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GoMiner: a resource for biological interpretation of genomic and proteomic data.
Zeeberg BR, Feng W, Wang G, Wang MD, Fojo AT, Sunshine M, Narasimhan S, Kane DW, Reinhold WC, Lababidi S, Bussey KJ, Riss J, Barrett JC, Weinstein JN
Genome Biol 2003, 4:R28
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1.


Research article    
Glucocorticoids with different chemical structures but similar glucocorticoid receptor potency regulate subsets of common and unique genes in human trabecular meshwork cells
Nehmé A, Lobenhofer EK, Stamer WD, Edelman JL
BMC Medical Genomics 2009, 2:58 (10 September 2009)
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Research    
Identification of secondary targets of N-containing bisphosphonates in mammalian cells via parallel competition analysis of the barcoded yeast deletion collection
Bivi N, Romanello M, Harrison R, Clarke I, Hoyle DC, Moro L, Ortolani F, Bonetti A, Quadrifoglio F, Tell G, Delneri D
Genome Biology 2009, 10:R93 (10 September 2009)
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Software    
SNAD: sequence name annotation-based designer
Sidorov IA, Reshetov DA, Gorbalenya AE
BMC Bioinformatics 2009, 10:251 (14 August 2009)
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Research article    
Distinct patterns of gene and protein expression elicited by organophosphorus pesticides in Caenorhabditis elegans
Lewis JA, Szilagyi M, Gehman E, Dennis WE, Jackson DA
BMC Genomics 2009, 10:202 (29 April 2009)
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Research article    
Gene set internal coherence in the context of functional profiling
Montaner D, Minguez P, Al-Shahrour F, Dopazo J
BMC Genomics 2009, 10:197 (27 April 2009)
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6.


Method    
Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure
Thomas R, Gohlke JM, Stopper GF, Parham FM, Portier CJ
Genome Biology 2009, 10:R44 (24 April 2009)
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7.


Research    
Early cellular signaling responses to axonal injury
Lukas TJ, Wang AL, Yuan M, Neufeld AH
Cell Communication and Signaling 2009, 7:5 (13 March 2009)
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8.


Methodology    
GO Explorer: A gene-ontology tool to aid in the interpretation of shotgun proteomics data
Carvalho PC, Fischer JSG, Chen EI, Domont GB, Carvalho MGC, Degrave WM, Yates JR, Barbosa VC
Proteome Science 2009, 7:6 (24 February 2009)
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Research article    
Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation
Huang AC, Hu L, Kauffman SA, Zhang W, Shmulevich I
BMC Systems Biology 2009, 3:20 (18 February 2009)
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10.


Software    
GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists
Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z
BMC Bioinformatics 2009, 10:48 (3 February 2009)
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Research    
A protein interaction based model for schizophrenia study
Hsu PC, Yang UC, Shih KH, Liu CM, Liu YL, Hwu HG
BMC Bioinformatics 2008, 9(Suppl 12):S23 (12 December 2008)
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12.


Research article    
Protein evolution in deep sea bacteria: an analysis of amino acids substitution rates
Campanaro S, Treu L, Valle G
BMC Evolutionary Biology 2008, 8:313 (13 November 2008)
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13.


Research article    
Transcriptomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in liver: Comparison of rat and mouse
Boutros PC, Yan R, Moffat ID, Pohjanvirta R, Okey AB
BMC Genomics 2008, 9:419 (16 September 2008)
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14.


Research    
Whole genome expression and biochemical correlates of extreme constitutional types defined in Ayurveda
Prasher B, Negi S, Aggarwal S, Mandal AK, Sethi TP, Deshmukh SR, Purohit SG, Sengupta S, Khanna S, Mohammad F, Garg G, Brahmachari SK, Indian Genome Variation Consortium , Mukerji M
Journal of Translational Medicine 2008, 6:48 (9 September 2008)
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15.


Research    
Susceptibility to glaucoma: differential comparison of the astrocyte transcriptome from glaucomatous African American and Caucasian American donors
Lukas TJ, Miao H, Chen L, Riordan SM, Li W, Crabb AM, Wise A, Du P, Lin SM, Hernandez MR
Genome Biology 2008, 9:R111 (9 July 2008)
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16.


Method    
Gene expression response in target organ and whole blood varies as a function of target organ injury phenotype
Lobenhofer EK, Auman JT, Blackshear PE, Boorman GA, Bushel PR, Cunningham ML, Fostel JM, Gerrish K, Heinloth AN, Irwin RD, Malarkey DE, Merrick BA, Sieber SO, Tucker CJ, Ward SM, Wilson RE, Hurban P, Tennant RW, Paules RS
Genome Biology 2008, 9:R100 (20 June 2008)
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17.


Database    
MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters
Law PJ, Claudel-Renard C, Joubert F, Louw AI, Berger DK
BMC Genomics 2008, 9:105 (28 February 2008)
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18.


Methodology article    
VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays
Kestler HA, Müller A, Kraus JM, Buchholz M, Gress TM, Liu H, Kane DW, Zeeberg BR, Weinstein JN
BMC Bioinformatics 2008, 9:67 (29 January 2008)
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19.


Software    
Literature Lab: a method of automated literature interrogation to infer biology from microarray analysis
Febbo PG, Mulligan MG, Slonina DA, Stegmaier K, Di Vizio D, Martinez PR, Loda M, Taylor SC
BMC Genomics 2007, 8:461 (18 December 2007)
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20.


Research article    
Dynamic gene expression in fish muscle during recovery growth induced by a fasting-refeeding schedule
Rescan PY, Montfort J, Rallière C, Le Cam A, Esquerré D, Hugot K
BMC Genomics 2007, 8:438 (28 November 2007)
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21.


Database    
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis
Sherman BT, Huang DW, Tan Q, Guo Y, Bour S, Liu D, Stephens R, Baseler MW, Lane HC, Lempicki RA
BMC Bioinformatics 2007, 8:426 (2 November 2007)
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22.


Research article    
Genes involved in TGF1-driven epithelial-mesenchymal transition of renal epithelial cells are topologically related in the human interactome map
Campanaro S, Picelli S, Torregrossa R, Colluto L, Ceol M, Del Prete D, D'Angelo A, Valle G, Anglani F
BMC Genomics 2007, 8:383 (22 October 2007)
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23.


Research article    
Androgen-induced masculinization in rainbow trout results in a marked dysregulation of early gonadal gene expression profiles
Baron D, Montfort J, Houlgatte R, Fostier A, Guiguen Y
BMC Genomics 2007, 8:357 (4 October 2007)
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24.


Research    
Comparative proteome analysis of human epithelial ovarian cancer
Gagné JP, Éthier C, Gagné P, Mercier G, Bonicalzi M, Mes-Masson AM, Droit A, Winstall E, Isabelle M, Poirier GG
Proteome Science 2007, 5:16 (24 September 2007)
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25.


Method    
The LeFE algorithm: embracing the complexity of gene expression in the interpretation of microarray data
Eichler GS, Reimers M, Kane D, Weinstein JN
Genome Biology 2007, 8:R187 (10 September 2007)
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26.


Research article    
Gene expression changes associated with Barrett's esophagus and Barrett's-associated adenocarcinoma cell lines after acid or bile salt exposure
Hao Y, Sood S, Triadafilopoulos G, Kim JH, Wang Z, Sahbaie P, Omary MB, Lowe AW
BMC Gastroenterology 2007, 7:24 (27 June 2007)
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27.


Research    
Toxicogenomic analysis of Caenorhabditis elegans reveals novel genes and pathways involved in the resistance to cadmium toxicity
Cui Y, McBride SJ, Boyd WA, Alper S, Freedman JH
Genome Biology 2007, 8:R122 (25 June 2007)
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28.


Research article    
CAG-encoded polyglutamine length polymorphism in the human genome
Butland SL, Devon RS, Huang Y, Mead CL, Meynert AM, Neal SJ, Lee SS, Wilkinson A, Yang GS, Yuen MMS, Hayden MR, Holt RA, Leavitt BR, Ouellette BFF
BMC Genomics 2007, 8:126 (22 May 2007)
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29.


Methodology article    
RNA quality in frozen breast cancer samples and the influence on gene expression analysis a comparison of three evaluation methods using microcapillary electrophoresis traces
Strand C, Enell J, Hedenfalk I, Fernö M
BMC Molecular Biology 2007, 8:38 (22 May 2007)
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30.


Method    
Revealing signaling pathway deregulation by using gene expression signatures and regulatory motif analysis
Liu Y, Ringnér M
Genome Biology 2007, 8:R77 (11 May 2007)
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31.


Research    
Decline of nucleotide excision repair capacity in aging Caenorhabditis elegans
Meyer JN, Boyd WA, Azzam GA, Haugen AC, Freedman JH, Van Houten B
Genome Biology 2007, 8:R70 (1 May 2007)
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32.


Database    
SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis
Kahn AB, Ryan MC, Liu H, Zeeberg BR, Jamison DC, Weinstein JN
BMC Bioinformatics 2007, 8:75 (5 March 2007)
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33.


Software    
FUNC: a package for detecting significant associations between gene sets and ontological annotations
Prüfer K, Muetzel B, Do HH, Weiss G, Khaitovich P, Rahm E, Pääbo S, Lachmann M, Enard W
BMC Bioinformatics 2007, 8:41 (6 February 2007)
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34.


Research    
Immune-mediated changes in actinic keratosis following topical treatment with imiquimod 5% cream
Torres A, Storey L, Anders M, Miller RL, Bulbulian BJ, Jin J, Raghavan S, Lee J, Slade HB, Birmachu W
Journal of Translational Medicine 2007, 5:7 (26 January 2007)
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35.


Software    
GO-2D: identifying 2-dimensional cellular-localized functional modules in Gene Ontology
Zhu J, Wang J, Guo Z, Zhang M, Yang D, Li Y, Wang D, Xiao G
BMC Genomics 2007, 8:30 (24 January 2007)
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36.


Review    
Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?
Birkholtz LM, Bastien O, Wells G, Grando D, Joubert F, Kasam V, Zimmermann M, Ortet P, Jacq N, Saïdani N, Roy S, Hofmann-Apitius M, Breton V, Louw AI, Maréchal E
Malaria Journal 2006, 5:110 (17 November 2006)
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37.


Software    
GeneTools application for functional annotation and statistical hypothesis testing
Beisvag V, Jünge FKR, Bergum H, Jølsum L, Lydersen S, Günther CC, Ramampiaro H, Langaas M, Sandvik AK, Lægreid A
BMC Bioinformatics 2006, 7:470 (24 October 2006)
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38.


Research    
Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways
Levine DM, Haynor DR, Castle JC, Stepaniants SB, Pellegrini M, Mao M, Johnson JM
Genome Biology 2006, 7:R93 (17 October 2006)
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39.


Software    
GOLEM: an interactive graph-based gene-ontology navigation and analysis tool
Sealfon RSG, Hibbs MA, Huttenhower C, Myers CL, Troyanskaya OG
BMC Bioinformatics 2006, 7:443 (10 October 2006)
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40.


Proceedings    
Differential gene expression in mouse primary hepatocytes exposed to the peroxisome proliferator-activated receptor agonists
Guo L, Fang H, Collins J, Fan X, Dial S, Wong A, Mehta K, Blann E, Shi L, Tong W, Dragan YP
BMC Bioinformatics 2006, 7(Suppl 2):S18 (26 September 2006)
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41.


Proceedings    
GOFFA: Gene Ontology For Functional Analysis A FDA Gene Ontology Tool for Analysis of Genomic and Proteomic Data
Sun H, Fang H, Chen T, Perkins R, Tong W
BMC Bioinformatics 2006, 7(Suppl 2):S23 (26 September 2006)
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42.


Research article    
A model of anti-angiogenesis: differential transcriptosome profiling of microvascular endothelial cells from diffuse systemic sclerosis patients
Giusti B, Fibbi G, Margheri F, Serratì S, Rossi L, Poggi F, Lapini I, Magi A, Del Rosso A, Cinelli M, Guiducci S, Kahaleh B, Bazzichi L, Bombardieri S, Matucci-Cerinic M, Gensini GF, Del Rosso M, Abbate R
Arthritis Research & Therapy 2006, 8:R115 (19 July 2006)
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43.




Research article    
A wing expressed sequence tag resource for Bicyclus anynana butterflies, an evo-devo model
Beldade P, Rudd S, Gruber JD, Long AD
BMC Genomics 2006, 7:130 (31 May 2006)
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44.


Research    
Large-scale and high-confidence proteomic analysis of human seminal plasma
Pilch B, Mann M
Genome Biology 2006, 7:R40 (18 May 2006)
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45.


Methodology article    
Combining evidence, biomedical literature and statistical dependence: new insights for functional annotation of gene sets
Aubry M, Monnier A, Chicault C, de Tayrac M, Galibert MD, Burgun A, Mosser J
BMC Bioinformatics 2006, 7:241 (4 May 2006)
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46.


Research article    
Transcription profiles of non-immortalized breast cancer cell lines
Fernandez-Cobo M, Holland JF, Pogo BGT
BMC Cancer 2006, 6:99 (20 April 2006)
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47.


Research article    
In vivo in vitro toxicogenomic comparison of TCDD-elicited gene expression in Hepa1c1c7 mouse hepatoma cells and C57BL/6 hepatic tissue
Dere E, Boverhof DR, Burgoon LD, Zacharewski TR
BMC Genomics 2006, 7:80 (12 April 2006)
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48.


Methodology article    
Amplification of the Gene Ontology annotation of Affymetrix probe sets
Muro EM, Perez-Iratxeta C, Andrade-Navarro MA
BMC Bioinformatics 2006, 7:159 (20 March 2006)
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49.


Software    
GOurmet: A tool for quantitative comparison and visualization of gene expression profiles based on gene ontology (GO) distributions
Doherty JM, Carmichael LK, Mills JC
BMC Bioinformatics 2006, 7:151 (17 March 2006)
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50.


Research    
Deciphering cellular states of innate tumor drug responses
Graudens E, Boulanger V, Mollard C, Mariage-Samson R, Barlet X, Grémy G, Couillault C, Lajémi M, Piatier-Tonneau D, Zaborski P, Eveno E, Auffray C, Imbeaud S
Genome Biology 2006, 7:R19 (15 March 2006)
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51.


Software    
GO-Diff: Mining functional differentiation between EST-based transcriptomes
Chen Z, Wang W, Ling XB, Liu JJ, Chen L
BMC Bioinformatics 2006, 7:72 (16 February 2006)
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52.


Research article    
Identification of blood biomarkers of rheumatoid arthritis by transcript profiling of peripheral blood mononuclear cells from the rat collagen-induced arthritis model
Shou J, Bull CM, Li L, Qian HR, Wei T, Luo S, Perkins D, Solenberg PJ, Tan SL, Chen XYC, Roehm NW, Wolos JA, Onyia JE
Arthritis Research & Therapy 2006, 8:R28 (10 January 2006)
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53.


Methodology article    
Finding biological process modifications in cancer tissues by mining gene expression correlations
Gamberoni G, Storari S, Volinia S
BMC Bioinformatics 2006, 7:6 (9 January 2006)
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54.


Research    
Primary and secondary transcriptional effects in the developing human Down syndrome brain and heart
Mao R, Wang X, Spitznagel EL, Frelin LP, Ting JC, Ding H, Kim J, Ruczinski I, Downey TJ, Pevsner J
Genome Biology 2005, 6:R107 (16 December 2005)
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55.


Research article    
Human promoter genomic composition demonstrates non-random groupings that reflect general cellular function
McNutt MC, Tongbai R, Cui W, Collins I, Freebern WJ, Montano I, Haggerty CM, Chandramouli GVR, Gardner K
BMC Bioinformatics 2005, 6:259 (18 October 2005)
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56.


Research article    
Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains
Campanaro S, Vezzi A, Vitulo N, Lauro FM, D'Angelo M, Simonato F, Cestaro A, Malacrida G, Bertoloni G, Valle G, Bartlett DH
BMC Genomics 2005, 6:122 (14 September 2005)
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57.


Methodology article    
Pathway level analysis of gene expression using singular value decomposition
Tomfohr J, Lu J, Kepler TB
BMC Bioinformatics 2005, 6:225 (12 September 2005)
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58.


Software    
L2L: a simple tool for discovering the hidden significance in microarray expression data
Newman JC, Weiner AM
Genome Biology 2005, 6:R81 (31 August 2005)
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59.


Research article    
Dynamic covariation between gene expression and proteome characteristics
Sharabiani MTA, Siermala M, Lehtinen TO, Vihinen M
BMC Bioinformatics 2005, 6:215 (30 August 2005)
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60.


Software    
DynGO: a tool for visualizing and mining of Gene Ontology and its associations
Liu H, Hu ZZ, Wu CH
BMC Bioinformatics 2005, 6:201 (9 August 2005)
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61.


Proceedings    
Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling
Fang H, Tong W, Perkins R, Shi L, Hong H, Cao X, Xie Q, Yim SH, Ward JM, Pitot HC, Dragan YP
BMC Bioinformatics 2005, 6(Suppl 2):S6 (15 July 2005)
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62.


Software    
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)
Zeeberg BR, Qin H, Narasimhan S, Sunshine M, Cao H, Kane DW, Reimers M, Stephens RM, Bryant D, Burt SK, Elnekave E, Hari DM, Wynn TA, Cunningham-Rundles C, Stewart DM, Nelson D, Weinstein JN
BMC Bioinformatics 2005, 6:168 (5 July 2005)
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63.


Research article    
Signal transduction pathway profiling of individual tumor samples
Breslin T, Krogh M, Peterson C, Troein C
BMC Bioinformatics 2005, 6:163 (29 June 2005)
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64.


Software    
FACT a framework for the functional interpretation of high-throughput experiments
Kokocinski F, Delhomme N, Wrobel G, Hummerich L, Toedt G, Lichter P
BMC Bioinformatics 2005, 6:161 (28 June 2005)
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65.


Methodology article    
PAGE: Parametric Analysis of Gene Set Enrichment
Kim SY, Volsky DJ
BMC Bioinformatics 2005, 6:144 (8 June 2005)
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66.


Research article    
Changes in the transcriptional profile of transporters in the intestine along the anterior-posterior and crypt-villus axes
Anderle P, Sengstag T, Mutch DM, Rumbo M, Praz V, Mansourian R, Delorenzi M, Williamson G, Roberts MA
BMC Genomics 2005, 6:69 (10 May 2005)
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67.


Methodology article    
Towards precise classification of cancers based on robust gene functional expression profiles
Guo Z, Zhang T, Li X, Wang Q, Xu J, Yu H, Zhu J, Wang H, Wang C, Topol EJ, Wang Q, Rao S
BMC Bioinformatics 2005, 6:58 (17 March 2005)
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68.


Research article    
Gene expression in the brain and kidney of rainbow trout in response to handling stress
Krasnov A, Koskinen H, Pehkonen P, Rexroad CE, Afanasyev S, Mölsä H
BMC Genomics 2005, 6:3 (6 January 2005)
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69.


Methodology article    
Comparing functional annotation analyses with Catmap
Breslin T, Edén P, Krogh M
BMC Bioinformatics 2004, 5:193 (9 December 2004)
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70.


Software    
GOToolBox: functional analysis of gene datasets based on Gene Ontology
Martin D, Brun C, Remy E, Mouren P, Thieffry D, Jacq B
Genome Biology 2004, 5:R101 (26 November 2004)
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71.


Research article    
Iterative class discovery and feature selection using Minimal Spanning Trees
Varma S, Simon R
BMC Bioinformatics 2004, 5:126 (8 September 2004)
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72.


Research article    
Handling multiple testing while interpreting microarrays with the Gene Ontology Database
Osier MV, Zhao H, Cheung KH
BMC Bioinformatics 2004, 5:124 (6 September 2004)
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73.


Methodology article    
Graph-based iterative Group Analysis enhances microarray interpretation
Breitling R, Amtmann A, Herzyk P
BMC Bioinformatics 2004, 5:100 (23 July 2004)
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74.


Research    
System-based proteomic analysis of the interferon response in human liver cells
Yan W, Lee H, Yi EC, Reiss D, Shannon P, Kwieciszewski BK, Coito C, Li X, Keller A, Eng J, Galitski T, Goodlett DR, Aebersold R, Katze MG
Genome Biology 2004, 5:R54 (22 July 2004)
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75.


Software    
Visualization and analysis of microarray and gene ontology data with treemaps
Baehrecke EH, Dang N, Babaria K, Shneiderman B
BMC Bioinformatics 2004, 5:84 (28 June 2004)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
76.


Correspondence    
Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics
Zeeberg BR, Riss J, Kane DW, Bussey KJ, Uchio E, Linehan WM, Barrett JC, Weinstein JN
BMC Bioinformatics 2004, 5:80 (23 June 2004)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] [6 comments]
77.


Methodology article    
Iterative Group Analysis (iGA): A simple tool to enhance sensitivity and facilitate interpretation of microarray experiments
Breitling R, Amtmann A, Herzyk P
BMC Bioinformatics 2004, 5:34 (29 March 2004)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
78.


Software    
GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies
Zhang B, Schmoyer D, Kirov S, Snoddy J
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