Discovery of biological networks from diverse functional genomic data
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* Corresponding author: Olga G Troyanskaya ogt@cs.princeton.edu
Genome Biology 2005, 6:R114 doi:10.1186/gb-2005-6-13-r114
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BioMed Central: 22 citations
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Research article
Removing bias against membrane proteins in interaction networks Glauber C Brito, David W Andrews BMC Systems Biology 2011, 5:169 (19 October 2011) |
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Methodology article
Integrative approaches to the prediction of protein functions based on the feature selection Seokha Ko, Hyunju Lee BMC Bioinformatics 2009, 10:455 (31 December 2009) |
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Software
Graphle: Interactive exploration of large, dense graphs Curtis Huttenhower, Sajid O Mehmood, Olga G Troyanskaya BMC Bioinformatics 2009, 10:417 (14 December 2009) |
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Research
Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function James C Costello, Mehmet M Dalkilic, Scott M Beason, Jeff R Gehlhausen, Rupali Patwardhan, Sumit Middha, Brian D Eads, Justen R Andrews Genome Biology 2009, 10:R97 (16 September 2009) The first computational interaction network built from |
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Research article
Ignacio Rodriguez-Llorente, Miguel A Caviedes, Mohammed Dary, Antonio J Palomares, Francisco M Cánovas, José M Peregrín-Alvarez BMC Systems Biology 2009, 3:63 (16 June 2009) |
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Proceedings
Xiaotong Lin, Mei Liu, Xue-wen Chen BMC Bioinformatics 2009, 10(Suppl 4):S5 (29 April 2009) |
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Database
Arnis Druka, Ilze Druka, Arthur G Centeno, Hongqiang Li, Zhaohui Sun, William TB Thomas, Nicola Bonar, Brian J Steffenson, Steven E Ullrich, Andris Kleinhofs, Roger P Wise, Timothy J Close, Elena Potokina, Zewei Luo, Carola Wagner, Günther F Schweizer, David F Marshall, Michael J Kearsey, Robert W Williams, Robbie Waugh BMC Genetics 2008, 9:73 (18 November 2008) |
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Method
Weidong Tian, Lan V Zhang, Murat Taşan, Francis D Gibbons, Oliver D King, Julie Park, Zeba Wunderlich, J Michael Cherry, Frederick P Roth Genome Biology 2008, 9(Suppl 1):S7 (27 June 2008) |
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Method
Wan Kim, Chase Krumpelman, Edward M Marcotte Genome Biology 2008, 9(Suppl 1):S5 (27 June 2008) |
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Method
Sara Mostafavi, Debajyoti Ray, David Warde-Farley, Chris Grouios, Quaid Morris Genome Biology 2008, 9(Suppl 1):S4 (27 June 2008) |
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Research
Predicting gene function in a hierarchical context with an ensemble of classifiers Yuanfang Guan, Chad L Myers, David C Hess, Zafer Barutcuoglu, Amy A Caudy, Olga G Troyanskaya Genome Biology 2008, 9(Suppl 1):S3 (27 June 2008) |
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Research
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence Lourdes Peña-Castillo, Murat Tasan, Chad L Myers, Hyunju Lee, Trupti Joshi, Chao Zhang, Yuanfang Guan, Michele Leone, Andrea Pagnani, Wan Kim, Chase Krumpelman, Weidong Tian, Guillaume Obozinski, Yanjun Qi, Sara Mostafavi, Guan Lin, Gabriel F Berriz, Francis D Gibbons, Gert Lanckriet, Jian Qiu, Charles Grant, Zafer Barutcuoglu, David P Hill, David Warde-Farley, Chris Grouios, Debajyoti Ray, Judith A Blake, Minghua Deng, Michael I Jordan, William S Noble, Quaid Morris, Judith Klein-Seetharaman, Ziv Bar-Joseph, Ting Chen, Fengzhu Sun, Olga G Troyanskaya, Edward M Marcotte, Dong Xu, Timothy R Hughes, Frederick P Roth et al. Genome Biology 2008, 9(Suppl 1):S2 (27 June 2008) |
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Research article
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) |
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Research article
Rank-based edge reconstruction for scale-free genetic regulatory networks Guanrao Chen, Peter Larsen, Eyad Almasri, Yang Dai BMC Bioinformatics 2008, 9:75 (31 January 2008) |
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Research article
Annotating novel genes by integrating synthetic lethals and genomic information Daniel Schöner, Markus Kalisch, Christian Leisner, Lukas Meier, Marc Sohrmann, Mahamadou Faty, Yves Barral, Matthias Peter, Wilhelm Gruissem, Peter Bühlmann BMC Systems Biology 2008, 2:3 (14 January 2008) |
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Commentary
Christopher A Maxwell, Víctor Moreno, Xavier Solé, Laia Gómez, Pilar Hernández, Ander Urruticoechea, Miguel Pujana Molecular Cancer 2008, 7:4 (10 January 2008) |
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Method
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. |
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Review
Inferring cellular networks – a review Florian Markowetz, Rainer Spang BMC Bioinformatics 2007, 8(Suppl 6):S5 (27 September 2007) |
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Method
Haidong Wang, Eran Segal, Asa Ben-Hur, Qian-Ru Li, Marc Vidal, Daphne Koller Genome Biology 2007, 8:R192 (14 September 2007) InSite is a computational method that integrates high-throughput protein and sequence data to infer the specific binding regions of interacting protein pairs. |
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Research article
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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Research article
A direct comparison of protein interaction confidence assignment schemes Silpa Suthram, Tomer Shlomi, Eytan Ruppin, Roded Sharan, Trey Ideker BMC Bioinformatics 2006, 7:360 (26 July 2006) |
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Research article
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.
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