Genome Biology

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Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering

Audrey P Gasch and Michael B Eisen*

Genome Biology 2002, 3:research0059-research0059.22 doi:10.1186/gb-2002-3-11-research0059

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BioMed Central: 25 citations

Research   Open Access

Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering

Dwight Kuo, Kai Tan, Guy Zinman, Timothy Ravasi, Ziv Bar-Joseph, Trey Ideker Genome Biology 2010, 11:R77 (23 July 2010)

Three yeast species respond to azole drugs in different ways and show different sensitivities to fluconazole

Proceedings   Open Access

Identifying promoter features of co-regulated genes with similar network motifs

Oscar Harari, Coral del Val, Rocío Romero-Zaliz, Dongwoo Shin, Henry Huang, Eduardo A Groisman, Igor Zwir BMC Bioinformatics 2009, 10(Suppl 4):S1 (29 April 2009)

Research   Open Access

Semi-supervised gene shaving method for predicting low variation biological pathways from genome-wide data

Dongxiao Zhu BMC Bioinformatics 2009, 10(Suppl 1):S54 (30 January 2009)

Software   Open Access

DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites

Evert-Jan Blom, Sacha AFT van Hijum, Klaas J Hofstede, Remko Silvis, Jos BTM Roerdink, Oscar P Kuipers BMC Bioinformatics 2008, 9:535 (16 December 2008)

Research   Open Access

Extending bicluster analysis to annotate unclassified ORFs and predict novel functional modules using expression data

Kenneth Bryan, Pádraig Cunningham BMC Genomics 2008, 9(Suppl 2):S20 (16 September 2008)

Proceedings   Open Access

Novel implementation of conditional co-regulation by graph theory to derive co-expressed genes from microarray data

Arun Rawat, Georg J Seifert, Youping Deng BMC Bioinformatics 2008, 9(Suppl 9):S7 (12 August 2008)

Research article   Open Access

A novel series of compositionally biased substitution matrices for comparing Plasmodium proteins

Kevin Brick, Elisabetta Pizzi BMC Bioinformatics 2008, 9:236 (16 May 2008)

Research   Open Access

Discovering multi–level structures in bio-molecular data through the Bernstein inequality

Alberto Bertoni, Giorgio Valentini BMC Bioinformatics 2008, 9(Suppl 2):S4 (26 March 2008)

Methodology article   Open Access Highly Accessed

Transcription factor target prediction using multiple short expression time series from Arabidopsis thaliana

Henning Redestig, Daniel Weicht, Joachim Selbig, Matthew A Hannah BMC Bioinformatics 2007, 8:454 (18 November 2007)

Research article   Open Access

On the detection of functionally coherent groups of protein domains with an extension to protein annotation

William A McLaughlin, Ken Chen, Tingjun Hou, Wei Wang BMC Bioinformatics 2007, 8:390 (16 October 2007)

Research   Open Access Highly Accessed

Global analysis of patterns of gene expression during Drosophila embryogenesis

Pavel Tomancak, Benjamin P Berman, Amy Beaton, Richard Weiszmann, Elaine Kwan, Volker Hartenstein, Susan E Celniker, Gerald M Rubin Genome Biology 2007, 8:R145 (23 July 2007)

Embryonic expression patterns for 6,003 (44%) of the 13,659 protein-coding genes identified in the Drosophila melanogaster genome were documented, of which 40% show tissue-restricted expression.

Software   Open Access Highly Accessed

Nearest Neighbor Networks: clustering expression data based on gene neighborhoods

Curtis Huttenhower, Avi I Flamholz, Jessica N Landis, Sauhard Sahi, Chad L Myers, Kellen L Olszewski, Matthew A Hibbs, Nathan O Siemers, Olga G Troyanskaya, Hilary A Coller BMC Bioinformatics 2007, 8:250 (12 July 2007)

Research   Open Access Highly Accessed

Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression

Shisong Ma, Hans J Bohnert Genome Biology 2007, 8:R49 (4 April 2007)

The integration of stress-dependent, tissue- and cell-specific expression profiles and 5'-regulatory sequence motif analysis defines a common stress transcriptome, identifies major motifs for stress response, and places stress response in the context of tissue and cell lineages in the Arabidopsis root.

Review   Free Highly Accessed

Expression genomics in breast cancer research: microarrays at the crossroads of biology and medicine

Lance D Miller, Edison T Liu Breast Cancer Research 2007, 9:206 (26 March 2007)

Methodology article   Open Access Highly Accessed

FLAME, a novel fuzzy clustering method for the analysis of DNA microarray data

Limin Fu, Enzo Medico BMC Bioinformatics 2007, 8:3 (4 January 2007)

Methodology article   Open Access Highly Accessed

Using local gene expression similarities to discover regulatory binding site modules

Bartek Wilczyński, Torgeir R Hvidsten, Andriy Kryshtafovych, Jerzy Tiuryn, Jan Komorowski, Krzysztof Fidelis BMC Bioinformatics 2006, 7:505 (17 November 2006)

Method   Open Access Highly Accessed

A classification based framework for quantitative description of large-scale microarray data

Dipen P Sangurdekar, Friedrich Srienc, Arkady B Khodursky Genome Biology 2006, 7:R32 (20 April 2006)

A new classification-based framework is presented that allows quantitative description of microarray data in terms of significance of co-expression within any gene group and condition-specific gene class activity.

Methodology article   Open Access

LS-NMF: A modified non-negative matrix factorization algorithm utilizing uncertainty estimates

Guoli Wang, Andrew V Kossenkov, Michael F Ochs BMC Bioinformatics 2006, 7:175 (28 March 2006)

Methodology article   Open Access

Determination of strongly overlapping signaling activity from microarray data

Ghislain Bidaut, Karsten Suhre, Jean-Michel Claverie, Michael F Ochs BMC Bioinformatics 2006, 7:99 (28 February 2006)

Methodology article   Open Access Highly Accessed

Biclustering of gene expression data by non-smooth non-negative matrix factorization

Pedro Carmona-Saez, Roberto D Pascual-Marqui, F Tirado, Jose M Carazo, Alberto Pascual-Montano BMC Bioinformatics 2006, 7:78 (17 February 2006)

Research article   Open Access Highly Accessed

Quantitative inference of dynamic regulatory pathways via microarray data

Wen-Chieh Chang, Chang-Wei Li, Bor-Sen Chen BMC Bioinformatics 2005, 6:44 (7 March 2005)

Method   Open Access Highly Accessed

MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model

Alan M Moses, Derek Y Chiang, Daniel A Pollard, Venky N Iyer, Michael B Eisen Genome Biology 2004, 5:R98 (30 November 2004)

MONKEY is a new method for identifying conserved transcription-factor binding sites from multiple-sequence alignments.

Software   Open Access

GeneXplorer: an interactive web application for microarray data visualization and analysis

Christian A Rees, Janos Demeter, John C Matese, David Botstein, Gavin Sherlock BMC Bioinformatics 2004, 5:141 (1 October 2004)

Software   Open Access

MiCoViTo: a tool for gene-centric comparison and visualization of yeast transcriptome states

Gaëlle Lelandais, Philippe Marc, Pierre Vincens, Claude Jacq, Stéphane Vialette BMC Bioinformatics 2004, 5:20 (3 March 2004)

Research article   Open Access Highly Accessed

DNA microarray data and contextual analysis of correlation graphs

Jacques Rougemont, Pascal Hingamp BMC Bioinformatics 2003, 4:15 (29 April 2003)