletal phenome using PATO. Conf Proc IEEE Eng Med Biol Soc 1: 7069-7072. 19964203 15
2009 Goncalves JP, Madeira SC, Oliveira AL BiGGEsTS: integrated environment for biclustering analysis of time series gene expression data. BMC Res Notes 2: 124. 19583847 7,10
2009 Gonzalez-Begne M, Lu B, Han X, Hagen FK, Hand AR, Melvin JE, Yates JR Proteomic analysis of human parotid gland exosomes by multidimensional protein identification technology (MudPIT). J Proteome Res 8: 1304-1314. Human salivary gland proteins 19199708 8,16
2009 Goodman M, Sterner KN, Islam M, Uddin M, Sherwood CC, Hof PR, Hou ZC, Lipovich L, Jia H, Grossman LI, Wildman DE Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries. Proc Natl Acad Sci U S A 106: 20824-20829. 19926857 16,18
2009 Gould CM|etAl ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Res 38: D167-180. 19920119 11
2009 Graham NS, Clutterbuck AL, James N, Lea RG, Mobasheri A, Broadley MR, May ST Equine transcriptome quantification using human GeneChip arrays can be improved using genomic DNA hybridisation and probe selection. Vet J 186: 323-327. Equine transcripts 19786357 7
2009 Granchi D, Ochoa G, Leonardi E, Devescovi V, Baglio SR, Osaba L, Baldini N, Ciapetti G Gene expression patterns related to osteogenic differentiation of bone marrow-derived mesenchymal stem cells during ex vivo expansion. Tissue Eng Part C Methods 16: 511-524. Rat mlain transcripts; propofol exposure 19686055 8,16
2009 Grillo G|etAl UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res 38: D75-80. 19880380 11
2009 Guda P, Chittur SV, Guda C Comparative analysis of protein-protein interactions in cancer-associated genes. Genomics Proteomics Bioinformatics 7: 25-36. Human transcripts; human proteins; cancer 19591789 7,8,16,17
2009 Guo CJ, Pan Q, Li DG, Sun H, Liu BW miR-15b and miR-16 are implicated in activation of the rat hepatic stellate cell: An essential role for apoptosis. J Hepatol 50: 766-778. rat liver miRNAs 19232449 7,16
2009 Guyonnet B, Marot G, Dacheux JL, Mercat MJ, Schwob S, Jaffrezic F, Gatti JL The adult boar testicular and epididymal transcriptomes. BMC Genomics 10: 369. Boar transcripts 19664223 7
2009 Hackenberg M, Lasso G, Matthiesen R ContDist: a tool for the analysis of quantitative gene and promoter properties. BMC Bioinformatics 10: 7. Human lymphocyte transcripts; B cell chronic lymphocytic leukemia 19128472 7,16
2009 Haegeman A, Jacob J, Vanholme B, Kyndt T, Mitreva M, Gheysen G Expressed sequence tags of the peanut pod nematode Ditylenchus africanus: the first transcriptome analysis of an Anguinid nematode. Mol Biochem Parasitol 167: 32-40. Ditylenchus africanus ESTs 19383517 5,7
2009 Han FM, Zhang XM, Xia QS, Wang JJ, Chen Y Gene expression profiling of mice liver tissue after intragastric administration of Chinese nutgall extract. Fen Zi Xi Bao Sheng Wu Xue Bao 42: 101-108. Mouse liver transcripts; Chinese nutgall 19537193 7
2009 Hang X|etAl Transcription and splicing regulation in human umbilical vein endothelial cells under hypoxic stress conditions by exon array. BMC Genomics 10: 126. Human umbilical vein endothelial cell transcripts; hypoxia 19320972 7,16
2009 Harel A, Inger A, Stelzer G, Strichman-Almashanu L, Dalah I, Safran M, Lancet D GIFtS: annotation landscape analysis with GeneCards. BMC Bioinformatics 10: 348. 19852797 3,11
2009 Harris TW|etAl WormBase: a comprehensive resource for nematode research. Nucleic Acids Res 38: D463-467. 19910365 1,11,15
2009 Hartung M, Kirsten T, Gross A, Rahm E OnEX: Exploring changes in life science ontologies. BMC Bioinformatics 10: 250. 19678926 10
2009 Hassan SS|etAl The transcriptome of cervical ripening in human pregnancy before the onset of labor at term: Identification of novel molecular functions involved in this process. J Matern Fetal Neonatal Med 22: 1183-1193. Human cervical transcripts 19883264 7,16
2009 Hatfield K, Oyan AM, Ersvaer E, Kalland KH, Lassalle P, Gjertsen BT, Bruserud O Primary human acute myeloid leukaemia cells increase the proliferation of microvascular endothelial cells through the release of soluble mediators. Br J Haematol 144: 53-68. Human blood cell transcripts; leukemia 19016730 7,16
2009 Hauser NC, Dukalska M, Fellenberg K, Rupp S From experimental setup to data analysis in transcriptomics: copper metabolism in the human pathogen Candida albicans. J Biophotonics 2: 262-268. Candida albicans transcripts 19367594 7
2009 He H, Cheng M, Yang X, Meng J, He A, Zheng X, Li Z, Guo P, Pan Z, Zhan X Preliminary molecular characterization of the human pathogen Angiostrongylus cantonensis. BMC Mol Biol 10: 97. Angiostrongylus cantonensis cDNAs 19852860 3,16
2009 He M, Wang Y, Li W PPI finder: a mining tool for human protein-protein interactions. PLoS ONE 4: e4554. Human proteins 19234603 8,10,16
2009 He Q, Berg A, Li Y, Vallejos CE, Wu R Mapping genes for plant structure, development and evolution: functional mapping meets ontology. Trends Genet 26: 39-46. 19945189 15
2009 Hebels DG, Jennen DG, Kleinjans JC, de Kok TM Molecular signatures of N-nitroso compounds in Caco-2 cells: implications for colon carcinogenesis. Toxicol Sci 108: 290-300. Human colon cancer cell line transcripts; nitroso compound exposure 19221148 7,16
2009 Hedegaard J|etAl Methods for interpreting lists of affected genes obtained in a DNA microarray experiment. BMC Proc 3 Suppl 4: S5. 19615118 7,10
2009 Hennetin J, Pehkonen P, Bellis M Construction and use of gene expression covariation matrix. BMC Bioinformatics 10: 214. 19594909 7
2009 Herbert JM, Buffa FM, Vorschmitt H, Egginton S, Bicknell R A new procedure for determining the genetic basis of a physiological process in a non-model species, illustrated by cold induced angiogenesis in the carp. BMC Genomics 10: 490. Carp genes 19852815 3,7
2009 Herrmann C, Berard S, Tichit L SimCT: a generic tool to visualize ontology based relationships for biological objects. Bioinformatics 25: 3197-3198. 19776214 10,15
2009 Hill DP, Berardini TZ, Howe DG, Van Auken KM Representing ontogeny through ontology: A developmental biologist's guide to the gene ontology. Mol Reprod Dev 77: 314-329. 19921742 1,2,3,13
2009 Hollenhorst PC, Chandler KJ, Poulsen RL, Johnson WE, Speck NA, Graves BJ DNA specificity determinants associate with distinct transcription factor functions. PLoS Genet 5: e1000778. 20019798 7,13
2009 Holmans P|etAl Gene Ontology analysis of GWA study data sets provides insights into the biology of bipolar disorder. Am J Hum Genet 85: 13-24. Human SNPs; bipolar disorder 19539887 10,13,16
2009 Hong SE, Heo HS, Kim DH, Kim MS, Kim CH, Lee J, Yoo MA, Yu BP, Leeuwenburgh C, Chung HY Revealing system-level correlations between aging and calorie restriction using a mouse transcriptome. Age (Dordr) 32: 15-30. Mouse transcripts 19590981 7,16,17
2009 Hossain MM, Ghanem N, Hoelker M, Rings F, Phatsara C, Tholen E, Schellander K, Tesfaye D Identification and characterization of miRNAs expressed in the bovine ovary. BMC Genomics 10: 443. Bovine ovary miRNAs 19765282 7
2009 Hsiao A, Subramaniam S Bivariate microarray analysis: statistical interpretation of two-channel functional genomics data. Syst Synth Biol 2: 95-9104. 19680790 7
2009 Hu JC, Karp PD, Keseler IM, Krummenacker M, Siegele DA What we can learn about Escherichia coli through application of Gene Ontology. Trends Microbiol 17: 269-278. E. coli genome 19576778 1,4,14
2009 Hu Y, Li P, Hao S, Liu L, Zhao J, Hou Y Differential expression of microRNAs in the placentae of Chinese patients with severe pre-eclampsia. Clin Chem Lab Med 47: 923-929. Human placental miRNAs; pre-eclampsia 19642860 7,16
2009 Hu Z, Hung JH, Wang Y, Chang YC, Huang CL, Huyck M, Delisi C VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. Nucleic Acids Res 37: W115-121. 19465394 10,17
2009 Hua YJ, Tang ZY, Tu K, Zhu L, Li YX, Xie L, Xiao HS Identification and target prediction of miRNAs specifically expressed in rat neural tissue. BMC Genomics 10: 214. Rat neural miRNAs 19426523 7
2009 Huang WL, Tung CW, Huang HL, Ho SY Predicting protein subnuclear localization using GO-amino-acid composition features. Biosystems 98: 73-79. 19583993 8,9
2009 Huang YC, Li Z, Carter JD, Soukup JM, Schwartz DA, Yang IV Fine ambient particles induce oxidative stress and metal binding genes in human alveolar macrophages. Am J Respir Cell Mol Biol 41: 544-552. Human lung transcripts; particulate pollution 19251948 7,16
2009 Hulsegge I, Kommadath A, Smits MA Globaltest and GOEAST: two different approaches for Gene Ontology analysis. BMC Proc 3 Suppl 4: S10. 19615110 10
2009 Hunter WB, Smith MT, Hunnicutt LE Analysis and functional annotation of expressed sequence tags from the Asian longhorned beetle, Anoplophora glabripennis. J Insect Sci 9: 21. Asian longhorned beetle ESTs 19619025 5
2009 Huntley RP, Binns D, Dimmer E, Barrell D, O'Donovan C, Apweiler R QuickGO: a user tutorial for the web-based Gene Ontology browser. Database (Oxford) 2009: bap010. 20157483 1,10
2009 Hur J, Schuyler AD, States DJ, Feldman EL SciMiner: Web-based literature mining tool for target identification and functional enrichment analysis. Bioinformatics 25: 838-840. 19188191 10,12
2009 Huss JW, Lindenbaum P, Martone M, Roberts D, Pizarro A, Valafar F, Hogenesch JB, Su AI The Gene Wiki: community intelligence applied to human gene annotation. Nucleic Acids Res 38: D633-639. 19755503 11
2009 Huttenhower C, Mehmood SO, Troyanskaya OG Graphle: Interactive exploration of large, dense graphs. BMC Bioinformatics 10: 417. 20003429 10
2009 Hvidsten TR, Laegreid A, Kryshtafovych A, Andersson G, Fidelis K, Komorowski J A comprehensive analysis of the structure-function relationship in proteins based on local structure similarity. PLoS One 4: e6266. 19603073 8,19
2009 Hwang T, Park T Identification of differentially expressed sub-networks based on multivariate ANOVA scoring method. BMC Bioinformatics 10: 128. 19405941 8,13,17
2009 Irles P, Belles X, Piulachs MD Identifying genes related to choriogenesis in insect panoistic ovaries by Suppression Subtractive Hybridization. BMC Genomics 10: 206. Cockroach genes 19405973 7
2009 Javierre BM|etAl Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus. Genome Res 20: 170-179. 20028698 13,16
2009 Jeong SK|etAl BiomarkerDigger: A versatile disease proteome database and analysis platform for the identification of plasma cancer biomarkers. Proteomics 9: 3729-3740. 19639590 8,11
2009 Jergil M, Kultima K, Gustafson AL, Dencker L, Stigson M Valproic acid-induced deregulation in vitro of genes associated in vivo with neural tube defects. Toxicol Sci 108: 132-148. Mouse embryonic cell line transcripts 19136453 7,16
2009 Jeron A, Pfoertner S, Bruder D, Geffers R, Hammerer P, Hofmann R, Buer J, Schrader AJ Frequency and gene expression profile of regulatory T cells in renal cell carcinoma. Tumour Biol 30: 160-170. Human T cell transcripts 19609102 7,16
2009 Jia L, Zhang L, Shao C, Song E, Sun W, Li M, Gao Y An attempt to understand kidney's protein handling function by comparing plasma and urine proteomes. PLoS ONE 4: e5146. Human plasma proteins; human urine proteins 19381340 8,16
2009 Jiang H, Yin Y, Zhang X, Hu S, Wang Q Chasing relationships between nutrition and reproduction: A comparative transcriptome analysis of hepatopancreas and testis from Eriocheir sinensis. Comp Biochem Physiol Part D Genomics Proteomics 4: 227-234. 20403758 7
2009 Jiang M, Ma Y, Chen C, Fu X, Yang S, Li X, Yu G, Mao Y, Xie Y, Li Y Androgen-Responsive Gene Database: Integrated knowledge on androgen-responsive genes. Mol Endocrinol 23: 1927-1933. Mammalian androgen-responsive genes 19762544 7,11,16
2009 Joenvaara S|etAl Caveolar transport through nasal epithelium of birch pollen allergen Bet v 1 in allergic patients. J Allergy Clin Immunol 124: 135-142.e1-21. Human nasal epithelial cell transcripts and proteins; allergy 19344938 7,8,16
2009 Joh JH, Kim KY, Lim JH, Son ES, Park HR, Park YJ, Kong WS, Yoo YB, Lee CS Comparative analysis of expressed sequence tags from Flammulina velutipes at different developmental stages. J Microbiol Biotechnol 19: 774-780. Flammulina velutipes ESTs 19734714 5
2009 Johnson R, Buckley NJ Gene dysregulation in Huntington's disease: REST, microRNAs and beyond. Neuromolecular Med 11: 183-199. 19458943 7,16,17
2009 Juncker AS, Larsen MV, Weinhold N, Nielsen M, Brunak S, Lund O Systematic characterisation of cellular localisation and expression profiles of proteins containing MHC ligands. PLoS One 4: e7448. Human proteins 19826487 7,8
2009 Jupiter D, Chen H, VanBuren V STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data. BMC Bioinformatics 10: 332. 19828039 7,10,17
2009 Kabanova S, Kleinbongard P, Volkmer J, Andree B, Kelm M, Jax TW Gene expression analysis of human red blood cells. Int J Med Sci 6: 156-159. Human red blood cell transcripts 19421340 7,16
2009 Kadish I, Thibault O, Blalock EM, Chen KC, Gant JC, Porter NM, Landfield PW Hippocampal and cognitive aging across the lifespan: a bioenergetic shift precedes and increased cholesterol trafficking parallels memory impairment. J Neurosci 29: 1805-1816. Rat hippocampus transcripts 19211887 7,16
2009 Kadupitige SR, Leung KC, Sellmeier J, Sivieng J, Catchpoole DR, Bain ME, Gaeta BA MINER: exploratory analysis of gene interaction networks by machine learning from expression data. BMC Genomics 10 Suppl 3: S17. 19958480 7,10
2009 Kang JS, Lee H, Moon IS, Lee Y, Koh YH, Je YH, Lim KJ, Lee SH Construction and characterization of subtractive stage-specific expressed sequence tag (EST) libraries of the pinewood nematode Bursaphelenchus xylophilus. Genomics 94: 70-77. Pinewood nematode ESTs 19289166 5,7
2009 Kapushesky M, Emam I, Holloway E, Kurnosov P, Zorin A, Malone J, Rustici G, Williams E, Parkinson H, Brazma A Gene Expression Atlas at the European Bioinformatics Institute. Nucleic Acids Res 38: D690-698. 19906730 11
2009 Karim N, Jones JT, Okada H, Kikuchi T Analysis of expressed sequence tags and identification of genes encoding cell-wall-degrading enzymes from the fungivorous nematode Aphelenchus avenae. BMC Genomics 10: 525. Aphelenchus avenae ESTs 19917084 5,7
2009 Kasuya J, Kaas G, Kitamoto T Effects of lithium chloride on the gene expression profiles in Drosophila heads. Neurosci Res 64: 413-420. Drosophila head transcripts; lithium 19410610 7
2009 Katz-Jaffe MG, McCallie BR, Preis KA, Filipovits J, Gardner DK Transcriptome analysis of in vivo and in vitro matured bovine MII oocytes. Theriogenology 71: 939-946. Bovine oocyte transcripts 19150733 7
2009 Keane OM, Maqbool N, McCulloch AF, McEwan JC, Dodds KG Generation of a preliminary bovine gene atlas, using expression clustering to annotate gene function. Genet Mol Res 8: 1013-1027. Bovine genes 19731199 7,17
2009 Keene SD, Greco TM, Parastatidis I, Lee SH, Hughes EG, Balice-Gordon RJ, Speicher DW, Ischiropoulos H Mass spectrometric and computational analysis of cytokine-induced alterations in the astrocyte secretome. Proteomics 9: 768-782. Astrocyte proteins 19132682 8
2009 Kelkar A, Deobagkar D A novel method to assess the full genome methylation profile using monoclonal antibody combined with the high throughput based microarray approach. Epigenetics 4: 415-420. 19755850 7,13
2009 Kim BY, Cao LH, Park H, Jeong S Reciprocal regulation of gene expression by Ephedra herba in mouse brain. Phytother Res 24: 531-537. Mouse brain transcripts 19655298 7,16,17
2009 Kim C, Lemke C, Paterson AH Functional dissection of drought-responsive gene expression patterns in Cynodon dactylon L. Plant Mol Biol 70: 1-16. Bermuda grass transcripts; drought response 19152115 7
2009 Kim CH, Lillehoj HS, Hong YH, Keeler CL, Lillehoj EP Comparison of global transcriptional responses to primary and secondary Eimeria acervulina infections in chickens. Dev Comp Immunol 34: 344-351. Chicken transcripts 19941894 7
2009 Kim DK, Kim CH, Lamont SJ, Keeler CL, Lillehoj HS Gene expression profiles of two B-complex disparate, genetically inbred Fayoumi chicken lines that differ in susceptibility to Eimeria maxima. Poult Sci 88: 1565-1579. Chicken transcripts 19590070 7
2009 Kim T, Kim E, Park SJ, Joo H PCHM: A bioinformatic resource for high-throughput human mitochondrial proteome searching and comparison. Comput Biol Med 39: 689-696. Human mitochondrial proteins 19541297 8,10,16
2009 Klucar L, Stano M, Hajduk M phiSITE: database of gene regulation in bacteriophages. Nucleic Acids Res 38: D366-370. 19900969 15
2009 Ko S, Lee H Integrative approaches to the prediction of protein functions based on the feature selection. BMC Bioinformatics 10: 455. 20043848 9
2009 Kobayashi D, Kumagai J, Morikawa T, Wilson-Morifuji M, Wilson A, Irie A, Araki N An integrated approach of differential mass spectrometry and gene ontology analysis identified novel proteins regulating neuronal differentiation and survival. Mol Cell Proteomics 8: 2350-2367. Rat cell line proteins 19525549 8,13
2009 Koh JL, Ding H, Costanzo M, Baryshnikova A, Toufighi K, Bader GD, Myers CL, Andrews BJ, Boone C DRYGIN: a database of quantitative genetic interaction networks in yeast. Nucleic Acids Res 38: D502-507. 19880385 11,17
2009 Kohonen J, Talikota S, Corander J, Auvinen P, Arjas E A Naive Bayes classifier for protein function prediction. In Silico Biol 9: 23-34. 19537159 9,10
2009 Koks S|etAl The differential transcriptome and ontology profiles of floating and cumulus granulosa cells in stimulated human antral follicles. Mol Hum Reprod 16: 229-240. Human ovarian follicle cell transcripts 19933312 7,16
2009 Korde LA, Lusa L, McShane L, Lebowitz PF, Lukes L, Camphausen K, Parker JS, Swain SM, Hunter K, Zujewski JA Gene expression pathway analysis to predict response to neoadjuvant docetaxel and capecitabine for breast cancer. Breast Cancer Res Treat 119: 685-699. Human breast transcripts 20012355 7,16
2009 Kossenkov AV, Ochs MF Matrix factorization for recovery of biological processes from microarray data. Methods Enzymol 467: 59-77. 19897089 7
2009 Kottmann R, Kostadinov I, Duhaime MB, Buttigieg PL, Yilmaz P, Hankeln W, Waldmann J, Gloeckner FO Megx.net: integrated database resource for marine ecological genomics. Nucleic Acids Res 38: D391-395. 19858098 15
2009 Kramer G, Sprenger RR, Back J, Dekker HL, Nessen MA, van Maarseveen JH, de Koning LJ, Hellingwerf KJ, de Jong L, de Koster CG Identification and quantitation of newly synthesized proteins in E. coli by enrichment of azido homoalanine-labeled peptides with diagonal chromatography. Mol Cell Proteomics 8: 1599-1611. E. coli proteins 19321432 8
2009 Krebs CJ, Khan S, Macdonald JW, Sorenson M, Robins DM The regulator of sex-limitation (Rsl) KRAB zinc finger proteins modulate sex-dependent and -independent liver metabolism. Physiol Genomics 38: 16-28. Mouse liver transcripts 19351907 7
2009 Krushevskaya D, Peterson H, Reimand J, Kull M, Vilo J VisHiC--hierarchical functional enrichment analysis of microarray data. Nucleic Acids Res 37: W587-592. 19483095 7,10
2009 Kubosaki A, Tomaru Y, Tagami M, Arner E, Miura H, Suzuki T, Suzuki M, Suzuki H, Hayashizaki Y Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation. Genome Biol 10: R41. Human monoblastoma cell transcripts 19374776 7
2009 Kumar S, Buza JJ, Burgess SC Genotype-dependent tumor regression in Marek's disease mediated at the level of tumor immunity. Cancer Microenviron 2: 23-31. Chicken lymphoma transcripts; Marek's disease 19308678 7,16
2009 Lando M, Holden M, Bergersen LC, Svendsrud DH, Stokke T, Sundfor K, Glad IK, Kristensen GB, Lyng H Gene dosage, expression, and ontology analysis identifies driver genes in the carcinogenesis and chemoradioresistance of cervical cancer. PLoS Genet 5: e1000719. Human cervical transcripts 19911042 7,16
2009 Lavrac N, Novak PK, Mozetic I, Podpecan V, Motaln H, Petek M, Gruden K Semantic subgroup discovery: Using ontologies in microarray data analysis. Conf Proc IEEE Eng Med Biol Soc 1: 5613-5616. 19964398 7
2009 Lazzari B, Caprera A, Cestaro A, Merelli I, Del Corvo M, Fontana P, Milanesi L, Velasco R, Stella A Ontology-oriented retrieval of putative microRNAs in Vitis vinifera via GrapeMiRNA: a web database of de novo predicted grape microRNAs. BMC Plant Biol 9: 82. Grape miRNAs 19563653 3,19
2009 Leach SM, Tipney H, Feng W, Baumgartner WA, Kasliwal P, Schuyler RP, Williams T, Spritz RA, Hunter L Biomedical discovery acceleration, with applications to craniofacial development. PLoS Comput Biol 5: e1000215. 19325874 13,15,17
2009 Lebrec JJ, Huizinga TW, Toes RE, Houwing-Duistermaat JJ, van Houwelingen HC Integration of gene ontology pathways with North American Rheumatoid Arthritis Consortium genome-wide association data via linear modeling. BMC Proc 3 Suppl 7: S94. 20018091 16,17
2009 Leder EH, Merila J, Primmer CR A flexible whole-genome microarray for transcriptomics in three-spine stickleback (Gasterosteus aculeatus). BMC Genomics 10: 426. Stickleback transcripts 19744352 7
2009 Lee AK, Mojtahed-Jaberi M, Kyriakou T, Aldecoa-Otalora Astarloa E, Arno M, Marshall NJ, Brain SD, O'Dell SD Effect of high-fat feeding on expression of genes controlling availability of dopamine in mouse hypothalamus. Nutrition 26: 411-422. Mouse hypothalamus transcripts; high-fat diet 19811894 7,16
2009 Lee D, Seo H, Park C, Park K WeGAS: A Web-Based Microbial Genome Annotation System. Biosci Biotechnol Biochem 73: 213-216. Human genes 19129632 7,13,16
2009 Lee KT, Byun MJ, Lim D, Kang KS, Kim NS, Oh JH, Chung CS, Park HS, Shin Y, Kim TH Full-length enriched cDNA library construction from tissues related to energy metabolism in pigs. Mol Cells 28: 529-536. Porcine ESTs 19937143 5
2009 Lee MJ, Park JH Pathway Analysis in HEK 293T cells overexpressing HIV-1 tat and nucleocapsid. J Microbiol Biotechnol 19: 1103-1108. Human cell line transcripts; HIV 19884766 7,16
2009 Lees J, Yeats C, Redfern O, Clegg A, Orengo C Gene3D: merging structure and function for a Thousand genomes. Nucleic Acids Res 38: D296-300. 19906693 11
2009 Leplae R, Lima-Mendez G, Toussaint A ACLAME: A CLAssification of Mobile genetic Elements, update 2010. Nucleic Acids Res 38: D57-61. 19933762 3,11
2009 Lewandrowski U, Wortelkamp S, Lohrig K, Zahedi RP, Wolters DA, Walter U, Sickmann A Platelet membrane proteomics: a novel repository for functional research. Blood 114: e10-19. 19436052 8
2009 Lewintre EJ, Martin CR, Montaner D, Marin M, Terol MJ, Farras R, Benet I, Calvete JJ, Dopazo J, Garcia-Conde J Analysis of chronic lymphotic leukemia transcriptomic profile: differences between molecular subgroups. Leuk Lymphoma 50: 68-79. Rat lung transcripts; rat blood proteins; respiratory allergy 19127482 7,8,16
2009 Li BW, Rush AC, Mitreva M, Yin Y, Spiro D, Ghedin E, Weil GJ Transcriptomes and pathways associated with infectivity, survival and immunogenicity in Brugia malayi L3. BMC Genomics 10: 267. Brugia malayi transcripts 19527522 7,16
2009 Li D, Su Z, Dong J, Wang T An expression database for roots of the model legume Medicago truncatula under salt stress. BMC Genomics 10: 517. 19906315 7,11
2009 Li H, He Y, Ding G, Wang C, Xie L, Li Y dbDEPC: a database of Differentially Expressed Proteins in human Cancers. Nucleic Acids Res 38: D658-664. 19900968 11
2009 Li H, Liang S Local network topology in human protein interaction data predicts functional association. PLoS One 4: e6410. 19641626 8,16,17,19
2009 Li JY, Chen X, Hosseini Moghaddam SH, Chen M, Wei H, Zhong BX Shotgun proteomics approach to characterizing the embryonic proteome of the silkworm, Bombyx mori, at labrum appearance stage. Insect Mol Biol 18: 649-660. Silkworm embryonic proteins 19754742 8
2009 Li L, Yang X, Jiang F, Dusting GJ, Wu Z Transcriptome-wide characterization of gene expression associated with unruptured intracranial aneurysms. Eur Neurol 62: 330-337. Human brain transcripts 19752560 7,16
2009 Li L, Zhang K, Lee J, Cordes S, Davis DP, Tang Z Discovering cancer genes by integrating network and functional properties. BMC Med Genomics 2: 61. 19765316 16,17
2009 Li M, Guo K, Kang XN, Sun L, Shu H, Li RL, Xu MH, Liu YK, Qin X, Li S [Protein profiles of multinodular hepatocellular carcinoma with multicentric occurrence or with intrahepatic metastasis.] Zhonghua Gan Zang Bing Za Zhi 17: 354-358. Human liver transcripts; hepatocellular carcinoma 19497201 7,16
2009 Li M, Zhao C Study on Tibetan Chicken embryonic adaptability to chronic hypoxia by revealing differential gene expression in heart tissue. Sci China C Life Sci 52: 284-295. Chicken heart transcripts 19294354 7
2009 Li T, Brouwer M Bioinformatic analysis of expressed sequence tags from grass shrimp Palaemonetes pugio exposed to environmental stressors. Comp Biochem Physiol Part D Genomics Proteomics 4: 187-195. 20403761 5,7
2009 Li W, McWilliam H, de la Torre AR, Grodowski A, Benediktovich I, Goujon M, Nauche S, Lopez R Non-redundant patent sequence databases with value-added annotations at two levels. Nucleic Acids Res 38: D52-56. 19884134 11
2009 Li WL, Rodrigo AG Covariation of branch lengths in phylogenies of functionally related genes. PLoS One 4: e8487. 20041191 9,17
2009 Li X, Wu HX, Dillon SK, Southerton SG Generation and analysis of expressed sequence tags from six developing xylem libraries in Pinus radiata D. Don. BMC Genomics 10: 41. Pine xylem ESTs 19159482 5,7
2009 Li Y, Yu JF, Yin L, Cui GZ [Concepts of ontology-based neuroinformatics and their relations.] Beijing Da Xue Xue Bao 41: 230-234. 19377637 14
2009 Li Z|etAl Consistent deregulation of gene expression between human and murine MLL rearrangement leukemias. Cancer Res 69: 1109-1116. Human transcripts; mouse transcripts; leukemia 19155294 7,16
2009 Lichtenfels R|etAl Systematic comparative protein expression profiling of clear cell renal cell carcinoma: A pilot study based on the separation of tissue specimen by two-dimensional electrophoresis. Mol Cell Proteomics 8: 2827-2842. Human kidney proteins 19752005 8,16
2009 Lin HC, Morcillo F, Dussert S, Tranchant-Dubreuil C, Tregear JW, Tranbarger TJ Transcriptome analysis during somatic embryogenesis of the tropical monocot Elaeis guineensis: evidence for conserved gene functions in early development. Plant Mol Biol 70: 173-192. Oil palm ESTs 19199047 5,7
2009 Lin X, Liu M, Chen XW Assessing reliability of protein-protein interactions by integrative analysis of data in model organisms. BMC Bioinformatics 10 Suppl 4: S5. 19426453 8,17
2009 Lin Y, Wu H Comparative analysis of aerobic and anaerobic prokaryotes to identify correlation between oxygen requirement and gene-gene functional association patterns. Genome Inform 23: 72-84. 20180263 13,18
2009 Lindeberg M, Biehl BS, Glasner JD, Perna NT, Collmer A, Collmer CW Gene Ontology annotation highlights shared and divergent pathogenic strategies of type III effector proteins deployed by the plant pathogen Pseudomonas syringae pv tomato DC3000 and animal pathogenic Escherichia coli strains. BMC Microbiol 9 Suppl 1: S4. 19278552 1,3,13,18
2009 Lindeberg M, Collmer A Gene Ontology for type III effectors: capturing processes at the host-pathogen interface. Trends Microbiol 17: 304-311. Pseudomonas syringae proteins 19576777 1,6
2009 Liu J, Faeder JR, Camacho CJ Toward a quantitative theory of intrinsically disordered proteins and their function. Proc Natl Acad Sci U S A 106: 19819-19823. 19903882 9,13
2009 Liu M, Chen XW, Jothi R Knowledge-guided inference of domain-domain interactions from incomplete protein-protein interaction networks. Bioinformatics 25: 2492-2499. 19667081 8,17
2009 Lopez D, Pazos F Gene ontology functional annotations at the structural domain level. Proteins 76: 598-607. Protein domain annotations 19241468 9
2009 Lopez Herraez D, Bauchet M, Tang K, Theunert C, Pugach I, Li J, Nandineni MR, Gross A, Scholz M, Stoneking M Genetic variation and recent positive selection in worldwide human populations: evidence from nearly 1 million SNPs. PLoS One 4: e7888. 19924308 10.1371/journal.pone.0007888 16,18
2009 Louie B, Higdon R, Kolker E A statistical model of protein sequence similarity and function similarity reveals overly-specific function predictions. PLoS One 4: e7546. 19844580 9
2009 Lu R, Markowetz F, Unwin RD, Leek JT, Airoldi EM, MacArthur BD, Lachmann A, Rozov R, Ma'ayan A, Boyer LA, Troyanskaya OG, Whetton AD, Lemischka IR Systems-level dynamic analyses of fate change in murine embryonic stem cells. Nature 462: 358-362. 19924215 7,8,17
2009 Lu X, Shao J, Li H, Yu Y Early whole-genome transcriptional response induced by benzo[a]pyrene diol epoxide in a normal human cell line. Genomics 93: 332-342. Human epithelial cell line transcripts; benzo[a]pyrene exposure 19150397 7,16
2009 Lutter D, Langmann T, Ugocsai P, Moehle C, Seibold E, Splettstoesser WD, Gruber P, Lang EW, Schmitz G Analyzing time-dependent microarray data using independent component analysis derived expression modes from human macrophages infected with F. tularensis holartica. J Biomed Inform 42: 605-611. Human macrophage transcripts 19535009 7,16
2009 Lv J, Su J, Wang F, Qi Y, Liu H, Zhang Y Detecting novel hypermethylated genes in Breast cancer benefiting from feature selection. Comput Biol Med 40: 159-167. 20044084 13,16
2009 Ma LJ, Li W, Zhang X, Huang DH, Zhang H, Xiao JY, Tian YQ Differential gene expression profiling of laryngeal squamous cell carcinoma by laser capture microdissection and complementary DNA microarrays. Arch Med Res 40: 114-123. Human laryngeal transcripts; cancer 19237021 7,16
2009 Ma XJ, Dahiya S, Richardson EA, Erlander M, Sgroi DC Gene expression profiling of tumor microenvironment during breast cancer progression. Breast Cancer Res 11: R7. Human breast tissue transcripts; breast cancer 19187537 7,16
2009 Ma XJ, Yin HJ, Chen KJ Differential gene expression profiles in coronary heart disease patients of blood stasis syndrome in traditional Chinese medicine and clinical role of target gene. Chin J Integr Med 15: 101-106. Human blood cell transcripts 19407946 7,16
2009 Mace LC, Yermalitskaya LV, Yi Y, Yang Z, Murray KT Transcriptional remodeling of rapidly stimulated HL-1 atrial myocytes exhibits concordance with human atrial fibrillation. J Mol Cell Cardiol 47: 485-492. Mouse heart cell transcripts 19615375 7,16
2009 Malone BM, Perkins AD, Bridges SM Integrating phenotype and gene expression data for predicting gene function. BMC Bioinformatics 10 Suppl 11: S20. 19811686 7,9,13
2009 Manadas B, English JA, Wynne KJ, Cotter DR, Dunn MJ Comparative analysis of OFFGel, SCX with pH gradient, and reverse phase at high pH for first dimensional separation of peptides from a membrane enriched protein fraction. Proteomics 9: 5194-5198. Mouse brain proteins 19771557 8
2009 Manning AK, Ngwa JS, Hendricks AE, Liu CT, Johnson AD, Dupuis J, Cupples LA Incorporating biological knowledge in the search for gene x gene interaction in genome-wide association studies. BMC Proc 3 Suppl 7: S81. 20018077 16,17
2009 Marco A, Marin I Interactome and Gene Ontology provide congruent yet subtly different views of a eukaryotic cell. BMC Syst Biol 3: 69. Saccharomyces proteins 19604360 8,17
2009 Mariappan D, Winkler J, Chen S, Schulz H, Hescheler J, Sachinidis A Transcriptional profiling of CD31(+) cells isolated from murine embryonic stem cells. Genes Cells 14: 243-260. Mouse embryonic stem cell transcripts 19170770 7
2009 Marino-Ramirez L, Tharakaraman K, Bodenreider O, Spouge J, Landsman D Identification of cis-regulatory elements in gene co-expression networks using A-GLAM. Methods Mol Biol 541: 1-20. 19381547 7,17
2009 Markljung E|etAl ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth. PLoS Biol 7: e1000256. Mouse cell line transcipts 20016685 7
2009 Marsico A, Scheubert K, Tuukkanen A, Henschel A, Winter C, Winnenburg R, Schroeder M MeMotif: a database of linear motifs in {alpha}-helical transmembrane proteins. Nucleic Acids Res 38: D181-189. 19910368 11
2009 Martin DN|etAl Differences in the tumor microenvironment between African-American and European-American breast cancer patients. PLoS ONE 4: e4531. Human breast transcripts; breast cancer 19225562 7,16,18
2009 Mas VR, Maluf DG, Archer KJ, Yanek K, Bornstein K, Fisher RA Proteomic analysis of HCV cirrhosis and HCV-induced HCC: identifying biomarkers for monitoring HCV-cirrhotic patients awaiting liver transplantation. Transplantation 87: 143-152. Human plasma transcripts; hepatits C 19136905 7,16
2009 Mason MJ, Fan G, Plath K, Zhou Q, Horvath S Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells. BMC Genomics 10: 327. Mouse embryonic stem cell transcripts 19619308 7,17
2009 Massanet R, Gallardo-Chacon JJ, Caminal P, Perera A Search of phenotype related candidate genes using gene ontology-based semantic similarity and protein interaction information: Application to Brugada syndrome. Conf Proc IEEE Eng Med Biol Soc 1: 7079-7082. 19963939 8,12,13,16
2009 Matsui T, Yamamoto T, Wyder S, Zdobnov EM, Kadowaki T Expression profiles of Urbilaterian genes uniquely shared between honey bee and vertebrates. BMC Genomics 10: 17. Mouse genes; honey bee genes 19138430 7,18
2009 Mazza R, Strozzi F, Caprera A, Ajmone-Marsan P, Williams JL The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species. BMC Genomics 10: 604. 20003425 18
2009 McCallie B, Schoolcraft WB, Katz-Jaffe MG Aberration of blastocyst microRNA expression is associated with human infertility. Fertil Steril 93: 2374-2382. Human blastocyst miRNAs; infertility 19296935 7,16
2009 McCarthy FM, Mahony TJ, Parcells MS, Burgess SC Understanding animal viruses using the Gene Ontology. Trends Microbiol 17: 328-335. Animal virus genomes 19577474 1,4
2009 McCord AM, Jamal M, Shankavarum UT, Lang FF, Camphausen K, Tofilon PJ Physiologic oxygen concentration enhances the stem-like properties of CD133+ human glioblastoma cells in vitro. Mol Cancer Res 7: 489-497. Human glioblastoma cell transcripts 19372578 7,16
2009 McHale CM|etAl Changes in the peripheral blood transcriptome associated with occupational benzene exposure identified by cross-comparison on two microarray platforms. Genomics 93: 343-349. Human blood transcripts; benzene exposure 19162166 7,16
2009 McQuade LR, Schmidt U, Pascovici D, Stojanov T, Baker MS Improved membrane proteomics coverage of human embryonic stem cells by peptide IPG-IEF. J Proteome Res 8: 5642-5649. Human embryonic stem cell proteins 19899800 8,16
2009 Meghana C, Troy H, Changsoon P, Daisuke K ESG: Extended Similarity Group method for automated protein function prediction. Bioinformatics 25: 1739-1745. 19435743 9,10
2009 Mehan MR, Nunez-Iglesias J, Kalakrishnan M, Waterman MS, Zhou XJ An integrative network approach to map the transcriptome to the phenome. J Comput Biol 16: 1023-1034. 19630539 7,13,17
2009 Meng J, Gao SJ, Huang Y Enrichment constrained time-dependent clustering analysis for finding meaningful temporal transcription modules. Bioinformatics 25: 1521-1527. 19351618 7
2009 Meng S, Brown DE, Ebbole DJ, Torto-Alalibo T, Oh YY, Deng J, Mitchell TK, Dean RA Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae. BMC Microbiol 9 Suppl 1: S8. Rice blast fungus genome 19278556 1,4,11
2009 Meng S, Torto-Alalibo T, Chibucos MC, Tyler BM, Dean RA Common processes in pathogenesis by fungal and oomycete plant pathogens, described with Gene Ontology terms. BMC Microbiol 9 Suppl 1: S7. 19278555 1,3,13,18
2009 Mercade J, Espinosa A, Adsuara JE, Adrados R, Segura J, Maes T Orymold: ontology based gene expression data integration and analysis tool applied to rice. BMC Bioinformatics 10: 158. 19463186 10
2009 Merelli I, Caprera A, Stella A, Del Corvo M, Milanesi L, Lazzari B The Human EST Ontology Explorer: a tissue-oriented visualization system for ontologies distribution in human EST collections. BMC Bioinformatics 10 Suppl 12: S2. 19828078 5,10,11
2009 Merkl R, Wiezer A GO4genome: A Prokaryotic Phylogeny Based on Genome Organization. J Mol Evol 68: 550-562. 19436929 18
2009 Metallo CM, Azarin SM, Moses LE, Ji L, de Pablo J, Palecek S Human embryonic stem cell-derived keratinocytes exhibit an epidermal transcription program and undergo epithelial morphogenesis in engineered tissue constructs. Tissue Eng Part A 16: 213-223. Human bone marrow transcripts 19686061 7,16
2009 Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, Abrego D, Colbourne JK, Willis BL, Matz MV Sequencing and de novo analysis of a coral larval transcriptome using 454 GS-Flx. BMC Genomics 10: 219. Acropora millepora larval transcripts 19435504 3,18
2009 Mi H, Thomas P PANTHER Pathway: An ontology-based pathway database coupled with data analysis tools. Methods Mol Biol 563: 123-140. 19597783 11,17
2009 Milks MW, Cripps JG, Lin H, Wang J, Robinson RT, Sargent JL, Whitfield ML, Gorham JD The role of Ifng in alterations in liver gene expression in a mouse model of fulminant autoimmune hepatitis. Liver Int 29: 1307-1315. Mouse liver transcripts; hepatitis 19490417 7,16
2009 Miller WR Clinical, pathological, proliferative and molecular responses associated with neoadjuvant aromatase inhibitor treatment in breast cancer. J Steroid Biochem Mol Biol 118: 273-276. Human breast transcripts 19837160 7,16
2009 Minarro-Gimenez JA, Madrid M, Fernandez-Breis JT OGO: an ontological approach for integrating knowledge about orthology. BMC Bioinformatics 10 Suppl 10: S13. 19796397 8
2009 Mithani SK, Bluebond-Langner R, Rodriguez ED Expression microarray identifies novel markers of free flap failure in a rat model. Ann Plast Surg 63: 323-326. Rat tissue transcripts; plastic surgery 19692897 7,16
2009 Mo WJ, Fu XP, Han XT, Yang GY, Zhang JG, Guo FH, Huang Y, Mao YM, Li Y, Xie Y A stochastic model for identifying differential gene pair co-expression patterns in prostate cancer progression. BMC Genomics 10: 340. Human prostate transcripts 19640296 7,16,17
2009 Mochida K, Yoshida T, Sakurai T, Ogihara Y, Shinozaki K TriFLDB: A database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomics. Plant Physiol 150: 1135-1146. Triticeae CDSs 19448038 3,11
2009 Mochida K, Yoshida T, Sakurai T, Yamaguchi-Shinozaki K, Shinozaki K, Tran LS In silico analysis of transcription factor repertoire and prediction of stress responsive transcription factors in soybean. DNA Res 16: 353-369. Soybean transcription factors 19884168 3,11
2009 Mohamed-Hussein ZA, Harun S Construction of a polycystic ovarian syndrome (PCOS) pathway based on the interactions of PCOS-related proteins retrieved from bibliomic data. Theor Biol Med Model 6: 18. Human ovarian transcripts 19723303 7,16
2009 Mongkoldhumrongkul N, Swain SC, Jayasinghe SN, Sturzenbaum S Bio-electrospraying the nematode Caenorhabditis elegans: studying whole-genome transcriptional responses and key life cycle parameters. J R Soc Interface 7: 595-601. Caenorhabditis elegans transcripts 19776148 7
2009 Montaner D, Minguez P, Al-Shahrour F, Dopazo J Gene set internal coherence in the context of functional profiling. BMC Genomics 10: 197. 19397819 7,17
2009 Montecchi-Palazzi L, Kerrien S, Reisinger F, Aranda B, Jones AR, Martens L, Hermjakob H The PSI semantic validator: a framework to check minimum information about a proteomics experiment compliance of proteomics data. Proteomics 9: 5112-5119. 19834897 8,10,15
2009 Mookherjee N, Hamill P, Gardy J, Blimkie D, Falsafi R, Chikatamarla A, Arenillas DJ, Doria S, Kollmann TR, Hancock RE Systems biology evaluation of immune responses induced by human host defence peptide LL-37 in mononuclear cells. Mol Biosyst 5: 483-496. Human immune cell transcripts 19381363 7,16,17
2009 Morgan H|etAl EuroPhenome: a repository for high-throughput mouse phenotyping data. Nucleic Acids Res 38: D577-585. 19933761 15
2009 Morrissey ER, Diaz-Uriarte R Pomelo II: finding differentially expressed genes. Nucleic Acids Res 37: W581-586. 19435879 7,10
2009 Mosca E, Bertoli G, Piscitelli E, Vilardo L, Reinbold RA, Zucchi I, Milanesi L Identification of functionally related genes using data mining and data integration: a breast cancer case study. BMC Bioinformatics 10 Suppl 12: S8. 19828084 12,17
2009 Mulder IE|etAl Environmentally-acquired bacteria influence microbial diversity and natural innate immune responses at gut surfaces. BMC Biol 7: 79. Pig mucosa-adherent microbe transcripts 19930542 13,16
2009 Muller B, Richards AJ, Jin B, Lu X GOGrapher: A Python library for GO graph representation and analysis. BMC Res Notes 2: 122. 19583843 10
2009 Muller J|etAl eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Res 38: D190-195. 19900971 11
2009 Murphy DM|etAl Global MYCN transcription factor binding analysis in neuroblastoma reveals association with distinct E-box motifs and regions of DNA hypermethylation. PLoS One 4: e8154. Neuroblastoma cell line transcripts 19997598 10.1371/journal.pone.0008154 7,16
2009 Murphy EF, Hooiveld GJ, Muller M, Calogero RA, Cashman KD The effect of trans-10, cis-12 conjugated linoleic acid on gene expression profiles related to lipid metabolism in human intestinal-like Caco-2 cells. Genes Nutr 4: 103-112. Human intestinal cell line transcripts; conjugated linoleic acid 19283423 7,16
2009 Nakao M, Okamoto S, Kohara M, Fujishiro T, Fujisawa T, Sato S, Tabata S, Kaneko T, Nakamura Y CyanoBase: the cyanobacteria genome database update 2010. Nucleic Acids Res 38: D379-381. 19880388 11
2009 Nakayasu ES, Gaynor MR, Sobreira TJ, Ross JA, Almeida IC Phosphoproteomic analysis of the human pathogen Trypanosoma cruzi at the epimastigote stage. Proteomics 9: 3489-3506. Trypanosoma cruzi proteins 19579231 8,16
2009 Nam S, Li M, Choi K, Balch C, Kim S, Nephew KP MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression. Nucleic Acids Res 37: W356-362. 19420067 7,10,19
2009 Nan Y, Jin F, Yang S, Tian Y, Xie Y, Fu E, Yu H Discovery of a set of biomarkers of human lung adenocarcinoma through cell-map proteomics and bioinformatics. Med Oncol 27: 1398-1406. Human lung proteins 20041319 8,16
2009 Nett JE, Lepak AJ, Marchillo K, Andes DR Time course global gene expression analysis of an in vivo Candida biofilm. J Infect Dis 200: 307-313. Candida albicans transcripts 19527170 7
2009 Ni J|etAl Gramene QTL database: development, content and applications. Database (Oxford) 2009: bap005. 20157478 1,11
2009 Nie H, Neerincx PB, Poel J, Ferrari F, Bicciato S, Leunissen JA, Groenen MA Microarray data mining using Bioconductor packages. BMC Proc 3 Suppl 4: S9. 19615122 7,10
2009 Ning Z, Jiang Z GO(Vis), a Gene Ontology visualization tool based on multi-dimensional values. Protein Pept Lett 17: 675-680. 19995339 10,13
2009 Nischan J, Gatalica Z, Curtis M, Lenk GM, Tromp G, Kuivaniemi H Binding sites for ETS family of transcription factors dominate the promoter regions of differentially expressed genes in abdominal aortic aneurysms. Circ Cardiovasc Genet 2: 565-572. 20031636 7,16
2009 Noy NF|etAl BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res 37: W170-173. 19483092 10,15
2009 O'Gorman GM, Park SD, Hill EW, Meade KG, Coussens PM, Agaba M, Naessens J, Kemp SJ, Machugh DE Transcriptional profiling of cattle infected with Trypanosoma congolense highlights gene expression signatures underlying trypanotolerance and trypanosusceptibility. BMC Genomics 10: 207. Bovine blood cell transcripts; trypanosome infection 19409086 7
2009 Ohdaira H, Nakagawa H, Yoshida K Profiling of molecular pathways regulated by microRNA 601. Comput Biol Chem 33: 429-433. Human lung cancer cell line transcripts; miRNA targets 19889580 7,16
2009 Olsvik PA, Holen E Characterization of an Atlantic cod (Gadus morhua) embryonic stem cell cDNA library. BMC Res Notes 2: 74. Cod ESTs 19416549 5
2009 Osborne JD, Flatow J, Holko M, Lin SM, Kibbe WA, Zhu LJ, Danila MI, Feng G, Chisholm RL Annotating the human genome with Disease Ontology. BMC Genomics 10 Suppl 1: S6. 19594883 15
2009 Osuna-Jimenez I, Williams TD, Prieto-Alamo MJ, Abril N, Chipman JK, Pueyo C Immune- and stress-related transcriptomic responses of Solea senegalensis stimulated with lipopolysaccharide and copper sulphate using heterologous cDNA microarrays. Fish Shellfish Immunol 26: 699-706. Sole transcripts 19264136 7
2009 Oti M, Huynen MA, Brunner HG The biological coherence of human phenome databases. Am J Hum Genet 85: 801-808. 20004759 13,16
2009 Otsuki N, Dang NH, Kumagai E, Kondo A, Iwata S, Morimoto C Aqueous extract of Carica papaya leaves exhibits anti-tumor activity and immunomodulatory effects. J Ethnopharmacol 127: 760-767. Human tumor cell line transcripts 19961915 7,16
2009 Oyan AM, Anensen N, Hellem Bo T, Stordrange L, Jonassen I, Bruserud O, Kalland KH, Gjertsen BT Genes of cell-cell interactions, chemotherapy detoxification and apoptosis are induced during chemotherapy of acute myeloid leukemia. BMC Cancer 9: 77. Human leukocyte transcripts 19265549 7,16
2009 Paic F|etAl Identification of Differentially Expressed Genes Between Osteoblasts and Osteocytes. Bone 45: 682-692. Mouse bone cell transcripts 19539797 7
2009 Palm T, Figarella-Branger D, Chapon F, Lacroix C, Gray F, Scaravilli F, Ellison DW, Salmon I, Vikkula M, Godfraind C Expression profiling of ependymomas unravels localization and tumor grade-specific tumorigenesis. Cancer 115: 3955-3968. Human macrophage transcripts 19536879 7,16
2009 Pandey G, Myers CL, Kumar V Incorporating functional inter-relationships into protein function prediction algorithms. BMC Bioinformatics 10: 142. 19435516 9
2009 Papachristoudis G, Diplaris S, Mitkas PA SoFoCles: Feature filtering for microarray classification based on Gene Ontology. J Biomed Inform 43: 1-14. 19576292 7,10
2009 Papapanou PN, Behle JH, Kebschull M, Celenti R, Wolf DL, Handfield M, Pavlidis P, Demmer RT Subgingival bacterial colonization profiles correlate with gingival tissue gene expression. BMC Microbiol 9: 221. Human gingival tissue transcripts; periodontitis 19835625 7,16
2009 Park SJ, Choi JS, Kim BC, Jho SW, Ryu JW, Park D, Lee KA, Bhak J, Kim SI PutidaNET: interactome database service and network analysis of Pseudomonas putida KT2440. BMC Genomics 10 Suppl 3: S18. Pseudomonas putida KT2440 proteome 19958481 8,11,17
2009 Pathak J, Solbrig HR, Buntrock JD, Johnson TM, Chute CG LexGrid: A framework for representing, storing, and querying biomedical terminologies from simple to sublime. J Am Med Inform Assoc 16: 305-315. 19261933 9,12
2009 Pelch KE, Schroder AL, Kimball PA, Sharpe-Timms KL, Wade Davis J, Nagel SC Aberrant gene expression profile in a mouse model of endometriosis mirrors that observed in women. Fertil Steril 93: 1615-1627.e18. Mouse uterine transcripts; endometriosis 19473656 7,16
2009 Peng ZY|etAl Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis. Nucleic Acids Res 37: D975-982. 19015126 3,11
2009 Perry JR, McCarthy MI, Hattersley AT, Zeggini E, The Wellcome Trust Case Control Consortium, Weedon MN, Frayling TM Interrogating Type 2 diabetes genome-wide association data using a biological pathway-based approach. Diabetes 58: 1463-1467. Human genes; diabetes 19252133 7,17
2009 Pesquita C, Faria D, Falcao AO, Lord P, Couto FM Semantic similarity in biomedical ontologies. PLoS Comput Biol 5: e1000443. 19649320 13,14
2009 Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database. Nucleic Acids Res 38: D443-447. 19884132 3,11
2009 Piek E|etAl Osteo-transcriptomics of human mesenchymal stem cells: Accelerated gene expression and osteoblast differentiation induced by vitamin D reveals c-MYC as an enhancer of BMP2-induced osteogenesis. Bone 46: 613-627. Human mesenchymal stem cells transcripts 19857615 7,16
2009 Plake C, Royer L, Winnenburg R, Hakenberg J, Schroeder M GoGene: gene annotation in the fast lane. Nucleic Acids Res 37: W300-304. 19465383 3,10,12
2009 Ponsuksili S, Murani E, Phatsara C, Schwerin M, Schellander K, Wimmers K Porcine muscle sensory attributes associate with major changes in gene networks involving CAPZB, ANKRD1, and CTBP2. Funct Integr Genomics 9: 455-471. Porcine genes 19597856 7,13,17
2009 Prasad PD, Stanton JA, Assinder SJ Expression of the actin-associated protein transgelin (SM22) is decreased in prostate cancer. Cell Tissue Res 339: 337-347. Human prostate cell line transcripts 20012321 7,16
2009 Proost S, Van Bel M, Sterck L, Billiau K, Van Parys T, Van de Peer Y, Vandepoele K PLAZA: A comparative genomics resource to study gene and genome evolution in plants. Plant Cell 21: 3718-3731. 20040540 10,11
2009 Qanbari S, Pimentel EC, Tetens J, Thaller G, Lichtner P, Sharifi AR, Simianer H A genome-wide scan for signatures of recent selection in Holstein cattle. Anim Genet 41: 377-389. 20096028 13,18
2009 Ramachandrarao SP, Zhu Y, Ravasi T, McGowan TA, Toh I, Dunn SR, Okada S, Shaw MA, Sharma K Pirfenidone Is Renoprotective in Diabetic Kidney Disease. J Am Soc Nephrol 20: 1765-1775. Mouse kidney proteins 19578007 8,16
2009 Rao PK, Singh CR, Jagannath C, Li Q A systems biology approach to study the phagosomal proteome modulated by mycobacterial infections. Int J Clin Exp Med 2: 233-247. Mouse macrophage proteins 19918316 8,13,16
2009 Rasaiyaah J, Noursadeghi M, Kellam P, Chain B Transcriptional and functional defects of dendritic cells derived from the MUTZ-3 leukaemia line. Immunology 127: 429-441. Human leukemia cell line transcripts 19538250 7,16
2009 Rattei T, Tischler P, Goetz S, Jehl MA, Hoser J, Arnold R, Conesa A, Mewes HW SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters. Nucleic Acids Res 38: D223-226. 19906725 11
2009 Ray SS, Bandyopadhyay S, Pal SK Combining multisource information through functional-annotation-based weighting: gene function prediction in yeast. IEEE Trans Biomed Eng 56: 229-236. 19272921 9
2009 Reams RR, Agrawal D, Davis MB, Yoder S, Odedina FT, Kumar N, Higginbotham JM, Akinremi T, Suther S, Soliman KF Microarray comparison of prostate tumor gene expression in African-American and Caucasian American males: a pilot project study. Infect Agent Cancer 4 Suppl 1: S3. Human prostate transcripts; prostate cancer 19208208 7,16
2009 Reiter R, Deutschle T, Wiegel T, Riechelmann H, Bartkowiak D Absence of inflammatory response from upper airway epithelial cells after x irradiation. Radiat Res 171: 274-282. Human bronchial epithelial cell line transcripts; inflammation; X-ray irradiation 19267554 7,16
2009 Reja R, Venkatakrishnan AJ, Lee J, Kim BC, Ryu JW, Gong S, Bhak J, Park D MitoInteractome: mitochondrial protein interactome database, and its application in 'aging network' analysis. BMC Genomics 10 Suppl 3: S20. Mitochondrial proteome 19958484 8,11,17
2009 Ren J, Liu Z, Gao X, Jin C, Ye M, Zou H, Wen L, Zhang Z, Xue Y, Yao X MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore. Nucleic Acids Res 38: D155-160. 19783819 11
2009 Rengel D, San Clemente H, Servant F, Ladouce N, Paux E, Wincker P, Couloux A, Sivadon P, Grima-Pettenati J A new genomic resource dedicated to wood formation in Eucalyptus. BMC Plant Biol 9: 36. Eucalyptus ESTs 19327132 5,11
2009 Renkonen J, Mattila P, Parviainen V, Joenvaara S, Toppila-Salmi S, Renkonen R A network analysis of the single nucleotide polymorphisms in acute allergic diseases. Allergy 65: 40-47. Human nasal epithelial transcripts 19796227 7,13,16,17
2009 Richardson L, Venkataraman S, Stevenson P, Yang Y, Burton N, Rao J, Fisher M, Baldock RA, Davidson DR, Christiansen JH EMAGE mouse embryo spatial gene expression database: 2010 update. Nucleic Acids Res 38: D703-709. 19767607 15
2009 Robine N, Lau NC, Balla S, Jin Z, Okamura K, Kuramochi-Miyagawa S, Blower MD, Lai EC A broadly conserved pathway generates 3'UTR-directed primary piRNAs. Curr Biol 19: 2066-2076. Mouse testis transcripts; Drosophila ovary transcripts 20022248 7,13
2009 Roe OD, Anderssen E, Helge E, Pettersen CH, Olsen KS, Sandeck H, Haaverstad R, Lundgren S, Larsson E Genome-wide profile of pleural mesothelioma versus parietal and visceral pleura: the emerging gene portrait of the mesothelioma phenotype. PLoS One 4: e6554. Human pleural transcripts; mesothelioma 19662092 7,16
2009 Roelofs D, Janssens TK, Timmermans MJ, Nota B, Marien J, Bochdanovits Z, Ylstra B, VAN Straalen NM Adaptive differences in gene expression associated with heavy metal tolerance in the soil arthropod Orchesella cincta. Mol Ecol 18: 3227-3239. Orchesella cincta cDNAs 19566677 7
2009 Rogers MF, Ben-Hur A The use of Gene Ontology evidence codes in preventing classifier assessment bias. Bioinformatics 25: 1173-1177. 19254922 9
2009 Rome S|etAl Microarray analysis of genes with impaired insulin regulation in the skeletal muscle of type 2 diabetic patients indicates the involvement of basic helix-loop-helix domain-containing, class B, 2 protein (BHLHB2). Diabetologia 52: 1899-1912. Human skeletal muscle transcripts; diabetes 19590847 7,16
2009 Romero R|etAl Isobaric labeling and tandem mass spectrometry: A novel approach for profiling and quantifying proteins differentially expressed in amniotic fluid in preterm labor with and without intra-amniotic infection/inflammation. J Matern Fetal Neonatal Med 23: 261-280. Human amniotic proteins 19670042 8,16
2009 Rot G, Parikh A, Curk T, Kuspa A, Shaulsky G, Zupan B dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface. BMC Bioinformatics 10: 265. Dictyostelium transcripts 19706156 7,11
2009 Rotter A|etAl Gene expression profiling in susceptible interaction of grapevine with its fungal pathogen Eutypa lata: extending MapMan ontology for grapevine. BMC Plant Biol 9: 104. Grape transcripts 19656401 7
2009 Roubelakis MG, Zotos P, Papachristoudis G, Michalopoulos I, Pappa KI, Anagnou NP, Kossida S Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application. BMC Bioinformatics 10 Suppl 6: S20. Human miRNAs 19534746 7,10
2009 Rower C, Vissers JP, Koy C, Kipping M, Hecker M, Reimer T, Gerber B, Thiesen HJ, Glocker MO Towards a proteome signature for invasive ductal breast carcinoma derived from label-free nanoscale LC-MS protein expression profiling of tumorous and glandular tissue. Anal Bioanal Chem 395: 2443-2456. Human breast proteins 19876624 8,16
2009 Roxas BA, Li Q Acid stress response of a mycobacterial proteome: insight from a gene ontology analysis. Int J Clin Exp Med 2: 309-328. Mycobacterium smegmatis proteome 20057975 8
2009 Roy S, Lane T, Werner-Washburne M, Martinez D Inference of functional networks of condition-specific response--a case study of quiescence in yeast. Pac Symp Biocomput 2009: 51-62. Yeast transcripts 19209695 7,17
2009 Ruepp A, Waegele B, Lechner M, Brauner B, Dunger-Kaltenbach I, Fobo G, Frishman G, Montrone C, Mewes HW CORUM: the comprehensive resource of mammalian protein complexes--2009. Nucleic Acids Res 38: D497-501. 19884131 11
2009 Ruths T, Ruths D, Nakhleh L GS2: an efficiently computable measure of GO-based similarity of gene sets. Bioinformatics 25: 1178-1184. 19289444 10,13
2009 Ryan RP, Koebnik R, Szurek B, Boureau T, Bernal A, Bogdanove A, Dow JM Passing GO (gene ontology) in plant pathogen biology: a report from the Xanthomonas Genomics Conference. Cell Microbiol 11: 1689-1696. 19804485 3
2009 Salem M, Kenney PB, Rexroad CE, Yao J Proteomic signature of muscle atrophy in rainbow trout. J Proteomics 73: 778-789. Trout muscle proteins 19903543 8
2009 Salih H, Adelson DL QTL global meta-analysis: are trait determining genes clustered? BMC Genomics 10: 184. 19393059 13
2009 Sam LT, Mendonca EA, Li J, Blake J, Friedman C, Lussier YA PhenoGO: an integrated resource for the multiscale mining of clinical and biological data. BMC Bioinformatics 10 Suppl 2: S8. 19208196 10,12
2009 Samarajiwa SA, Forster S, Auchettl K, Hertzog PJ INTERFEROME: the database of interferon regulated genes. Nucleic Acids Res 37: D852-857. 18996892 11
2009 Samwald M, Chen H, Ruttenberg A, Lim E, Marenco L, Miller P, Shepherd G, Cheung KH Semantic SenseLab: Implementing the vision of the Semantic Web in neuroscience. Artif Intell Med 48: 21-28. 20006477 13,15
2009 Sandra V, Inge N, Jef H, Hilda W, Greet S, Paul VC, Rosette VD Gene profiles of THP-1 macrophages after in vitro exposure to respiratory (non)-sensitizing chemicals: identification of discriminating genetic markers and pathway analysis. Toxicol In Vitro 23: 1151-1162. Human macrophage transcripts 19527780 7,16
2009 Sanfilippo A, Baddeley B, Beagley N, McDermott J, Riensche R, Taylor R, Gopalan B Using the gene ontology to enrich biological pathways. Int J Comput Biol Drug Des 2: 221-235. 20090161 13,17
2009 Sarson AJ, Wang Y, Kang Z, Dowd SE, Lu Y, Yu H, Han Y, Zhou H, Gong J Gene expression profiling within the spleen of Clostridium perfringens-challenged Broilers fed antibiotic-medicated and non-medicated diets. BMC Genomics 10: 260. Chicken transcripts; antibiotic treatment 19500416 7
2009 Sartor MA|etAl Genomewide analysis of aryl hydrocarbon receptor binding targets reveals an extensive array of gene clusters that control morphogenetic and developmental programs. Environ Health Perspect 117: 1139-1146. Mouse hepatoma cell transcripts 19654925 7
2009 Sathiyamoorthy S, In JG, Gayathri S, Kim YJ, Yang DC Generation and gene ontology based analysis of expressed sequence tags (EST) from a Panax ginseng C. A. Meyer roots. Mol Biol Rep 37: 3465-3472. Ginseng ESTs 19943115 5
2009 Sato K, Shin-I T, Seki M, Shinozaki K, Yoshida H, Takeda K, Yamazaki Y, Conte M, Kohara Y Development of 5006 full-length CDNAs in barley: a tool for accessing cereal genomics resources. DNA Res 16: 81-89. Barley cDNAs 19150987 3
2009 Satoh JI, Obayashi S, Tabunoki H, Wakana T, Kim SU Stable Expression of Neurogenin 1 Induces LGR5, a Novel Stem Cell Marker, in an Immortalized Human Neural Stem Cell Line HB1.F3. Cell Mol Neurobiol 30: 415-426. Human neural cell line transcripts 19813087 7,16
2009 Scaglione D, Acquadro A, Portis E, Taylor CA, Lanteri S, Knapp SJ Ontology and diversity of transcript-associated microsatellites mined from a globe artichoke EST database. BMC Genomics 10: 454. Artichoke ESTs 19785740 5,7
2009 Scatolini M, Grand MM, Grosso E, Venesio T, Pisacane A, Balsamo A, Sirovich R, Risio M, Chiorino G Altered molecular pathways in melanocytic lesions. Int J Cancer 126: 1869-1881. Human melanocytic transcripts 19795447 7,16
2009 Schlicker A, Albrecht M FunSimMat update: new features for exploring functional similarity. Nucleic Acids Res 38: D244-248. 19923227 11,19
2009 Schober D, Smith B, Lewis SE, Kusnierczyk W, Lomax J, Mungall C, Taylor CF, Rocca-Serra P, Sansone SA Survey-based naming conventions for use in OBO Foundry ontology development. BMC Bioinformatics 10: 125. 19397794 1,15
2009 Schriml LM|etAl GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database. Nucleic Acids Res 38: D754-764. 19850722 15
2009 Sebestyen E, Nagy T, Suhai S, Barta E DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes. BMC Bioinformatics 10 Suppl 6: S6. 19534755 7,10,18
2009 Sekigawa T, Tajima A, Hasegawa T, Hasegawa Y, Inoue H, Sano Y, Matsune S, Kurono Y, Inoue I Gene-expression profiles in human nasal polyp tissues and identification of genetic susceptibility in aspirin-intolerant asthma. Clin Exp Allergy 39: 972-981. Human nasal polyp transcripts; asthma 19489917 7,16
2009 Sellam A, Tebbji F, Nantel A Role of Ndt80p in sterol metabolism regulation and azole resistance in Candida albicans. Eukaryot Cell 8: 1174-1183. Candida albicans promoters 19542309 7
2009 Selpi S, Bryant CH, Kemp GJ, Sarv J, Kristiansson E, Sunnerhagen P Predicting functional upstream open reading frames in Saccharomyces cerevisiae. BMC Bioinformatics 10: 451. 20042076 13,19
2009 Senthil K, Wasnik NG, Kim YJ, Yang DC Generation and analysis of expressed sequence tags from leaf and root of Withania somnifera (Ashwgandha). Mol Biol Rep 37: 893-902. Withania somnifera ESTs 19669665 5,7
2009 Sequeira A|etAl Global brain gene expression analysis links glutamatergic and GABAergic alterations to suicide and major depression. PLoS One 4: e6585. Human brain transcripts; depression; suicide 19668376 7,16
2009 Shah NH, Jonquet C, Chiang AP, Butte AJ, Chen R, Musen MA Ontology-driven indexing of public datasets for translational bioinformatics. BMC Bioinformatics 10 Suppl 2: S1. 19208184 15
2009 Sharma RK, Bhardwaj P, Negi R, Mohapatra T, Ahuja PS Identification, characterization and utilization of unigene derived microsatellite markers in tea (Camellia sinensis, L). BMC Plant Biol 9: 53. Tea ESTs 19426565 5
2009 Sharma SM|etAl Insights into the pathogenesis of axial spondyloarthropathy based on gene expression profiles. Arthritis Res Ther 11: R168. Human blood cell transcripts 19900269 7,16
2009 Shaw DR Searching the Mouse Genome Informatics (MGI) resources for information on mouse biology from genotype to phenotype. Curr Protoc Bioinformatics Chapter 1: Unit1.7. Mouse genome 19274630 1,4,11,15
2009 Shen HB, Chou KC Gpos-mPLoc: a top-down approach to improve the quality of predicting subcellular localization of Gram-positive bacterial proteins. Protein Pept Lett 16: 1478-1484. 20001911 9,10
2009 Shen T, Shou T, Yan X, Dong H, Zou Y, Gao J, Zeng R, Hua Y, Zhang J, Li L [Screening of differentially expressed genes from patients with Bardet-Biedl syndrome by gene chip analysis.] Zhonghua Yi Xue Yi Chuan Xue Za Zhi 26: 648-652. Human peripheral blood mononuclear cell transcripts 19953487 7,16
2009 Shen Y, Sun W, Li KC Dynamic weighted clustering with noise set. Bioinformatics 26: 341-347. 20007256 7
2009 Shi C|etAl Genomics of human intracranial aneurysm wall. Stroke 40: 1252-1261. Human arterial wall transcripts; intracranial aneurysm 19228845 7,16
2009 Shimizu M, Tainaka H, Oba T, Mizuo K, Umezawa M, Takeda K Maternal exposure to nanoparticulate titanium dioxide during the prenatal period alters gene expression related to brain development in the mouse. Part Fibre Toxicol 6: 20. Mouse brain transcripts; nanoparticle exposure 19640265 7,16
2009 Shu QY, Wischnitzki E, Liu ZA, Ren HX, Han XY, Hao Q, Gao FF, Xu SX, Wang LS Functional annotation of expressed sequence tags as a tool to understand the molecular mechanism controlling flower bud development in tree peony. Physiol Plant 135: 436-449. Tree peony ESTs 19292824 5
2009 Simon M, Hancock JM Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins. Genome Biol 10: R59. 19486509 13,18
2009 Singh P, Alley TL, Wright SM, Kamdar S, Schott W, Wilpan RY, Mills KD, Graber JH Global changes in processing of mRNA 3' untranslated regions characterize clinically distinct cancer subtypes. Cancer Res 69: 9422-9430. Mouse transcripts; human tumor transcripts; B-cell leukemia/lymphoma 19934316 7,13,16
2009 Sinha A, Shahzad K, Latif F, Cadeiras M, von Bayern MP, Oz S, Naka Y, Deng MC Peripheral Blood Mononuclear Cell Transcriptome Profiles Suggest T-cell Immunosuppression after Uncomplicated Mechanical Circulatory Support Device Surgery. Hum Immunol 71: 164-169. Human blood cell transcripts 19879911 7,16
2009 Siu KW, Desouza LV, Scorilas A, Romaschin AD, Honey RJ, Stewart R, Pace K, Youssef Y, Chow TF, Yousef GM Differential Protein Expressions in Renal Cell Carcinoma: New Biomarker Discovery by Mass Spectrometry. J Proteome Res 8: 3797-3807. Human kidney proteins 19610612 8,16
2009 Skarman A, Jiang L, Henrik H, Buitenhuis B, Hedegaard J, Conley LN, Sorensen P Gene set analysis methods applied to chicken microarray expression data. BMC Proc 3 Suppl 4: S8. Chicken transcripts 19615121 7
2009 Skrzypek MS, Arnaud MB, Costanzo MC, Inglis DO, Shah P, Binkley G, Miyasato SR, Sherlock G New tools at the Candida Genome Database: biochemical pathways and full-text literature search. Nucleic Acids Res 38: D428-432. 19808938 1,11
2009 Sleiman PM|etAl Characterisation of a novel NR4A2 mutation in Parkinson's disease brain. Neurosci Lett 457: 75-79. Human neuronal transcripts; Parkinson's disease 19429166 7,16
2009 Smialowski P|etAl The Negatome database: a reference set of non-interacting protein pairs. Nucleic Acids Res 38: D540-544. 19920129 11
2009 Smith CL, Eppig JT The Mammalian Phenotype Ontology: enabling robust annotation and comparative analysis. Wiley Interdiscip Rev Syst Biol Med 1: 390-399. 20052305 15
2009 Soderlund C Computational techniques for elucidating plant-pathogen interactions from large-scale experiments on fungi and oomycetes. Brief Bioinform 10: 654-663. 19933211 11,13
2009 Soh J|etAl Spatiotemporal integration of molecular and anatomical data in virtual reality using semantic mapping. Int J Nanomedicine 4: 79-89. 19421373 15
2009 Soldatos TG, O'Donoghue SI, Satagopam VP, Jensen LJ, Brown NP, Barbosa-Silva A, Schneider R Martini: using literature keywords to compare gene sets. Nucleic Acids Res 38: 26-38. 19858102 13
2009 Song J, Singh M How and when should interactome-derived clusters be used to predict functional modules and protein function? Bioinformatics 25: 3143-3150. Saccharomyces proteins 19770263 8,9,17
2009 Song MO, Li J, Freedman JH Physiological and toxicological transcriptome changes in HepG2 cells exposed to copper. Physiol Genomics 38: 386-401. Human liver cell line transcripts; copper exposure 19549813 7,16
2009 Song YB, Jhun MA, Park T, Huh WK Quantitative proteomic analysis of ribosomal protein L35b mutant of Saccharomyces cerevisiae. Biochim Biophys Acta 1804: 676-683. Saccharomyces ribosomal proteins 19879384 8
2009 Soos V, Sebestyen E, Juhasz A, Pinter J, Light ME, Van Staden J, Balazs E Stress-related genes define essential steps in the response of maize seedlings to smoke-water. Funct Integr Genomics 9: 231-242. Maize transcripts 19139936 7
2009 Sowa ME, Bennett EJ, Gygi SP, Harper JW Defining the human deubiquitinating enzyme interaction landscape. Cell 138: 389-403. Human proteins; deubiquitination 19615732 17
2009 Sprung RW, Brock JW, Tanksley JP, Li M, Washington MK, Slebos RJ, Liebler DC Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis. Mol Cell Proteomics 8: 1988-1998. 19467989 8
2009 Stelzer G, Inger A, Olender T, Iny-Stein T, Dalah I, Harel A, Safran M, Lancet D GeneDecks: paralog hunting and gene-set distillation with GeneCards annotation. OMICS 13: 477-487. 20001862 10,11
2009 Stockhammer OW, Zakrzewska A, Hegedus Z, Spaink HP, Meijer AH Transcriptome profiling and functional analyses of the zebrafish embryonic innate immune response to Salmonella infection. J Immunol 182: 5641-5653. Zebrafish embryonic transcripts; Salmonella infection 19380811 7
2009 Stockwin LH, Vistica DT, Kenney S, Schrump DS, Butcher DO, Raffeld M, Shoemaker RH Gene expression profiling of alveolar soft-part sarcoma (ASPS). BMC Cancer 9: 22. Human alveolar transcripts; sarcoma 19146682 7,16
2009 Storm MP, Kumpfmueller B, Thompson B, Kolde R, Vilo J, Hummel O, Schulz H, Welham MJ Characterization of the phosphoinositide 3-kinase-dependent transcriptome in murine embryonic stem cells: identification of novel regulators of pluripotency. Stem Cells 27: 764-775. Mouse embryonic stem cell transcripts; pluripotency 19350676 7
2009 Strath J, Georgopoulos LJ, Kellam P, Blair GE Identification of genes differentially expressed as result of adenovirus type 5- and adenovirus type 12-transformation. BMC Genomics 10: 67. Rat kidney cell line transcripts 19200380 7
2009 Su Z, Zeng Y, Gu X A preliminary analysis of gene pleiotropy estimated from protein sequences. J Exp Zoolog B Mol Dev Evol 314B: 115-122. 19637279 13
2009 Sun CH, Kim MS, Han Y, Yi GS COFECO: composite function annotation enriched by protein complex data. Nucleic Acids Res 37: W350-355. 19429688 3,10,17
2009 Sun J, Han L, Zhao Z Gene- and evidence-based candidate gene selection for schizophrenia and gene feature analysis. Artif Intell Med 48: 99-9106. 19944577 13,16
2009 Suzuki K, Machiyama F, Nishino S, Watanabe Y, Kashiwagi K, Kashiwagi A, Yoshizato K Molecular features of thyroid hormone-regulated skin remodeling in Xenopus laevis during metamorphosis. Dev Growth Differ 51: 411-427. Xenopus skin transcripts 19382937 7
2009 Taher L, Ovcharenko I Variable locus length in the human genome leads to ascertainment bias in functional inference for noncoding elements. Bioinformatics 25: 578-584. 19168912 3,13
2009 Takahashi Y, Forrest AR, Maeno E, Hashimoto T, Daub CO, Yasuda J MiR-107 and MiR-185 can induce cell cycle arrest in human non small cell lung cancer cell lines. PLoS One 4: e6677. Human miRNA targets; lung cancer 19688090 7,16
2009 Taki K|etAl Microarray analysis of differentially expressed genes in the kidneys and testes of mice after long-term irradiation with low-dose-rate gamma-rays. J Radiat Res (Tokyo) 50: 241-252. Mouse kidney transcripts; mouse testis transcripts; gamma radiation exposure 19398854 7,16
2009 Tang Z, Choi JH, Hemmerich C, Sarangi A, Colbourne JK, Dong Q ESTPiper - a web-based analysis pipeline for expressed sequence tags. BMC Genomics 10: 174. 19383159 5,10
2009 Tastan O, Qi Y, Carbonell JG, Klein-Seetharaman J Prediction of interactions between HIV-1 and human proteins by information integration. Pac Symp Biocomput 2009: 516-527. 19209727 17,19
2009 Taylor JM, Street TL, Hao L, Copley R, Taylor MS, Hayden PJ, Stolper G, Mott R, Hein J, Moffatt MF, Cookson WO Dynamic and physical clustering of gene expression during epidermal barrier formation in differentiating keratinocytes. PLoS One 4: e7651. Human keratinocyte transcripts 19888454 7,16
2009 Tazi KA, Quioc JJ, Abdel-Razek W, Tellier Z, Guichard C, Ogier-Denis E, Lebrec D, Moreau R Protein array technology to investigate cytokine production by monocytes from patients with advanced alcoholic cirrhosis: An ex vivo pilot study. Hepatol Res 39: 706-715. Human peripheral blood monocyte proteins; cirrhosis 19473436 8,16
2009 Tchagang AB, Bui KV, McGinnis T, Benos PV Extracting biologically significant patterns from short time series gene expression data. BMC Bioinformatics 10: 255. 19695084 7,10
2009 Teerapornpuntakit J, Dorkkam N, Wongdee K, Krishnamra N, Charoenphandhu N Endurance swimming stimulates transepithelial calcium transport and alters the expression of genes related to calcium absorption in the intestine of rats. Am J Physiol Endocrinol Metab 296: E775-786. Rat intestinal transcripts; endurance exercise 19176351 7,16
2009 Teixeira MC, Raposo LR, Mira NP, Lourenco AB, Sa-Correia I Genome-wide identification of Saccharomyces cerevisiae genes required for maximal tolerance to ethanol. Appl Environ Microbiol 75: 5761-5772. Yeast genes; ethanol tolerance 19633105 13
2009 Teixeira VH, Olaso R, Martin-Magniette ML, Lasbleiz S, Jacq L, Oliveira CR, Hilliquin P, Gut I, Cornelis F, Petit-Teixeira E Transcriptome analysis describing new immunity and defense genes in peripheral blood mononuclear cells of rheumatoid arthritis patients. PLoS One 4: e6803. Human peripheral blood mononuclear cell transcripts; rheumatoid arthritis 19710928 7,16
2009 Terrapon N, Gascuel O, Marechal E, Breehelin L Detection of new protein domains using co-occurrence: application to Plasmodium falciparum. Bioinformatics 25: 3077-3083. 19786484 9
2009 Thiemann A, Fu J, Schrag TA, Melchinger AE, Frisch M, Scholten S Correlation between parental transcriptome and field data for the characterization of heterosis in Zea mays L. Theor Appl Genet 120: 401-413. Maize transcripts 19888564 7
2009 Thompson P, Iqbal SA, McNaught J, Ananiadou S Construction of an annotated corpus to support biomedical information extraction. BMC Bioinformatics 10: 349. 19852798 15
2009 Throude M|etAl Structure and expression analysis of rice paleo duplications. Nucleic Acids Res 37: 1248-1259. Rice genes 19136467 18
2009 Tian F, Chen J, Bao S, Shi L, Liu X, Grossman R A graph model based study on regulatory impacts of transcription factors of Drosophila melanogaster and comparison across species. Biochem Biophys Res Commun 386: 559-562. 19538943 7,17,18
2009 Tian W, Samatova NF Pairwise alignment of interaction networks by fast identification of maximal conserved patterns. Pac Symp Biocomput 2009: 99-110. 19209698 17,18
2009 Timmermans MJ, Roelofs D, Nota B, Ylstra B, Holmstrup M Sugar sweet springtails: on the transcriptional response of Folsomia candida (Collembola) to desiccation stress. Insect Mol Biol 18: 737-746. Folsomia candida transcripts 19788701 7
2009 Tomas A, Fernandes LT, Sanchez A, Segales J Time course differential gene expression in response to porcine circovirus type 2 subclinical infection. Vet Res 41: 12. Porcine blood transcripts 19825344 7
2009 Tong JC, Lim SJ, Muh HC, Chew FT, Tammi MT Allergen Atlas: a comprehensive knowledge center and analysis resource for allergen information. Bioinformatics 25: 979-980. 19213741 11
2009 Torma A, Pitkanen JP, Huopaniemi L, Mattila P, Renkonen R Concordant gene regulation related to perturbations of three GDP-mannose-related genes. FEMS Yeast Res 9: 63-72. Yeast proteins 19133071 7,8
2009 Toronen P, Pehkonen P, Holm L Generation of Gene Ontology benchmark datasets with various types of positive signal. BMC Bioinformatics 10: 319. 19811632 10
2009 Torto-Alalibo T, Collmer CW, Gwinn-Giglio M The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium: community development of new Gene Ontology terms describing biological processes involved in microbe-host interactions. BMC Microbiol 9 Suppl 1: S1. 19278549 1,3,13
2009 Torto-Alalibo T, Collmer CW, Lindeberg M, Bird D, Collmer A, Tyler BM Common and contrasting themes in host cell-targeted effectors from bacterial, fungal, oomycete and nematode plant symbionts described using the Gene Ontology. BMC Microbiol 9 Suppl 1: S3. 19278551 1,3,13,18
2009 Torto-Alalibo T, Meng S, Dean RA Infection strategies of filamentous microbes described with the Gene Ontology. Trends Microbiol 17: 320-327. Filamentous microbe genomes 19577927 1,4
2009 Toyama R, Chen X, Jhawar N, Aamar E, Epstein J, Reany N, Alon S, Gothilf Y, Klein DC, Dawid IB Transcriptome analysis of the zebrafish pineal gland. Dev Dyn 238: 1813-1826. Zebrafish pineal transcripts 19504458 7
2009 Trimmer PA, Bennett JP The cybrid model of sporadic Parkinson's disease. Exp Neurol 218: 320-325. Human cytoplasmic hybrid genes; Parkinson's disease 19328199 7,16
2009 Tripathi AK, Sha W, Shulaev V, Stins MF, Sullivan DJ Plasmodium falciparum infected erythrocytes induce NF-{kappa}B regulated inflammatory pathways in human cerebral endothelium. Blood 114: 4243-4252. Human brain transcripts; cerebral malaria 19713460 7,16
2009 Tseng LH, Chen I, Lin YH, Chen MY, Lo TS, Lee CL Genome-based expression profiles study for the pathogenesis of pelvic organ prolapse: an array of 33 genes model. Int Urogynecol J Pelvic Floor Dysfunct 21: 79-84. Human pelvic connective tissue transcripts 19756343 7,16
2009 Tseng LH, Chen I, Lin YH, Liang CC, Lloyd LK Genome-based expression profiling study following spinal cord injury in the rat: An array of 48-gene model. Neurourol Urodyn 29: 1439-1443. Rat bladder transcripts 19618445 7,16
2009 Tseng TT, Tyler BM, Setubal JC Protein secretion systems in bacterial-host associations, and their description in the Gene Ontology. BMC Microbiol 9 Suppl 1: S2. 19278550 1,3,13
2009 Tsoi LC, Boehnke M, Klein RL, Zheng WJ Evaluation of genome-wide association study results through development of ontology fingerprint. Bioinformatics 25: 1314-1320. 19349285 12,13
2009 Tsuritani K, Takeda J, Sakagami J, Ishii A, Eriksson T, Hara T, Ishibashi H, Koshihara Y, Yamada K, Yoneda Y Cytokine Receptor-Like Factor 1 is highly expressed in damaged human knee osteoarthritic cartilage and involved in osteoarthritis downstream of TGF-beta. Calcif Tissue Int 86: 47-57. Human cartilage transcripts 19921088 7,16
2009 Tuller T, Kupiec M, Ruppin E Co-evolutionary networks of genes and cellular processes across fungal species. Genome Biol 10: R48. 19416514 17,18
2009 Tuller T, Rubinstein U, Bar D, Gurevitch M, Ruppin E, Kupiec M Higher-order genomic organization of cellular functions in yeast. J Comput Biol 16: 303-316. 19193148 13,18
2009 Tyagi A, Ryme J, Brodin D, Ostlund Farrants AK, Visa N SWI/SNF associates with nascent pre-mRNPs and regulates alternative pre-mRNA processing. PLoS Genet 5: e1000470. Drosophila transcripts 19424417 7
2009 Tyler BM Viewing the microbial world through the lens of the Gene Ontology. Trends Microbiol 17: 259-261. Microbial genomes 19577929 1,4
2009 Uchiyama I, Higuchi T, Kawai M MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity. Nucleic Acids Res 38: D361-365. 19906735 11
2009 Uebing-Czipura AU, Dawson HD, Rutherford MS, Scherba G Transcriptome profile and cytogenetic analysis of immortalized neuronally restricted progenitor cells derived from the porcine olfactory bulb. Anim Biotechnol 20: 186-215. Porcine olfactory bulb neuroblast cell line transcripts 19937495 7
2009 Uittenbogaard M, Baxter KK, Chiaramello A NeuroD6 genomic signature bridging neuronal differentiation to survival via the molecular chaperone network. J Neurosci Res 88: 33-54. Human neuronal cell transcripts; neurogenesis 19610105 7,16
2009 Umezawa M, Tanaka N, Tainaka H, Takeda K, Ihara T, Sugamata M Microarray analysis provides insight into the early step of pathophysiology of mouse endometriosis model induced by autotransplantation of endometrium. Life Sci 84: 832-837. Mouse peritoneal transcripts; endometriosis 19345696 7,16
2009 Van Auken K, Jaffery J, Chan JN, Muller HM, Sternberg PW Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) cellular component curation. BMC Bioinformatics 10: 228. C. elegans proteins 19622167 1,6,9,12
2009 Vandepoele K, Quimbaya M, Casneuf T, De Veylder L, Van de Peer Y Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks. Plant Physiol 150: 535-546. Arabidopsis transcripts 19357200 7,17
2009 Vanopstal K, Vander Stichele R, Laureys G, Buysschaert J Vocabularies and Retrieval Tools in Biomedicine: Disentangling the Terminological Knot. J Med Syst epub 20703537 14
2009 Varshney RK|etAl A comprehensive resource of drought- and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.). BMC Genomics 10: 523. Chickpea ESTs 19912666 5
2009 Vega VB, Woo XY, Hamidi H, Yeo HC, Yeo ZX, Bourque G, Clarke ND Inferring direct regulatory targets of a transcription factor in the DREAM2 challenge. Ann N Y Acad Sci 1158: 215-223. 19348643 7,17
2009 Velankar S|etAl PDBe: Protein Data Bank in Europe. Nucleic Acids Res 38: D308-317. 19858099 11
2009 Venier P|etAl MytiBase: a knowledgebase of mussel (M. galloprovincialis) transcribed sequences. BMC Genomics 10: 72. Mussel ESTs 19203376 5,7
2009 Vera J, Kwon T, Schmitz U, Kolch W, Exploration of homodimer receptor: homodimer protein interactions. Int J Bioinform Res Appl 5: 447-457. 19640831 8,17
2009 Verspoor K, Dvorkin D, Cohen KB, Hunter L Ontology quality assurance through analysis of term transformations. Bioinformatics 25: i77-84. 19478020 13,14
2009 Vinogradov AE, Anatskaya OV Loss of protein interactions and regulatory divergence in yeast whole-genome duplicates. Genomics 93: 534-542. 19272438 18
2009 Vo TT, Jung EM, Dang VH, Yoo YM, Choi KC, Yu FH, Jeung EB Di-(2 ethylhexyl) phthalate and flutamide alter gene expression in the testis of immature male rats. Reprod Biol Endocrinol 7: 104. Rat testis transcripts 19781091 7,16
2009 Waldeck W, Pipkorn R, Korn B, Mueller G, Schick M, Toth K, Wiessler M, Didinger B, Braun K Transporter molecules influence the gene expression in HeLa cells. Int J Med Sci 6: 18-27. HeLa cell transcripts; drug delivery 19214198 7,16
2009 Walters KA, Syder AJ, Lederer SL, Diamond DL, Paeper B, Rice CM, Katze MG Genomic analysis reveals a potential role for cell cycle perturbation in HCV-mediated apoptosis of cultured hepatocytes. PLoS Pathog 5: e1000269. Human liver cell line transcripts; hepatitis C 19148281 10.1371/journal.ppat.1000269 7,16
2009 Wang H, Gao Y, Jin X, Xiao J Expression of contactin associated protein-like 2 in a subset of hepatic progenitor cell compartment identified by gene expression profiling in hepatitis B virus-positive cirrhosis. Liver Int 30: 126-138. Human liver transcripts 19889080 7,16
2009 Wang J, Kim JM, Donovan DM, Becker KG, Li MD Significant modulation of mitochondrial electron transport system by nicotine in various rat brain regions. Mitochondrion 9: 186-195. Rat brain transcripts; nicotine exposure 19460297 7,16
2009 Wang L|etAl Genome-wide transcriptional profiling reveals microRNA-correlated genes and biological processes in human lymphoblastoid cell lines. PLoS ONE 4: e5878. Human lymphoblastoid cell line miRNAs 19517021 7,16
2009 Wang N, Xue L, Yuan A, Xu D Identification of mouse 8-cell embryo stage-specific genes by Digital Differential Display. Exp Anim 58: 547-556. Mouse genes; embryonic development 19897940 7
2009 Wang SY, Shen XY, Wu CY, Pan F, Shen YY, Sheng HH, Chen XM, Gao HJ Analysis of whole genomic expression profiles of Helicobacter pylori related chronic atrophic gastritis with IL-1B-31CC/-511TT genotypes. J Dig Dis 10: 99-9106. Human stomach transcripts; Helicobacter pylori infection; gastritis 19426391 7,16
2009 Wang Y, Leung FC A study on genomic distribution and sequence features of human long inverted repeats reveals species-specific intronic inverted repeats. FEBS J 276: 1986-1998. Human long inverted repeats 19243432 13,18
2009 Wang Y, Leung FC In silico prediction of two classes of honeybee genes with CpG deficiency or CpG enrichment and sorting according to Gene Ontology classes. J Mol Evol 68: 700-705. Honeybee genes 19466376 7
2009 Wang YY, Ye ZY, Zhao ZS, Tao HQ, Li SG Systems biology approach to identification of biomarkers for metastatic progression in gastric cancer. J Cancer Res Clin Oncol epub Human genes; gastric cancer 19649653 7,16,17
2009 Wang Z, Zhang Q Genome-Wide Identification and Evolutionary Analysis of the Animal Specific ETS Transcription Factor Family. Evol Bioinform Online 5: 119-131. Animal transcriptomes 20011068 7
2009 Washington NL, Haendel MA, Mungall CJ, Ashburner M, Westerfield M, Lewis SE Linking human diseases to animal models using ontology-based phenotype annotation. PLoS Biol 7: e1000247. 19956802 10.1371/journal.pbio.1000247 1,13,15
2009 Watanabe-Fukuda Y|etAl Orengedokuto and berberine improve indomethacin-induced small intestinal injury via adenosine. J Gastroenterol 44: 380-389. Mouse small intestinal transcripts; enteropathy; orengedokuto; berberine 19319464 7,16
2009 Way KJ|etAl The generation and properties of human macrophage populations from hemopoietic stem cells. J Leukoc Biol 85: 766-778. Human macrophage transcripts 19181863 7,16
2009 Webb R|etAl Variants within MECP2, a key transcription regulator, are associated with increased susceptibility to lupus and differential gene expression in patients with systemic lupus erythematosus. Arthritis Rheum 60: 1076-1084. Human B cell transcripts; lupus 19333917 7,16
2009 Werner A, Carlile M, Swan D What do natural antisense transcripts regulate? RNA Biol 6: 43-48. 19098462 7
2009 Wessells H, Sullivan CJ, Tsubota Y, Engel KL, Kim B, Olson NE, Thorner D, Chitaley K Transcriptional profiling of human cavernosal endothelial cells reveals distinctive cell adhesion phenotype and role for Claudin 11 in vascular barrier function. Physiol Genomics 39: 100-108. Human cavernosal endothelial cell transcripts; penile erection 19622796 7,16
2009 Wetterbom A, Gyllensten U, Cavelier L, Bergstrom TF Genome-wide analysis of chimpanzee genes with premature termination codons. BMC Genomics 10: 56. Chimpanzee genes 19178713 13,18
2009 Wilkinson P|etAl EMMA--mouse mutant resources for the international scientific community. Nucleic Acids Res 38: D570-576. 19783817 15
2009 Williams TD|etAl Hepatic transcriptomic and metabolomic responses in the stickleback (Gasterosteus aculeatus) exposed to environmentally relevant concentrations of dibenzanthrocene. Environ Sci Technol 43: 6341-6348. Stickleback transcripts; dibenzanthracene exposure 19746735 7
2009 Wilson D, Pethica R, Zhou Y, Talbot C, Vogel C, Madera M, Chothia C, Gough J SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny. Nucleic Acids Res 37: D380-386. 19036790 6,11
2009 Wiwanitkit V "Interaction between bcl2 and jun B in primary cutaneous lymphoma: a gene ontology approach": a comment on the new approach in dermatology. Indian J Dermatol 54: 298. 20161870 16
2009 Wiwanitkit V Interaction between interferon regulatory factor-1 and human papillomavirus E7 oncogene in cervical cancer: an ontology study. Taiwan J Obstet Gynecol 48: 138-141. 19574175 13,16
2009 Wortman JR|etAl The 2008 update of the Aspergillus nidulans genome annotation: a community effort. Fungal Genet Biol 46 Suppl 1: S2-13. Aspergillus nidulans genome 19146970 4
2009 Wren JD A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide. Bioinformatics 25: 1694-1701. Human genes 19447786 7,9
2009 Wu J, Xu X, Xiao J, Xu L, Yi H, Gao S, Liu J, Bao Q, Zhao F, Li X FlyPhy: a phylogenomic analysis platform for Drosophila genes and gene families. BMC Bioinformatics 10: 123. Drosophila genes 19393099 3,18
2009 Wu Q|etAl Transcript profiles of Panax quinquefolius from flower, leaf and root bring new insights into genes related to ginsenosides biosynthesis and transcriptional regulation. Physiol Plant 138: 134-149. Ginseng ESTs 19947964 7
2009 Wu X, Ghimbovschi S, Aujla PK, Rose MC, Pena MT Expression profiling of inflammatory mediators in pediatric sinus mucosa. Arch Otolaryngol Head Neck Surg 135: 65-72. Human sinus mucosa transcripts; chronic rhinosinusitis 19153309 7,16
2009 Wurm Y, Uva P, Ricci F, Wang J, Jemielity S, Iseli C, Falquet L, Keller L Fourmidable: a database for ant genomics. BMC Genomics 10: 5. Human myometrial transcripts; human cervical transcripts; labor 19126223 7,16
2009 Xi L, Moscou MJ, Meng Y, Xu W, Caldo RA, Shaver M, Nettleton D, Wise RP Transcript-based cloning of RRP46, a regulator of rRNA processing and R gene-independent cell death in barley-powdery mildew interactions. Plant Cell 21: 3280-3295. Barley transcripts 19861556 7
2009 Xiong W, Niu PY, Zhu WT, Chen J Tenascin-C as a prognostic biomarker in osteosarcoma? Chin Med J (Engl) 122: 2737-2743. Human osteosarcoma cell line transcripts 19951606 7,16
2009 Xu T, Gu J, Zhou Y, Du L Improving detection of differentially expressed gene sets by applying cluster enrichment analysis to Gene Ontology. BMC Bioinformatics 10: 240. 19653916 7,10
2009 Xu XQ, Soo SY, Sun W, Zweigerdt R Global expression profile of highly enriched cardiomyocytes derived from human embryonic stem cells. Stem Cells 27: 2163-2174. Human cardiomyocyte transcripts 19658189 7,16
2009 Xuan W, Dai M, Mirel B, Song J, Athey B, Watson SJ, Meng F Open Biomedical Ontology-based Medline exploration. BMC Bioinformatics 10 Suppl 5: S6. 19426463 10,15
2009 Yamasaki C|etAl H-InvDB in 2009: extended database and data mining resources for human genes and transcripts. Nucleic Acids Res 38: D626-632. 19933760 11
2009 Yamazaki Y|etAl NBRP databases: databases of biological resources in Japan. Nucleic Acids Res 38: D26-32. 19934255 11
2009 Yan H, Zhou W, Wei L, Zhong F, Yang Y Proteomic analysis of astrocytic secretion that regulates neurogenesis using quantitative amine-specific isobaric tagging. Biochem Biophys Res Commun 391: 1187-1191. Rat astrocyte proteins 20005204 8
2009 Yan J, Yang X, Mortin MA, Shahabuddin M Malaria sporozoite antigen-directed genome-wide response in transgenic Drosophila. 47: 196-203. Drosophila transcripts; Plasmodium falciparum antigens 19241390 7,16
2009 Yan J, Yang X, Mortin MA, Shahabuddin M Malaria sporozoite antigen-directed genome-wide response in transgenic Drosophila. Genesis 47: 196-203. Plasmodium falciparum transcripts 19241390 7,16
2009 Yan W|etAl Systematic comparison of the human saliva and plasma proteomes. Proteomics Clin Appl 3: 116-134. Human proteins 19898684 8,16
2009 Yang CC, Lin YS, Hsu CC, Tsai MH, Wu SC, Cheng WT Seasonal effect on sperm messenger RNA profile of domestic swine (Sus Scrofa). Anim Reprod Sci 119: 76-84. Porcine speerm transcripts 20056359 7
2009 Yang E, Androulakis IP Assessing and selecting gene expression signals based upon the quality of the measured dynamics. BMC Bioinformatics 10: 55. 19208252 7
2009 Yang H, Zhou Z, Zhang H, Chen M, Li J, Ma Y, Zhong B Shotgun proteomic analysis of the fat body during metamorphosis of domesticated silkworm (Bombyx mori). Amino Acids 38: 1333-1342. Silkworm proteins 19730979 8
2009 Yang X, Zhou Y, Jin R, Chan C Reconstruct modular phenotype-specific gene networks by knowledge-driven matrix factorization. Bioinformatics 25: 2236-2243. 19542155 7,10,17
2009 Yao HP, Chen L, Xiang X, Guo AQ, Lu XM, Wu XF Proteomics identification and annotation of proteins of cell line of Bombyx mori, BmN cell. Biosci Rep 30: 209-215. Silkworm proteins 19496755 8
2009 Yin LM, Jiang GH, Wang Y, Wang Y, Liu YY, Jin WR, Xu YD, Zhang QH, Yang YQ Use of serial analysis of gene expression to reveal the specific regulation of gene expression profile in asthmatic rats treated by acupuncture. J Biomed Sci 16: 46. Rat lung transcripts; asthma; acupuncture 19419550 7,16
2009 Yoo DR, Chong SA, Nam MJ Proteome profiling of arsenic trioxide-treated human hepatic cancer cells. Cancer Genomics Proteomics 6: 269-274. Human hepatic cancer cell proteins 19996132 8,16
2009 Yoshihara K|etAl Gene expression profiling of advanced-stage serous ovarian cancers distinguishes novel subclasses and implicates ZEB2 in tumor progression and prognosis. Cancer Sci 100: 1421-1428. Human ovarian transcripts; ovarian cancer 19486012 7,16
2009 Yu Y, Tu K, Zheng S, Li Y, Ding G, Ping J, Hao P, Li Y GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction. BMC Bioinformatics 10: 264. 19703314 7,10,13
2009 Zagorski J, Obraztsova M, Gellar MA, Kline JA, Watts JA Transcriptional changes in right ventricular tissues are enriched in the outflow tract compared to the apex during chronic pulmonary embolism in rats. Physiol Genomics 39: 61-71. Rat heart transcripts 19602618 7,16
2009 Zagrobelny M, Scheibye-Alsing K, Bjerg Jensen N, Lindberg Moller B, Gorodkin J, Bak S 454 pyrosequencing based transcriptome analysis of Zygaena filipendulae with focus on genes involved in biosynthesis of cyanogenic glucosides. BMC Genomics 10: 574. Zygaena filipendulae transcripts 19954531 7
2009 Zeng J, Cao XQ, Zhao H, Yan H Finding human promoter groups based on DNA physical properties. Phys Rev E Stat Nonlin Soft Matter Phys 80: 041917. 19905352 7,13
2009 Zhang C, Fei SZ, Warnke S, Li L, Hannapel D Identification of genes associated with cold acclimation in perennial ryegrass. J Plant Physiol 166: 1436-1445. Ryegrass ESTs 19375818 5,7
2009 Zhang D, Popesku JT, Martyniuk CJ, Xiong H, Duarte-Guterman P, Yao L, Xia X, Trudeau VL Profiling neuroendocrine gene expression changes following fadrozole-induced estrogen decline in the female goldfish. Physiol Genomics 38: 351-361. Goldfish brain transcripts 19509080 7
2009 Zhang D, Xiong H, Mennigen JA, Popesku JT, Marlatt VL, Martyniuk CJ, Crump K, Cossins AR, Xia X, Trudeau VL Defining global neuroendocrine gene expression patterns associated with reproductive seasonality in fish. PLoS ONE 4: e5816. Goldfish brain transcripts 19503831 7
2009 Zhang F, Lu M, Zhang QP, Zhang FC, Gao W, Cui QH [Prediction of the microRNAs related to cardiovascular diseases by bioinformatics.] Beijing Da Xue Xue Bao 41: 112-116. Human miRNAs; cardiovascular disease 19221578 7,13,16
2009 Zhang X, Liu Y, Feng C, Yang S, Wang Y, Wu AS, Yue Y Proteomic profiling of the insoluble fractions in the rat hippocampus post-propofol anesthesia. Neurosci Lett 465: 165-170. Human keratinocyte transcripts 19682543 7,16
2009 Zhang X|etAl Expression profiles of early esophageal squamous cell carcinoma by cDNA microarray. Cancer Genet Cytogenet 194: 23-29. Human esophageal transcripts 19737650 7,16
2009 Zhang Y, Chen J, Tang X, Wang F, Jiang L, Xiong X, Wang M, Rong M, Liu Z, Liang S Transcriptome analysis of the venom glands of the Chinese wolf spider Lycosa singoriensis. Zoology (Jena) 113: 10-18. Wolf spider transcripts 19875276 7
2009 Zhang Y, Lv J, Liu H, Zhu J, Su J, Wu Q, Qi Y, Wang F, Li X HHMD: the human histone modification database. Nucleic Acids Res 38: D149-154. 19892823 11
2009 Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW Reverse engineering module networks by PSO-RNN hybrid modeling. BMC Genomics 10 Suppl 1: S15. 19594874 17
2009 Zhang Y, Ye Y, Shen D, Jiang K, Zhang H, Sun W, Zhang J, Xu F, Cui Z, Wang S Identification of transgelin-2 as a biomarker of colorectal cancer by laser capture microdissection and quantitative proteome analysis. Cancer Sci 101: 523-529. Human mucosal epithelial transcripts 19930159 8,16
2009 Zhang Z, Wu R, Li P, Liu F, Zhang W, Zhang P, Li P, Wang Y Baicalin administration is effective in positive regulation of twenty-four ischemia/reperfusion-related proteins identified by a proteomic study. Neurochem Int 54: 488-496. Mouse cerebral artery proteins; baicalin treatment 19428793 8,16
2009 Zhang Z, Zhang B, Nie X, Liu Q, Xie F, Shang D Transcriptome analysis and identification of genes related to immune function in skin of the chinese brown frog. Zoolog Sci 26: 80-86. Chinese brown frog skin transcripts 19267615 5,7
2009 Zhao C, Putnik M, Gustafsson JA, Dahlman-Wright K Microarray analysis of altered gene expression in ERbeta-overexpressing HEK293 cells. Endocrine 36: 224-232. Human kidney cell line transcripts 19680825 7,16
2009 Zhao J, Klyne G, Benson E, Gudmannsdottir E, White-Cooper H, Shotton D FlyTED: the Drosophila Testis Gene Expression Database. Nucleic Acids Res 38: D710-715. 19934263 15
2009 Zheng HT, Borchert C, Kim HG GOClonto: An ontological clustering approach for conceptualizing PubMed abstracts. J Biomed Inform 43: 31-40. 19635585 10,12
2009 Zhou QY, Fang MD, Huang TH, Li CC, Yu M, Zhao SH Detection of differentially expressed genes between Erhualian and Large White placentas on day 75 and 90 of gestation. BMC Genomics 10: 337. Porcine placental transcripts 19630995 7
2009 Zhou X, Su Z, Sammons RD, Peng Y, Tranel PJ, Stewart CN, Yuan JS Novel software package for cross-platform transcriptome analysis (CPTRA). BMC Bioinformatics 10 Suppl 11: S16. 19811681 7,10
2009 Zhou YB, Huang ZX, Ren CP, Zhu B, Yao KT [Screening and preliminary analysis of the apoptosis- and proliferation-related genes in nasopharyngeal carcinoma.] Nan Fang Yi Ke Da Xue Xue Bao 29: 645-647. Human transcripts; nasopharyngeal carcinoma 19403385 7,16
2009 Zhu W, Yang L, Du Z Layered functional network analysis of gene expression in human heart failure. PLoS One 4: e6288. Human heart transcripts; human heart proteins 19629191 7,8,16,17
2009 Zou Y, Su Z, Yang J, Zeng Y, Gu X Uncovering genetic regulatory network divergence between duplicate genes using yeast eQTL landscape. J Exp Zoolog B Mol Dev Evol 312: 722-733. Yeast QTLs 19373876 13,17,18
2009 Zuo C, Liang S, Wang Z, Li H, Zheng W, Ma W Enriching protein-protein and functional interaction networks in human embryonic stem cells. Int J Mol Med 23: 811-819. Human embryonic stem cell proteins 19424609 8,16,17
2009 de Boer BA, Ruijter JM, Voorbraak FP, Moorman AF More than a decade of developmental gene expression atlases: where are we now? Nucleic Acids Res 37: 7349-7359. 19822576 11,15
2009 de Matos P, Alcantara R, Dekker A, Ennis M, Hastings J, Haug K, Spiteri I, Turner S, Steinbeck C Chemical Entities of Biological Interest: an update. Nucleic Acids Res 38: D249-254. 19854951 15
2009 de Sousa Abreu R|etAl Genomic analyses of Musashi1 downstream targets show a strong association with cancer related processes. J Biol Chem 284: 12125-12135. Human kidney cell line transcripts 19258308 7,16
2009 de Tayrac M, Le S, Aubry M, Mosser J, Husson F Simultaneous analysis of distinct Omics data sets with integration of biological knowledge: Multiple Factor Analysis approach. BMC Genomics 10: 32. 19154582 7,13,17
2009 van Beijnum JR, Petersen K, Griffioen AW Tumor endothelium is characterized by a matrix remodeling signature. Front Biosci (Schol Ed) 1: 216-225. Human tumor transcripts 19482697 7,16
2009 van Lunteren E, Moyer M Gene expression profiling in the type 1 diabetes rat diaphragm. PLoS One 4: e7832. Rat diaphragm transcripts 19915678 10.1371/journal.pone.0007832 7,16
2009 van Oostrom O, de Kleijn DP, Fledderus JO, Pescatori M, Stubbs A, Tuinenburg A, Lim SK, Verhaar MC Folic acid supplementation normalizes the endothelial progenitor cell transcriptome of patients with type 1 diabetes: a case-control pilot study. Cardiovasc Diabetol 8: 47. Human endothelial progenitor cell transcripts; type I diabetes 19706161 7,16
2010 Aarthi S, Raj GD, Raman M, Blake D, Subramaniam C, Tomley F Expressed sequence tags from Eimeria brunetti-preliminary analysis and functional annotation. Parasitol Res epub 21161277 5
2010 Abdelsadik A, Roeder T Chronic activation of the epithelial immune system of the fruit fly's salivary glands has a negative effect on organismal growth and induces a peculiar set of target genes. BMC Genomics 11: 265. 20420686 7
2010 Abril JF, Cebria F, Rodriguez-Esteban G, Horn T, Fraguas S, Calvo B, Bartscherer K, Salo E Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea. BMC Genomics 11: 731. 21194483 3,7
2010 Accetturo M, Creanza TM, Santoro C, Tria G, Giordano A, Battagliero S, Vaccina A, Scioscia G, Leo P Finding new genes for non-syndromic hearing loss through an in silico prioritization study. PLoS One epub 20927407 16,19
2010 Ahmed A, Frey G, Michel CJ Essential molecular functions associated with the circular code evolution. J Theor Biol 264: 613-622. 20153338 13,18
2010 Al-Swailem AM|etAl Sequencing, analysis, and annotation of expressed sequence tags for Camelus dromedarius. PLoS One 5: e10720. Camel ESTs 20502665 5
2010 Alam HB, Hashmi S, Finkelstein RA, Frankelstein RA, Shuja F, Fukudome EY, Li Y, Liu B, Demoya M, Velmahos GC Alterations in gene expression after induction of profound hypothermia for the treatment of lethal hemorrhage. J Trauma 68: 1084-1098. 20453763 7,16
2010 Alam-Faruque Y, Dimmer EC, Huntley RP, O'Donovan C, Scambler P, Apweiler R The renal gene ontology annotation initiative. Organogenesis 6: 71-75. 20885853 1,6
2010 Albrethsen J|etAl Sub-nuclear proteomics in colorectal cancer:Identification of proteins enriched in the nuclear matrix fraction and regulation in adenoma to carcinoma progression. Mol Cell Proteomics 9: 988-981005. Human colorectal cancer proteins 20089989 8,16
2010 Alterovitz G|etAl Ontology engineering. Nat Biotechnol 28: 128-130. 20139945 1,2,3,13,14
2010 Altomare DA, Rybak SM, Pei J, Maizel JV, Cheung M, Testa JR, Shogen K Onconase responsive genes in human mesothelioma cells: implications for an RNA damaging therapeutic agent. BMC Cancer 10: 34. Human mesothelioma cell link transcripts 20137089 7,16
2010 Alves RD, Eijken M, Swagemakers S, Chiba H, Titulaer MK, Burgers PC, Luider TM, van Leeuwen JP Proteomic analysis of human osteoblastic cells: relevant proteins and functional categories for differentiation. J Proteome Res 9: 4688-4700. 20690663 8,16
2010 Ammari M, McCarthy FM, Nanduri B, Pinchuk LM Analysis of Bovine Viral Diarrhea Viruses-infected monocytes: identification of cytopathic and non-cytopathic biotype differences. BMC Bioinformatics 11 Suppl 6: S9. 20946620 8,17
2010 Amos W, Bryant C Using human demographic history to infer natural selection reveals contrasting patterns on different families of immune genes. Proc Biol Sci epub 21068042 18
2010 Amthauer HA, Tsatsoulis C Classifying genes to the correct Gene Ontology Slim term in Saccharomyces cerevisiae using neighbouring genes with classification learning. BMC Genomics 11: 340. 20509921 9
2010 An J, Choi KP, Wells CA, Chen YP Identifying co-regulating microrna groups. J Bioinform Comput Biol 8: 99-9115. miRNA targets 20183876 7
2010 Antonescu C, Antonescu V, Sultana R, Quackenbush J Using the DFCI gene index databases for biological discovery. Curr Protoc Bioinformatics Chapter 1: Unit1.6.1-36. 20205187 11
2010 Aparicio A, Tzelepi V, Araujo JC, Guo CC, Liang S, Troncoso P, Logothetis CJ, Navone NM, Maity SN Neuroendocrine prostate cancer xenografts with large-cell and small-cell features derived from a single patient's tumor: Morphological, immunohistochemical, and gene expression profiles. Prostate epub 21086505 7,16
2010 Argout X|etAl The genome of Theobroma cacao. Nat Genet 43: 101-108. Chocolate 21186351 4
2010 Arlt VM, Zuo J, Trenz K, Roufosse CA, Lord GM, Nortier JL, Schmeiser HH, Hollstein M, Phillips DH Gene expression changes induced by the human carcinogen aristolochic acid I in renal and hepatic tissue of mice. Int J Cancer 128: 21-32. Mouse kidney transcripts; mouse liver transcripts 20232387 7,16
2010 Arrais JP, Fernandes J, Pereira J, Oliveira JL GeneBrowser 2: an application to explore and identify common biological traits in a set of genes. BMC Bioinformatics 11: 389. 20663121 10
2010 Arya GH, Weber AL, Wang P, Magwire MM, Serrano Negron YL, Mackay TF, Anholt RR Natural variation, functional pleiotropy and transcriptional contexts of odorant binding protein genes in Drosophila melanogaster. Genetics 186: 1475-1485. 20870963 7,13,18
2010 Babik W, Stuglik M, Qi W, Kuenzli M, Kuduk K, Koteja P, Radwan J Heart transcriptome of the bank vole (Myodes glareolus): towards understanding the evolutionary variation in metabolic rate. BMC Genomics 11: 390. 20565972 7,18
2010 Backes C, Meese E, Lenhof HP, Keller A A dictionary on microRNAs and their putative target pathways. Nucleic Acids Res 38: 4476-4486. miRNA targets 20299343 7,17
2010 Bakthavatsalam D, Gomer RH The secreted proteome profile of developing Dictyostelium discoideum cells. Proteomics 10: 2556-2559. 20422638 8
2010 Balasinor NH, D'Souza R, Nanaware P, Idicula-Thomas S, Kedia-Mokashi N, He Z, Dym M Effect of high intratesticular estrogen on global gene expression and testicular cell number in rats. Reprod Biol Endocrinol 8: 72. 20573204 7,16
2010 Bandyopadhyay D, Huan J, Liu J, Prins J, Snoeyink J, Wang W, Tropsha A Functional neighbors: inferring relationships between nonhomologous protein families using family-specific packing motifs. IEEE Trans Inf Technol Biomed 14: 1137-1143. 20570776 9,13
2010 Barrantes I, Glockner G, Meyer S, Marwan W Transcriptomic changes arising during light-induced sporulation in Physarum polycephalum. BMC Genomics 11: 115. Physarum polycephalum transcripts 20163733 7
2010 Barton VN, Foreman NK, Donson AM, Birks DK, Handler MH, Vibhakar R Aurora kinase A as a rational target for therapy in glioblastoma. J Neurosurg Pediatr 6: 98-9105. 20593995 7,16
2010 Bauer S, Gagneur J, Robinson PN GOing Bayesian: model-based gene set analysis of genome-scale data. Nucleic Acids Res 38: 3523-3532. 20172960 7,13
2010 Beaver JE, Tasan M, Gibbons FD, Tian W, Hughes TR, Roth FP FuncBase: a resource for quantitative gene function annotation. Bioinformatics 26: 1806-1807. 20495000 11
2010 Beckham JT, Wilmink GJ, Opalenik SR, Mackanos MA, Abraham AA, Takahashi K, Contag CH, Takahashi T, Jansen ED Microarray analysis of cellular thermotolerance. Lasers Surg Med 42: 752-765. 21246580 7
2010 Benabderrahmane S, Smail-Tabbone M, Poch O, Napoli A, Devignes MD IntelliGO: a new vector-based semantic similarity measure including annotation origin. BMC Bioinformatics 11: 588. 21122125 10
2010 Bennett KL|etAl Proteomic analysis of human cataract aqueous humour: Comparison of one-dimensional gel LCMS with two-dimensional LCMS of unlabelled and iTRAQ-labelled specimens. J Proteomics 74: 151-166. 20940065 8,16
2010 Benoit M, Thuny F, Le Priol Y, Lepidi H, Bastonero S, Casalta JP, Collart F, Capo C, Raoult D, Mege JL The transcriptional programme of human heart valves reveals the natural history of infective endocarditis. PLoS One 5: e8939. Human heart valve transcripts 20126625 10.1371/journal.pone.0008939 7,16
2010 Bentsink L|etAl Natural variation for seed dormancy in Arabidopsis is regulated by additive genetic and molecular pathways. Proc Natl Acad Sci U S A 107: 4264-4269. Arabidopsis genes 20145108 7,13
2010 Bercu JP, Jolly RA, Flagella KM, Baker TK, Romero P, Stevens JL Toxicogenomics and cancer risk assessment: A framework for key event analysis and dose-response assessment for nongenotoxic carcinogens. Regul Toxicol Pharmacol 58: 369-381. 20801182 7,16
2010 Bermejo-Alvarez P, Rizos D, Rath D, Lonergan P, Gutierrez-Adan A Sex determines the expression level of one third of the actively expressed genes in bovine blastocysts. Proc Natl Acad Sci U S A 107: 3394-3399. Bovine blastocyst transcripts 20133684 7
2010 Bermejo-Martin JF|etAl Host adaptive immunity deficiency in severe pandemic influenza. Crit Care 14: R167. 20840779 7,8,16
2010 Bettencourt R, Pinheiro M, Egas C, Gomes P, Afonso M, Shank T, Santos RS High-throughput sequencing and analysis of the gill tissue transcriptome from the deep-sea hydrothermal vent mussel Bathymodiolus azoricus. BMC Genomics 11: 559. 20937131 7,18
2010 Bhasin M, Yuan L, Keskin DB, Otu HH, Libermann TA, Oettgen P Bioinformatic identification and characterization of human endothelial cell-restricted genes. BMC Genomics 11: 342. 20509943 7,16
2010 Bian F, Liu W, Yoon KC, Lu R, Zhou N, Ma P, Pflugfelder SC, Li DQ Molecular signatures and biological pathway profiles of human corneal epithelial progenitor cells. Int J Biochem Cell Biol 42: 1142-1153. Human corneal epithelial stem cell transcripts 20363357 7,16
2010 Blake JA, Bult CJ, Kadin JA, Richardson JE, Eppig JT, the Mouse Genome Database Group The mouse genome database (MGD): premier model organism resource for mammalian genomics and genetics. Nucleic Acids Res 39: D842-848. 21051359 1,4,11
2010 Blalock EM|etAl Aging-related gene expression in hippocampus proper compared with dentate gyrus is selectively associated with metabolic syndrome variables in rhesus monkeys. J Neurosci 30: 6058-6071. 20427664 7,16
2010 Borchardt T, Looso M, Bruckskotten M, Weis P, Kruse J, Braun T Analysis of newly established EST databases reveals similarities between heart regeneration in newt and fish. BMC Genomics 11: 4. Notophthalmus viridescens ESTs 20047682 5,7
2010 Borgan E|etAl Merging transcriptomics and metabolomics - advances in breast cancer profiling. BMC Cancer 10: 628. 21080935 7,8,16
2010 Borlawsky TB, Li J, Shagina L, Crowson MG, Liu Y, Friedman C, Lussier YA Evaluation of an ontology-anchored natural language-based approach for asserting multi-scale biomolecular networks for systems medicine. AMIA Summits Transl Sci Proc 2010: 6-10. 21347135 12,15
2010 Bossers K, Wirz KT, Meerhoff GF, Essing AH, van Dongen JW, Houba P, Kruse CG, Verhaagen J, Swaab DF Concerted changes in transcripts in the prefrontal cortex precede neuropathology in Alzheimer's disease. Brain 133: 3699-3723. 20889584 7,16
2010 Bowden P, Pendrak V, Zhu P, Marshall JG Meta sequence analysis of human blood peptides and their parent proteins. J Proteomics 73: 1163-1175. Human blood proteins 20170764 8,16
2010 Bratlie MS, Johansen J, Sherman BT, Huang da W, Lempicki RA, Drablos F Gene duplications in prokaryotes can be associated with environmental adaptation. BMC Genomics 11: 588. 20961426 18
2010 Bruckskotten M, Looso M, Cemic F, Konzer A, Hemberger J, Kruger M, Braun T PCA2GO: a new multivariate statistics based method to identify highly expressed GO-Terms. BMC Bioinformatics 11: 336. 20565932 10
2010 Buffin E, Gho M Laser microdissection of sensory organ precursor cells of Drosophila microchaetes. PLoS One 5: e9285. Drosophila transcripts 20174573 7
2010 Buske FA, Boden M, Bauer DC, Bailey TL Assigning roles to DNA regulatory motifs using comparative genomics. Bioinformatics 26: 860-866. 20147307 9,10
2010 Cacciotto C, Addis MF, Pagnozzi D, Chessa B, Coradduzza E, Carcangiu L, Uzzau S, Alberti A, Pittau M The liposoluble proteome of Mycoplasma agalactiae: an insight into the minimal protein complement of a bacterial membrane. BMC Microbiol 10: 225. 20738845 8
2010 Camina-Tato M|etAl Gender-associated differences of perforin polymorphisms in the susceptibility to multiple sclerosis. J Immunol 185: 5392-5404. 20921521 13,16
2010 Cardoso KC, Da Silva MJ, Costa GG, Torres TT, Del Bem LE, Vidal RO, Menossi M, Hyslop S A transcriptomic analysis of gene expression in the venom gland of the snake Bothrops alternatus (urutu). BMC Genomics 11: 605. 20977763 7
2010 Carvalho PC, Yates Iii JR, Barbosa VC Analyzing shotgun proteomic data with PatternLab for proteomics. Curr Protoc Bioinformatics Chapter 13: Unit 13.13.1-15. 20521246 10
2010 Castagnone-Sereno P, Danchin EG, Deleury E, Guillemaud T, Malausa T, Abad P Genome-wide survey and analysis of microsatellites in nematodes, with a focus on the plant-parasitic species Meloidogyne incognita. BMC Genomics 11: 598. 20973953 13,18
2010 Cha S, Imielinski MB, Rejtar T, Richardson EA, Thakur D, Sgroi DC, Karger BL In Situ proteomic analysis of human breast cancer epithelial cells using laser capture microdissection (LCM)-LC/MS: Annotation by protein set enrichment analysis (PSEA) and gene ontology (GO). Mol Cell Proteomics 9: 2529-2544. 20739354 8,16
2010 Chakrabarti AK, Vipat VC, Mukherjee S, Singh R, Pawar SD, Mishra AC Host gene expression profiling in influenza A virus-infected lung epithelial (A549) cells: a comparative analysis between highly pathogenic and modified H5N1 viruses. Virol J 7: 219. 20828378 7,16
2010 Champelovier P, El Atifi-Borel M, Issartel JP, Boutonnat J, Berger F, Seigneurin D Inhibition of c-Jun N-terminal kinase by SP600125: a cDNA microarray analysis. Cancer Genomics Proteomics 7: 87-92. Human leukemia cell transcripts 20335523 7,16
2010 Chan SS, Li HJ, Hsueh YC, Lee DS, Chen JH, Hwang SM, Chen CY, Shih E, Hsieh PC Fibroblast growth factor-10 promotes cardiomyocyte differentiation from embryonic and induced pluripotent stem cells. PLoS One 5: e14414. 21203390 7,16
2010 Chang HW, Cheng YH, Chuang LY, Yang CH SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping. BMC Bioinformatics 11: 173. 20377871 10,13
2010 Chao SK, Lin J, Brouwer-Visser J, Smith AB, Horwitz SB, McDaid HM Resistance to discodermolide, a microtubule-stabilizing agent and senescence inducer, is 4E-BP1-dependent. Proc Natl Acad Sci U S A 108: 391-396. 21173253 7,16
2010 Chateauvieux S, Eifes S, Morceau F, Grigorakaki C, Schnekenburger M, Henry E, Dicato M, Diederich M Valproic acid perturbs hematopoietic homeostasis by inhibition of erythroid differentiation and activation of the myelo-monocytic pathway. Biochem Pharmacol 81: 498-509. 21108933 7,16
2010 Chelaifa H, Mahe F, Ainouche M Transcriptome divergence between the hexaploid salt-marsh sister species Spartina maritima and Spartina alterniflora (Poaceae). Mol Ecol 19: 2050-2063. 20550634 7,18
2010 Chen F, Lee Y, Jiang Y, Wang S, Peatman E, Abernathy J, Liu H, Liu S, Kucuktas H, Ke C, Liu Z Identification and characterization of full-length cDNAs in channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus). PLoS One 5: e11546. 20634964 5
2010 Chen GK, Thomas DC Using biological knowledge to discover higher order interactions in genetic association studies. Genet Epidemiol 34: 863-878. 21104889 13,16,17
2010 Chen J, Sam L, Huang Y, Lee Y, Li J, Liu Y, Xing HR, Lussier YA Protein interaction network underpins concordant prognosis among heterogeneous breast cancer signatures. J Biomed Inform 43: 385-396. Human proteins; breast cancer 20350617 8,16,17
2010 Chen W, Lin H Prediction of midbody, centrosome and kinetochore proteins based on gene ontology information. Biochem Biophys Res Commun 401: 382-384. 20854791 9,19
2010 Chen Z, Tang J Using gene ontology to enhance effectiveness of similarity measures for microarray data. Int J Data Min Bioinform 4: 520-534. 21133039 7
2010 Chen Z, Ye H, Zhou L, Cheng CH, Chen L A gene family-based method for interspecies comparisons of sequencing-based transcriptomes and its use in environmental adaptation analysis. J Genet Genomics 37: 205-218. 20347830 7,13,18
2010 Cheng CY, Hu YJ Extracting the abstraction pyramid from complex networks. BMC Bioinformatics 11: 411. 20682075 10,17
2010 Cheng L, Lu W, Kulkarni B, Pejovic T, Yan X, Chiang JH, Hood L, Odunsi K, Lin B Analysis of chemotherapy response programs in ovarian cancers by the next-generation sequencing technologies. Gynecol Oncol 117: 159-169. Human ovarian transcripts 20181382 7,16
2010 Chi SM Prediction of protein subcellular localization by weighted gene ontology terms. Biochem Biophys Res Commun 399: 402-405. 20678488 9
2010 Chin CH, Chen SH, Ho CW, Ko MT, Lin CY A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles. BMC Bioinformatics 11 Suppl 1: S25. 20122197 8,17
2010 Chiriac A, Nelson TJ, Faustino RS, Behfar A, Terzic A Cardiogenic induction of pluripotent stem cells streamlined through a conserved SDF-1/VEGF/BMP2 integrated network. PLoS One 5: e9943. 20376342 7,17
2010 Choi JH, Kijimoto T, Snell-Rood E, Tae H, Yang Y, Moczek AP, Andrews J Gene discovery in the horned beetle Onthophagus taurus. BMC Genomics 11: 703. 21156066 5
2010 Choi YJ, Yun HK, Park KS, Noh JH, Heo YY, Kim SH, Kim DW, Lee HJ Transcriptional profiling of ESTs responsive to Rhizobium vitis from 'Tamnara' grapevines (Vitis sp.). J Plant Physiol 167: 1084-1092. 20398958 5
2010 Chong HK, Infante AM, Seo YK, Jeon TI, Zhang Y, Edwards PA, Xie X, Osborne TF Genome-wide interrogation of hepatic FXR reveals an asymmetric IR-1 motif and synergy with LRH-1. Nucleic Acids Res 38: 6007-6017. 20483916 7
2010 Chou KC, Shen HB A new method for predicting the subcellular localization of eukaryotic proteins with both single and multiple sites: Euk-mPLoc 2.0. PLoS One 5: e9931. 20368981 9,10
2010 Chou KC, Shen HB Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization. PLoS One 5: e11335. 20596258 9,10
2010 Chowdhary R, Bajic VB, Dong D, Wong L, Liu JS Genome-wide analysis of regions similar to promoters of histone genes. BMC Syst Biol 4 Suppl 1: S4. 20522254 7,19
2010 Chute CG Distributed biomedical terminology development: from experiments to open process. Yearb Med Inform epub 20938572 14
2010 Cibrian-Jaramillo A, De la Torre-Barcena JE, Lee EK, Katari MS, Little DP, Stevenson DW, Martienssen R, Coruzzi GM, DeSalle R Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution. Genome Biol Evol 2: 225-239. 20624728 18
2010 Coleman SJ, Zeng Z, Wang K, Luo S, Khrebtukova I, Mienaltowski MJ, Schroth GP, Liu J, MacLeod JN Structural annotation of equine protein-coding genes determined by mRNA sequencing. Anim Genet 41 Suppl 2: 121-130. 21070285 5,7
2010 Coletta A, Pinney JW, Solis DY, Marsh J, Pettifer SR, Attwood TK Low-complexity regions within protein sequences have position-dependent roles. BMC Syst Biol 4: 43. 20385029 13,17
2010 Collino F, Deregibus MC, Bruno S, Sterpone L, Aghemo G, Viltono L, Tetta C, Camussi G Microvesicles derived from adult human bone marrow and tissue specific mesenchymal stem cells shuttle selected pattern of miRNAs. PLoS One 5: e11803. 20668554 7,16
2010 Coombs KM, Berard A, Xu W, Krokhin O, Meng X, Cortens JP, Kobasa D, Wilkins J, Brown EG Quantitative proteomic analyses of influenza virus-infected cultured human lung cells. J Virol 84: 10888-10906. 20702633 8,16
2010 Cornette R|etAl Identification of anhydrobiosis-related genes from an expressed sequence tag database in the cryptobiotic midge Polypedilum vanderplanki (diptera; chironomidae). J Biol Chem 285: 35889-35899. 20833722 5,7
2010 Cornman RS The distribution of GYR- and YLP-like motifs in Drosophila suggests a general role in cuticle assembly and other protein-protein interactions. PLoS One epub 20824096 13
2010 Costain WJ, Haqqani AS, Rasquinha I, Giguere MS, Slinn J, Zurakowski B, Stanimirovic DB Proteomic analysis of synaptosomal protein expression reveals that cerebral ischemia alters lysosomal Psap processing. Proteomics 10: 3272-3291. 20718007 8,16
2010 Coulet A, Shah NH, Garten Y, Musen M, Altman RB Using text to build semantic networks for pharmacogenomics. J Biomed Inform 43: 1009-1019. 20723615 15
2010 Critzer FJ, D'Souza DH, Saxton AM, Golden DA Increased transcription of the phosphate-specific transport system of Escherichia coli O157:H7 after exposure to sodium benzoate. J Food Prot 73: 819-824. 20501031 7,16
2010 Crul T, Testelmans D, Spruit MA, Troosters T, Gosselink R, Geeraerts I, Decramer M, Gayan-Ramirez G Gene expression profiling in vastus lateralis muscle during an acute exacerbation of COPD. Cell Physiol Biochem 25: 491-500. Human muscle transcripts 20332630 7,16
2010 Cui L, Guo X, Qi Y, Qi X, Ge Y, Shi Z, Wu T, Shan J, Shan Y, Zhu Z, Wang H Identification of microRNAs involved in the host response to enterovirus 71 infection by a deep sequencing approach. J Biomed Biotechnol 2010: 425939. 20625495 7,16
2010 D'Alessandro A, Scaloni A, Zolla L Human milk proteins: an interactomics and updated functional overview. J Proteome Res 9: 3339-3373. 20443637 8,16,17
2010 D'Amato A, Bachi A, Fasoli E, Boschetti E, Peltre G, Senechal H, Sutra JP, Citterio A, Righetti PG In-depth exploration of Hevea brasiliensis latex proteome and "hidden allergens" via combinatorial peptide ligand libraries. J Proteomics 73: 1368-1380. Hevea brasiliensis latex proteins 20226888 6,8
2010 Dai YX, Lang JH, Zhu L, Liu ZF, Pan LY, Sun DW [Microarray analysis of gene expression profiles in pelvic organ prolapse.] Zhonghua Fu Chan Ke Za Zhi 45: 342-347. 20646442 7,16
2010 Dangaria SJ, Ito Y, Luan X, Diekwisch TG Differentiation of neural-crest-derived intermediate pluripotent progenitors into committed periodontal populations involves unique molecular signature changes, cohort shifts, and epigenetic modifications. Stem Cells Dev 20: 39-52. 20604680 7
2010 Das S, Ehlers JD, Close TJ, Roberts PA Transcriptional profiling of root-knot nematode induced feeding sites in cowpea (Vigna unguiculata L. Walp.) using a soybean genome array. BMC Genomics 11: 480. 20723233 7
2010 Das S, Foley N, Bryan K, Watters KM, Bray I, Murphy DM, Buckley PG, Stallings RL MicroRNA mediates DNA demethylation events triggered by retinoic acid during neuroblastoma cell differentiation. Cancer Res 70: 7874-7881. 20841484 7,16
2010 Das S, Idicula SM KMeans greedy search hybrid algorithm for biclustering gene expression data. Adv Exp Med Biol 680: 181-188. 20865500 7
2010 Davidsen PK, Gallagher IJ, Hartman JW, Tarnopolsky MA, Dela F, Helge JW, Timmons JA, Phillips SM High responders to resistance exercise training demonstrate differential regulation of skeletal muscle microRNA expression. J Appl Physiol 110: 309-317. 21030674 7,16
2010 Davila Lopez M, Martinez Guerra JJ, Samuelsson T Analysis of gene order conservation in eukaryotes identifies transcriptionally and functionally linked genes. PLoS One 5: e10654. 20498846 7,18
2010 Davis MJ, Sehgal MS, Ragan MA Automatic, context-specific generation of Gene Ontology slims. BMC Bioinformatics 11: 498. 20929524 10
2010 De Bodt S, Carvajal D, Hollunder J, Van den Cruyce J, Movahedi S, Inze D CORNET: a user-friendly tool for data mining and integration. Plant Physiol 152: 1167-1179. 20053712 10
2010 De la Cruz-Hernandez E|etAl Transcriptional changes induced by epigenetic therapy with hydralazine and magnesium valproate in cervical carcinoma. Oncol Rep 25: 399-407. 21152880 7,16,17
2010 Deegan JI, Dimmer EC, Mungall CJ Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development. BMC Bioinformatics 11: 530. 20973947 1,3,13
2010 Denecke B, Wickert L, Liu Y, Ciuclan L, Dooley S, Meindl-Beinker NM Smad7 dependent expression signature highlights BMP2 and HK2 signaling in HSC transdifferentiation. World J Gastroenterol 16: 5211-5224. 21049555 7
2010 Deng X, Liang J, Lin ZX, Wu FS, Zhang YP, Zhang ZW Natural taurine promotes apoptosis of human hepatic stellate cells in proteomics analysis. World J Gastroenterol 16: 1916-1923. 20397272 8,16
2010 Desai J, Flatow JM, Song J, Zhu LJ, Du P, Huang CC, Lu H, Lin SM, Kibbe WA Visual Presentation as a Welcome Alternative to Textual Presentation of Gene Annotation Information. Adv Exp Med Biol 680: 709-715. 20865558 10
2010 Desgagne-Penix I, Khan MF, Schriemer DC, Cram D, Nowak J, Facchini PJ Integration of deep transcriptome and proteome analyses reveals the components of alkaloid metabolism in opium poppy cell cultures. BMC Plant Biol 10: 252. 21083930 7,8
2010 Dharmawardhana P, Brunner AM, Strauss SH Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa. BMC Genomics 11: 150. Populus trichocarpa transcripts 20199690 7
2010 Di Camillo B, Sanavia T, Iori E, Bronte V, Roncaglia E, Maran A, Avogaro A, Toffolo G, Cobelli C The transcriptional response in human umbilical vein endothelial cells exposed to insulin: a dynamic gene expression approach. PLoS One 5: e14390. 21203503 7,16
2010 Di Matteo A, Sacco A, Anacleria M, Pezzotti M, Delledonne M, Ferrarini A, Frusciante L, Barone A The ascorbic acid content of tomato fruits is associated with the expression of genes involved in pectin degradation. BMC Plant Biol 10: 163. 20691085 7
2010 Dias PJ, Teixeira MC, Telo JP, Sa-Correia I Insights into the mechanisms of toxicity and tolerance to the agricultural fungicide mancozeb in yeast, as suggested by a chemogenomic approach. OMICS 14: 211-227. 20337531 13
2010 Diehl AD|etAl Hematopoietic cell types: Prototype for a revised cell ontology. J Biomed Inform epub 20123131 13,15
2010 Diez D, Wheelock AM, Goto S, Haeggstrom JZ, Paulsson-Berne G, Hansson GK, Hedin U, Gabrielsen A, Wheelock CE The use of network analyses for elucidating mechanisms in cardiovascular disease. Mol Biosyst 6: 289-304. 20094647 7,16,17
2010 Ding Y, Lu B, Meng LN, Fan YH, Guo Y, Shen Y, Chen S [Proteomic expression analysis of colonic mucosa in a rat model of irritable bowel syndrome.] Zhonghua Yi Xue Za Zhi 90: 564-569. Rat colon mucosa proteins 20367971 8,16
2010 Dondero F, Negri A, Boatti L, Marsano F, Mignone F, Viarengo A Transcriptomic and proteomic effects of a neonicotinoid insecticide mixture in the marine mussel (Mytilus galloprovincialis, Lam.). Sci Total Environ 408: 3775-3786. 20417955 7,8
2010 Done B, Khatri P, Done A, Draghici S Predicting novel human gene ontology annotations using semantic analysis. IEEE/ACM Trans Comput Biol Bioinform 7: 91-99. 20150671 9,12
2010 Doolittle JM, Gomez SM Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens. Virol J 7: 82. 20426868 16,17,19
2010 Dorsey JF, Dowling ML, Kim M, Voong R, Kao GD Modulation of the anti-cancer efficacy of microtubule-targeting agents by cellular growth conditions. Cancer Biol Ther epub 20234172 13,16
2010 Doss MX|etAl Global transcriptomic analysis of murine embryonic stem cell-derived brachyury (T) cells. Genes Cells epub Mouse mesodermal cell transcripts 20184659 7
2010 Doxey AC, Cheng Z, Moffatt BA, McConkey BJ Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d. BMC Struct Biol 10: 23. 20678238 8,19
2010 Drahushchenko OO, Tokovenko BT, Obolens'ka MIu [Initial analysis of the results of the genome-wide search for the genes responsive to interferon alpha] Ukr Biokhim Zh 82: 82-89. 20684232 7
2010 Du Z, Zhou X, Ling Y, Zhang Z, Su Z agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38 Suppl: W64-70. 20435677 10,11
2010 Durmus Tekir S, Umit P, Eren Toku A, Ulgen KO Reconstruction of protein-protein interaction network of insulin signaling in homo sapiens. J Biomed Biotechnol 2010: 690925. 21197403 8,16,17
2010 Eijgelaar WJ, Horrevoets AJ, Bijnens AP, Daemen MJ, Verhaegh WF Equivalence testing in microarray analysis: Similarities in the transcriptome of human atherosclerotic and non-atherosclerotic macrophages. Physiol Genomics epub Human macrophage transcripts 20068025 7,16
2010 Ekblom R, Balakrishnan CN, Burke T, Slate J Digital gene expression analysis of the zebra finch genome. BMC Genomics 11: 219. Zebra finch transcripts 20359325 7
2010 Ellis J, Sinclair D, Morrison D, Al-Qassab S, Springett K, Ivens A Microarray analyses of mouse responses to infection by Neospora caninum identifies disease associated cellular pathways in the host response. Mol Biochem Parasitol 174: 117-127. 20817048 7
2010 Eng D, Campbell A, Hilton T, Leid M, Gross MK, Kioussi C Prediction of regulatory networks in mouse abdominal wall. Gene 469: 1-8. 20797427 7,17
2010 Engelhorn J, Turck F Metaanalysis of ChIP-chip data. Methods Mol Biol 631: 185-207. 20204876 7,13
2010 Engreitz JM, Daigle BJ, Marshall JJ, Altman RB Independent component analysis: Mining microarray data for fundamental human gene expression modules. J Biomed Inform 43: 932-944. 20619355 7,16,17
2010 Fang H|etAl An FDA bioinformatics tool for microbial genomics research on molecular characterization of bacterial foodborne pathogens using microarrays. BMC Bioinformatics 11 Suppl 6: S4. 20946615 7,10
2010 Fardin P, Cornero A, Barla A, Mosci S, Acquaviva M, Rosasco L, Gambini C, Verri A, Varesio L Identification of multiple hypoxia signatures in neuroblastoma cell lines by l1-l2 regularization and data reduction. J Biomed Biotechnol 2010: 878709. 20652058 7,16
2010 Farias LP, Tararam CA, Miyasato PA, Nishiyama MY, Oliveira KC, Kawano T, Verjovski-Almeida S, Leite LC Screening the Schistosoma mansoni transcriptome for genes differentially expressed in the schistosomulum stage in search for vaccine candidates. Parasitol Res 108: 123-135. 20852890 7,16
2010 Farnsworth A, Flaman AS, Prasad SS, Gravel C, Williams A, Yauk CL, Li X Acetaminophen modulates the transcriptional response to recombinant interferon-beta. PLoS One 5: e11031. 20544007 7,16
2010 Feinberg AP|etAl Personalized epigenomic signatures that are stable over time and covary with body mass index. Sci Transl Med 2: 49ra67. 20844285 13,16
2010 Feng G, Du P, Krett NL, Tessel M, Rosen S, Kibbe WA, Lin SM A collection of bioconductor methods to visualize gene-list annotations. BMC Res Notes 3: 10. 20180973 10
2010 Feng JF, Zhang KM, Jiang JY, Gao GY, Fu X, Liang YM Effect of therapeutic mild hypothermia on the genomics of the hippocampus after moderate traumatic brain injury in rats. Neurosurgery 67: 730-742. 20651628 7,16
2010 Finamore F, Pieroni L, Ronci M, Marzano V, Mortera SL, Romano M, Cortese C, Federici G, Urbani A Proteomics investigation of human platelets by shotgun nUPLC-MSE and 2DE experimental strategies: a comparative study. Blood Transfus 8 Suppl 3: s140-148. 20606744 8,16
2010 Freudenberg J, Lee AT, Siminovitch KA, Amos CI, Ballard D, Li W, Gregersen PK Locus category based analysis of a large genome-wide association study of rheumatoid arthritis. Hum Mol Genet 19: 3863-3872. 20639398 13,16
2010 Fung DC, Wilkins MR, Hart D, Hong SH Using the clustered circular layout as an informative method for visualizing protein-protein interaction networks. Proteomics 10: 2723-2727. 20480505 17
2010 Galindo RC, Munoz PM, de Miguel MJ, Marin CM, Labairu J, Revilla M, Blasco JM, Gortazar C, de la Fuente J Gene expression changes in spleens of the wildlife reservoir species, Eurasian wild boar (Sus scrofa), naturally infected with Brucella suis biovar 2. J Genet Genomics 37: 725-736. 21115167 7
2010 Gallach M, Chandrasekaran C, Betran E Analyses of nuclearly encoded mitochondrial genes suggest gene duplication as a mechanism for resolving intralocus sexually antagonistic conflict in Drosophila. Genome Biol Evol 2: 835-850. 21037198 17,18
2010 Gallagher IJ|etAl Integration of microRNA changes in vivo identifies novel molecular features of muscle insulin resistance in type 2 diabetes. Genome Med 2: 9. Human muscle transcripts 20353613 7,16
2010 Gan LP, Zhang WY, Niu YS, Xu L, Xi J, Ji MM, Xu SQ Construction and application of an electronic spatiotemporal expression profile and gene ontology analysis platform based on the EST database of the silkworm, Bombyx mori. J Insect Sci 10: 114. 20874595 5,7,10
2010 Garcia-Herrero S, Garrido N, Martinez-Conejero JA, Remohi J, Pellicer A, Meseguer M Ontological evaluation of transcriptional differences between sperm of infertile males and fertile donors using microarray analysis. J Assist Reprod Genet 27: 111-120. Human sperm transcripts 20127162 7,16
2010 Gasiorowski JZ, Liliensiek SJ, Russell P, Stephan DA, Nealey PF, Murphy CJ Alterations in gene expression of human vascular endothelial cells associated with nanotopographic cues. Biomaterials 31: 8882-8888. 20832112 7,16
2010 Ghandhi SA, Ming L, Ivanov VN, Hei TK, Amundson SA Regulation of early signaling and gene expression in the alpha-particle and bystander response of IMR-90 human fibroblasts. BMC Med Genomics 3: 31. 20670442 7,16
2010 Gharib SA, Dayyat EA, Khalyfa A, Kim J, Clair HB, Kucia M, Gozal D Intermittent hypoxia mobilizes bone marrow-derived very small embryonic-like stem cells and activates developmental transcriptional programs in mice. Sleep 33: 1439-1446. 21102985 7,16
2010 Ghigo E, Barry AO, Pretat L, Al Moussawi K, Desnues B, Capo C, Kornfeld H, Mege JL IL-16 promotes T. whipplei replication by inhibiting phagosome conversion and modulating macrophage activation. PLoS One 5: e13561. 21042409 7,16
2010 Gilardoni PA, Schuck S, Jungling R, Rotter B, Baldwin IT, Bonaventure G SuperSAGE analysis of the Nicotiana attenuata transcriptome after fatty acid-amino acid elicitation (FAC): identification of early mediators of insect responses. BMC Plant Biol 10: 66. 20398280 7
2010 Gillespie M, Shamovsky V, D'Eustachio P Human and chicken TLR pathways: manual curation and computer-based orthology analysis. Mamm Genome 22: 130-138. 21052677 1,11,17,18
2010 Glessner JT|etAl Strong synaptic transmission impact by copy number variations in schizophrenia. Proc Natl Acad Sci U S A 107: 10584-10589. 20489179 13,16
2010 Goertsches RH, Hecker M, Koczan D, Serrano-Fernandez P, Moeller S, Thiesen HJ, Zettl UK Long-term genome-wide blood RNA expression profiles yield novel molecular response candidates for IFN-beta-1b treatment in relapsing remitting MS. Pharmacogenomics 11: 147-161. Human blood cell transcripts; multiple sclerosis 20136355 7,16
2010 Gomez P, Hackett TL, Moore MM, Knight DA, Tebbutt SJ Functional genomics of human bronchial epithelial cells directly interacting with conidia of Aspergillus fumigatus. BMC Genomics 11: 358. 20525375 7,16
2010 Gordon FE, Nutt CL, Cheunsuchon P, Nakayama Y, Provencher KA, Rice KA, Zhou Y, Zhang X, Klibanski A Increased expression of angiogenic genes in the brains of mouse meg3-null embryos. Endocrinology 151: 2443-2452. 20392836 7,16
2010 Gottstein B, Wittwer M, Schild M, Merli M, Leib SL, Mueller N, Mueller J, Jaggi R Hepatic gene expression profile in mice perorally infected with Echinococcus multilocularis eggs. PLoS One 5: e9779. Mouse liver transcripts; echinococcosis 20368974 7,16
2010 Grassi L, Fusco D, Sellerio A, Cora D, Bassetti B, Caselle M, Lagomarsino MC Identity and divergence of protein domain architectures after the yeast whole-genome duplication event. Mol Biosyst 6: 2305-2315. 20820472 18
2010 Gregersen LH, Jacobsen AB, Frankel LB, Wen J, Krogh A, Lund AH MicroRNA-145 targets YES and STAT1 in colon cancer cells. PLoS One 5: e8836. Human colon cancer cell line miRNAs 20098684 7,16
2010 Gu F, Hsu HK, Hsu PY, Wu J, Ma Y, Parvin J, Huang TH, Jin VX Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data. BMC Syst Biol 4: 170. 21167036 13,16,17
2010 Gu Y, Yang D, Zou J, Ma W, Wu R, Zhao W, Zhang Y, Xiao H, Gong X, Zhang M, Zhu J, Guo Z Systematic interpretation of comutated genes in large-scale cancer mutation profiles. Mol Cancer Ther 9: 2186-2195. 20663929 13,16,17
2010 Guan Y, Ackert-Bicknell CL, Kell B, Troyanskaya OG, Hibbs MA Functional genomics complements quantitative genetics in identifying disease-gene associations. PLoS Comput Biol 6: e1000991. 21085640 13,16,17
2010 Gudjonsson JE, Ding J, Johnston A, Tejasvi T, Guzman AM, Nair RP, Voorhees JJ, Abecasis GR, Elder JT Assessment of the Psoriatic Transcriptome in a Large Sample: Additional Regulated Genes and Comparisons with In Vitro Models. J Invest Dermatol 130: 1829-1840. Human skin transcripts; psoriasis 20220767 7,16
2010 Gunther OP, Lin D, Balshaw RF, Ng RT, Hollander Z, Wilson-McManus J, McMaster WR, McManus BM, Keown PA, Biomarkers in Transplantation Team Effects of sample timing and treatment on gene expression in early acute renal allograft rejection. Transplantation 91: 323-329. 21107303 7,16
2010 Guo AY, Sun J, Jia P, Zhao Z Network analysis of EtOH-related candidate genes. Chem Biodivers 7: 1142-1152. 20491071 17
2010 Guo J, Tian D, McKinney BA, Hartman JL Recursive expectation-maximization clustering: a method for identifying buffering mechanisms composed of phenomic modules. Chaos 20: 026103. 20590332 13,18
2010 Guo S, Zheng Y, Joung JG, Liu S, Zhang Z, Crasta OR, Sobral BW, Xu Y, Huang S, Fei Z Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. BMC Genomics 11: 384. 20565788 7
2010 Gupta MK|etAl Global transcriptional profiles of beating clusters derived from human induced pluripotent stem cells and embryonic stem cells are highly similar. BMC Dev Biol 10: 98. 20843318 7,16
2010 Gust KA, Wilbanks MS, Guan X, Pirooznia M, Habib T, Yoo L, Wintz H, Vulpe CD, Perkins EJ Investigations of transcript expression in fathead minnow (Pimephales promelas) brain tissue reveal toxicological impacts of RDX exposure. Aquat Toxicol 101: 135-145. 20965580 7
2010 Hamoudi RA|etAl Differential expression of NF-kappaB target genes in MALT lymphoma with and without chromosome translocation: insights into molecular mechanism. Leukemia 24: 1487-1497. 20520640 7,16
2010 Hansen L, Marino-Ramirez L, Landsman D Many sequence-specific chromatin modifying protein-binding motifs show strong positional preferences for potential regulatory regions in the Saccharomyces cerevisiae genome. Nucleic Acids Res 38: 1772-1779. 20047965 7
2010 Hao T, Ma HW, Zhao XM, Goryanin I Compartmentalization of the Edinburgh Human Metabolic Network. BMC Bioinformatics 11: 393. 20649990 17
2010 Harhay GP|etAl An atlas of Bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation. Genome Biol 11: R102. 20961407 7,11
2010 Hashimoto JG, Forquer MR, Tanchuck MA, Finn DA, Wiren KM Importance of genetic background for risk of relapse shown in altered prefrontal cortex gene expression during abstinence following chronic alcohol intoxication. Neuroscience 173: 57-75. 21081154 7,16
2010 Hassan SS|etAl The molecular basis for sonographic cervical shortening at term: identification of differentially expressed genes and the epithelial-mesenchymal transition as a function of cervical length. Am J Obstet Gynecol 203: 472.e1-472.e14. 20817141 7,16
2010 Hawkins T, Chitale M, Kihara D Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP. BMC Bioinformatics 11: 265. 20482861 9,17
2010 Hayashi Y, Kajimoto K, Iida S, Sato Y, Mizufune S, Kaji N, Kamiya H, Baba Y, Harashima H DNA microarray analysis of whole blood cells and insulin-sensitive tissues reveals the usefulness of blood RNA profiling as a source of markers for predicting type 2 diabetes. Biol Pharm Bull 33: 1033-1042. 20522973 7,16
2010 Hayes KR, Beatty M, Meng X, Simmons CR, Habben JE, Danilevskaya ON Maize global transcriptomics reveals pervasive leaf diurnal rhythms but rhythms in developing ears are largely limited to the core oscillator. PLoS One 5: e12887. 20886102 7
2010 He MM, Shi JT, Zhu XH, Jin W, Wang P, Zhang J, Wagn KK [Genomic distribution of AML1-ETO fusion protein binding sites] Zhongguo Shi Yan Xue Ye Xue Za Zhi 18: 553-558. 20561400 13,16
2010 He X, Sarma MS, Ling X, Chee B, Zhai C, Schatz B Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model. BMC Bioinformatics 11: 272. 20487560 10
2010 Heimeier RA, Das B, Buchholz DR, Fiorentino M, Shi YB Studies on Xenopus laevis intestine reveal biological pathways underlying vertebrate gut adaptation from embryo to adult. Genome Biol 11: R55. 20482879 7
2010 Helleman J, Smid M, Jansen MP, van der Burg ME, Berns EM Pathway analysis of gene lists associated with platinum-based chemotherapy resistance in ovarian cancer: The big picture. Gynecol Oncol 117: 170-176. Human genes; ovarian cancer 20132968 16,17
2010 Herranz R, Benguria A, Lavan DA, Lopez-Vidriero I, Gasset G, Javier Medina F, van Loon JJ, Marco R Spaceflight-related suboptimal conditions can accentuate the altered gravity response of Drosophila transcriptome. Mol Ecol epub 20819157 7
2010 Hershey AD, Burdine D, Kabbouche MA, Powers SW Genomic expression patterns in medication overuse headaches. Cephalalgia 31: 161-171. 20974594 7,16
2010 Hildebrand J, Rutze M, Walz N, Gallinat S, Wenck H, Deppert W, Grundhoff A, Knott A A Comprehensive Analysis of MicroRNA Expression During Human Keratinocyte Differentiation In Vitro and In Vivo. J Invest Dermatol 131: 20-29. 20827281 7,16
2010 Ho MR, Chen CH, Lin WC Gene-oriented ortholog database: a functional comparison platform for orthologous loci. Database (Oxford) 2010: baq002. 20428317 11,18
2010 Hoang LT|etAl The early whole-blood transcriptional signature of dengue and features associated with progression to dengue shock syndrome in Vietnamese children and young adults. J Virol 84: 12982-12994. 20943967 7,16
2010 Hodgin JB|etAl A molecular profile of focal segmental glomerulosclerosis from formalin-fixed, paraffin-embedded tissue. Am J Pathol 177: 1674-1686. 20847290 7,16
2010 Hoehndorf R, Ngonga Ngomo AC, Kelso J Applying the functional abnormality ontology pattern to anatomical functions. J Biomed Semantics 1: 4. 20618982 14,15
2010 Hoenemann C, Richardt S, Kruger K, Zimmer AD, Hohe A, Rensing SA Large impact of the apoplast on somatic embryogenesis in Cyclamen persicum offers possibilities for improved developmental control in vitro. BMC Plant Biol 10: 77. 20426818 7
2010 Hoffmann J|etAl Mast cells promote lung vascular remodeling in pulmonary hypertension. Eur Respir J epub 21148228 7,16
2010 Holman AG, Mefford ME, O'Connor N, Gabuzda D HIVBrainSeqDB: a database of annotated HIV envelope sequences from brain and other anatomical sites. AIDS Res Ther 7: 43. 21156070 15
2010 Hook SE, Lampi MA, Febbo EJ, Ward JA, Parkerton TF Temporal patterns in the transcriptomic response of rainbow trout, Oncorhynchus mykiss, to crude oil. Aquat Toxicol 99: 320-329. 20541815 7
2010 Hori TS, Gamperl AK, Afonso LO, Johnson SC, Hubert S, Kimball J, Bowman S, Rise ML Heat-shock responsive genes identified and validated in Atlantic cod (Gadus morhua) liver, head kidney and skeletal muscle using genomic techniques. BMC Genomics 11: 72. Atlantic cod ESTs 20109224 5,7
2010 Horiba T, Nishimura I, Nakai Y, Abe K, Sato R Naringenin chalcone improves adipocyte functions by enhancing adiponectin production. Mol Cell Endocrinol 323: 208-214. Mouse cell line transcripts 20363289 7,16
2010 Hou X, Li Q, Huang T Microarray analysis of gene expression profiles in the bovine mammary gland during lactation. Sci China Life Sci 53: 248-256. 20596835 7
2010 Hoyle D|etAl Shared changes in gene expression in frontal cortex of four genetically modified mouse models of depression. Eur Neuropsychopharmacol 21: 3-10. 21030216 7,16
2010 Hsieh CH, Jeng SF, Wu CJ, Lu TH, Yang JC, Chen YC, Lin CJ, Rau CS Altered Expression of the MicroRNAS and Their Potential Target Genes in the Soleus Muscle After Peripheral Denervation and Reinnervation in Rats. J Trauma 70: 472-480. 20693912 7
2010 Hu J, Wan J, Hackler L, Zack DJ, Qian J Computational analysis of tissue-specific gene networks: application to murine retinal functional studies. Bioinformatics 26: 2289-2297. 20616386 7,8,16,17
2010 Huang HC, Zheng S, VanBuren V, Zhao Z Discovering disease-specific biomarker genes for cancer diagnosis and prognosis. Technol Cancer Res Treat 9: 219-230. 20441232 7,13,16
2010 Huang SY|etAl Differential expression of porcine testis proteins during postnatal development. Anim Reprod Sci 123: 221-233. 21183296 8
2010 Iancu OD, Darakjian P, Walter NA, Malmanger B, Oberbeck D, Belknap J, McWeeney S, Hitzemann R Genetic diversity and striatal gene networks: focus on the heterogeneous stock-collaborative cross (HS-CC) mouse. BMC Genomics 11: 585. 20959017 7,17,18
2010 Isabelle M, Moreel X, Gagne JP, Rouleau M, Ethier C, Gagne P, Hendzel MJ, Poirier GG Investigation of PARP-1, PARP-2, and PARG interactomes by affinity-purification mass spectrometry. Proteome Sci 8: 22. 20388209 8,16
2010 Iwamoto T|etAl Gene pathways associated with prognosis and chemotherapy sensitivity in molecular subtypes of breast cancer. J Natl Cancer Inst 103: 264-272. 21191116 7,16,17
2010 Iwasawa S, Yamano Y, Takiguchi Y, Tanzawa H, Tatsumi K, Uzawa K Upregulation of thioredoxin reductase 1 in human oral squamous cell carcinoma. Oncol Rep 25: 637-644. 21206984 7,16
2010 Jablonski MM, Freeman NE, Orr WE, Templeton JP, Lu L, Williams RW, Geisert EE Genetic pathways regulating glutamate levels in retinal Muller cells. Neurochem Res epub 20882406 7
2010 Jaeger SA, Chan ET, Berger MF, Stottmann R, Hughes TR, Bulyk ML Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites. Genomics 95: 185-195. 20079828 7,13
2010 Jagtap S, Meganathan K, Gaspar J, Wagh V, Winkler J, Hescheler J, Sachinidis A Cytosine arabinoside induces ectoderm and inhibits mesoderm expression in human embryonic stem cells during multi-lineage differentiation. Br J Pharmacol epub 21198554 7,16
2010 Jain S, Bader GD An improved method for scoring protein-protein interactions using semantic similarity within the Gene Ontology. BMC Bioinformatics 11: 562. 21078182 8,17
2010 Jani SD, Argraves GL, Barth JL, Argraves WS GeneMesh: a web-based microarray analysis tool for relating differentially expressed genes to MeSH terms. BMC Bioinformatics 11: 166. 20359363 7,10
2010 Janse CJ, Kroeze H, van Wigcheren A, Mededovic S, Fonager J, Franke-Fayard B, Waters AP, Khan SM A genotype and phenotype database of genetically modified malaria-parasites. Trends Parasitol 27: 31-39. 20663715 11,13
2010 Janvilisri T, Scaria J, Chang YF Transcriptional profiling of Clostridium difficile and Caco-2 cells during infection. J Infect Dis 202: 282-290. 20521945 7,16
2010 Jelier R, Goeman JJ, Hettne KM, Schuemie MJ, den Dunnen JT, 't Hoen PA Literature-aided interpretation of gene expression data with the weighted global test. Brief Bioinform epub 21183478 3,9,12
2010 Jeong SK, Lee EY, Cho JY, Lee HJ, Jeong AS, Cho SY, Paik YK Data management and functional annotation of the Korean reference plasma proteome. Proteomics 10: 1250-1255. Human plasma proteome 20175082 8,11,16
2010 Jerhammar F, Ceder R, Garvin S, Grenman R, Grafstrom RC, Roberg K Fibronectin 1 is a potential biomarker for radioresistance in head and neck squamous cell carcinoma. Cancer Biol Ther 10: 1244-1251. 20930522 7,16
2010 Jia M, Choi SY, Reiners D, Wurtele ES, Dickerson JA MetNetGE: interactive views of biological networks and ontologies. BMC Bioinformatics 11: 469. 20849585 10
2010 Jia P, Sun J, Guo AY, Zhao Z SZGR: a comprehensive schizophrenia gene resource. Mol Psychiatry 15: 453-462. 20424623 11,16
2010 Jiang JY, Xiong H, Cao M, Xia X, Sirard MA, Tsang BK Mural granulosa cell gene expression associated with oocyte developmental competence. J Ovarian Res 3: 6. Rat mural granulosa cell transcripts 20205929 7
2010 Jiang L, Zhang D, Zhang Y, Peng L, Chen J, Liang S Venomics of the spider Ornithoctonus huwena based on transcriptomic versus proteomic analysis. Comp Biochem Physiol Part D Genomics Proteomics 5: 81-88. 20403776 7,8
2010 Jiang X, Gold D, Kolaczyk ED Network-based auto-probit modeling for protein function prediction. Biometrics epub 21133881 9,17
2010 Jin B, Lu X Identifying informative subsets of the Gene Ontology with information bottleneck methods. Bioinformatics 26: 2445-2451. 20702400 12
2010 Jing L, Ng MK Prior knowledge based mining functional modules from Yeast PPI networks with gene ontology. BMC Bioinformatics 11 Suppl 11: S3. 21172053 12,17
2010 Johnson EC, Doser T, Cepurna WO, Dyck J, Jia L, Guo Y, Lambert W, Morrison JC Cell proliferation and interleukin-6 type cytokine signaling are implicated by gene expression responses in early optic nerve head injury in rat glaucoma. Invest Ophthalmol Vis Sci 52: 504-518. 20847120 7,16
2010 Jonchere V, Rehault-Godbert S, Hennequet-Antier C, Cabau C, Sibut V, Cogburn LA, Nys Y, Gautron J Gene expression profiling to identify eggshell proteins involved in physical defense of the chicken egg. BMC Genomics 11: 57. Chicken eggshell proteins 20092629 8
2010 Jordheim LP, Plesa A, Dreano M, Cros-Perrial E, Keime C, Herveau S, Demangel D, Vendrell JA, Dumontet C Sensitivity and gene expression profile of fresh human acute myeloid leukemia cells exposed ex vivo to AS602868. Cancer Chemother Pharmacol epub 20844879 7,16
2010 Jorge EC, Melo CM, Rosario MF, Rossi JR, Ledur MC, Moura AS, Coutinho LL Chicken skeletal muscle-associated macroarray for gene discovery. Genet Mol Res 9: 188-207. Chicken muscle ESTs 20198575 5
2010 Jumbo-Lucioni P, Ayroles JF, Chambers MM, Jordan KW, Leips J, Mackay TF, De Luca M Systems genetics analysis of body weight and energy metabolism traits in Drosophila melanogaster. BMC Genomics 11: 297. 20459830 13,18
2010 Jung J, Ryu T, Hwang Y, Lee E, Lee D Prediction of extracellular matrix proteins based on distinctive sequence and domain characteristics. J Comput Biol 17: 97-9105. 20078400 9,19
2010 Jung J, Yi G, Sukno SA, Thon MR PoGO: Prediction of Gene Ontology terms for fungal proteins. BMC Bioinformatics 11: 215. 20429880 9
2010 Kadl A|etAl Identification of a novel macrophage phenotype that develops in response to atherogenic phospholipids via Nrf2. Circ Res 107: 737-746. 20651288 7,16
2010 Kahn AB, Zeeberg BR, Ryan MC, Jamison DC, Rockoff DM, Pommier Y, Weinstein JN Ontogenomic study of the relationship between number of gene splice variants and GO categorization. Bioinformatics 26: 1945-1949. 20616384 13
2010 Kang BY, Ko S, Kim DW SICAGO: Semi-supervised cluster analysis using semantic distance between gene pairs in Gene Ontology. Bioinformatics 26: 1384-1385. 20348546 10
2010 Kang HG, Paik KH, Cho HY, Lee BH, Ha IS, Choi Y, Cheong HI Transcriptome analysis of the response of cultured murine podocytes to puromycin aminonucleoside. Nephron Exp Nephrol 115: e1-e8. Mouse podocyte cell line transcripts 20185935 7,16
2010 Kapferer I, Schmidt S, Gstir R, Durstberger G, Huber LA, Vietor I Gene-expression profiles of epithelial cells treated with EMD in vitro: analysis using complementary DNA arrays. J Periodontal Res 46: 118-125. 21108644 7,16
2010 Katara P, Grover A, Kuntal H, Sharma V In silico prediction of drug targets in Vibrio cholerae. Protoplasma epub 21174131 7,19
2010 Katz-Jaffe MG, McCallie BR, Janesch A, Filipovits JA, Schoolcraft WB, Gardner DK Blastocysts from patients with polycystic ovaries exhibit altered transcriptome and secretome. Reprod Biomed Online 21: 520-526. 20797904 7,8,16
2010 Kedziorek DA, Muja N, Walczak P, Ruiz-Cabello J, Gilad AA, Jie CC, Bulte JW Gene expression profiling reveals early cellular responses to intracellular magnetic labeling with superparamagnetic iron oxide nanoparticles. Magn Reson Med 63: 1031-1043. Rat neural stem cell transcripts 20373404 7,16
2010 Kelly RJ, Vincent DE, Friedberg I IPRStats: visualization of the functional potential of an InterProScan run. BMC Bioinformatics 11 Suppl 12: S13. 21210980 10
2010 Kim JH, Na CY, Choi SY, Kim HW, Du Kim Y, Kwon JB, Chung MY, Hong JM, Park CB Integration of gene-expression profiles and pathway analysis in ascending thoracic aortic aneurysms. Ann Vasc Surg 24: 538-549. 20451796 7,16,17
2010 Kim KM, Caetano-Anolles G Emergence and evolution of modern molecular functions inferred from phylogenomic analysis of ontological data. Mol Biol Evol 27: 1710-1733. 20418223 18
2010 Kim S, Min WK, Chun S, Lee W, Chung HJ, Choi SJ, Yang SE, Yang YS, Yoo JI Protein expression profiles during osteogenic differentiation of mesenchymal stem cells derived from human umbilical cord blood. Tohoku J Exp Med 221: 141-150. 20495303 8,16
2010 Kim S, Park J, Park SY, Mitchell TK, Lee YH Identification and analysis of in planta expressed genes of Magnaporthe oryzae. BMC Genomics 11: 104. Magnaporthe oryzae ESTs; rice ESTs 20146797 5,7
2010 Klie S, Nikoloski Z, Selbig J Biological cluster evaluation for gene function prediction. J Comput Biol epub 20059365 9
2010 Knowles-Barley S, Longair M, Armstrong JD BrainTrap: a database of 3D protein expression patterns in the Drosophila brain. Database (Oxford) 2010: baq005. 20624714 15
2010 Ko GJ, Grigoryev DN, Linfert D, Jang HR, Watkins T, Cheadle C, Racusen LC, Rabb H Transcriptional analysis of kidneys during repair from AKI reveals possible roles for NGAL and KIM-1 as biomarkers of AKI to CKD transition. Am J Physiol Renal Physiol 298: F1472-1483. Mouse kidney transcripts 20181666 7,16
2010 Kobayashi S, Stice JP, Kazmin D, Wittmann BM, Kimbrel EA, Edwards DP, Chang CY, McDonnell DP Mechanisms of progesterone receptor inhibition of inflammatory responses in cellular models of breast cancer. Mol Endocrinol 24: 2292-2302. 20980435 7,16
2010 Kourmpetis YA, van Dijk AD, Bink MC, van Ham RC, ter Braak CJ Bayesian Markov Random Field analysis for protein function prediction based on network data. PLoS One 5: e9293. 10.1371/journal.pone.0009293 20195360 8,9,17
2010 Kozlowski P, de Mezer M, Krzyzosiak WJ Trinucleotide repeats in human genome and exome. Nucleic Acids Res 38: 4027-4039. 20215431 13,16
2010 Kubota M, Kasahara T, Iwamoto K, Komori A, Ishiwata M, Miyauchi T, Kato T Therapeutic implications of down-regulation of cyclophilin D in bipolar disorder. Int J Neuropsychopharmacol 13: 1355-1368. 20392297 7,16
2010 Kugita M|etAl Global gene expression profiling in early-stage polycystic kidney disease in the Han:SPRD Cy rat identifies a role for RXR signaling. Am J Physiol Renal Physiol 300: F177-188. 20926632 7,16
2010 Kulkarni BB, Tighe PJ, Mohammed I, Yeung AM, Powe DG, Hopkinson A, Shanmuganathan VA, Dua HS Comparative transcriptional profiling of the limbal epithelial crypt demonstrates its putative stem cell niche characteristics. BMC Genomics 11: 526. 20920242 7
2010 Kultima K, Jergil M, Salter H, Gustafson AL, Dencker L, Stigson M Early transcriptional responses in mouse embryos as a basis for selection of molecular markers predictive of valproic acid teratogenicity. Reprod Toxicol 30: 457-468. 20546886 7,16
2010 Kumar G, Ranganathan S Network analysis of human protein location. BMC Bioinformatics 11 Suppl 7: S9. 21106131 8,16,17
2010 Kumar M, Gromiha MM, Raghava GP SVM based prediction of RNA-binding proteins using binding residues and evolutionary information. J Mol Recognit epub 20677174 19
2010 Kustra R, Zagdanski A Data-fusion in clustering microarray data: balancing discovery and interpretability. IEEE/ACM Trans Comput Biol Bioinform 7: 50-63. 20150668 7
2010 Kwon J, Lee B, Chung H Gerontome: a web-based database server for aging-related genes and analysis pipelines. BMC Genomics 11 Suppl 4: S20. 21143804 3,11
2010 Lachmann A, Ma'ayan A Lists2Networks: Integrated analysis of gene/protein lists. BMC Bioinformatics 11: 87. 20152038 10,17
2010 Lammers G, Gilissen C, Nillesen ST, Uijtdewilligen PJ, Wismans RG, Veltman JA, Daamen WF, van Kuppevelt TH High density gene expression microarrays and gene ontology analysis for identifying processes in implanted tissue engineering constructs. Biomaterials 31: 8299-8312. 20727583 7,16
2010 Landa P, Storchova H, Hodek J, Vankova R, Podlipna R, Marsik P, Ovesna J, Vanek T Transferases and transporters mediate the detoxification and capacity to tolerate trinitrotoluene in Arabidopsis. Funct Integr Genomics 10: 547-559. 20532806 7
2010 Lanz RB, Bulynko Y, Malovannaya A, Labhart P, Wang L, Li W, Qin J, Harper M, O'Malley BW Global characterization of transcriptional impact of the SRC-3 coregulator. Mol Endocrinol 24: 859-872. Human breast cancer cell transcripts, proteins 20181721 7,8,16
2010 Laurila JB, Naderi N, Witte R, Riazanov A, Kouznetsov A, Baker CJ Algorithms and semantic infrastructure for mutation impact extraction and grounding. BMC Genomics 11 Suppl 4: S24. 21143808 12,13,19
2010 Lavallee-Adam M, Coulombe B, Blanchette M Detection of locally over-represented GO terms in protein-protein interaction networks. J Comput Biol 17: 443-457. 20377456 8,17
2010 Lawson C, Gieske M, Murdoch B, Ye P, Li Y, Hassold T, Hunt PA Gene Expression in the Fetal Mouse Ovary Is Altered by Exposure to Low Doses of Bisphenol A. Biol Reprod 84: 79-86. 20739668 7,16
2010 Le Brigand K, Robbe-Sermesant K, Mari B, Barbry P MiRonTop: mining microRNAs targets across large scale gene expression studies. Bioinformatics 26: 3131-3132. 20959382 7,10,12
2010 Leal GA, Gomes LH, Albuquerque PS, Tavares FC, Figueira A Searching for Moniliophthora perniciosa pathogenicity genes. Fungal Biol 114: 842-854. 20943194 7,18
2010 Leaver MJ, Taggart JB, Villeneuve L, Bron JE, Guy DR, Bishop SC, Houston RD, Matika O, Tocher DR Heritability and mechanisms of n-3 long chain polyunsaturated fatty acid deposition in the flesh of Atlantic salmon. Comp Biochem Physiol Part D Genomics Proteomics 6: 62-69. 20451480 7
2010 Lee LN, Baban D, Ronan EO, Ragoussis J, Beverley PC, Tchilian EZ Chemokine gene expression in lung CD8 T cells correlates with protective immunity in mice immunized intra-nasally with Adenovirus-85A. BMC Med Genomics 3: 46. 20942964 7,16
2010 Lee SH, Gondro C, van der Werf J, Kim NK, Lim DJ, Park EW, Oh SJ, Gibson JP, Thompson JM Use of a bovine genome array to identify new biological pathways for beef marbling in Hanwoo (Korean Cattle). BMC Genomics 11: 623. 21062493 7
2010 Lee SM|etAl Systems-level comparison of host responses induced by pandemic and seasonal influenza A H1N1 viruses in primary human type I-like alveolar epithelial cells in vitro. Respir Res 11: 147. 21029402 7,16
2010 Lee WP, Tzou WS Fast revelation of the motif mode for a yeast protein interaction network through intelligent agent-based distributed computing. Protein Pept Lett 17: 1091-1101. 20509852 8,17
2010 Lee Y, Li J, Gamazon E, Chen JL, Tikhomirov A, Cox NJ, Lussier YA Biomolecular systems of disease buried across multiple GWAS unveiled by information theory and ontology. AMIA Summits Transl Sci Proc 2010: 31-35. 21347143 12,13,16
2010 Leekitcharoenphon P, Taweemuang U, Palittapongarnpim P, Kotewong R, Supasiri T, Sonthayanon B Predicted sub-populations in a marine shrimp proteome as revealed by combined EST and cDNA data from multiple Penaeus species. BMC Res Notes 3: 295. 21067619 8
2010 Lenka SK, Katiyar A, Chinnusamy V, Bansal KC Comparative analysis of drought-responsive transcriptome in Indica rice genotypes with contrasting drought tolerance. Plant Biotechnol J epub 20809928 7
2010 Leonelli S Documenting the emergence of bio-ontologies: or, why researching bioinformatics requires HPSSB. Hist Philos Life Sci 32: 105-125. 20848809 14
2010 Leung MC, Bowley KL, Squires EJ Examination of testicular gene expression patterns in yorkshire pigs with high and low levels of boar taint. Anim Biotechnol 21: 77-87. Porcine testicular transcripts 20379884 7
2010 Levison SE, McLaughlin JT, Zeef LA, Fisher P, Grencis RK, Pennock JL Colonic transcriptional profiling in resistance and susceptibility to trichuriasis: Phenotyping a chronic colitis and lessons for iatrogenic helminthosis. Inflamm Bowel Dis 16: 2065-2079. 20687192 7,16
2010 Li D, Deng Z, Chen C, Xia Z, Wu M, He P, Chen S Identification and characterization of genes associated with tapping panel dryness from Hevea brasiliensis latex using suppression subtractive hybridization. BMC Plant Biol 10: 140. 20618931 7
2010 Li G, Wu Z, Li X, Ning X, Li Y, Yang G Biological role of MicroRNA-103 based on expression profile and target genes analysis in pigs. Mol Biol Rep epub 21152985 7
2010 Li H, Ma WL, Zuo CQ, Liang S, Ye Y, Zheng WL [Functional prediction of KIAA0101 gene in human non-small cell lung cancer.] Nan Fang Yi Ke Da Xue Xue Bao 30: 157-159. Human transcripts; lung cancer 20118010 7,16
2010 Li J, Duncan DT, Zhang B CanProVar: a human cancer proteome variation database. Hum Mutat 31: 219-228. 20052754 8,10
2010 Li J, Fan Y, Chen J, Yao KT, Huang ZX Microarray analysis of differentially expressed genes between nasopharyngeal carcinoma cell lines 5-8F and 6-10B. Cancer Genet Cytogenet 196: 23-30. Human nasopharyngeal carcinoma cell line transcripts 16 19963132 7
2010 Li J, Yuan Z, Zhang Z The cellular robustness by genetic redundancy in budding yeast. PLoS Genet 6: e1001187. 21079672 13,18
2010 Li JD, Feng QC, Li JS Differential gene expression profiling of oesophageal squamous cell carcinoma by DNA microarray and bioinformatics analysis. J Int Med Res 38: 1904-1912. 21226993 7,16,17
2010 Li JY, Hosseini Moghaddam SH, Chen JE, Chen M, Zhong BX Shotgun proteomic analysis on the embryos of silkworm Bombyx mori at the end of organogenesis. Insect Biochem Mol Biol 40: 293-302. Silkworm proteins 20138214 8
2010 Li X, Chen GH, Zhang WY, Zhang X Genome-wide transcriptional analysis of maize endosperm in response to ae wx double mutations. J Genet Genomics 37: 749-762. 21115169 7
2010 Li Y, Chan EY, Li J, Ni C, Peng X, Rosenzweig E, Tumpey TM, Katze MG MicroRNA expression and virulence in pandemic influenza virus infected mice. J Virol 84: 3023-3032. Mouse miRNAS; influenza virus infection 20071585 7,16
2010 Li Y, Hu X, Lin H, Yang Z A Framework for Semi-Supervised Feature Generation and its Applications in Biomedical Literature Mining. IEEE/ACM Trans Comput Biol Bioinform 8: 294-307. 20876938 12
2010 Li Y, Lam KS, Dasgupta N, Ye P A yeast's eye view of mammalian reproduction: cross-species gene co-expression in meiotic prophase. BMC Syst Biol 4: 125. 20819218 7,12,16,18
2010 Li Y, Luo HM, Sun C, Song JY, Sun YZ, Wu Q, Wang N, Yao H, Steinmetz A, Chen SL EST analysis reveals putative genes involved in glycyrrhizin biosynthesis. BMC Genomics 11: 268. 20423525 5,7
2010 Lillycrop KA, Rodford J, Garratt ES, Slater-Jefferies JL, Godfrey KM, Gluckman PD, Hanson MA, Burdge GC Maternal protein restriction with or without folic acid supplementation during pregnancy alters the hepatic transcriptome in adult male rats. Br J Nutr 103: 1711-1719. Rat liver transcripts 20211039 7,16
2010 Lin M, Chen W, Huang J, Gao H, Ye Y, Song Z, Shen X MicroRNA expression profiles in human colorectal cancers with liver metastases. Oncol Rep 25: 739-747. 21174058 7,16
2010 Lin S, Cheung WK, Chen S, Lu G, Wang Z, Xie D, Li K, Lin MC, Kung HF Computational identification and characterization of primate-specific microRNAs in human genome. Comput Biol Chem 34: 232-241. 20863765 7,13,18
2010 Lin YR, Wei HY, Tsai TL, Lin TH HDAPD: a web tool for searching the disease-associated protein structures. BMC Bioinformatics 11: 88. 20158919 10,11
2010 Lindenmeyer MT, Eichinger F, Sen K, Anders HJ, Edenhofer I, Mattinzoli D, Kretzler M, Rastaldi MP, Cohen CD Systematic analysis of a novel human renal glomerulus-enriched gene expression dataset. PLoS One 5: e11545. 20634963 7,16
2010 Liu F, Li W, Li Z, Zhang S, Chen S, Su S High-abundance mRNAs in Apis mellifera: Comparison between nurses and foragers. J Insect Physiol 57: 274-279. 21115016 7
2010 Liu F|etAl Gene expression profiles deciphering rice phenotypic variation between Nipponbare (Japonica) and 93-11 (Indica) during oxidative stress. PLoS One 5: e8632. Rice transcripts 20072620 7
2010 Liu G, Ding M, Chen J, Huang J, Wang H, Jing Q, Shen B Computational analysis of microRNA function in heart development. Acta Biochim Biophys Sin (Shanghai) 42: 662-670. 20716610 7,11,13,17
2010 Liu H, Zhao X, Wang F, Jiang X, Zhang S, Ye M, Zhao ZK, Zou H The proteome analysis of oleaginous yeast Lipomyces starkeyi. FEMS Yeast Res 11: 42-51. 21040454 8
2010 Liu J, Zheng S, Liu L, Li L, Feng Q Protein profiles of the midgut of Spodoptera litura larvae at the sixth instar feeding stage by shotgun ESI-MS approach. J Proteome Res 9: 2117-2147. Spodoptera litura larval proteins 20345177 6,8
2010 Liu WY, Zhao CJ Genome-wide identification and analysis of the chicken basic helix-loop-helix factors. Comp Funct Genomics epub 20454632 3
2010 Liu Y, Ng M Shrunken methodology to genome-wide SNPs selection and construction of SNPs networks. BMC Syst Biol 4 Suppl 2: S5. 20840732 16,17
2010 Liu YJ, Guo YF, Zhang LS, Pei YF, Yu N, Yu P, Papasian CJ, Deng HW Biological Pathway-Based Genome-Wide Association Analysis Identified the Vasoactive Intestinal Peptide (VIP) Pathway Important for Obesity. Obesity (Silver Spring) 18: 2339-2346. 20379146 13,16
2010 Liu Y|etAl Shotgun proteomics and network analysis between plasma membrane and extracellular matrix proteins from rat Olfactory Ensheathing cells. Cell Transplant 19: 133-146. Rat olfactory ensheathing cell proteome 20350363 8,17
2010 Liu Z, Chen S ER regulates an evolutionarily conserved apoptosis pathway. Biochem Biophys Res Commun 400: 34-38. 20691160 7
2010 Lo YS, Chen YC, Yang JM 3D-interologs: an evolution database of physical protein- protein interactions across multiple genomes. BMC Genomics 11 Suppl 3: S7. 21143789 8,11,17,18
2010 Lo YS, Lin CY, Yang JM PCFamily: a web server for searching homologous protein complexes. Nucleic Acids Res 38 Suppl: W516-522. 20511590 10,11
2010 Lockstone HE, Sanderson S, Kulakova N, Baban D, Leonard A, Kok WL, McGowan S, McMichael AJ, Ho LP Gene-set analysis of lung samples provides insight into pathogenesis of progressive, fibrotic pulmonary sarcoidosis. Am J Respir Crit Care Med 181: 1367-1375. Human lung transcripts 20194811 7,16
2010 Logan CA, Somero GN Transcriptional responses to thermal acclimation in the eurythermal fish Gillichthys mirabilis (Cooper 1864). Am J Physiol Regul Integr Comp Physiol 299: R843-852. 20610827 7
2010 Lokanathan Y, Mohd-Adnan A, Wan KL, Nathan S Transcriptome analysis of the Cryptocaryon irritans tomont stage identifies potential genes for the detection and control of cryptocaryonosis. BMC Genomics 11: 76. Cryptocaryon irritans ESTs 20113487 5
2010 Lopez-Garcia B, Gandia M, Munoz A, Carmona L, Marcos JF A genomic approach highlights common and diverse effects and determinants of susceptibility on the yeast Saccharomyces cerevisiae exposed to distinct antimicrobial peptides. BMC Microbiol 10: 289. 21078184 7,13
2010 Louie B, Bergen S, Higdon R, Kolker E Quantifying protein function specificity in the Gene Ontology. Stand Genomic Sci 2: 238-244. 21304708 13
2010 Louie B, Higdon R, Kolker E The necessity of adjusting tests of protein category enrichment in discovery proteomics. Bioinformatics 26: 3007-3011. 21068002 8
2010 Lu B, Yin L, Xu L, Peng J Application of proteomic and bioinformatic techniques for studying the hepatoprotective effect of dioscin against CCl4-induced liver damage in mice. Planta Med epub 20979020 8,16
2010 Lu C, Xiao C, Chen G, Jiang M, Zha Q, Yan X, Kong W, Lu A Cold and heat pattern of rheumatoid arthritis in traditional Chinese medicine: distinct molecular signatures indentified by microarray expression profiles in CD4-positive T cell. Rheumatol Int epub 20658292 16,17
2010 Lui JC, Forcinito P, Chang M, Chen W, Barnes KM, Baron J Coordinated postnatal down-regulation of multiple growth-promoting genes: evidence for a genetic program limiting organ growth. FASEB J 24: 3083-3092. Rat organ transcripts 20371622 7,16
2010 Luo C, Lam E ANCORP: a high-resolution approach that generates distinct chromatin state models from multiple genome-wide datasets. Plant J 63: 339-351. 20444227 7,13
2010 Luo H, Li Y, Sun C, Wu Q, Song J, Sun Y, Steinmetz A, Chen S Comparison of 454-ESTs from Huperzia serrata and Phlegmariurus carinatus reveals putative genes involved in lycopodium alkaloid biosynthesis and developmental regulation. BMC Plant Biol 10: 209. 20854695 5,7
2010 Ma'ayan A, He JC Protein kinase target discovery from genome-wide messenger RNA expression profiling. Mt Sinai J Med 77: 345-349. 20687179 7,13
2010 MacPherson JI, Dickerson JE, Pinney JW, Robertson DL Patterns of HIV-1 protein interaction identify perturbed host-cellular subsystems. PLoS Comput Biol 6: e1000863. 20686668 8,16,17
2010 Macagno ER|etAl Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes. BMC Genomics 11: 407. Leech ESTs 20579359 5
2010 Maity S, Goel SI, Roy S, Ghorai S, Bhattacharyya S, Venugopalan A, Ghosh AK Analysis of transcripts expressed in one-day-old larvae and fifth instar silk glands of tasar silkworm, Antheraea mylitta. Comp Funct Genomics epub 20454581 5,11
2010 Mali B, Grohme MA, Forster F, Dandekar T, Schnolzer M, Reuter D, Welnicz W, Schill RO, Frohme M Transcriptome survey of the anhydrobiotic tardigrade Milnesium tardigradum in comparison with Hypsibius dujardini and Richtersius coronifer. BMC Genomics 11: 168. Tardigrade ESTs 20226016 5,7
2010 Malik R, Dulla K, Nigg EA, Koerner R From proteome lists to biological impact tools and strategies for the analysis of large MS data sets. Proteomics 10: 1270-1283. 20077408 8,10
2010 Mallanna SK, Ormsbee BD, Iacovino M, Gilmore JM, Cox JL, Kyba M, Washburn MP, Rizzino A Proteomic Analysis of Sox2-associated Proteins During Early Stages of Mouse Embryonic Stem Cell Differentiation Identifies Sox21 as a Novel Regulator of Stem Cell Fate. Stem Cells 28: 1715-1727. 20687156 8
2010 Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H Modeling Sample Variables with an Experimental Factor Ontology. Bioinformatics 26: 1112-1118. 20200009 15
2010 Manda P, Freeman MG, Bridges SM, Jankun-Kelly TJ, Nanduri B, McCarthy FM, Burgess SC GOModeler--a tool for hypothesis-testing of functional genomics datasets. BMC Bioinformatics 11 Suppl 6: S29. 20946613 1,7,10
2010 Manickavelu A, Kawaura K, Oishi K, Shin-I T, Kohara Y, Yahiaoui N, Keller B, Suzuki A, Yano K, Ogihara Y Comparative gene expression analysis of susceptible and resistant near-isogenic lines in common wheat infected by Puccinia triticina. DNA Res 17: 211-222. Puccinia triticina ESTs 20360266 5
2010 Mansuy V, Geller S, Rey JP, Campagne C, Boccard J, Poulain P, Prevot V, Pralong FP Phenotypic and molecular characterization of proliferating and differentiated GnRH-expressing GnV-3 cells. Mol Cell Endocrinol 332: 97-9105. 20937356 7
2010 Marcon F, Silvestrini F, Siniscalchi E, Palli D, Saieva C, Crebelli R Gene expression in response to ionizing radiation and family history of gastric cancer. Fam Cancer epub 21061175 7,16
2010 Marques FZ, Campain AE, Yang YH, Morris BJ Meta-analysis of genome-wide gene expression differences in onset and maintenance phases of genetic hypertension. Hypertension 56: 319-324. 20585107 7,16
2010 Martin A, Ochagavia ME, Rabasa LC, Miranda J, Fernandez-de-Cossio J, Bringas R BisoGenet: a new tool for gene network building, visualization and analysis. BMC Bioinformatics 11: 91. 20163717 10,17
2010 Martin SA, Douglas A, Houlihan DF, Secombes CJ Starvation alters the liver transcriptome of the innate immune response in Atlantic salmon (Salmo salar). BMC Genomics 11: 418. 20602791 7
2010 Martinez-Romero M|etAl Artificial intelligence techniques for colorectal cancer drug metabolism: ontology and complex network. Curr Drug Metab 11: 347-368. 20446907 16,17
2010 Martyniuk CJ, Kroll KJ, Doperalski NJ, Barber DS, Denslow ND Genomic and proteomic responses to environmentally relevant exposures to dieldrin: indicators of neurodegeneration? Toxicol Sci 117: 190-199. 20584760 7,8,16,17
2010 Massanet-Vila R, Gallardo-Chacon JJ, Caminal P, Perera A An information theory-based tool for characterizing the interaction environment of a protein. Conf Proc IEEE Eng Med Biol Soc 1: 5529-5532. 21096470 8,10
2010 Mathur S, Dinakarpandian D Automated ontological gene annotation for computing disease similarity. AMIA Summits Transl Sci Proc 2010: 12-16. 21347137 15
2010 Matsuoka K, Komori H, Nose M, Endo Y, Sawasaki T Simple screening method for autoantigen proteins using the N-terminal biotinylated protein library produced by wheat cell-free synthesis. J Proteome Res 9: 4264-4273. 20575507 13,16
2010 Mbeunkui F, Scholl EH, Opperman CH, Goshe MB, Bird DM Proteomic and bioinformatic analysis of the root-knot nematode Meloidogyne hapla: the basis for plant parasitism. J Proteome Res 9: 5370-5381. 20804128 7,8,18
2010 McGary KL, Park TJ, Woods JO, Cha HJ, Wallingford JB, Marcotte EM Systematic discovery of nonobvious human disease models through orthologous phenotypes. Proc Natl Acad Sci U S A 107: 6544-6549. 20308572 13,16,18
2010 McGivney BA, McGettigan PA, Browne JA, Evans AC, Fonseca RG, Loftus BJ, Lohan A, MacHugh DE, Murphy BA, Katz LM, Hill EW Characterization of the equine skeletal muscle transcriptome identifies novel functional responses to exercise training. BMC Genomics 11: 398. 20573200 7
2010 Mehan MR, Nunez-Iglesias J, Dai C, Waterman MS, Zhou XJ An integrative modular approach to systematically predict gene-phenotype associations. BMC Bioinformatics 11 Suppl 1: S62. 20122238 7,16,17,19
2010 Mei-Ling L, Xin-Quan S, Meng-Chun J Differentially expressed genes in early gestational chorionic villi after administration of mifepristone. Gynecol Endocrinol epub 20569099 7,16
2010 Melis M, Hernandez J, Siegel EM, McLoughlin JM, Ly QP, Nair RM, Lewis JM, Jensen EH, Alvarado MD, Coppola D, Eschrich S, Bloom GC, Yeatman TJ, Shibata D Gene expression profiling of colorectal mucinous adenocarcinomas. Dis Colon Rectum 53: 936-943. 20485009 7,16
2010 Meng X, Chang Y, Qiu X, Wang X Generation and analysis of expressed sequence tags from adductor muscle of Japanese scallop Mizuhopecten yessoensis. Comp Biochem Physiol Part D Genomics Proteomics 5: 288-294. 20832371 5
2010 Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, Thomas PD PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res 38: D204-210. 20015972 1,3,18
2010 Middleton S, Song T, Nayak S Length constraints of multi-domain proteins in metazoans. Bioinformation 4: 441-444. 20975906 13,18
2010 Mienaltowski MJ, Huang L, Bathke AC, Stromberg AJ, Macleod JN Transcriptional comparisons between equine articular repair tissue, neonatal cartilage, cultured chondrocytes and mesenchymal stromal cells. Brief Funct Genomic Proteomic 9: 238-250. Equine cartilage transcripts 20348544 7,16
2010 Min JL, Barrett A, Watts T, Pettersson FH, Lockstone HE, Lindgren CM, Taylor JM, Allen M, Zondervan KT, McCarthy MI Variability of gene expression profiles in human blood and lymphoblastoid cell lines. BMC Genomics 11: 96. Human cell line transcripts 20141636 7,16
2010 Miozzi L, Provero P, Accotto GP ORTom: a multi-species approach based on conserved co-expression to identify putative functional relationships among genes in tomato. Plant Mol Biol 73: 519-532. 20411302 7,17,18
2010 Mitsuhashi T|etAl Global gene profiling and comprehensive bioinformatics analysis of a 46,XY female with pericentric inversion of the Y chromosome. Congenit Anom (Kyoto) 50: 40-51. 20201967 7,12,16
2010 Mittal A, Middleditch M, Ruggiero K, Loveday B, Delahunt B, Jullig M, Cooper GJ, Windsor JA, Phillips AR Changes in the mesenteric lymph proteome induced by haemorrhagic shock. Shock 34: 140-149. Rat lymph proteins 20160674 8,16
2010 Mittal P|etAl Characterization of the myometrial transcriptome and biological pathways of spontaneous human labor at term. J Perinat Med 38: 617-643. 20629487 7,16
2010 Mizoguchi T, Arakawa Y, Kobayashi M, Fujishima M Influence of Chlorella powder intake during swimming stress in mice. Biochem Biophys Res Commun 404: 121-126. 21095179 7,17
2010 Moberg C, Catalano RD, Charnock-Jones DS, Olovsson M VEGF-A and serum withdrawal induced changes in the transcript profile in human endometrial endothelial cells. Reprod Sci 17: 590-611. Human endometrial endothelial cell transcripts 20360594 7,16
2010 Moehninsi , Miura K, Nakajyo H, Yamada K, Hasegawa K, Shigemori H Comparative transcriptional profiling-based identification of raphanusanin-inducible genes. BMC Plant Biol 10: 111. 20553608 7
2010 Mohamad N, Boden M The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression. BMC Syst Biol 4: 44. 20388198 8
2010 Montaner D, Dopazo J Multidimensional gene set analysis of genomic data. PLoS One 5: e10348. 20436964 7,8,13,17
2010 Moreira EG, Yu X, Robinson JF, Griffith W, Hong SW, Beyer RP, Bammler TK, Faustman EM Toxicogenomic profiling in maternal and fetal rodent brains following gestational exposure to chlorpyrifos. Toxicol Appl Pharmacol 245: 310-325. Mouse brain transcripts; chlorpyrifos exposure 20350560 7,16
2010 Moreno-Vinasco L, Garcia JG Receptor tyrosine kinase inhibitors in rodent pulmonary hypertension. Adv Exp Med Biol 661: 419-434. Rat transcripts 20204746 7,16
2010 Mosca E, Alfieri R, Merelli I, Viti F, Calabria A, Milanesi L A multilevel data integration resource for breast cancer study. BMC Syst Biol 4: 76. 20525248 11,16,17
2010 Moskvina V|etAl Genetic Differences between Five European Populations. Hum Hered 70: 141-149. 20616560 18
2010 Moutselos K, Maglogiannis I, Chatziioannou A Delineation and interpretation of gene networks towards their effect in cellular physiology- A reverse engineering approach for the identification of critical molecular players, through the use of ontologies. Conf Proc IEEE Eng Med Biol Soc 1: 6709-6712. 21096082 7,17
2010 Mu Y, Ding F, Cui P, Ao J, Hu S, Chen X Transcriptome and expression profiling analysis revealed changes of multiple signaling pathways involved in immunity in the large yellow croaker during Aeromonas hydrophila infection. BMC Genomics 11: 506. 20858287 3,7
2010 Mukhopadhyay A, Bandyopadhyay S, Maulik U Multi-class clustering of cancer subtypes through SVM based ensemble of pareto-optimal solutions for gene marker identification. PLoS One 5: e13803. 21103052 7,16
2010 Mullen MA, Olson KJ, Dallaire P, Major F, Assmann SM, Bevilacqua PC RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles. Nucleic Acids Res 38: 8149-8163. 20860998 13
2010 Mun GI, Boo YC Identification of CD44 as a senescence-induced cell adhesion gene responsible for the enhanced monocyte recruitment to senescent endothelial cells. Am J Physiol Heart Circ Physiol 298: H2102-2111. 20382854 7,16
2010 Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J Cross-product extensions of the Gene Ontology. J Biomed Inform epub 20152934 1,2,15
2010 Murchison EP|etAl The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer. Science 327: 84-87. Tasmanian devil transcripts 20044575 7
2010 Murphy DM, Buckley PG, Bryan K, Watters KM, Koster J, van Sluis P, Molenaar J, Versteeg R, Stallings RL Dissection of the oncogenic MYCN transcriptional network reveals a large set of clinically relevant cell cycle genes as drivers of neuroblastoma tumorigenesis. Mol Carcinog epub 21190229 7,16,17
2010 Murphy JP, Pinto DM Temporal proteomic analysis of IGF-1R signalling in MCF-7 breast adenocarcinoma cells. Proteomics 10: 1847-1860. Human breast adenocarcinoma cell line transcripts 20213678 7,16
2010 Naciff JM, Khambatta ZS, Reichling TD, Carr GJ, Tiesman JP, Singleton DW, Khan SA, Daston GP The genomic response of Ishikawa cells to bisphenol A exposure is dose- and time-dependent. Toxicology 270: 137-149. Human cell line transcripts; bisphenol A exposure 20170705 7,16
2010 Naeem H, Kuffner R, Csaba G, Zimmer R miRSel: Automated extraction of associations between microRNAs and genes from the biomedical literature. BMC Bioinformatics 11: 135. 20233441 11
2010 Naegle KM, Gymrek M, Joughin BA, Wagner JP, Welsch RE, Yaffe MB, Lauffenburger DA, White FM PTMScout: A web resource for analysis of high-throughput post-translational proteomic studies. Mol Cell Proteomics 9: 2558-2570. 20631208 8,10,11
2010 Neibergs HL, Settles ML, Whitlock RH, Taylor JF GSEA-SNP identifies genes associated with Johne's disease in cattle. Mamm Genome 21: 419-425. 20706723 7
2010 Ni CW, Qiu H, Rezvan A, Kwon K, Nam D, Son DJ, Visvader JE, Jo H Discovery of novel mechanosensitive genes in vivo using mouse carotid artery endothelium exposed to disturbed flow. Blood 116: e66-73. 20551377 7,16
2010 Nie H, Crooijmans RP, Lammers A, van Schothorst EM, Keijer J, Neerincx PB, Leunissen JA, Megens HJ, Groenen MA Gene expression in chicken reveals correlation with structural genomic features and conserved patterns of transcription in the terrestrial vertebrates. PLoS One 5: e11990. 20700537 7,18
2010 Niedoszytko M, Bruinenberg M, Van Doormaal JJ, De Monchy JG, Nedoszytko B, Koppelman GH, Nawijn MC, Wijmenga C, Jassem E, Elberink JN Gene expression analysis predicts insect venom anaphylaxis in indolent systemic mastocytosis. Allergy epub 21143240 7,16
2010 Nilo R|etAl Proteomic analysis of peach fruit mesocarp softening and chilling injury using difference gel electrophoresis (DIGE). BMC Genomics 11: 43. Peach proteins 20082721 8
2010 Ning K, Ng HK, Srihari S, Leong HW, Nesvizhskii AI Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology. BMC Bioinformatics 11: 505. 20939873 8,17
2010 Nishimura S|etAl Marine antifungal theonellamides target 3beta-hydroxysterol to activate Rho1 signaling. Nat Chem Biol 6: 519-526. 20543850 13
2010 Nishiuchi S, Fujihara K, Liu S, Takano T Analysis of expressed sequence tags from a NaHCO(3)-treated alkali-tolerant plant, Chloris virgata. Plant Physiol Biochem 48: 247-255. Chloris virgata ESTs 20199868 5,7
2010 Niu C, Wang Y, Yue J, Ning B, Gao Z, Liang L [Identification of exotoxin-specific motifs/domains in bacterial exotoxin sequences and corresponding gene ontology analysis]. Wei Sheng Wu Xue Bao 50: 1246-1250. 21090266 11,13
2010 Noorbakhsh F, Ramachandran R, Barsby N, Ellestad KK, Leblanc A, Dickie P, Baker G, Hollenberg MD, Cohen EA, Power C MicroRNA profiling reveals new aspects of HIV neurodegeneration: caspase-6 regulates astrocyte survival. FASEB J 24: 1799-1812. Human brain miRNAs; HIV infection 20097875 7,16
2010 Nudelman G, Ge Y, Hu J, Kumar M, Seto J, Duke JL, Kleinstein SH, Hayot F, Sealfon SC, Wetmur JG Coregulation mapping based on individual phenotypic variation in response to virus infection. Immunome Res 6: 2. Human dendritic cell transcripts 20298589 7,16,18
2010 Numayama-Tsuruta K, Arai Y, Takahashi M, Sasaki-Hoshino M, Funatsu N, Nakamura S, Osumi N Downstream genes of Pax6 revealed by comprehensive transcriptome profiling in the developing rat hindbrain. BMC Dev Biol 10: 6. Rat brain transcripts 20082710 7
2010 O'Donoghue LE, Ptitsyn AA, Kamstock DA, Siebert J, Thomas RS, Duval DL Expression profiling in canine osteosarcoma: identification of biomarkers and pathways associated with outcome. BMC Cancer 10: 506. 20860831 7
2010 Ochoa MT, Teles R, Haas BE, Zaghi D, Li H, Sarno EN, Rea TH, Modlin RL, Lee DJ A role for interleukin-5 in promoting increased immunoglobulin M at the site of disease in leprosy. Immunology 131: 405-414. 20561085 7,16
2010 Ogando DG, Dahlquist KD, Alizadeh M, Kunchithapautham K, Li J, Yu N, LaVail MM, Rohrer B, Vollrath D, Danciger M Candidate genes for chromosomes 6 and 10 quantitative trait loci for age-related retinal degeneration in mice. Mol Vis 16: 1004-1018. 20577653 7,13,16
2010 Ogata Y, Suzuki H, Shibata D CoP: a database for characterizing co-expressed gene modules with biological information in plants. Bioinformatics 26: 1267-1268. 20305269 7,10
2010 Oh JJ, Taschereau EO, Koegel AK, Ginther CL, Rotow JK, Isfahani KZ, Slamon DJ RBM5/H37 tumor suppressor, located at the lung cancer hot spot 3p21.3, alters expression of genes involved in metastasis. Lung Cancer 70: 253-262. Human cell line transcripts 20338664 7,16
2010 Ojalvo LS, Whittaker CA, Condeelis JS, Pollard JW Gene expression analysis of macrophages that facilitate tumor invasion supports a role for Wnt-signaling in mediating their activity in primary mammary tumors. J Immunol 184: 702-712. Mouse macrophage transcripts; breast cancer 20018620 7,16
2010 Oppelt A, Humann FC, Fuessl M, Azevedo SV, Marco Antonio DS, Heinze J, Hartfelder K Suppression subtractive hybridization analysis reveals expression of conserved and novel genes in male accessory glands of the ant Leptothorax gredleri. BMC Evol Biol 10: 273. 20825642 7,18
2010 Ostrup E, Bauersachs S, Blum H, Wolf E, Hyttel P Differential endometrial gene expression in pregnant and nonpregnant sows. Biol Reprod 83: 277-285. 20393170 7
2010 Otto TD|etAl ProteinWorldDB: Querying radical pairwise alignments among protein sets from complete genomes. Bioinformatics 26: 705-707. 20089515 8,11
2010 Ozaki S|etAl Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module. DNA Res 17: 105-116. Tomato transcripts 20130013 7
2010 Ozsait B, Komurcu-Bayrak E, Levula M, Erginel-Unaltuna N, Kahonen M, Rai M, Lehtimaki T, Laaksonen R Niemann-Pick type C fibroblasts have a distinct microRNA profile related to lipid metabolism and certain cellular components. Biochem Biophys Res Commun 403: 316-321. 21075073 7,16
2010 Pallavicini A, Randelli E, Modonut M, Casani D, Scapigliati G, Buonocore F Searching for immunomodulatory sequences in sea bass (Dicentrarchus labrax L.): transcripts analysis from thymus. Fish Shellfish Immunol 29: 571-578. 20685619 5,7
2010 Palmer RD|etAl Malignant germ cell tumors display common microRNA profiles resulting in global changes in expression of messenger RNA targets. Cancer Res 70: 2911-2923. Human germ cell transcripts 20332240 7,16
2010 Pandey AK, Munjal N, Datta M Gene expression profiling and network analysis reveals lipid and steroid metabolism to be the most favored by TNFalpha in HepG2 cells. PLoS One 5: e9063. Human hepatocellular liver carcinoma cell line transcripts 20140224 7,16,17
2010 Pandit SB, Brylinski M, Zhou H, Gao M, Arakaki AK, Skolnick J PSiFR: an integrated resource for prediction of protein structure and function. Bioinformatics 26: 687-688. 20080513 9,10,19
2010 Park B, Han K An ontology-based search engine for protein-protein interactions. BMC Bioinformatics 11 Suppl 1: S23. 20122195 8,12,17
2010 Parmentier G, Bastian FB, Robinson-Rechavi M Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy. Bioinformatics 26: 1766-1771. 20519284 15
2010 Parton A, Bayne CJ, Barnes DW Analysis and functional annotation of expressed sequence tags from in vitro cell lines of elasmobranchs: Spiny dogfish shark (Squalus acanthias) and little skate (Leucoraja erinacea). Comp Biochem Physiol Part D Genomics Proteomics 5: 199-206. 20471924 5
2010 Paulo JA, Lee LS, Wu B, Repas K, Banks PA, Conwell DL, Steen H Proteomic analysis of endoscopically (endoscopic pancreatic function test) collected gastroduodenal fluid using in-gel tryptic digestion followed by LC-MS/MS. Proteomics Clin Appl 4: 715-725. 21137089 8,16
2010 Paulo JA, Lee LS, Wu B, Repas K, Mortele KJ, Banks PA, Steen H, Conwell DL Identification of pancreas-specific proteins in endoscopically (endoscopic pancreatic function test) collected pancreatic fluid with liquid chromatography- tandem mass spectrometry. Pancreas 39: 889-896. Human pancreatic fluid proteins 20182389 8,16
2010 Pavlou M, Kulasingam V, Sauter ER, Kliethermes B, Diamandis EP Nipple aspirate fluid proteome of healthy females and patients with breast cancer. Clin Chem 56: 848-855. Human nipple aspirate fluid proteome 20348408 8,16
2010 Peddinti D, Memili E, Burgess SC Proteomics-based systems biology modeling of bovine germinal vesicle stage oocyte and cumulus cell interaction. PLoS One 5: e11240. 20574525 8,17
2010 Peidis P, Giannakouros T, Burow ME, Williams RW, Scott RE Systems genetics analyses predict a transcription role for P2P-R: molecular confirmation that P2P-R is a transcriptional co-repressor. BMC Syst Biol 4: 14. 20184719 7,17
2010 Pellagatti A|etAl Deregulated gene expression pathways in myelodysplastic syndrome hematopoietic stem cells. Leukemia 24: 756-764. Human hematopoietic stem cell transcripts 20220779 7,16
2010 Perreau VM|etAl A domain level interaction network of amyloid precursor protein and Abeta of Alzheimer's disease. Proteomics 10: 2377-2395. 20391539 8,16,17
2010 Peterson SM, Zhang J, Weber G, Freeman JL Global gene expression analysis reveals dynamic and developmental stage dependent enrichment of lead (Pb)-induced neurological gene alterations. Environ Health Perspect epub 21147602 7,16
2010 Pieroni L, Finamore F, Ronci M, Mattoscio D, Marzano V, Mortera SL, Quattrucci S, Federici G, Romano M, Urbani A Proteomics investigation of human platelets in healthy donors and cystic fibrosis patients by shotgun nUPLC-MS(E) and 2DE: a comparative study. Mol Biosyst 7: 630-639. 21072441 8,16
2010 Pinto PI, Matsumura H, Thorne MA, Power DM, Terauchi R, Reinhardt R, Canario AV Gill transcriptome response to changes in environmental calcium in the green spotted puffer fish. BMC Genomics 11: 476. 20716350 7
2010 Pirooznia M, Pozhitkov A, Perkins EJ, Deng Y, Brouwer M Generation, analysis and functional annotation of expressed sequence tags from the sheepshead minnow (Cyprinodon variegatus). BMC Genomics 11 Suppl 2: S4. 21047385 5
2010 Pisanu S, Ghisaura S, Pagnozzi D, Biosa G, Tanca A, Roggio T, Uzzau S, Addis MF The sheep milk fat globule membrane proteome. J Proteomics 74: 350-358. 21147282 6,8
2010 Piubelli C, Vighini M, Mathe AA, Domenici E, Carboni L Escitalopram affects cytoskeleton and synaptic plasticity pathways in a rat gene-environment interaction model of depression as revealed by proteomics. Part II: environmental challenge. Int J Neuropsychopharmacol epub 21054913 8,16
2010 Piubelli C, Vighini M, Mathe AA, Domenici E, Carboni L Escitalopram modulates neuron-remodelling proteins in a rat gene-environment interaction model of depression as revealed by proteomics. Part I: genetic background. Int J Neuropsychopharmacol epub 21054914 8,16
2010 Pollanen E|etAl Power training and postmenopausal hormone therapy affect transcriptional control of specific co-regulated gene clusters in skeletal muscle. Age (Dordr) 32: 347-363. 20640546 7,16
2010 Popesku JT, Martyniuk CJ, Denslow ND, Trudeau VL Rapid dopaminergic modulation of the fish hypothalamic transcriptome and proteome. PLoS One 5: e12338. 20808832 7,8
2010 Porcu G, Wilson C, Di Giandomenico D, Ragnini-Wilson A A yeast-based genomic strategy highlights the cell protein networks altered by FTase inhibitor peptidomimetics. Mol Cancer 9: 197. 20653956 7,16,17
2010 Posnack NG, Lee NH, Brown R, Sarvazyan N Gene expression profiling of DEHP-treated cardiomyocytes reveals potential causes of phthalate arrhythmogenicity. Toxicology 279: 54-64. 20920545 7,16
2010 Prakash SK|etAl Rare copy number variants disrupt genes regulating vascular smooth muscle cell adhesion and contractility in sporadic thoracic aortic aneurysms and dissections. Am J Hum Genet 87: 743-756. 21092924 7,16,17
2010 Prentis PJ, Woolfit M, Thomas-Hall SR, Ortiz-Barrientos D, Pavasovic A, Lowe AJ, Schenk PM Massively parallel sequencing and analysis of expressed sequence tags in a successful invasive plant. Ann Bot 106: 1009-1017. 20929896 5
2010 Pruss BM|etAl Environmental and genetic factors that contribute to Escherichia coli K-12 biofilm formation. Arch Microbiol 192: 715-728. 20559621 7,13
2010 Puniyani K, Faloutsos C, Xing EP SPEX2: automated concise extraction of spatial gene expression patterns from Fly embryo ISH images. Bioinformatics 26: i47-56. 20529936 7,13
2010 Quest DJ, Land ML, Brettin TS, Cottingham RW Next generation models for storage and representation of microbial biological annotation. BMC Bioinformatics 11 Suppl 6: S15. 20946598 3,11,14,15
2010 Rajasekaran S, Mi T, Merlin JC, Oommen A, Gradie P, Schiller MR Partitioning of minimotifs based on function with improved prediction accuracy. PLoS One 5: e12276. 20808856 13,19
2010 Rajicic N|etAl Identification and interpretation of longitudinal gene expression changes in trauma. PLoS One 5: e14380. 21187951 7,16
2010 Rao A, Kumar MK, Joseph T, Bulusu G Cerebral malaria: insights from host-parasite protein-protein interactions. Malar J 9: 155. 20529383 8,16,17
2010 Rawat A, Gust KA, Deng Y, Garcia-Reyero N, Quinn MJ, Johnson MS, Indest KJ, Elasri MO, Perkins EJ From raw materials to validated system: the construction of a genomic library and microarray to interpret systemic perturbations in Northern bobwhite. Physiol Genomics 42: 219-235. 20406850 3,7
2010 Rawat A, Gust KA, Elasri MO, Perkins EJ Quail Genomics: a knowledgebase for Northern bobwhite. BMC Bioinformatics 11 Suppl 6: S13. 20946596 5,11
2010 Raymond F, Metairon S, Kussmann M, Colomer J, Nascimento A, Mormeneo E, Garcia-Martinez C, Gomez-Foix AM Comparative gene expression profiling between human cultured myotubes and skeletal muscle tissue. BMC Genomics 11: 125. Human muscle transcripts 20175888 7,16
2010 Rebholz-Schuhmann D, Kavaliauskas S, Pezik P PaperMaker: validation of biomedical scientific publications. Bioinformatics 26: 982-984. 20200010 10,12
2010 Redell JB, Zhao J, Dash PK Altered expression of miRNA-21 and its targets in the hippocampus after traumatic brain injury. J Neurosci Res epub 21154462 7,16
2010 Richards AJ, Muller B, Shotwell M, Cowart LA, Rohrer B, Lu X Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph. Bioinformatics 26: i79-87. 20529941 10
2010 Richter CA, Garcia-Reyero N, Martyniuk C, Knoebl I, Pope M, Wright-Osment MK, Denslow ND, Tillitt DE Gene expression changes in female zebrafish (Danio rerio) brain in response to acute exposure to methylmercury. Environ Toxicol Chem 30: 301-308. 21082716 7
2010 Rider AK, Siwo G, Chawla NV, Ferdig M, Emrich SJ A statistical approach to finding overlooked genetic associations. BMC Bioinformatics 11: 526. 20964847 13
2010 Riewe SD, Mans JJ, Hirano T, Katz J, Shiverick KT, Brown TA, Lamont RJ Human trophoblast responses to Porphyromonas gingivalis infection. Mol Oral Microbiol 25: 252-259. 20618699 7,18
2010 Riggins CW, Peng Y, Stewart CN, Tranel PJ Characterization of de novo transcriptome for waterhemp (Amaranthus tuberculatus) using GS-FLX 454 pyrosequencing and its application for studies of herbicide target-site genes. Pest Manag Sci 66: 1042-1052. 20680963 3,7
2010 Robinson JF, Guerrette Z, Yu X, Hong S, Faustman EM A systems-based approach to investigate dose- and time-dependent methylmercury-induced gene expression response in C57BL/6 mouse embryos undergoing neurulation. Birth Defects Res B Dev Reprod Toxicol 89: 188-200. 20540155 7,16
2010 Robinson JF, Port JA, Yu X, Faustman EM Integrating genetic and toxicogenomic information for determining underlying susceptibility to developmental disorders. Birth Defects Res A Clin Mol Teratol 88: 920-930. 20706997 7,13,16
2010 Robinson PN, Mundlos S The human phenotype ontology. Clin Genet 77: 525-534. 20412080 15
2010 Rodelsperger C, Dieterich C CYNTENATOR: progressive gene order alignment of 17 vertebrate genomes. PLoS One 5: e8861. 20126624 10.1371/journal.pone.0008861 13,18
2010 Romero-Ruiz A, Mejias R, Diaz-Martin J, Lopez-Barneo J, Gao L Mesencephalic and striatal protein profiles in mice over-expressing glucose-6-phosphate dehydrogenase in dopaminergic neurons. J Proteomics 73: 1747-1757. 20594931 8,16
2010 Ronneberg JA|etAl Methylation profiling with a panel of cancer related genes: Association with estrogen receptor, TP53 mutation status and expression subtypes in sporadic breast cancer. Mol Oncol 5: 61-76. 21212030 7,13,16
2010 Rooney JP, Patil A, Joseph F, Endres L, Begley U, Zappala MR, Cunningham RP, Begley TJ Cross-species functionome analysis identifies proteins associated with DNA repair, translation and aerobic respiration as conserved modulators of UV-toxicity. Genomics 97: 133-147. 21195161 13,18
2010 Roslan R, Othman RM, Shah ZA, Kasim S, Asmuni H, Taliba J, Hassan R, Zakaria Z Utilizing shared interacting domain patterns and Gene Ontology information to improve protein-protein interaction prediction. Comput Biol Med 40: 555-564. 20417930 17,19
2010 Rossi L, Lapini I, Magi A, Pratesi G, Lavitrano M, Biasi GM, Pulli R, Pratesi C, Abbate R, Giusti B Carotid Artery Disease: Novel Pathophysiological Mechanisms Identified by Gene-expression Profiling of Peripheral Blood. Eur J Vasc Endovasc Surg 40: 549-558. 20709579 7,16
2010 Rossouw D, van den Dool AH, Jacobson D, Bauer FF Comparative transcriptomic and proteomic profiling of industrial wine yeast strains. Appl Environ Microbiol 76: 3911-3923. 20418425 7,8
2010 Rothem DE, Rothem L, Dahan A, Eliakim R, Soudry M Nicotinic modulation of gene expression in osteoblast cells, MG-63. Bone epub 21168537 7,16
2010 Roy A, Kucukural A, Zhang Y I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 5: 725-738. 20360767 9,10
2010 Ruppen I, Grau L, Orenes-Pinero E, Ashman K, Gil M, Algaba F, Bellmunt J, Sanchez-Carbayo M Differential protein expression profiling by iTRAQ-2DLC-MS/MS of human bladder cancer EJ138 cells transfected with the metastasis suppressor KiSS-1 gene. Mol Cell Proteomics 9: 2276-2291. Human bladder cancer cell line proteins 20139371 8,16
2010 Ryan JC, Morey JS, Bottein MY, Ramsdell JS, Van Dolah FM Gene expression profiling in brain of mice exposed to the marine neurotoxin ciguatoxin reveals an acute anti-inflammatory, neuroprotective response. BMC Neurosci 11: 107. 20796285 7,16
2010 Rybarczyk-Filho JL, Castro MA, Dalmolin RJ, Moreira JC, Brunnet LG, de Almeida RM Towards a genome-wide transcriptogram: the Saccharomyces cerevisiae case. Nucleic Acids Res epub 21169199 7,17
2010 Saadi A|etAl Stromal genes discriminate preinvasive from invasive disease, predict outcome, and highlight inflammatory pathways in digestive cancers. Proc Natl Acad Sci U S A 107: 2177-2182. Human gastrointestinal transcripts 20080664 7,16
2010 Sabatier R|etAl A gene expression signature identifies two prognostic subgroups of basal breast cancer. Breast Cancer Res Treat epub 20490655 7,16
2010 Sadowski MI, Taylor WR On the evolutionary origins of "Fold Space Continuity": A study of topological convergence and divergence in mixed alpha-beta domains. J Struct Biol 172: 244-252. 20691788 13
2010 Salem M, Rexroad CE, Wang J, Thorgaard GH, Yao J Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches. BMC Genomics 11: 564. 20942956 7
2010 Sanchez BC, Carter B, Hammers HR, Sepulveda MS Transcriptional response of hepatic largemouth bass (Micropterus salmoides) mRNA upon exposure to environmental contaminants. J Appl Toxicol epub 20589742 7
2010 Sansanwal P, Li L, Hsieh SC, Sarwal MM Insights into novel cellular injury mechanisms by gene expression profiling in nephropathic cystinosis. J Inherit Metab Dis 33: 775-786. 20865335 7,16
2010 Santora RJ, Lie ML, Grigoryev DN, Nasir O, Moore FA, Hassoun HT Therapeutic distant organ effects of regional hypothermia during mesenteric ischemia-reperfusion injury. J Vasc Surg 52: 1003-1014. 20678877 7,16
2010 Sanzol J Dating and functional characterization of duplicated genes in the apple (Malus domestica Borkh.) by analyzing EST data. BMC Plant Biol 10: 87. 20470375 5,18
2010 Sarac OS, Atalay V, Cetin-Atalay R GOPred: GO molecular function prediction by combined classifiers. PLoS One 5: e12382. 20824206 9,10
2010 Sardana D, Vasa S, Vepachedu N, Chen J, Gudivada RC, Aronow BJ, Jegga AG PhenoHM: human-mouse comparative phenome-genome server. Nucleic Acids Res 38 Suppl: W165-174. 20507906 15
2010 Sarma SN, Kim YJ, Ryu JC Gene expression profiles of human promyelocytic leukemia cell lines exposed to volatile organic compounds. Toxicology 271: 122-130. Human cell line transcripts 20359517 7,16
2010 Sathiyamoorthy S, In JG, Gayathri S, Kim YJ, Yang DCh Gene ontology study of methyl jasmonate-treated and non-treated hairy roots of Panax ginseng to identify genes involved in secondary metabolic pathway. Genetika 46: 932-939. 20795497 5,7
2010 Sathiyamoorthy S, In JG, Lee OR, Lee BS, Devi SR, Yang DC In silico gene expression analysis in Codonopsis lanceolata root. Mol Biol Rep epub 21088900 5,7
2010 Sato K, Nakagawa H, Tajima A, Yoshida K, Inoue I ANRIL is implicated in the regulation of nucleus and potential transcriptional target of E2F1. Oncol Rep 24: 701-707. 20664976 7,16
2010 Sbacchi S, Acquadro F, Calo I, Cali F, Romano V Functional annotation of genes overlapping copy number variants in autistic patients: focus on axon pathfinding. Curr Genomics 11: 136-145. 20885821 13,16
2010 Schlicker A, Lengauer T, Albrecht M Improving disease gene prioritization using the semantic similarity of Gene Ontology terms. Bioinformatics 26: i561-567. 20823322 16,19
2010 Schoenhuth A, Salari R, Hormozdiari F, Cherkasov A, Sahinalp SC Towards improved assessment of functional similarity in large-scale screens: a study on indel length. J Comput Biol 17: 1-20. 20078394 18
2010 Schultz J, Koczan D, Schmitz U, Ibrahim SM, Pilch D, Landsberg J, Kunz M Tumor-promoting role of signal transducer and activator of transcription (Stat)1 in late-stage melanoma growth. Clin Exp Metastasis 27: 133-140. Human melanoma transcripts; metastasis 20180146 7,16
2010 Schulz R, Proudhon C, Bestor TH, Woodfine K, Lin CS, Lin SP, Prissette M, Oakey RJ, Bourc'his D The parental non-equivalence of imprinting control regions during mammalian development and evolution. PLoS Genet 6: e1001214. 21124941 7,18
2010 Schwind S|etAl Prognostic significance of expression of a single microRNA, miR-181a, in cytogenetically normal acute myeloid leukemia: A cancer and leukemia Group B study. J Clin Oncol 28: 5257-5264. 21079133 7,16
2010 Sephton CF|etAl Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes. J Biol Chem 286: 1204-1215. 21051541 13,16
2010 Sha Z, Wang S, Zhuang Z, Wang Q, Wang Q, Li P, Ding H, Wang N, Liu Z, Chen S Generation and analysis of 10 000 ESTs from the half-smooth tongue sole Cynoglossus semilaevis and identification of microsatellite and SNP markers. J Fish Biol 76: 1190-1204. 20409170 5
2010 Shahzad K, Cadeiras M, Memon S, Zeeberg B, Klingler T, Sinha A, Tabak EG, Unniachan S, Deng MC Gene expression signatures of peripheral blood mononuclear cells during the early post-transplant period in patients developing cardiac allograft vasculopathy. J Transplant 2010: 719696. 21234308 7,16
2010 Shameer K, Madan LL, Veeranna S, Gopal B, Sowdhamini R PeptideMine--a webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes. BMC Bioinformatics 11: 473. 20858292 8,10
2010 Sharakhova MV, George P, Brusentsova IV, Leman SC, Bailey JA, Smith CD, Sharakhov IV Genome mapping and characterization of the Anopheles gambiae heterochromatin. BMC Genomics 11: 459. 20684766 3
2010 Sharma A, Chavali S, Tabassum R, Tandon N, Bharadwaj D Gene prioritization in Type 2 Diabetes using domain interactions and network analysis. BMC Genomics 11: 84. Human proteins; diabetes 20122255 8,16,17
2010 Sharma M, Halligan BD, Wakim BT, Savin VJ, Cohen EP, Moulder JE The urine proteome for radiation biodosimetry: effect of total body vs. local kidney irradiation. Health Phys 98: 186-195. Rat urine proteins 20065682 8,16
2010 Sharma P, Ignatchenko V, Grace K, Ursprung C, Kislinger T, Gramolini AO Endoplasmic reticulum protein targeting of phospholamban: a common role for an N-terminal di-arginine motif in ER retention? PLoS One 5: e11496. 20634894 13,16
2010 Sharma PK, Mittal N, Deswal S, Roy N Calorie restriction up-regulates iron and copper transport genes in Saccharomyces cerevisiae. Mol Biosyst 7: 394-402. 21031176 7
2010 Shen HB, Chou KC Gneg-mPLoc: A top-down strategy to enhance the quality of predicting subcellular localization of Gram-negative bacterial proteins. J Theor Biol 264: 326-333. 20093124 9,19
2010 Shen HB, Chou KC Virus-mPLoc: a fusion classifier for viral protein subcellular location prediction by incorporating multiple sites. J Biomol Struct Dyn 28: 175-186. 20645651 9,10
2010 Sheng X, Song X, Yu Y, Niu L, Li S, Li H, Wei C, Liu T, Zhang L, Du L Characterization of microRNAs from sheep (Ovis aries) using computational and experimental analyses. Mol Biol Rep epub Sheep miRNAs 20140706 3,7
2010 Sheyn D, Pelled G, Netanely D, Domany E, Gazit D The Effect of Simulated Microgravity on Human Mesenchymal Stem Cells Cultured in an Osteogenic Differentiation System: A Bioinformatics Study. Tissue Eng Part A 16: 3403-3412. 20807102 7,16
2010 Shi F, Leckie C, MacIntyre G, Haviv I, Boussioutas A, Kowalczyk A A bi-ordering approach to linking gene expression with clinical annotations in gastric cancer. BMC Bioinformatics 11: 477. 20860844 7,16,17
2010 Shi T, Huang H, Barker MS Ancient genome duplications during the evolution of kiwifruit (Actinidia) and related Ericales. Ann Bot 106: 497-504. 20576738 18
2010 Shi W|etAl Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes. Pharmacogenomics J 10: 310-323. 20676069 7
2010 Shi Z, Derow CK, Zhang B Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression. BMC Syst Biol 4: 74. 20507583 7,16,17
2010 Slavkov I, Gjorgjioski V, Struyf J, Dzeroski S Finding explained groups of time-course gene expression profiles with predictive clustering trees. Mol Biosyst 6: 729-740. 20237651 7
2010 Sleumer MC, Mah AK, Baillie DL, Jones SJ Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans. Nucleic Acids Res 38: 2990-3004. 20100800 12,13
2010 Smith WJ, Li Y, Ingham A, Collis E, McWilliam SM, Dixon TJ, Norris BJ, Mortimer SI, Moore RJ, Reverter A A genomics-informed, SNP association study reveals FBLN1 and FABP4 as contributing to resistance to fleece rot in Australian Merino sheep. BMC Vet Res 6: 27. 20500888 7
2010 Smits M|etAl miR-101 is down-regulated in glioblastoma resulting in EZH2-induced proliferation, migration, and angiogenesis. Oncotarget 1: 710-720. 21321380 7,16
2010 Snyder EM, Small CL, Bomgardner D, Xu B, Evanoff R, Griswold MD, Hinton BT Gene expression in the efferent ducts, epididymis, and vas deferens during embryonic development of the mouse. Dev Dyn 239: 2479-2491. 20652947 7
2010 Sohn P, Cox M, Chen D, Serra R Molecular profiling of the developing mouse axial skeleton: a role for Tgfbr2 in the development of the intervertebral disc. BMC Dev Biol 10: 29. Mouse vertebral transcripts 20214815 7
2010 Sokolov A, Ben-Hur A Hierarchical classification of gene ontology terms using the GOstruct method. J Bioinform Comput Biol 8: 357-376. 20401950 9
2010 Som A, Harder C, Greber B, Siatkowski M, Paudel Y, Warsow G, Cap C, Scholer H, Fuellen G The PluriNetWork: An Electronic Representation of the Network Underlying Pluripotency in Mouse, and Its Applications. PLoS One 5: e15165. 21179244 11,17
2010 Sompallae R, Callegari S, Kamranvar SA, Masucci MG Transcription profiling of Epstein-Barr virus nuclear antigen (EBNA)-1 expressing cells suggests targeting of chromatin remodeling complexes. PLoS One 5: e12052. 20706582 7,16
2010 Spade DJ, Griffitt RJ, Liu L, Brown-Peterson NJ, Kroll KJ, Feswick A, Glazer RA, Barber DS, Denslow ND Queen conch (Strombus gigas) testis regresses during the reproductive season at nearshore sites in the Florida Keys. PLoS One 5: e12737. 20856805 3,7
2010 Spin JM, Quertermous T, Tsao PS Chromatin remodeling pathways in smooth muscle cell differentiation, and evidence for an integral role for p300. PLoS One 5: e14301. 21179216 7,16
2010 Stanley D, Bandara A, Fraser S, Chambers PJ, Stanley GA The ethanol stress response and ethanol tolerance of Saccharomyces cerevisiae. J Appl Microbiol 109: 13-24. Saccharomyces genes; ethanol exposure 20070446 7
2010 Stanley D, Chambers PJ, Stanley GA, Borneman A, Fraser S Transcriptional changes associated with ethanol tolerance in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 88: 231-239. 20661734 7
2010 Stanley D, Fraser S, Stanley GA, Chambers PJ Retrotransposon expression in ethanol-stressed Saccharomyces cerevisiae. Appl Microbiol Biotechnol 87: 1447-1454. 20393705 7
2010 Starossom SC, Imitola J, Wang Y, Cao L, Khoury SJ Subventricular zone microglia transcriptional networks. Brain Behav Immun epub 21074605 7,16,17
2010 Stephenson TJ, McIntyre CL, Collet C, Xue GP TaNF-YC11, one of the light-upregulated NF-YC members in Triticum aestivum, is co-regulated with photosynthesis-related genes. Funct Integr Genomics 10: 265-276. Wheat transcripts 20111976 7
2010 Stone MD, Odland RM, McGowan T, Onsongo G, Tang C, Rhodus NL, Jagtap P, Bandhakavi S, Griffin TJ Novel in situ collection of tumor interstitial fluid from a head and neck squamous carcinoma reveals a unique proteome with diagnostic potential. Clin Proteomics 6: 75-82. 20930922 8,16
2010 Strunnikova NV|etAl Transcriptome analysis and molecular signature of human retinal pigment epithelium. Hum Mol Genet 19: 2468-2486. Human retinal pigment epithelium transcripts 20360305 7,16
2010 Sun J, Zhao Z Functional features, biological pathways, and protein interaction networks of addiction-related genes. Chem Biodivers 7: 1153-1162. 20491072 16,17
2010 Sun YX, Jia JP [Microarray analysis of human primary astrocytes activated by beta amyloid peptide and alpha1-antichymotrypsin] Zhonghua Yi Xue Za Zhi 90: 763-767. 20627023 7,16
2010 Suvorov A, Takser L Global gene expression analysis in the livers of rat offspring perinatally exposed to low doses of 2,2',4,4'-tetrabromodiphenyl ether. Environ Health Perspect 118: 97-9102. Rat liver transcripts 20056577 7,16
2010 Tam NN, Szeto CY, Freudenberg JM, Fullenkamp AN, Medvedovic M, Ho SM Research resource: estrogen-driven prolactin-mediated gene-expression networks in hormone-induced prostatic intraepithelial neoplasia. Mol Endocrinol 24: 2207-2217. 20861223 7,16
2010 Taniguchi M, Penner GB, Beauchemin KA, Oba M, Guan LL Comparative analysis of gene expression profiles in ruminal tissue from Holstein dairy cows fed high or low concentrate diets. Comp Biochem Physiol Part D Genomics Proteomics 5: 274-279. 20732839 7
2010 Tanizawa H, Iwasaki O, Tanaka A, Capizzi JR, Wickramasinghe P, Lee M, Fu Z, Noma KI Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation. Nucleic Acids Res 38: 8164-8177. 21030438 7,13,17
2010 Tatebe K, Zeytun A, Ribeiro RM, Hoffmann R, Harrod KS, Forst CV Response network analysis of differential gene expression in human epithelial lung cells during avian influenza infections. BMC Bioinformatics 11: 170. Human lung epithelial cell transcripts 20370926 7,16,17
2010 Tchagang AB, Gawronski A, Berube H, Phan S, Famili F, Pan Y GOAL: a software tool for assessing biological significance of genes groups. BMC Bioinformatics 11: 229. 20459620 10
2010 Teh SL, Chan WS, Abdullah JO, Namasivayam P Development of expressed sequence tag resources for Vanda Mimi Palmer and data mining for EST-SSR. Mol Biol Rep epub 21116862 5,7
2010 Teixeira MC, Raposo LR, Palma M, Sa-Correia I Identification of genes required for maximal tolerance to high-glucose concentrations, as those present in industrial alcoholic fermentation media, through a chemogenomics approach. OMICS 14: 201-210. Saccharomyces genes 20210661 13
2010 Thewes V, Orso F, Jager R, Eckert D, Schafer S, Kirfel G, Garbe S, Taverna D, Schorle H Interference with activator protein-2 transcription factors leads to induction of apoptosis and an increase in chemo- and radiation-sensitivity in breast cancer cells. BMC Cancer 10: 192. 20459791 7,16
2010 Thurlow JK|etAl Spectral clustering of microarray data elucidates the roles of microenvironment remodeling and immune responses in survival of head and neck squamous cell carcinoma. J Clin Oncol 28: 2881-2888. 20458058 7,16
2010 Tino G, Zhao H, Yan H Searching for co-expressed genes in three-color cDNA microarray data using a probabilistic model-based Hough transform. IEEE/ACM Trans Comput Biol Bioinform epub 21116039 7
2010 Tirrell R, Evani U, Berman AE, Mooney SD, Musen MA, Shah NH An ontology-neutral framework for enrichment analysis. AMIA Annu Symp Proc 2010: 797-801. 21347088 10
2010 Tomaszewski M|etAl Genetic architecture of ambulatory blood pressure in the general population: Insights from cardiovascular gene-centric array. Hypertension 56: 1069-1076. 21060006 7,16,18
2010 Torto-Alalibo T|etAl Unifying themes in microbial associations with animal and plant hosts described using the gene ontology. Microbiol Mol Biol Rev 74: 479-503. 21119014 1,3,13
2010 Tran DH, Satou K, Ho TB, Pham TH Computational discovery of miR-TF regulatory modules in human genome. Bioinformation 4: 371-377. 20975901 7
2010 Tsoumani KT, Augustinos AA, Kakani EG, Drosopoulou E, Mavragani-Tsipidou P, Mathiopoulos KD Isolation, annotation and applications of expressed sequence tags from the olive fly, Bactrocera oleae. Mol Genet Genomics 285: 33-45. 20978910 5
2010 Tuju CL, Lu GT, Zeng CQ [Systematic analysis of cis-nested gene pairs in the human genome]. Yi Chuan 32: 914-920. 20870612 18
2010 Uchida K, Nakajima H, Hirai T, Yayama T, Chen KB, Kobayashi S, Roberts S, Johnson WE, Baba H Microarray analysis of expression of cell death-associated genes in rat spinal cord cells exposed to cyclic tensile stresses in vitro. BMC Neurosci 11: 84. 20663127 7
2010 Ueno S|etAl Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak. BMC Genomics 11: 650. 21092232 5
2010 Uhl GR, Drgon T, Johnson C, Ramoni MF, Behm FM, Rose JE Genome wide association for smoking cessation success in a trial of precessation nicotine replacement. Mol Med 16: 513-526. 20811658 13,16
2010 Ulitsky I, Maron-Katz A, Shavit S, Sagir D, Linhart C, Elkon R, Tanay A, Sharan R, Shiloh Y, Shamir R Expander: from expression microarrays to networks and functions. Nat Protoc 5: 303-322. 20134430 7,10
2010 Urbich C|etAl Proteomic characterisation of human early pro-angiogenic cells. J Mol Cell Cardiol 50: 333-336. 21147123 8,16
2010 Valentini G True Path Rule hierarchical ensembles for genome-wide gene function prediction. IEEE/ACM Trans Comput Biol Bioinform epub 20479498 9
2010 Varghese S, Xu H, Bartlett D, Hughes M, Pingpank JF, Beresnev T, Alexander HR Isolated hepatic perfusion with high-dose melphalan results in immediate alterations in tumor gene expression in patients with metastatic ocular melanoma. Ann Surg Oncol 17: 1870-1877. Human ocular melanoma liver metastasis transcripts 20221901 7,16
2010 Varkonyi T|etAl Microarray Profiling Reveals That Placental Transcriptomes of Early-onset HELLP Syndrome and Preeclampsia Are Similar. Placenta 32S1: S21-S29. 20541258 7,16
2010 Veeramani B, Bader JS Predicting functional associations from metabolism using bi-partite network algorithms. BMC Syst Biol 4: 95. 20630077 9,17
2010 Vidal RO, Mondego JM, Pot D, Ambrosio AB, Andrade AC, Pereira LF, Colombo CA, Vieira LG, Carazzolle MF, Pereira GA A high-throughput data mining of single nucleotide polymorphisms in coffea species expressed sequence tags suggests differential homeologous gene expression in the allotetraploid Coffea arabica. Plant Physiol 154: 1053-1066. 20864545 5,7
2010 Vinod MS, Sankararamasubramanian HM, Priyanka R, Ganesan G, Parida A Gene expression analysis of volatile-rich male flowers of dioecious Pandanus fascicularis using expressed sequence tags. J Plant Physiol 167: 914-919. Pandanus fascicularis ESTs 20149480 5
2010 Vock C, Nitz I, Doering F Transcriptom-based identification of a putative role for the human Acyl-CoA-Binding-Protein (ACBP) in vesicular trafficking. Cell Mol Biol (Noisy-le-grand) 56 Suppl: OL1261-1265. Human transcripts 20219168 7,16
2010 Vogl C, Flatt T, Fuhrmann B, Hofmann E, Wallner B, Stiefvater R, Kovarik P, Strobl B, Muller M Transcriptome analysis reveals a major impact of tyrosine kinase 2 (Tyk2) on the expression of interferon responsive and metabolic genes. BMC Genomics 11: 199. Mouse macrophage transcripts 20338026 7,16
2010 Vooder T, Valk K, Kolde R, Roosipuu R, Vilo J, Metspalu A Gene Expression-Based Approaches in Differentiation of Metastases and Second Primary Tumour. Case Rep Oncol 3: 255-261. 20740207 7,16
2010 Walker CG, Meier S, Littlejohn MD, Lehnert K, Roche JR, Mitchell MD Modulation of the maternal immune system by the pre-implantation embryo. BMC Genomics 11: 474. 20707927 7
2010 Wang H, Zhang H, Wong YH, Voolstra C, Ravasi T, B Bajic V, Qian PY Rapid transcriptome and proteome profiling of a non-model marine invertebrate, Bugula neritina. Proteomics 10: 2972-2981. 20540116 7,8
2010 Wang J, Li M, Chen J, Pan Y A Fast Hierarchical Clustering Algorithm for Functional Modules Discovery in Protein Interaction Networks. IEEE/ACM Trans Comput Biol Bioinform epub 20733244 17
2010 Wang J, Yu H, Xie W, Xing Y, Yu S, Xu C, Li X, Xiao J, Zhang Q A global analysis of QTLs for expression variations in rice shoots at the early seedling stage. Plant J 63: 1063-1074. 20626655 7,13
2010 Wang N, Zhao DH, Wu CA, Tian W, Xiao B, Hu JW [Shotgun proteomic analysis of intervertebral disc tissues from fetal and adult subjects] Zhonghua Yi Xue Za Zhi 90: 610-613. 20450784 8,16
2010 Wang WK, Ho CW, Hung KH, Wang KH, Huang CC, Araki H, Hwang CC, Hsu TW, Osada N, Chiang TY Multilocus analysis of genetic divergence between outcrossing Arabidopsis species: evidence of genome-wide admixture. New Phytol 188: 488-500. 20673288 13,18
2010 Wang XW, Luan JB, Li JM, Bao YY, Zhang CX, Liu SS De novo characterization of a whitefly transcriptome and analysis of its gene expression during development. BMC Genomics 11: 400. 20573269 7
2010 Wang Y, Li Z, He C, Wang D, Yuan X, Chen J, Jin J MicroRNAs expression signatures are associated with lineage and survival in acute leukemias. Blood Cells Mol Dis 44: 191-197. Human miRNAs; leukemia 20110180 7,16
2010 Wang Z, Du J, Lam SH, Mathavan S, Matsudaira P, Gong Z Morphological and molecular evidence for functional organization along the rostrocaudal axis of the adult zebrafish intestine. BMC Genomics 11: 392. 20565988 7
2010 Wang Z, Fang B, Chen J, Zhang X, Luo Z, Huang L, Chen X, Li Y De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas). BMC Genomics 11: 726. 21182800 3,7
2010 Wang Z, Libault M, Joshi T, Valliyodan B, Nguyen H, Xu D, Stacey G, Cheng J SoyDB: a knowledge database of soybean transcription factors. BMC Plant Biol 10: 14. 20082720 3,11
2010 Warren AS, Anandakrishnan R, Zhang L Functional bias in molecular evolution rate of Arabidopsis thaliana. BMC Evol Biol 10: 125. 20433764 18
2010 Waterhouse RM, Zdobnov EM, Kriventseva EV Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi. Genome Biol Evol 3: 75-86. 21148284 18
2010 Weekes MP, Antrobus R, Lill JR, Duncan LM, Hor S, Lehner PJ Comparative analysis of techniques to purify plasma membrane proteins. J Biomol Tech 21: 108-115. 20808639 8
2010 Whan V, Hobbs M, McWilliam S, Lynn DJ, Strandberg Lutzow Y, Khatkar M, Barendse W, Raadsma H, Tellam RL Bovine proteins containing poly-glutamine repeats are often polymorphic and enriched for components of transcriptional regulatory complexes. BMC Genomics 11: 654. 21092319 7,13,16
2010 Whistler T, Chiang CF, Lonergan W, Hollier M, Unger ER Implementation of exon arrays: alternative splicing during T-cell proliferation as determined by whole genome analysis. BMC Genomics 11: 496. 20840771 7,16
2010 Wilhelm BT|etAl RNA-seq analysis of two closely related leukemia clones that differ in their self-renewal capacity. Blood 117: e27-38. 20980679 7,16
2010 Wisniewski JR, Nagaraj N, Zougman A, Gnad F, Mann M Brain phosphoproteome obtained by a FASP-based method reveals plasma membrane protein topology. J Proteome Res 9: 3280-3289. 20415495 8
2010 Wiwanitki V Function association of tissue inhibitor of metalloproteinase-1 and malignant melanoma: systomics approach. Acta Dermatovenerol Croat 18: 68. 20361890 7,16
2010 Wollmer MA Cholesterol-related genes in Alzheimer's disease. Biochim Biophys Acta 1801: 762-773. 20580938 13,16
2010 Wong WW|etAl Characterization of the apoptotic response of human leukemia cells to organosulfur compounds. BMC Cancer 10: 351. 20598143 7,16
2010 Wongsurawat T, Leelatanawit R, Thamniemdee N, Uawisetwathana U, Karoonuthaisiri N, Menasveta P, Klinbunga S Identification of testis-relevant genes using in silico analysis from testis ESTs and cDNA microarray in the black tiger shrimp (Penaeus monodon). BMC Mol Biol 11: 55. 20696033 5,7
2010 Wright CM|etAl ADAM28: a potential oncogene involved in asbestos-related lung adenocarcinomas. Genes Chromosomes Cancer 49: 688-698. 20544843 7,16
2010 Wu G, Feng X, Stein L A human functional protein interaction network and its application to cancer data analysis. Genome Biol 11: R53. 20482850 8,16,17
2010 Wu Q, Sun C, Luo H, Li Y, Niu Y, Sun Y, Lu A, Chen S Transcriptome Analysis of Taxus cuspidata Needles Based on 454 Pyrosequencing. Planta Med epub 20862637 5
2010 Wu T, Qin Z, Zhou X, Feng Z, Du Y Transcriptome profile analysis of floral sex determination in cucumber. J Plant Physiol 167: 905-913. Cucumber transcripts 20303197 7
2010 Wu Z, Zhang W, Lu Y, Lu C Transcriptome profiling of zebrafish infected with Streptococcus suis. Microb Pathog 48: 178-187. Zebrafish transcripts 20206250 7
2010 Wylie CJ, Hendricks TJ, Zhang B, Wang L, Lu P, Leahy P, Fox S, Maeno H, Deneris ES Distinct transcriptomes define rostral and caudal serotonin neurons. J Neurosci 30: 670-684. Mouse neuronal transcripts 20071532 7
2010 Xia XQ, McClelland M, Wang Y TabSQL: a MySQL tool to facilitate mapping user data to public databases. BMC Bioinformatics 11: 342. 20573251 10
2010 Xiao J, Jones-Brando L, Talbot CC, Yolken RH Differential effects of three canonical Toxoplasma strains on gene expression in human neuroepithelial cells. Infect Immun 79: 1363-1373. 21149591 7,16,17
2010 Xiao YL, Redman JC, Monaghan EL, Zhuang J, Underwood BA, Moskal WA, Wang W, Wu HC, Town CD High throughput generation of promoter reporter (GFP) transgenic lines of low expressing genes in Arabidopsis and analysis of their expression patterns. Plant Methods 6: 18. 20687964 15
2010 Xie F, Frazier TP, Zhang B Identification and characterization of microRNAs and their targets in the bioenergy plant switchgrass (Panicum virgatum). Planta 232: 417-434. 20461402 3,7
2010 Xie F, Frazier TP, Zhang B Identification, characterization and expression analysis of MicroRNAs and their targets in the potato (Solanum tuberosum). Gene 473: 8-22. 20933063 7
2010 Xie S, Wang F, Yan D, Zhou G, Ye M, Zou H [Application of online two-dimensional separation system using monolithic columns for proteome analysis of human cartilage] Se Pu 28: 140-145. 20556951 8,16
2010 Xiong B, Wu J, Burk DL, Xue M, Jiang H, Shen J BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server. BMC Bioinformatics 11: 47. 20100327 10,11
2010 Xu J, Kelly R, Fang H, Tong W ArrayTrack: a free FDA bioinformatics tool to support emerging biomedical research--an update. Hum Genomics 4: 428-434. 20846933 10
2010 Xu J|etAl MiRNA-miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features. Nucleic Acids Res 39: 825-836. 20929877 17
2010 Xu X|etAl Quantitative proteomics study of breast cancer cell lines isolated from a single patient: Discovery of TIMM17A as a marker for breast cancer. Proteomics 10: 1374-1390. Human breast proteins 20198662 8,16
2010 Xu Y, Zhang M, Wang Y, Kadambi P, Dave V, Lu LJ, Whitsett JA A systems approach to mapping transcriptional networks controlling surfactant homeostasis. BMC Genomics 11: 451. 20659319 7,16,17
2010 Xu YD, Cui JM, Wang Y, Yin LM, Gao CK, Liu YY, Yang YQ The early asthmatic response is associated with glycolysis, calcium binding and mitochondria activity as revealed by proteomic analysis in rats. Respir Res 11: 107. 20691077 8,16
2010 Xu YZ, Thuraisingam T, Morais DA, Rola-Pleszczynski M, Radzioch D Nuclear translocation of {beta}-actin is involved in transcriptional regulation during macrophage differentiation of HL-60 cells. Mol Biol Cell 21: 811-820. Human leukemia cell line genes 20053683 7,16
2010 Yang Y, Lu BL Protein subcellular multi-localization prediction using a min-max modular support vector machine. Int J Neural Syst 20: 13-28. 20180250 9,13
2010 Yang Y, Qu Y, Lu X Global gene expression analysis of the effects of gold nanoparticles on human dermal fibroblasts. J Biomed Nanotechnol 6: 234-246. 21179940 7,16
2010 Yao JQ, Liu QH, Chen X, Yang Q, Xu ZY, Hu F, Wang L, Li JM Hsp90 inhibitor 17-allylamino-17-demethoxygeldanamycin inhibits the proliferation of ARPE-19 cells. J Biomed Sci 17: 30. 20416086 7,17
2010 Young MD, Wakefield MJ, Smyth GK, Oshlack A Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol 11: R14. 20132535 10
2010 Young ND|etAl Unlocking the transcriptomes of two carcinogenic parasites, Clonorchis sinensis and Opisthorchis viverrini. PLoS Negl Trop Dis 4: e719. 20582164 7,16
2010 Yu G, Li F, Qin Y, Bo X, Wu Y, Wang S GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics 26: 976-978. 20179076 10
2010 Yu J, Yin P, Liu F, Cheng G, Guo K, Lu A, Zhu X, Luan W, Xu J Effect of heat stress on porcine small intestine: A morphological and gene expression study. Comp Biochem Physiol A Mol Integr Physiol 156: 119-128. Porcine intestinal transcripts 20096800 7
2010 Yu L, Gao L, Li K A method based on local density and random walks for complexes detection in protein interaction networks. J Bioinform Comput Biol 8: 47-62. 21155019 8,17
2010 Yu M, Xiang F, Beyer RP, Farin FM, Bammler TK, Chin MT Transcription factor CHF1/Hey2 regulates specific pathways in serum stimulated primary cardiac myocytes: Implications for cardiac hypertrophy. Curr Genomics 11: 287-296. 21119893 7,16
2010 Yu Y, Xu T, Yu Y, Hao P, Li X Association of tissue lineage and gene expression: conservatively and differentially expressed genes define common and special functions of tissues. BMC Bioinformatics 11 Suppl 11: S1. 21172044 7,13
2010 Zeisberger SM, Zoller S, Riegel M, Chen S, Krenning G, Harmsen MC, Sachinidis A, Zisch AH Optimization of the culturing conditions of human umbilical cord blood-derived endothelial colony-forming cells under xeno-free conditions applying a transcriptomic approach. Genes Cells 15: 671-687. 20497237 7,16
2010 Zeng J, Zhu S, Liew AW, Yan H Multiconstrained gene clustering based on generalized projections. BMC Bioinformatics 11: 164. 20356386 13
2010 Zeng S, Xiao G, Guo J, Fei Z, Xu Y, Roe BA, Wang Y Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim. BMC Genomics 11: 94. Epimedium sagittatum ESTs 20141623 5
2010 Zhang F, Chen JY Discovery of pathway biomarkers from coupled proteomics and systems biology methods. BMC Genomics 11 Suppl 2: S12. 21047379 8,13,16,17
2010 Zhang H, Gao XS, Zhao J, Xiong W, Zhang M, Li HZ, Zhou DM, Jin X, Zhang DS Differential gene expression profiles of DNA repair genes in esophageal cancer cells after X-ray irradiation. Chin J Cancer 29: 865-872. 20868556 7,16
2010 Zhang J, Li F, Jiang H, Yu Y, Liu C, Li S, Wang B, Xiang J Proteomic analysis of differentially expressed proteins in lymphoid organ of Fenneropenaeus chinensis response to Vibrio anguillarum stimulation. Fish Shellfish Immunol 29: 186-194. 20394824 8
2010 Zhang L|etAl Plasma membrane proteome analysis of the early effect of alcohol on liver: implications for alcoholic liver disease. Acta Biochim Biophys Sin (Shanghai) 43: 19-29. 21134885 8,16
2010 Zhang S, Cao J, Kong YM, Scheuermann RH GO-Bayes: Gene Ontology-based over-representation analysis using a Bayesian approach. Bioinformatics 26: 905-911. 20176581 7,13,17
2010 Zhang SO, Mathur S, Hattem G, Tassy O, Pourquie O Sex-dimorphic gene expression and ineffective dosage compensation of Z-linked genes in gastrulating chicken embryos. BMC Genomics 11: 13. Chicken primitive streak transcripts 20055996 7
2010 Zhang X, Huang B, Zhou X, Chen C Quantitative proteomic analysis of S-nitrosated proteins in diabetic mouse liver with ICAT switch method. Protein Cell 1: 675-687. 21203939 8,16
2010 Zhang Y, De S, Garner JR, Smith K, Wang SA, Becker KG Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information. BMC Med Genomics 3: 1. 20092628 15
2010 Zhang Y, Liu X, Zhang W, Han R Differential gene expression of the honey bees Apis mellifera and A. cerana induced by Varroa destructor infection. J Insect Physiol 56: 1207-1218. Honey bee transcripts; varroa mite infection 20346951 7
2010 Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration. PLoS One 5: e10268. 20422009 7,16,17
2010 Zhang Y, Zan L, Wang H Screening candidate genes related to tenderness trait in Qinchuan cattle by genome array. Mol Biol Rep 38: 2007-2014. 20848214 7
2010 Zheng HT, Borchert C, Jiang Y A knowledge-driven approach to biomedical document conceptualization. Artif Intell Med 49: 67-78. 20371168 12
2010 Zhou X, Han P, Li J, Zhang X, Huang B, Ruan HQ, Chen C ESNOQ, proteomic quantification of endogenous S-nitrosation. PLoS One 5: e10015. 20368813 8,13
2010 Zhu LJ, Gazin C, Lawson ND, Pages H, Lin SM, Lapointe DS, Green MR ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics 11: 237. 20459804 10
2010 Zu X, Yu L, Sun Y, Tian J, Liu F, Sun Q, He S, Sun G, Luo W, Jiang Y Global mapping of ZBTB7A transcription factor binding sites in HepG2 cells. Cell Mol Biol Lett 15: 260-271. Human cell line transcripts 20336405 7,16
2010 Zwenger SR, Alsaggaf R, Basu C Does expressed sequenced tags (EST) library of Salsola iberica (tumbleweed) help to understand plant responses to environmental stresses? Plant Signal Behav epub 20935479 5
2010 [No Authors Listed] In this issue. Proteomics epub 20552582 8
2010 [No authors listed] [Somatic polyploidy associated metabolic changes revealed by modular biology] Tsitologiia 52: 52-62. 20302017 7,13,17
2010 de Lima Morais DA, Harrison PM Large-scale evidence for conservation of NMD candidature across mammals. PLoS One 5: e11695. 20657786 13,18
2010 van Dartel DA, Pennings JL, Robinson JF, Kleinjans JC, Piersma AH Discriminating classes of developmental toxicants using gene expression profiling in the embryonic stem cell test. Toxicol Lett 201: 143-151. 21195148 7,16
2010 van Lunteren E, Spiegler S, Moyer M Differential expression of lipid and carbohydrate metabolism genes in upper airway versus diaphragm muscle. Sleep 33: 363-370. Rat muscle transcripts 20337195 7,16
2010 van den Berg BH, McCarthy FM, Lamont SJ, Burgess SC Re-annotation is an essential step in systems biology modeling of functional genomics data. PLoS One 5: e10642. 20498845 1,3,7,17
2010 van der Zande M, Walboomers XF, Brannvall M, Olalde B, Jurado MJ, Alava JI, Jansen JA Genetic profiling of osteoblast-like cells cultured on a novel bone reconstructive material, consisting of poly-L-lactide, carbon nanotubes and microhydroxyapatite, in the presence of bone morphogenetic protein-2. Acta Biomater 6: 4352-4360. 20601234 7,16
2010 von Toerne C, Sieg C, Kaufmann U, Diedrichs-Mohring M, Nelson PJ, Wildner G Effector T cells driving monophasic vs. relapsing/remitting experimental autoimmune uveitis show unique pathway signatures. Mol Immunol 48: 272-280. 20727594 7,16
2011 Agarwal SM, Raghav D, Singh H, Raghava GP CCDB: a curated database of genes involved in cervix cancer. Nucleic Acids Res 39: D975-979. 21045064 11,16
2011 Almeida LM, Basu U, Khaniya B, Taniguchi M, Williams JL, Moore SS, Guan le L Gene expression in the medulla following oral infection of cattle with bovine spongiform encephalopathy. J Toxicol Environ Health A 74: 110-126. 21218340 7
2011 Arighi CN A tutorial on protein ontology resources for proteomic studies. Methods Mol Biol 694: 77-90. 21082429 15
2011 Arnaiz O, Sperling L ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia. Nucleic Acids Res 39: D632-636. 20952411 4,11
2011 Basu U, Almeida L, Olson NE, Meng Y, Williams JL, Moore SS, Guan le L Transcriptome analysis of the medulla tissue from cattle in response to bovine spongiform encephalopathy using digital gene expression tag profiling. J Toxicol Environ Health A 74: 127-137. 21218341 7
2011 Beck D, Ayers S, Wen J, Brandl MB, Pham TD, Webb P, Chang CC, Zhou X Integrative analysis of next generation sequencing for small non-coding RNAs and transcriptional regulation in Myelodysplastic Syndromes. BMC Med Genomics 4: 19. 21342535 7,16
2011 Beisvag V|etAl Contributions of the EMERALD project to assessing and improving microarray data quality. Biotechniques 50: 27-31. 21231919 15
2011 Blanca J, Canizares J, Roig C, Ziarsolo P, Nuez F, Pico B Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genomics 12: 104. 21310031 5
2011 Boekel J, Kallskog O, Ryden-Aulin M, Rhen M, Richter-Dahlfors A Comparative tissue transcriptomics reveal prompt inter-organ communication in response to local bacterial kidney infection. BMC Genomics 12: 123. 21338499 7,16
2011 Boltana S, Reyes-Lopez F, Morera D, Goetz F, Mackenzie SA Divergent responses to peptidoglycans derived from different E. coli serotypes influence inflammatory outcome in trout, Oncorhynchus mykiss, macrophages. BMC Genomics 12: 34. 21235753 7
2011 Chatziioannou AA, Moulos P Exploiting statistical methodologies and controlled vocabularies for prioritized functional analysis of genomic experiments: the StRAnGER web application. Front Neurosci 5: 8. 21293737 10,13
2011 Chen XW, Jeong JC, Dermyer P KUPS: constructing datasets of interacting and non-interacting protein pairs with associated attributions. Nucleic Acids Res 39: D750-754. 20952400 8,11,17
2011 Cheng PJ, Wang TH, Huang SY, Kao CC, Lu JH, Hsiao CH, Steven Shaw SW Differential proteomics analysis of amniotic fluid in pregnancies of increased nuchal translucency with normal karyotype. Prenat Diagn epub 21312199 8,16
2011 Cheuk BL, Cheng SW Differential expression of elastin assembly genes in patients with Stanford Type A aortic dissection using microarray analysis. J Vasc Surg epub 21276682 7,16
2011 Childers CP|etAl Bovine Genome Database: integrated tools for genome annotation and discovery. Nucleic Acids Res 39: D830-834. 21123190 3,11
2011 Chum WW, Kwan HS, Au CH, Kwok IS, Fung YW Cataloging and profiling genes expressed in Lentinula edodes fruiting body by massive cDNA pyrosequencing and LongSAGE. Fungal Genet Biol epub 21281728 3,7
2011 Davis AP, King BL, Mockus S, Murphy CG, Saraceni-Richards C, Rosenstein M, Wiegers T, Mattingly CJ The Comparative Toxicogenomics Database: update 2011. Nucleic Acids Res 39: D1067-1072. 20864448 11
2011 Echt CS, Saha S, Krutovsky KV, Wimalanathan K, Erpelding JE, Liang C, Nelson CD An annotated genetic map of loblolly pine based on microsatellite and cDNA markers. BMC Genet 12: 17. 21269494 5
2011 Fang X, Yoon JG, Li L, Tsai YS, Zheng S, Hood L, Goodlett DR, Foltz G, Lin B Landscape of the SOX2 protein-protein interactome. Proteomics 11: 921-934. 21280222 8,16,17
2011 Fernandino JI|etAl Analysis of sexually dimorphic expression of genes at early gonadogenesis of pejerrey Odontesthes bonariensis using a heterologous microarray. Sex Dev epub 21325793 7
2011 Fokas E, You A, Juricko J, Engenhart-Cabillic R, An HX Genetic alterations after carbon ion irradiation in human lung adenocarcinoma cells. Int J Oncol 38: 161-168. 21109937 7,16
2011 Folly BB, Weffort-Santos AM, Fathman CC, Soares LR Dengue-2 structural proteins associate with human proteins to produce a coagulation and innate immune response biased interactome. BMC Infect Dis 11: 34. 21281507 8,16,17
2011 Freitas AA, Vasieva O, de Magalhaes JP A data mining approach for classifying DNA repair genes into ageing-related or non-ageing-related. BMC Genomics 12: 27. 21226956 12,16
2011 Fu CH, Chen YW, Hsiao YY, Pan ZJ, Liu ZJ, Huang YM, Tsai WC, Chen HH OrchidBase: A collection of sequences of transcriptome derived from orchids. Plant Cell Physiol 52: 238-243. 21245031 5,11
2011 Gabert BJ, Kultz D Osmoprotective proteome adjustments in mouse kidney papilla. Biochim Biophys Acta 1814: 435-448. 21236367 8
2011 Gan L, Liu X, Xiang Z, He N Microarray-based gene expression profiles of silkworm brains. BMC Neurosci 12: 8. 21247463 7
2011 Gasparini F, Shimeld SM Analysis of a botryllid enriched-full-lenght cDNA library: insight into the evolution of splice leader trans-splicing in tunicates. Dev Genes Evol epub 21331664 5
2011 Goetz S, Arnold R, Sebastian-Leon P, Martin-Rodriguez S, Tischler P, Jehl MA, Dopazo J, Rattei T, Conesa A B2G-FAR, a species centered GO annotation repository. Bioinformatics epub 21335611 3,11
2011 Gonsalves SE, Moses AM, Razak Z, Robert F, Westwood JT Whole-genome analysis reveals that active heat shock factor binding sites are mostly associated with non-heat shock genes in Drosophila melanogaster. PLoS One 6: e15934. 21264254 7,13
2011 Gremse M, Chang A, Schomburg I, Grote A, Scheer M, Ebeling C, Schomburg D The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. Nucleic Acids Res 39: D507-513. 21030441 15
2011 Gutierrez-Roelens I, Galant C, Theate I, Lories R, Durez P, Nzeusseu-Toukap A, Van den Eynde B, Houssiau F, Lauwerys B Rituximab treatment induces the expression of genes involved in healing processes in the rheumatoid arthritis synovium. Arthritis Rheum epub 21337318 7,16
2011 Ha M, Ng D, Li WH, Chen ZJ Coordinated histone modifications are associated with gene expression variation within and between species. Genome Res epub 21324879 7,13
2011 Huang T, Wan S, Xu Z, Zheng Y, Feng KY, Li HP, Kong X, Cai YD Analysis and prediction of translation rate based on sequence and functional features of the mRNA. PLoS One 6: e16036. 21253596 13,19
2011 Inostroza-Ponta M, Berretta R, Moscato P QAPgrid: A two level QAP-based approach for large-scale data analysis and visualization. PLoS One 6: e14468. 21267077 13
2011 Jorgensen HB, Sorensen P, Cooper GA, Lorenzen E, Lorenzen N, Hansen MH, Koop BF, Henryon M General and family-specific gene expression responses to viral hemorrhagic septicaemia virus infection in rainbow trout (Oncorhynchus mykiss). Mol Immunol epub 21345492 7
2011 Kang TH, Guibinga GH, Friedmann T HPRT deficiency coordinately dysregulates canonical Wnt and presenilin-1 signaling: A neuro-developmental regulatory role for a housekeeping gene? PLoS One 6: e16572. 21305049 7,8,16
2011 Keilwagen J, Grau J, Paponov IA, Posch S, Strickert M, Grosse I De-novo discovery of differentially abundant transcription factor binding sites including their positional preference. PLoS Comput Biol 7: e1001070. 21347314 7,13
2011 Kendler KS, Kalsi G, Holmans PA, Sanders AR, Aggen SH, Dick DM, Aliev F, Shi J, Levinson DF, Gejman PV Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample. Alcohol Clin Exp Res epub 21314694 13,16
2011 Kim YH|etAl Epigenomic Analysis of Aberrantly Methylated Genes in Colorectal Cancer Identifies Genes Commonly Affected by Epigenetic Alterations. Ann Surg Oncol epub 21298349 7,13,16
2011 Klein C, Troedsson MH Transcriptional Profiling of Equine Conceptuses Reveals New Aspects of Embryo-Maternal Communication in the Horse. Biol Reprod epub 21209420 7
2011 Knox C|etAl DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs. Nucleic Acids Res 39: D1035-1041. 21059682 11
2011 Lee JH, Gonzalez GH Towards integrative gene prioritization in Alzheimer's disease. Pac Symp Biocomput epub 21121028 7,8,16,17
2011 Liao M, Zou S, Weng J, Hou L, Yang L, Zhao Z, Bao J, Jing Z A microRNA profile comparison between thoracic aortic dissection and normal thoracic aorta indicates the potential role of microRNAs in contributing to thoracic aortic dissection pathogenesis. J Vasc Surg epub 21334170 7,13,16
2011 Liu H, Liu W, Liao Y, Cheng L, Liu Q, Ren X, Shi L, Tu X, Wang QK, Guo AY CADgene: a comprehensive database for coronary artery disease genes. Nucleic Acids Res 39: D991-996. 21045063 11,16
2011 Liu Z, Cao J, Gao X, Zhou Y, Wen L, Yang X, Yao X, Ren J, Xue Y CPLA 1.0: an integrated database of protein lysine acetylation. Nucleic Acids Res 39: D1029-1034. 21059677 11
2011 Maglott D, Ostell J, Pruitt KD, Tatusova T Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 39: D52-57. 21115458 11
2011 Martyniuk CJ, Spade DJ, Blum JL, Kroll KJ, Denslow ND Methoxychlor affects multiple hormone signaling pathways in the largemouth bass (Micropterus salmoides) liver. Aquat Toxicol 101: 483-492. 21276474 7
2011 Masuno K, Haldar SM, Jeyaraj D, Mailloux C, Huang X, Panettieri Jr RA, Jain MK, Gerber AN Expression profiling identifies Klf15 as a glucocorticoid target that regulates airway hyperresponsiveness. Am J Respir Cell Mol Biol epub 21257922 7,16
2011 McCarthy FM|etAl AgBase: supporting functional modeling in agricultural organisms. Nucleic Acids Res 39: D497-506. 21075795 1,3,10,11
2011 McDermott JE, Archuleta M, Stevens SL, Stenzel-Poore MP, Sanfilippo A Defining the players in higher-order networks: predictive modeling for reverse engineering functional influence networks. Pac Symp Biocomput epub 21121059 16,17
2011 McGarvey PB, Zhang J, Natale DA, Wu CH, Huang H Protein-centric data integration for functional analysis of comparative proteomics data. Methods Mol Biol 694: 323-339. 21082443 8
2011 Mei S, Wang F, Zhou S Gene ontology based transfer learning for protein subcellular localization. BMC Bioinformatics 12: 44. 21284890 9
2011 Mittal P, Romero R, Tarca AL, Draghici S, Nhan-Chang CL, Chaiworapongsa T, Hotra J, Gomez R, Kusanovic JP, Lee DC, Kim CJ, Hassan SS A molecular signature of an arrest of descent in human parturition. Am J Obstet Gynecol 204: 177.e15-33. 21284969 7,16
2011 Mohammadi A, Saraee MH, Salehi M Identification of disease-causing genes using microarray data mining and Gene Ontology. BMC Med Genomics 4: 12. 21269461 7,12,16
2011 Molina C|etAl The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE. BMC Plant Biol 11: 31. 21320317 7
2011 Mondal M, Schilling B, Folger J, Steibel JP, Buchnick H, Zalman Y, Ireland JJ, Meidan R, Smith GW Deciphering the luteal transcriptome: Potential mechanisms mediating stage specific luteolytic response of the corpus luteum to prostaglandin F2{alpha} Physiol Genomics epub 21325060 7
2011 Mondego JM|etAl An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora. BMC Plant Biol 11: 30. 21303543 5,7
2011 Nepomuceno JA, Troncoso A, Aguilar-Ruiz JS Biclustering of gene expression data by correlation-based scatter search. BioData Min 4: 3. 21261986 7
2011 Noack F, Ribbat-Idel J, Thorns C, Chiriac A, Axt-Fliedner R, Diedrich K, Feller AC miRNA expression profiling in formalin-fixed and paraffin-embedded placental tissue samples from pregnancies with severe preeclampsia. J Perinat Med epub 21309633 7,16
2011 Panhuis TM, Broitman-Maduro G, Uhrig J, Maduro M, Reznick DN Analysis of expressed sequence tags from the placenta of the live-bearing fish Poeciliopsis (Poeciliidae). J Hered epub 21339338 5
2011 Park D, Singh R, Baym M, Liao CS, Berger B IsoBase: a database of functionally related proteins across PPI networks. Nucleic Acids Res 39: D295-300. 21177658 11,17,18
2011 Parkinson H|etAl ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res 39: D1002-1004. 21071405 15
2011 Pfister S, Jones VJ, Power M, Truisi GL, Khoo PL, Steiner KA, Kanai-Azuma M, Kanai Y, Tam PP, Loebel DA Sox17-dependent gene expression and early heart and gut development in Sox17-deficient mouse embryos. Int J Dev Biol epub 21305474 7
2011 Posekany A, Felsenstein K, Sykacek P Biological assessment of robust noise models in microarray data analysis. Bioinformatics epub 21252077 7
2011 Prat Y, Fromer M, Linial N, Linial M Recovering key biological constituents through sparse representation of gene expression. Bioinformatics 27: 655-661. 21258061 7,19
2011 Rastogi S, Rost B LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana. Nucleic Acids Res 39: D230-234. 21071420 11
2011 Redell JB, Zhao J, Dash PK Altered expression of miRNA-21 and its targets in the hippocampus after traumatic brain injury. J Neurosci Res 89: 212-221. 21162128 7,16
2011 Risling M, Ochsman T, Carlstedt T, Linda H, Plantman S, Rostami E, Angeria M, Skold MK On acute gene expression changes after ventral root replantation. Front Neurol 1: 159. 21228913 7,16
2011 Rogers ED, Henry TB, Twiner MJ, Gouffon JS, McPherson JT, Boyer GL, Sayler GS, Wilhelm SW Global gene expression profiling in larval zebrafish exposed to microcystin-LR and microcystis reveals endocrine disrupting effects of Cyanobacteria. Environ Sci Technol epub 21280650 7,16
2011 Rouard M, Guignon V, Aluome C, Laporte MA, Droc G, Walde C, Zmasek CM, Perin C, Conte MG GreenPhylDB v2.0: comparative and functional genomics in plants. Nucleic Acids Res 39: D1095-1102. 20864446 10,11
2011 Schindelman G, Fernandes JS, Bastiani CA, Yook K, Sternberg PW Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community. BMC Bioinformatics 12: 32. 21261995 1,15
2011 Scott MS, Boisvert FM, Lamond AI, Barton GJ PNAC: a protein nucleolar association classifier. BMC Genomics 12: 74. 21272300 8,9,13
2011 Smoot M, Ono K, Ideker T, Maere S PiNGO : a Cytoscape plugin to find candidate genes in biological networks. Bioinformatics epub 21278188 10,17
2011 Stephenson TJ, McIntyre CL, Collet C, Xue GP TaNF-YB3 is involved in the regulation of photosynthesis genes in Triticum aestivum. Funct Integr Genomics epub 21327447 7
2011 Sun PG, Gao L, Han S Prediction of human disease-related gene clusters by clustering analysis. Int J Biol Sci 7: 61-73. 21278917 16,17,19
2011 Sun X, Mei S, Tao H, Wang G, Su L, Jiang S, Deng C, Xiong Y, Li F Microarray profiling for differential gene expression in PMSG-hCG stimulated preovulatory ovarian follicles of Chinese Taihu and Large White sows. BMC Genomics 12: 111. 21324170 7
2011 Tan M, Alshalalfa M, Alhajj R, Polat F Influence of prior knowledge in constraint-based learning of gene regulatory networks. IEEE/ACM Trans Comput Biol Bioinform 8: 130-142. 21071802 7,17
2011 Taylor RC, Sanfilippo A, McDermott JE, Baddeley B, Riensche R, Jensen R, Verhagen M, Pustejovsky J Enriching regulatory networks by bootstrap learning using optimised GO-based gene similarity and gene links mined from PubMed abstracts. Int J Comput Biol Drug Des 4: 56-82. 21330694 12,17
2011 Templin T, Amundson SA, Brenner DJ, Smilenov LB Whole mouse blood microRNA as biomarkers for exposure to gamma-rays and (56)Fe ion. Int J Radiat Biol epub 21271940 7,16
2011 Trehanpati N, Sukriti S, Geffers R, Hissar S, Riese P, Toepfer T, Guzman CA, Sarin SK gene expression profiles of T cells from hepatitis E virus infected patients in acute and resolving phase. J Clin Immunol epub 21287396 7,16
2011 Turcan S, Vetter DE, Maron JL, Wei X, Slonim DK Mining functionally relevant gene sets for analyzing physiologically novel clinical expression data. Pac Symp Biocomput epub 21121032 7,16,17,19
2011 Twine NA, Janitz K, Wilkins MR, Janitz M Whole transcriptome sequencing reveals gene expression and splicing differences in brain regions affected by Alzheimer's disease. PLoS One 6: e16266. 21283692 7,13,16
2011 Villeneuve C, Baricault L, Canelle L, Barboule N, Racca C, Monsarrat B, Magnaldo T, Larminat F Mitochondrial proteomic approach reveals GAL7 as a novel BCL-2 binding protein in human cells. Mol Biol Cell epub 21289092 8,16
2011 Virok DP, Simon D, Bozso Z, Rajko R, Datki Z, Balint E, Szegedi V, Janaky T, Penke B, Fulop L Protein array based interactome analysis of amyloid-beta indicates an inhibition of protein translation. J Proteome Res epub 21244100 8,16
2011 Wang JH|etAl Modeling the cumulative genetic risk for multiple sclerosis from genome wide association data. Genome Med 3: 3. 21244703 13,16
2011 Wang L, Huang J, Jiang M, Sun L Survivin (BIRC5) cell cycle computational network in human no-tumor hepatitis/cirrhosis and hepatocellular carcinoma transformation. J Cell Biochem epub 21312234 7,16,17
2011 Wissler L, Codoner FM, Gu J, Reusch TB, Olsen JL, Procaccini G, Bornberg-Bauer E Back to the Sea twice: identifying candidate plant genes for molecular evolution to marine life. BMC Evol Biol 11: 8. 21226908 13,18
2011 Wu P, Wang X, Qin GX, Liu T, Jiang YF, Li MW, Guo XJ Microarray analysis of the gene expression profile in the midgut of silkworm infected with cytoplasmic polyhedrosis virus. Mol Biol Rep 38: 333-341. Silkworm transcripts 20349281 7
2011 Wu XM, Shao XQ, Meng XX, Zhang XN, Zhu L, Liu SX, Lin J, Xiao HS Genome-wide analysis of microRNA and mRNA expression signatures in hydroxycamptothecin-resistant gastric cancer cells. Acta Pharmacol Sin 32: 259-269. 21293479 7,16
2011 Xiao R, Power RF, Mallonee D, Crowdus C, Brennan KM, Ao T, Pierce JL, Dawson KA A comparative transcriptomic study of vitamin E and an algae-based antioxidant as antioxidative agents: Investigation of replacing vitamin E with the algae-based antioxidant in broiler diets. Poult Sci 90: 136-146. 21177453 7
2011 Yang B, Sayers S, Xiang Z, He Y Protegen: a web-based protective antigen database and analysis system. Nucleic Acids Res 39: D1073-1078. 20959289 15
2011 Yang X, Ye Y, Wang G, Huang H, Yu D, Liang S VeryGene: linking tissue-specific genes to diseases, drugs and beyond for knowledge discovery. Physiol Genomics epub 21245417 11
2011 Yu Y, Yuan D, Liang S, Li X, Wang X, Lin Z, Zhang X Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC1 population between Gossypium hirsutum and G. barbadense. BMC Genomics 12: 15. 21214949 5
2011 Zeeberg BR|etAl RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis. BMC Bioinformatics 12: 52. 21310028 7,8,10
2011 Zhang H, Jin J, Tang L, Zhao Y, Gu X, Gao G, Luo J PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database. Nucleic Acids Res 39: D1114-1117. 21097470 11
2011 Zhou Q, Ching AK, Leung WK, Szeto CY, Ho SM, Chan PK, Yuan YF, Lai PB, Yeo W, Wong N Novel therapeutic potential in targeting microtubules by nanoparticle albumin-bound paclitaxel in hepatocellular carcinoma. Int J Oncol 38: 721-731. 21240457 7,16
2011 de Lima Morais DA, Fang H, Rackham OJ, Wilson D, Pethica R, Chothia C, Gough J SUPERFAMILY 1.75 including a domain-centric gene ontology method. Nucleic Acids Res 39: D427-434. 21062816 11
2011 du Plessis L, Skunca N, Dessimoz C The what, where, how and why of gene ontology--a primer for bioinformaticians. Brief Bioinform epub 21330331 2