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Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network

Lan V Zhang, Oliver D King, Sharyl L Wong, Debra S Goldberg, Amy HY Tong, Guillaume Lesage, Brenda Andrews, Howard Bussey, Charles Boone and Frederick P Roth*

Journal of Biology 2005, 4:6 doi:10.1186/jbiol23

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BioMed Central: 17 citations

Research article   Open Access

Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs

Fergal Casey, Nevan Krogan, Denis C Shields, Gerard Cagney BMC Systems Biology 2011, 5:133 (22 August 2011)

Methodology article   Open Access

Extracting quantitative genetic interaction phenotypes from matrix combinatorial RNAi

Elin Axelsson, Thomas Sandmann, Thomas Horn, Michael Boutros, Wolfgang Huber , Bernd Fischer BMC Bioinformatics 2011, 12:342 (17 August 2011)

Proceedings   Open Access

Discovering conditional co-regulated protein complexes by integrating diverse data sources

Fei Luo, Juan Liu, Jinyan Li BMC Systems Biology 2010, 4(Suppl 2):S4 (13 September 2010)

Research article   Open Access

Composite functional module inference: detecting cooperation between transcriptional regulation and protein interaction by mantel test

Chao Wu, Fan Zhang, Xia Li, Shihua Zhang, Jiang Li, Fei Su, Kongning Li, Yuqing Yan BMC Systems Biology 2010, 4:82 (10 June 2010)

Method   Open Access Highly Accessed

Towards accurate imputation of quantitative genetic interactions

Igor Ulitsky, Nevan J Krogan, Ron Shamir Genome Biology 2009, 10:R140 (10 December 2009)

A new method for calculating quantitative genetic interactions allows for the inference of 190,000 new genetic interactions in Saccharomyces cerevisae.

Research article   Open Access

The capacity for multistability in small gene regulatory networks

Dan Siegal-Gaskins, Erich Grotewold, Gregory D Smith BMC Systems Biology 2009, 3:96 (21 September 2009)

Research article   Open Access

Triangle network motifs predict complexes by complementing high-error interactomes with structural information

Bill Andreopoulos, Christof Winter, Dirk Labudde, Michael Schroeder BMC Bioinformatics 2009, 10:196 (27 June 2009)

Software   Open Access Highly Accessed

NetGrep: fast network schema searches in interactomes

Eric Banks, Elena Nabieva, Ryan Peterson, Mona Singh Genome Biology 2008, 9:R138 (18 September 2008)

NetGrep is a system for searching protein interaction networks for matches to user-supplied network schemas.

Method   Open Access

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function

Sara Mostafavi, Debajyoti Ray, David Warde-Farley, Chris Grouios, Quaid Morris Genome Biology 2008, 9(Suppl 1):S4 (27 June 2008)

Method   Open Access Highly Accessed

Network motif analysis of a multi-mode genetic-interaction network

R James Taylor, Andrew F Siegel, Timothy Galitski Genome Biology 2007, 8:R160 (2 August 2007)

Statistical and computational methods for the extraction of biological information from dense multi-mode genetic-interaction networks were developed and implemented in open-source software.

Research article   Open Access Highly Accessed

Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae

Illés J Farkas, Chuang Wu, Chakra Chennubhotla, Ivet Bahar, Zoltán N Oltvai BMC Bioinformatics 2006, 7:478 (28 October 2006)

Research   Open Access Highly Accessed

Design principles of molecular networks revealed by global comparisons and composite motifs

Haiyuan Yu, Yu Xia, Valery Trifonov, Mark Gerstein Genome Biology 2006, 7:R55 (19 July 2006)

A global comparison of the four basic molecular networks in yeast - regulatory, co-expression, interaction and metabolic - reveals general design principles.

Research article   Open Access Highly Accessed

Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae

Teresa Reguly, Ashton Breitkreutz, Lorrie Boucher, Bobby-Joe Breitkreutz, Gary C Hon, Chad L Myers, Ainslie Parsons, Helena Friesen, Rose Oughtred, Amy Tong, Chris Stark, Yuen Ho, David Botstein, Brenda Andrews, Charles Boone, Olga G Troyanskya, Trey Ideker, Kara Dolinski, Nizar N Batada, Mike Tyers Journal of Biology 2006, 5:11 (8 June 2006)

A new literature-based yeast database documents over 33,000 biological interactions, manually curated from the primary literature, and provides an invaluable resource to benchmark high-throughput methods in the study of complex networks.

Research article   Open Access

Differential evolutionary conservation of motif modes in the yeast protein interaction network

Wei-Po Lee, Bing-Chiang Jeng, Tun-Wen Pai, Chin-Pei Tsai, Chang-Yung Yu, Wen-Shyong Tzou BMC Genomics 2006, 7:89 (25 April 2006)

Research   Open Access Highly Accessed

Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins

Jay R Hesselberth, John P Miller, Anna Golob, Jason E Stajich, Gregory A Michaud, Stanley Fields Genome Biology 2006, 7:R30 (10 April 2006)

A protein interaction map for 12 of the 13 WW domains present in the proteins of S. cerevisiae was generated by using protein microarray data.

Minireview   Free

Untangling the web of functional and physical interactions in yeast

Markus J Herrgård, Bernhard Ø Palsson Journal of Biology 2005, 4:5 (8 June 2005)

Research news   Free Highly Accessed

A road map of yeast interactions

Jonathan B Weitzman Journal of Biology 2005, 4:4 (1 June 2005)