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	Unpublished		http://www.geneontology.org/gene.ontology.discussion.shtml|full				1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 <em>Dictyostelium discoideum</em>.	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 Ontology<sup>TM</sup> Consortium	The Plant Ontology<sup>TM</sup> 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&amp;type=&amp;item=&amp;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&amp;type=&amp;item=&amp;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
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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
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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	Cor&#224; 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
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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
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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
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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
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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
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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
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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
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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
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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
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2004	Midford PE	Ontologies for behavior.	Bioinformatics	20: 3700-3701.			15284105		15
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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
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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
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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
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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
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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
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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
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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
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2004	Prlic A, Domingues FS, Lackner P, Sippl MJ	WILMA-automated annotation of protein sequences.	Bioinformatics	20: 127-128.			14693821		9
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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
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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
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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
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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
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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
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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
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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
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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
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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
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2005	Bard JB	Anatomics: the intersection of anatomy and bioinformatics.	J Anat	206: 1-16.			15679867		15
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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
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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
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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
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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
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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 &amp; 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
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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 &amp; 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 &amp; 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 &amp; 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
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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
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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
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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
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2010	Katara P, Grover A, Kuntal H, Sharma V	In silico prediction of drug targets in Vibrio cholerae.	Protoplasma	epub			21174131		7,19
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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