BMC Bioinformatics

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Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks

Cecily J Wolfe*, Isaac S Kohane and Atul J Butte

BMC Bioinformatics 2005, 6:227 doi:10.1186/1471-2105-6-227

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BioMed Central: 21 citations

Research   Open Access

Construction of gene regulatory networks using biclustering and bayesian networks

Fadhl M Alakwaa, Nahed H Solouma, Yasser M Kadah Theoretical Biology and Medical Modelling 2011, 8:39 (22 October 2011)

Research article   Open Access Highly Accessed

Gene coexpression clusters and putative regulatory elements underlying seed storage reserve accumulation in Arabidopsis

Fred Y Peng, Randall J Weselake BMC Genomics 2011, 12:286 (2 June 2011)

Research article   Open Access Highly Accessed

Genes and gene expression modules associated with caloric restriction and aging in the laboratory mouse

William R Swindell BMC Genomics 2009, 10:585 (7 December 2009)

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Mining for coexpression across hundreds of datasets using novel rank aggregation and visualization methods

Priit Adler, Raivo Kolde, Meelis Kull, Aleksandr Tkachenko, Hedi Peterson, Jüri Reimand, Jaak Vilo Genome Biology 2009, 10:R139 (4 December 2009)

The MEM web resource allows users to search for co-expressed genes across all microarray datasets in the ArrayExpress database.

Proceedings   Open Access

Measuring similarity between gene expression profiles: a Bayesian approach

Viet-Anh Nguyen, Pietro Lió BMC Genomics 2009, 10(Suppl 3):S14 (3 December 2009)

Proceedings   Open Access

Threshold selection in gene co-expression networks using spectral graph theory techniques

Andy D Perkins, Michael A Langston BMC Bioinformatics 2009, 10(Suppl 11):S4 (8 October 2009)

Research article   Open Access

Meta-coexpression conservation analysis of microarray data: a "subset" approach provides insight into brain-derived neurotrophic factor regulation

Tamara Aid-Pavlidis, Pavlos Pavlidis, Tõnis Timmusk BMC Genomics 2009, 10:420 (8 September 2009)

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Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network

Osnat Atias, Benny Chor, Daniel A Chamovitz BMC Systems Biology 2009, 3:86 (3 September 2009)

Methodology article   Open Access Highly Accessed

CLEAN: CLustering Enrichment ANalysis

Johannes M Freudenberg, Vineet K Joshi, Zhen Hu, Mario Medvedovic BMC Bioinformatics 2009, 10:234 (29 July 2009)

Methodology article   Open Access Highly Accessed

Construction and use of gene expression covariation matrix

Jérôme Hennetin, Petri Pehkonen, Michel Bellis BMC Bioinformatics 2009, 10:214 (13 July 2009)

Methodology article   Open Access

Assessing and selecting gene expression signals based upon the quality of the measured dynamics

Eric Yang, Ioannis P Androulakis BMC Bioinformatics 2009, 10:55 (10 February 2009)

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Systems medicine: the future of medical genomics and healthcare

Charles Auffray, Zhu Chen, Leroy Hood Genome Med 2009, 1:2 (20 January 2009)

Systems approaches to medicine will transform the way drugs are developed and will enable medicine to become predictive, personalized, preventive and participatory.

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A comparison of four clustering methods for brain expression microarray data

Alexander L Richards, Peter Holmans, Michael C O'Donovan, Michael J Owen, Lesley Jones BMC Bioinformatics 2008, 9:490 (25 November 2008)

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Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources

Evert Blom, Rainer Breitling, Klaas Hofstede, Jos BTM Roerdink, Sacha AFT van Hijum, Oscar P Kuipers BMC Genomics 2008, 9:495 (21 October 2008)

Research   Open Access

Mining tissue specificity, gene connectivity and disease association to reveal a set of genes that modify the action of disease causing genes

Antonio Reverter, Aaron Ingham, Brian P Dalrymple BioData Mining 2008, 1:8 (19 September 2008)

A new algorithm, which mines databases of tissue specificity, gene connectivity and disease association, has identified a new group of genes that interact with disease causing genes and impact on disease outcomes.

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Perceiving molecular evolution processes in Escherichia coli by comprehensive metabolite and gene expression profiling

Chandran Vijayendran, Aiko Barsch, Karl Friehs, Karsten Niehaus, Anke Becker, Erwin Flaschel Genome Biology 2008, 9:R72 (10 April 2008)

Transcript and metabolite abundance changes were analyzed in evolved and ancestor strains of Escherichia coli in three different evolutionary conditions

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Inferring cellular networks – a review

Florian Markowetz, Rainer Spang BMC Bioinformatics 2007, 8(Suppl 6):S5 (27 September 2007)

Methodology article   Open Access Highly Accessed

EDISA: extracting biclusters from multiple time-series of gene expression profiles

Jochen Supper, Martin Strauch, Dierk Wanke, Klaus Harter, Andreas Zell BMC Bioinformatics 2007, 8:334 (12 September 2007)

Methodology article   Open Access

Bioinformatics analysis of the early inflammatory response in a rat thermal injury model

Eric Yang, Timothy Maguire, Martin L Yarmush, Francois Berthiaume, Ioannis P Androulakis BMC Bioinformatics 2007, 8:10 (10 January 2007)

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Global similarity and local divergence in human and mouse gene co-expression networks

Panayiotis Tsaparas, Leonardo Mariño-Ramírez, Olivier Bodenreider, Eugene V Koonin, I King Jordan BMC Evolutionary Biology 2006, 6:70 (12 September 2006)

Human and mouse co-expression gene networks are frequently highly divergent at the local level but essentially identical at the global level.

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Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks

David J Reiss, Nitin S Baliga, Richard Bonneau BMC Bioinformatics 2006, 7:280 (2 June 2006)