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Identifying biological themes within lists of genes with EASE.
Hosack DA, Dennis G, Sherman BT, Lane HC, Lempicki RA
Genome Biol 2003, 4:R70
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Research article    
Gene expression profiles in developing nephrons using Lim1 metanephric mesenchyme-specific conditional mutant mice
Chen YT, Kobayashi A, Kwan KM, Johnson RL, Behringer RR
BMC Nephrology 2006, 7:1 (7 February 2006)
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Preliminary evidence of mitochondrial dysfunction associated with post-infective fatigue after acute infection with Epstein Barr Virus
Vernon SD, Whistler T, Cameron B, Hickie IB, Reeves WC, Lloyd A
BMC Infectious Diseases 2006, 6:15 (31 January 2006)
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81.


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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cGMP-independent nitric oxide signaling and regulation of the cell cycle
Cui X, Zhang J, Ma P, Myers DE, Goldberg IG, Sittler KJ, Barb JJ, Munson PJ, Cintron AP, McCoy JP, Wang S, Danner RL
BMC Genomics 2005, 6:151 (3 November 2005)
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Genome-wide gene expression in response to parasitoid attack in Drosophila
Wertheim B, Kraaijeveld AR, Schuster E, Blanc E, Hopkins M, Pletcher SD, Strand MR, Partridge L, Godfray HCJ
Genome Biology 2005, 6:R94 (31 October 2005)
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84.


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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85.


Research article    
Epidermal growth factor (EGF) withdrawal masks gene expression differences in the study of pituitary adenylate cyclase-activating polypeptide (PACAP) activation of primary neural stem cell proliferation
Sievertzon M, Wirta V, Mercer A, Frisén J, Lundeberg J
BMC Neuroscience 2005, 6:55 (28 August 2005)
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Comparing independent microarray studies: the case of human embryonic stem cells
Suárez-Fariñas M, Noggle S, Heke M, Hemmati-Brivanlou A, Magnasco MO
BMC Genomics 2005, 6:99 (22 July 2005)
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87.


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Global gene expression analysis in time series following N-acetyl L-cysteine induced epithelial differentiation of human normal and cancer cells in vitro
Gustafsson AC, Kupershmidt I, Edlundh-Rose E, Greco G, Serafino A, Krasnowska EK, Lundeberg T, Bracci-Laudiero L, Romano MC, Parasassi T, Lundeberg J
BMC Cancer 2005, 5:75 (7 July 2005)
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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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Research    
Genomic analysis of metabolic pathway gene expression in mice
Ghazalpour A, Doss S, Sheth SS, Ingram-Drake LA, Schadt EE, Lusis AJ, Drake TA
Genome Biology 2005, 6:R59 (1 July 2005)
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Methodology article    
Theme discovery from gene lists for identification and viewing of multiple functional groups
Pehkonen P, Wong G, Törönen P
BMC Bioinformatics 2005, 6:162 (29 June 2005)
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91.


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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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PAGE: Parametric Analysis of Gene Set Enrichment
Kim SY, Volsky DJ
BMC Bioinformatics 2005, 6:144 (8 June 2005)
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93.


Correspondence    
Considerations when using the significance analysis of microarrays (SAM) algorithm
Larsson O, Wahlestedt C, Timmons JA
BMC Bioinformatics 2005, 6:129 (29 May 2005)
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94.


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Gene expression profile of cervical tissue compared to exfoliated cells: Impact on biomarker discovery
Steinau M, Lee DR, Rajeevan MS, Vernon SD, Ruffin MT, Unger ER
BMC Genomics 2005, 6:64 (5 May 2005)
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95.


Methodology article    
Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments
Liu H, Tarima S, Borders AS, Getchell TV, Getchell ML, Stromberg AJ
BMC Bioinformatics 2005, 6:106 (25 April 2005)
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96.


Research article    
Transcriptome analysis in primary neural stem cells using a tag cDNA amplification method
Sievertzon M, Wirta V, Mercer A, Meletis K, Erlandsson R, Wikström L, Frisén J, Lundeberg J
BMC Neuroscience 2005, 6:28 (15 April 2005)
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97.


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Promoter features related to tissue specificity as measured by Shannon entropy
Schug J, Schuller WP, Kappen C, Salbaum JM, Bucan M, Stoeckert CJ
Genome Biology 2005, 6:R33 (29 March 2005)
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98.


Research article    
Gene expression signature of estrogen receptor status in breast cancer
Abba MC, Hu Y, Sun H, Drake JA, Gaddis S, Baggerly K, Sahin A, Aldaz CM
BMC Genomics 2005, 6:37 (11 March 2005)
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99.


Method    
Genomic analysis of early murine mammary gland development using novel probe-level algorithms
Master SR, Stoddard AJ, Bailey LC, Pan TC, Dugan KD, Chodosh LA
Genome Biology 2005, 6:R20 (1 February 2005)
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100.


Software    
GECKO: a complete large-scale gene expression analysis platform
Theilhaber J, Ulyanov A, Malanthara A, Cole J, Xu D, Nahf R, Heuer M, Brockel C, Bushnell S
BMC Bioinformatics 2004, 5:195 (10 December 2004)
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101.


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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102.


Research    
Gene expression profiling of epithelial ovarian tumours correlated with malignant potential
Warrenfeltz S, Pavlik S, Datta S, Kraemer ET, Benigno B, McDonald JF
Molecular Cancer 2004, 3:27 (7 October 2004)
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103.


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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104.


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)
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105.


Software    
PubMatrix: a tool for multiplex literature mining
Becker KG, Hosack DA, Dennis G, Lempicki RA, Bright TJ, Cheadle C, Engel J
BMC Bioinformatics 2003, 4:61 (10 December 2003)
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