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Discovery of biological networks from diverse functional genomic data
Chad L Myers, Drew Robson, Adam Wible, Matthew A Hibbs, Camelia Chiriac, Chandra L Theesfeld, Kara Dolinski, Olga G Troyanskaya
Genome Biol. 2005; 6(13): R114. Published online 2005 December 19. doi: 10.1186/gb-2005-6-13-r114
PMCID:
PMC1414113
Abstract Full Text PDF–805K Supplementary Material

Is Cited by the Following 63 Articles in this Archive:

ScreenTroll: a searchable database to compare genome-wide yeast screens
Peter H. Thorpe, John C. Dittmar, Rodney Rothstein
Database (Oxford) 2012; 2012: bas022. Published online 2012 April 20. doi: 10.1093/database/bas022
PMCID:
PMC3330810
Abstract Full Text PDF–531K
“Guilt by Association” Is the Exception Rather Than the Rule in Gene Networks
Jesse Gillis, Paul Pavlidis
PLoS Comput Biol. 2012 March; 8(3): e1002444. Published online 2012 March 29. doi: 10.1371/journal.pcbi.1002444
PMCID:
PMC3315453
Abstract Full Text PDF–414K Supplementary Material
CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations
Julie Park, Maria C. Costanzo, Rama Balakrishnan, J. Michael Cherry, Eurie L. Hong
Database (Oxford) 2012; 2012: bas001. Published online 2012 February 13. doi: 10.1093/database/bas001
PMCID:
PMC3308158
Abstract Full Text PDF–437K
Yeast: An Experimental Organism for 21st Century Biology
David Botstein, Gerald R. Fink
Genetics. 2011 November; 189(3): 695–704. doi: 10.1534/genetics.111.130765
PMCID:
PMC3213361
Free in PMC on 2012/11/01
Removing bias against membrane proteins in interaction networks
Glauber C Brito, David W Andrews
BMC Syst Biol. 2011; 5: 169. Published online 2011 October 19. doi: 10.1186/1752-0509-5-169
PMCID:
PMC3213014
Abstract Full Text PDF–1.6M Supplementary Material
Small sets of interacting proteins suggest functional linkage mechanisms via Bayesian analogical reasoning
Edoardo M. Airoldi, Katherine A. Heller, Ricardo Silva
Bioinformatics. 2011 July 1; 27(13): i374–i382. Published online 2011 June 14. doi: 10.1093/bioinformatics/btr236
PMCID:
PMC3117334
Abstract Full Text
Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis
Artem Lysenko, Michael Defoin-Platel, Keywan Hassani-Pak, Jan Taubert, Charlie Hodgman, Christopher J Rawlings, Mansoor Saqi
BMC Bioinformatics. 2011; 12: 203. Published online 2011 May 25. doi: 10.1186/1471-2105-12-203
PMCID:
PMC3118170
Abstract Full Text PDF–1.2M Supplementary Material
Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study
Maria C. Costanzo, Julie Park, Rama Balakrishnan, J. Michael Cherry, Eurie L. Hong
Database (Oxford) 2011; 2011: bar004. Published online 2011 March 15. doi: 10.1093/database/bar004
PMCID:
PMC3067894
Abstract Full Text PDF–238K
Accurate Quantification of Functional Analogy among Close Homologs
Maria D. Chikina, Olga G. Troyanskaya
PLoS Comput Biol. 2011 February; 7(2): e1001074. Published online 2011 February 3. doi: 10.1371/journal.pcbi.1001074
PMCID:
PMC3033368
Abstract Full Text PDF–1.4M Supplementary Material
Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana
Ana Pop, Curtis Huttenhower, Anjali Iyer-Pascuzzi, Philip N Benfey, Olga G Troyanskaya
BMC Syst Biol. 2010; 4: 180. Published online 2010 December 31. doi: 10.1186/1752-0509-4-180
PMCID:
PMC3023688
Abstract Full Text PDF–838K Supplementary Material
A Scalable Approach for Discovering Conserved Active Subnetworks across Species
Raamesh Deshpande, Shikha Sharma, Catherine M. Verfaillie, Wei-Shou Hu, Chad L. Myers
PLoS Comput Biol. 2010 December; 6(12): e1001028. Published online 2010 December 9. doi: 10.1371/journal.pcbi.1001028
PMCID:
PMC3000367
Abstract Full Text PDF–879K Supplementary Material
Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components
Christopher Y. Park, David C. Hess, Curtis Huttenhower, Olga G. Troyanskaya
PLoS Comput Biol. 2010 November; 6(11): e1001009. Published online 2010 November 24. doi: 10.1371/journal.pcbi.1001009
PMCID:
PMC2991250
Abstract Full Text PDF–1.9M Supplementary Material
Functional Genomics Complements Quantitative Genetics in Identifying Disease-Gene Associations
Yuanfang Guan, Cheryl L. Ackert-Bicknell, Braden Kell, Olga G. Troyanskaya, Matthew A. Hibbs
PLoS Comput Biol. 2010 November; 6(11): e1000991. Published online 2010 November 11. doi: 10.1371/journal.pcbi.1000991
PMCID:
PMC2978695
Abstract Full Text PDF–1.0M Supplementary Material
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function
David Warde-Farley, Sylva L. Donaldson, Ovi Comes, Khalid Zuberi, Rashad Badrawi, Pauline Chao, Max Franz, Chris Grouios, Farzana Kazi, Christian Tannus Lopes, Anson Maitland, Sara Mostafavi, Jason Montojo, Quentin Shao, George Wright, Gary D. Bader, Quaid Morris
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W214–W220. Published online 2010 June 21. doi: 10.1093/nar/gkq537
PMCID:
PMC2896186
Abstract Full Text PDF–8.6M Supplementary Material
A Quick Guide to Large-Scale Genomic Data Mining
Curtis Huttenhower, Oliver Hofmann
PLoS Comput Biol. 2010 May; 6(5): e1000779. Published online 2010 May 27. doi: 10.1371/journal.pcbi.1000779
PMCID:
PMC2877728
Full Text PDF–882K Supplementary Material
Genetic interactions between a phospholipase A2 and the Rim101 pathway components in S. cerevisiae reveal a role for this pathway in response to changes in membrane composition and shape
M. Mattiazzi, A. Jambhekar, P. Kaferle, J. L. DeRisi, I. Križaj, U. Petrovič
Mol Genet Genomics. 2010 June; 283(6): 519–530. Published online 2010 April 9. doi: 10.1007/s00438-010-0533-8
PMCID:
PMC2872012
Abstract Full Text PDF–562K Supplementary Material
Systematic Planning of Genome-Scale Experiments in Poorly Studied Species
Yuanfang Guan, Maitreya Dunham, Amy Caudy, Olga Troyanskaya
PLoS Comput Biol. 2010 March; 6(3): e1000698. Published online 2010 March 5. doi: 10.1371/journal.pcbi.1000698
PMCID:
PMC2832676
Abstract Full Text PDF–1.6M Supplementary Material
How to Understand the Cell by Breaking It: Network Analysis of Gene Perturbation Screens
Florian Markowetz
PLoS Comput Biol. 2010 February; 6(2): e1000655. Published online 2010 February 26. doi: 10.1371/journal.pcbi.1000655
PMCID:
PMC2829042
Full Text PDF–323K
Integrative approaches to the prediction of protein functions based on the feature selection
Seokha Ko, Hyunju Lee
BMC Bioinformatics. 2009; 10: 455. Published online 2009 December 31. doi: 10.1186/1471-2105-10-455
PMCID:
PMC2813249
Abstract Full Text PDF–2.9M Supplementary Material
Graphle: Interactive exploration of large, dense graphs
Curtis Huttenhower, Sajid O Mehmood, Olga G Troyanskaya
BMC Bioinformatics. 2009; 10: 417. Published online 2009 December 14. doi: 10.1186/1471-2105-10-417
PMCID:
PMC2803856
Abstract Full Text PDF–526K
The Modular Organization of Protein Interactions in Escherichia coli
José M. Peregrín-Alvarez, Xuejian Xiong, Chong Su, John Parkinson
PLoS Comput Biol. 2009 October; 5(10): e1000523. Published online 2009 October 2. doi: 10.1371/journal.pcbi.1000523
PMCID:
PMC2739439
Abstract Full Text PDF–1.0M Supplementary Material
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 Biol. 2009; 10(9): R97. Published online 2009 September 16. doi: 10.1186/gb-2009-10-9-r97
PMCID:
PMC2768986
Abstract Full Text PDF–2.6M Supplementary Material
The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction
Curtis Huttenhower, Matthew A. Hibbs, Chad L. Myers, Amy A. Caudy, David C. Hess, Olga G. Troyanskaya
Bioinformatics. 2009 September 15; 25(18): 2404–2410. Published online 2009 June 26. doi: 10.1093/bioinformatics/btp397
PMCID:
PMC2735660
Abstract Full Text PDF–285K
The Symbiosis Interactome: a computational approach reveals novel components, functional interactions and modules in Sinorhizobium meliloti
Ignacio Rodriguez-Llorente, Miguel A Caviedes, Mohammed Dary, Antonio J Palomares, Francisco M Cánovas, José M Peregrín-Alvarez
BMC Syst Biol. 2009; 3: 63. Published online 2009 June 16. doi: 10.1186/1752-0509-3-63
PMCID:
PMC2701930
Abstract Full Text PDF–1.2M Supplementary Material
Assessing reliability of protein-protein interactions by integrative analysis of data in model organisms
Xiaotong Lin, Mei Liu, Xue-wen Chen
BMC Bioinformatics. 2009; 10(Suppl 4): S5. Published online 2009 April 29. doi: 10.1186/1471-2105-10-S4-S5
PMCID:
PMC2681066
Abstract Full Text PDF–1.4M
Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins
Pingzhao Hu, Sarath Chandra Janga, Mohan Babu, J. Javier Díaz-Mejía, Gareth Butland, Wenhong Yang, Oxana Pogoutse, Xinghua Guo, Sadhna Phanse, Peter Wong, Shamanta Chandran, Constantine Christopoulos, Anaies Nazarians-Armavil, Negin Karimi Nasseri, Gabriel Musso, Mehrab Ali, Nazila Nazemof, Veronika Eroukova, Ashkan Golshani, Alberto Paccanaro, Jack F Greenblatt, Gabriel Moreno-Hagelsieb, Andrew Emili
PLoS Biol. 2009 April; 7(4): e1000096. Published online 2009 April 28. doi: 10.1371/journal.pbio.1000096
PMCID:
PMC2672614
Abstract Full Text Supplementary Material
Web-Queryable Large-Scale Data Sets for Hypothesis Generation in Plant Biology
Siobhan M. Brady, Nicholas J. Provart
Plant Cell. 2009 April; 21(4): 1034–1051. doi: 10.1105/tpc.109.066050
PMCID:
PMC2685637
Abstract Full Text PDF–887K
Biomedical Discovery Acceleration, with Applications to Craniofacial Development
Sonia M. Leach, Hannah Tipney, Weiguo Feng, William A. Baumgartner, Jr., Priyanka Kasliwal, Ronald P. Schuyler, Trevor Williams, Richard A. Spritz, Lawrence Hunter
PLoS Comput Biol. 2009 March; 5(3): e1000215. Published online 2009 March 27. doi: 10.1371/journal.pcbi.1000215
PMCID:
PMC2653649
Abstract Full Text PDF–1.6M Supplementary Material
Computationally Driven, Quantitative Experiments Discover Genes Required for Mitochondrial Biogenesis
David C. Hess, Chad L. Myers, Curtis Huttenhower, Matthew A. Hibbs, Alicia P. Hayes, Jadine Paw, John J. Clore, Rosa M. Mendoza, Bryan San Luis, Corey Nislow, Guri Giaever, Michael Costanzo, Olga G. Troyanskaya, Amy A. Caudy
PLoS Genet. 2009 March; 5(3): e1000407. Published online 2009 March 20. doi: 10.1371/journal.pgen.1000407
PMCID:
PMC2648979
Abstract Full Text PDF–1.6M Supplementary Material
Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis
Matthew A. Hibbs, Chad L. Myers, Curtis Huttenhower, David C. Hess, Kai Li, Amy A. Caudy, Olga G. Troyanskaya
PLoS Comput Biol. 2009 March; 5(3): e1000322. Published online 2009 March 20. doi: 10.1371/journal.pcbi.1000322
PMCID:
PMC2654405
Abstract Full Text PDF–987K Supplementary Material
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