Genome Biology

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The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists

Da W Huang, Brad T Sherman, Qina Tan, Jack R Collins, W Gregory Alvord, Jean Roayaei, Robert Stephens, Michael W Baseler, H Clifford Lane and Richard A Lempicki*

Genome Biology 2007, 8:R183 doi:10.1186/gb-2007-8-9-r183

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BioMed Central: 18 citations

Research article   Open Access

Muscle wasting and the temporal gene expression pattern in a novel rat intensive care unit model

Monica Llano-Diez, Ann-Marie Gustafson, Carl Olsson, Hanna Goransson , Lars Larsson BMC Genomics 2011, 12:602 (13 December 2011)

Methodology article   Open Access Highly Accessed

AIGO: Towards a unified framework for the Analysis and the Inter-comparison of GO functional annotations

Michael Defoin-Platel, Matthew M Hindle, Artem Lysenko, Stephen J Powers, Dimah Z Habash, Christopher J Rawlings, Mansoor Saqi BMC Bioinformatics 2011, 12:431 (3 November 2011)

Proceedings   Open Access

Jejunal gene expression patterns correlate with severity of systemic infection in chicken

Dirkjan Schokker, Mari A Smits, Johanna MJ Rebel BMC Proceedings 2011, 5(Suppl 4):S4 (3 June 2011)

Research article   Open Access

Revealing and avoiding bias in semantic similarity scores for protein pairs

Jing Wang, Xianxiao Zhou, Jing Zhu, Chenggui Zhou, Zheng Guo BMC Bioinformatics 2010, 11:290 (28 May 2010)

Research   Open Access

The dissection of transcriptional modules regulated by various drugs of abuse in the mouse striatum

Marcin Piechota, Michal Korostynski, Wojciech Solecki, Agnieszka Gieryk, Michal Slezak, Wiktor Bilecki, Barbara Ziolkowska, Elzbieta Kostrzewa, Iwona Cymerman, Lukasz Swiech, Jacek Jaworski, Ryszard Przewlocki Genome Biology 2010, 11:R48 (4 May 2010)

The transcriptional response to six commonly-abused drugs was assessed in the mouse brain revealing common modules of drug-induced genes.

Research article   Open Access Highly Accessed

Effect of training-sample size and classification difficulty on the accuracy of genomic predictors

Vlad Popovici, Weijie Chen, Brandon D Gallas, Christos Hatzis, Weiwei Shi, Frank W Samuelson, Yuri Nikolsky, Marina Tsyganova, Alex Ishkin, Tatiana Nikolskaya, Kenneth R Hess, Vicente Valero, Daniel Booser, Mauro Delorenzi, Gabriel N Hortobagyi, Leming Shi, W Fraser Symmans, Lajos Pusztai Breast Cancer Research 2010, 12:R5 (11 January 2010)

Methodology article   Open Access

Generation of Gene Ontology benchmark datasets with various types of positive signal

Petri Törönen, Petri Pehkonen, Liisa Holm BMC Bioinformatics 2009, 10:319 (7 October 2009)

Proceedings   Open Access

A systems biology approach to the identification and analysis of transcriptional regulatory networks in osteocytes

Angela K Dean, Stephen E Harris, Ivo Kalajzic, Jianhua Ruan BMC Bioinformatics 2009, 10(Suppl 9):S5 (17 September 2009)

Proceedings   Open Access

BioNetBuilder2.0: bringing systems biology to chicken and other model organisms

Jay H Konieczka, Kevin Drew, Alex Pine, Kevin Belasco, Sean Davey, Tatiana A Yatskievych, Richard Bonneau, Parker B Antin BMC Genomics 2009, 10(Suppl 2):S6 (14 July 2009)

Research article   Open Access

Impaired immune function in Gulf War Illness

Toni Whistler, Mary Fletcher, William Lonergan, Xiao-R Zeng, Jin-Mann Lin, Arthur LaPerriere, Suzanne D Vernon, Nancy G Klimas BMC Medical Genomics 2009, 2:12 (5 March 2009)

Patients with Gulf War Illness have altered gene expression associated with natural killer cell functions, a condition exacerbated by vigorous exercise, implying they have impaired immune function compared to healthy people.

Software   Open Access

EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data

Christoph Bock, Konstantin Halachev, Joachim Büch, Thomas Lengauer Genome Biology 2009, 10:R14 (10 February 2009)

EpiGRAPH is a genome-scale data-mining software tool that enables users to identify epigenetic and gene regulatory features in large datasets of genomic regions.

Research article   Open Access

Generation and analysis of expressed sequence tags from six developing xylem libraries in Pinus radiata D. Don

Xinguo Li, Harry X Wu, Shannon K Dillon, Simon G Southerton BMC Genomics 2009, 10:41 (21 January 2009)

Software article   Open Access Highly Accessed

Fast Gene Ontology based clustering for microarray experiments

Kristian Ovaska, Marko Laakso, Sampsa Hautaniemi BioData Mining 2008, 1:11 (21 November 2008)

Software   Open Access Highly Accessed

ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets

Patrick J Killion, Vishwanath R Iyer Genome Biology 2008, 9:R159 (12 November 2008)

ArrayPlex is a software package that centrally provides a large number of flexible toolsets useful for functional genomics.

Methodology article   Open Access Highly Accessed

Assessment of protein set coherence using functional annotations

Monica Chagoyen, Jose M Carazo, Alberto Pascual-Montano BMC Bioinformatics 2008, 9:444 (20 October 2008)

A novel approach to evaluating the homogeneity of protein sets on the basis of the global similarity of their Gene Ontology functional annotations compliments methods for validating microarray clusters and protein-protein interaction networks.

Research   Open Access Highly Accessed

Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases

Monika Ray, Jianhua Ruan, Weixiong Zhang Genome Biology 2008, 9:R148 (8 October 2008)

Analysis of microarray data reveals extensive links between Alzheimer’s disease and cardiovascular diseases.

Proceedings   Open Access

Systems biology approach to identification of biomarkers for metastatic progression in cancer

Andrey A Ptitsyn, Michael M Weil, Douglas H Thamm BMC Bioinformatics 2008, 9(Suppl 9):S8 (12 August 2008)

Research article   Open Access Highly Accessed

Gene Ontology term overlap as a measure of gene functional similarity

Meeta Mistry, Paul Pavlidis BMC Bioinformatics 2008, 9:327 (4 August 2008)