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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 and Mike Tyers*

Journal of Biology 2006, 5:11 doi:10.1186/jbiol36

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Proceedings   Open Access

Network-based functional enrichment

Christopher L Poirel, Clifford C Owens, T M Murali BMC Bioinformatics 2011, 12(Suppl 13):S14 (30 November 2011)

Research   Open Access

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text

Martin Krallinger, Miguel Vazquez, Florian Leitner, David Salgado, Andrew Chatr-aryamontri, Andrew Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers, Gerold Schneider, Fabio Rinaldi, Robert Leaman, Graciela Gonzalez, Sergio Matos, Sun Kim, W Wilbur, Luis Rocha, Hagit Shatkay, Ashish V Tendulkar, Shashank Agarwal, Feifan Liu, Xinglong Wang, Rafal Rak, Keith Noto, Charles Elkan, Zhiyong Lu et al. BMC Bioinformatics 2011, 12(Suppl 8):S3 (3 October 2011)

Research article   Open Access Highly Accessed

Noise reduction in protein-protein interaction graphs by the implementation of a novel weighting scheme

George D Kritikos, Charalampos Moschopoulos, Michalis Vazirgiannis, Sophia Kossida BMC Bioinformatics 2011, 12:239 (16 June 2011)

Research article   Open Access Highly Accessed

Mining protein networks for synthetic genetic interactions

Sri R Paladugu, Shan Zhao, Animesh Ray, Alpan Raval BMC Bioinformatics 2008, 9:426 (9 October 2008)

Database   Open Access

DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions

Jingkai Yu, Svetlana Pacifico, Guozhen Liu, Russell L Finley BMC Genomics 2008, 9:461 (7 October 2008)

Research article   Open Access

Systematic genetic array analysis links the Saccharomyces cerevisiae SAGA/SLIK and NuA4 component Tra1 to multiple cellular processes

Stephen MT Hoke, Julie Guzzo, Brenda Andrews, Christopher J Brandl BMC Genetics 2008, 9:46 (10 July 2008)

Method   Open Access

Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy

Wan Kim, Chase Krumpelman, Edward M Marcotte Genome Biology 2008, 9(Suppl 1):S5 (27 June 2008)

Methodology article   Open Access Highly Accessed

Inferring the role of transcription factors in regulatory networks

Philippe Veber, Carito Guziolowski, Michel Le Borgne, Ovidiu Radulescu, Anne Siegel BMC Bioinformatics 2008, 9:228 (6 May 2008)

Research article   Open Access

High-precision high-coverage functional inference from integrated data sources

Bolan Linghu, Evan S Snitkin, Dustin T Holloway, Adam M Gustafson, Yu Xia, Charles DeLisi BMC Bioinformatics 2008, 9:119 (25 February 2008)

Research article   Open Access

Identifying protein complexes directly from high-throughput TAP data with Markov random fields

Wasinee Rungsarityotin, Roland Krause, Arno Schödl, Alexander Schliep BMC Bioinformatics 2007, 8:482 (19 December 2007)

Methodology article   Open Access Highly Accessed

Generating confidence intervals on biological networks

Thomas Thorne, Michael PH Stumpf BMC Bioinformatics 2007, 8:467 (30 November 2007)

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Using protein complexes to predict phenotypic effects of gene mutation

Hunter B Fraser, Joshua B Plotkin Genome Biology 2007, 8:R252 (27 November 2007)

The best predictor of a protein's knockout phenotype is shown to be the knockout phenotype of other proteins that are present in a protein complex with it.

Research article   Open Access

Reuse of structural domain–domain interactions in protein networks

Benjamin Schuster-Böckler, Alex Bateman BMC Bioinformatics 2007, 8:259 (18 July 2007)

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Probabilistic prediction and ranking of human protein-protein interactions

Michelle S Scott, Geoffrey J Barton BMC Bioinformatics 2007, 8:239 (5 July 2007)

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A proteome-wide protein interaction map for Campylobacter jejuni

Jodi R Parrish, Jingkai Yu, Guozhen Liu, Julie A Hines, Jason E Chan, Bernie A Mangiola, Huamei Zhang, Svetlana Pacifico, Farshad Fotouhi, Victor J DiRita, Trey Ideker, Phillip Andrews, Russell L Finley Genome Biology 2007, 8:R130 (5 July 2007)

'Systematic identification of protein interactions for the bacterium Campylobacter jejuni using high-throughput yeast two-hybrid screens detected interactions for 80% of the organism's proteins.

Research article   Open Access

A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality

G Traver Hart, Insuk Lee, Edward M Marcotte BMC Bioinformatics 2007, 8:236 (2 July 2007)

Research   Open Access

ProtNet: a tool for stochastic simulations of protein interaction networks dynamics

Massimo Bernaschi, Filippo Castiglione, Alessandra Ferranti, Caius Gavrila, Michele Tinti, Gianni Cesareni BMC Bioinformatics 2007, 8(Suppl 1):S4 (8 March 2007)

Opinion   Free

How complete are current yeast and human protein-interaction networks?

G Traver Hart, Arun K Ramani, Edward M Marcotte Genome Biology 2006, 7:120 (1 December 2006)

How can protein-interaction networks can be made more complete?

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The interaction map of yeast: terra incognita?

Joe Mellor, Charles DeLisi Journal of Biology 2006, 5:10 (8 June 2006)