Genome Biology

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A first-draft human protein-interaction map

Ben Lehner and Andrew G Fraser*

Genome Biology 2004, 5:R63 doi:10.1186/gb-2004-5-9-r63

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Sensitive Detection of Pathway Perturbations in Cancers

Corban G Rivera, Brett M Tyler, TM Murali BMC Bioinformatics 2012, 13(Suppl 3):S9 (21 March 2012)

Software   Open Access Highly Accessed

Bio::Homology::InterologWalk - A Perl module to build putative protein-protein interaction networks through interolog mapping

Giuseppe Gallone, T Ian Simpson, J Douglas Armstrong, Andrew P Jarman BMC Bioinformatics 2011, 12:289 (18 July 2011)

Research   Open Access

Global protein interactome exploration through mining genome-scale data in Arabidopsis thaliana

Feng Xu, Guang Li, Chen Zhao, Yuhua Li, Peng Li, Jian Cui, Youping Deng, Tieliu Shi BMC Genomics 2010, 11(Suppl 2):S2 (2 November 2010)

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Response of the mosquito protein interaction network to dengue infection

Xiang Guo, Yao Xu, Guowu Bian, Andrew D Pike, Yan Xie, Zhiyong Xi BMC Genomics 2010, 11:380 (16 June 2010)

Research   Open Access

Evaluation of the collaborative network of highly correlating skin proteins and its change following treatment with glucocorticoids

Uwe Klinge, Nicolette Farman, Anette Fiebeler Theoretical Biology and Medical Modelling 2010, 7:16 (28 May 2010)

Research article   Open Access Highly Accessed

Building and analyzing protein interactome networks by cross-species comparisons

Amy M Wiles, Mark Doderer, Jianhua Ruan, Ting-Ting Gu, Dashnamoorthy Ravi, Barron Blackman, Alexander JR Bishop BMC Systems Biology 2010, 4:36 (30 March 2010)

Method   Open Access Highly Accessed

Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network

Bolan Linghu, Evan S Snitkin, Zhenjun Hu, Yu Xia, Charles DeLisi Genome Biology 2009, 10:R91 (3 September 2009)

An evidence-weighted functional-linkage network of human genes reveals associations among diseases that share no known disease genes and have dissimilar phenotypes

Research article   Open Access Highly Accessed

Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression

Stefanie De Bodt, Sebastian Proost, Klaas Vandepoele, Pierre Rouzé, Yves Van de Peer BMC Genomics 2009, 10:288 (29 June 2009)

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Protein-protein interaction as a predictor of subcellular location

Chang Shin, Simon Wong, Melissa J Davis, Mark A Ragan BMC Systems Biology 2009, 3:28 (25 February 2009)

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The prediction of protein-protein interaction networks in rice blast fungus

Fei He, Yan Zhang, Hao Chen, Ziding Zhang, You-Liang Peng BMC Genomics 2008, 9:519 (2 November 2008)

Research article   Open Access

Interspecies data mining to predict novel ING-protein interactions in human

Paul MK Gordon, Mohamed A Soliman, Pinaki Bose, Quang Trinh, Christoph W Sensen, Karl Riabowol BMC Genomics 2008, 9:426 (18 September 2008)

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Deducing topology of protein-protein interaction networks from experimentally measured sub-networks

Ling Yang, Thomas M Vondriska, Zhangang Han, W Robb MacLellan, James N Weiss, Zhilin Qu BMC Bioinformatics 2008, 9:301 (3 July 2008)

More accurate topologies of protein-protein interaction networks can be deduced by building core sub-networks using filtered information from experimental data sets.

Research article   Open Access

A simple principle concerning the robustness of protein complex activity to changes in gene expression

Jennifer I Semple, Tanya Vavouri, Ben Lehner BMC Systems Biology 2008, 2:1 (2 January 2008)

Method   Open Access Highly Accessed

Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes

Kriston L McGary, Insuk Lee, Edward M Marcotte Genome Biology 2007, 8:R258 (5 December 2007)

Loss-of-function phenotypes of yeast genes can be predicted from the loss-of-function phenotypes of their neighbours in functional gene networks. This could potentially be applied to the prediction of human disease genes.

Research   Open Access Highly Accessed

Integrative analysis for finding genes and networks involved in diabetes and other complex diseases

Regine Bergholdt, Zenia M Størling, Kasper Lage, E Olof Karlberg, Páll Í Ólason, Mogens Aalund, Jørn Nerup, Søren Brunak, Christopher T Workman, Flemming Pociot Genome Biology 2007, 8:R253 (28 November 2007)

An integrative analysis combining genetic interactions and protein interactions can be used to identify candidate genes/proteins for type 1 diabetes and other complex diseases.

Research article   Open Access

Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining

Xochitl C Morgan, Shulin Ni, Daniel P Miranker, Vishwanath R Iyer BMC Bioinformatics 2007, 8:445 (15 November 2007)

Methodology article   Open Access Highly Accessed

InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes

Jingchun Sun, Yan Sun, Guohui Ding, Qi Liu, Chuan Wang, Youyu He, Tieliu Shi, Yixue Li, Zhongming Zhao BMC Bioinformatics 2007, 8:414 (26 October 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)

Software   Open Access

FlyMine: an integrated database for Drosophila and Anopheles genomics

Rachel Lyne, Richard Smith, Kim Rutherford, Matthew Wakeling, Andrew Varley, Francois Guillier, Hilde Janssens, Wenyan Ji, Peter Mclaren, Philip North, Debashis Rana, Tom Riley, Julie Sullivan, Xavier Watkins, Mark Woodbridge, Kathryn Lilley, Steve Russell, Michael Ashburner, Kenji Mizuguchi, Gos Micklem Genome Biology 2007, 8:R129 (5 July 2007)

This novel web-based database provides unique accessibility and querying of integrated genomic and proteomic data for Drosophila and Anopheles.

Research article   Open Access

Evidence for systems-level molecular mechanisms of tumorigenesis

Pilar Hernández, Jaime Huerta-Cepas, David Montaner, Fátima Al-Shahrour, Joan Valls, Laia Gómez, Gabriel Capellá, Joaquín Dopazo, Miguel Pujana BMC Genomics 2007, 8:185 (20 June 2007)

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Reconstruction of human protein interolog network using evolutionary conserved network

Tao-Wei Huang, Chung-Yen Lin, Cheng-Yan Kao BMC Bioinformatics 2007, 8:152 (10 May 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?

Research article   Open Access

An integrated approach to the prediction of domain-domain interactions

Hyunju Lee, Minghua Deng, Fengzhu Sun, Ting Chen BMC Bioinformatics 2006, 7:269 (25 May 2006)

Research article   Open Access

Topology and weights in a protein domain interaction network – a novel way to predict protein interactions

Stefan Wuchty BMC Genomics 2006, 7:122 (23 May 2006)

Software   Open Access

Ulysses - an application for the projection of molecular interactions across species

Danielle Kemmer, Yong Huang, Sohrab P Shah, Jonathan Lim, Jochen Brumm, Macaire MS Yuen, John Ling, Tao Xu, Wyeth W Wasserman, BF Francis Ouellette Genome Biology 2005, 6:R106 (2 December 2005)

Ulysses, a new software for the parallel analysis and display of protein interactions detected in various species, is described.

Research article   Open Access

HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms

Maria Persico, Arnaud Ceol, Caius Gavrila, Robert Hoffmann, Arnaldo Florio, Gianni Cesareni BMC Bioinformatics 2005, 6(Suppl 4):S21 (1 December 2005)

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Tools enabling the elucidation of molecular pathways active in human disease: Application to Hepatitis C virus infection

David J Reiss, Iliana Avila-Campillo, Vesteinn Thorsson, Benno Schwikowski, Timothy Galitski BMC Bioinformatics 2005, 6:154 (20 June 2005)

Research article   Open Access

Filtering high-throughput protein-protein interaction data using a combination of genomic features

Ashwini Patil, Haruki Nakamura BMC Bioinformatics 2005, 6:100 (18 April 2005)

Gene ontology annotations, sequence alignment and structural information of Pfam domains have been combined to create a method of validating high-thoroughput protein-protein interaction data that functions with a sensitivity of 90% and specificity of 63%.

Research   Open Access Highly Accessed

Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome

Arun K Ramani, Razvan C Bunescu, Raymond J Mooney, Edward M Marcotte Genome Biology 2005, 6:R40 (15 April 2005)

In order to consolidate the known human proteins interactions two tests were developed to measure the relative accuracy of the available interaction data. In addition, 6,580 interactions among 3,737 human proteins were recovered from Medline abstracts and combined with existing interaction data to obtain a network of 31,609 interactions among 7,748 human proteins, accurate to the same degree as the existing data sets.

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Ontological visualization of protein-protein interactions

Harold J Drabkin, Christopher Hollenbeck, David P Hill, Judith A Blake BMC Bioinformatics 2005, 6:29 (11 February 2005)