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Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function
Weidong Tian, Lan V Zhang, Murat Taşan, Francis D Gibbons, Oliver D King, Julie Park, Zeba Wunderlich, J Michael Cherry, Frederick P Roth
Genome Biol. 2008; 9(Suppl 1): S7. Published online 2008 June 27. doi: 10.1186/gb-2008-9-s1-s7
PMCID:
PMC2447541
Abstract Full Text PDF–1.6M Supplementary Material
 Is Cited by the Following 10 Articles in this Archive:
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
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
A Genome-Wide Gene Function Prediction Resource for Drosophila melanogaster
Han Yan, Kavitha Venkatesan, John E. Beaver, Niels Klitgord, Muhammed A. Yildirim, Tong Hao, David E. Hill, Michael E. Cusick, Norbert Perrimon, Frederick P. Roth, Marc Vidal
PLoS One. 2010; 5(8): e12139. Published online 2010 August 12. doi: 10.1371/journal.pone.0012139
PMCID:
PMC2920829
Abstract Full Text PDF–2.8M Supplementary Material
Predicting genetic modifier loci using functional gene networks
Insuk Lee, Ben Lehner, Tanya Vavouri, Junha Shin, Andrew G. Fraser, Edward M. Marcotte
Genome Res. 2010 August; 20(8): 1143–1153. doi: 10.1101/gr.102749.109
PMCID:
PMC2909577
Abstract Full Text PDF–1.1M
It’s the machine that matters: Predicting gene function and phenotype from protein networks
Peggy I. Wang, Edward M. Marcotte
J Proteomics. Author manuscript; available in PMC 2011 October 10.
Published in final edited form as: J Proteomics. 2010 October 10; 73(11): 2277–2289. Published online 2010 July 15. doi: 10.1016/j.jprot.2010.07.005
PMCID:
PMC2953423
Abstract Full Text PDF–4.2M
FuncBase : a resource for quantitative gene function annotation
John E. Beaver, Murat Taşan, Francis D. Gibbons, Weidong Tian, Timothy R. Hughes, Frederick P. Roth
Bioinformatics. 2010 July 15; 26(14): 1806–1807. Published online 2010 May 21. doi: 10.1093/bioinformatics/btq265
PMCID:
PMC2894510
Abstract Full Text PDF–173K
Representing Ontogeny Through Ontology: A Developmental Biologist’s Guide to The Gene Ontology
David P. Hill, Tanya Z. Berardini, Douglas G. Howe, Kimberly M. Van Auken
Mol Reprod Dev. Author manuscript; available in PMC 2011 April 1.
Published in final edited form as: Mol Reprod Dev. 2010 April; 77(4): 314–329. doi: 10.1002/mrd.21130
PMCID:
PMC2830379
Abstract Full Text PDF–837K
Genomics Portals: integrative web-platform for mining genomics data
Kaustubh Shinde, Mukta Phatak, Freudenberg M Johannes, Jing Chen, Qian Li, Joshi K Vineet, Zhen Hu, Krishnendu Ghosh, Jaroslaw Meller, Mario Medvedovic
BMC Genomics. 2010; 11: 27. Published online 2010 January 13. doi: 10.1186/1471-2164-11-27
PMCID:
PMC2824719
Abstract Full Text PDF–2.3M Supplementary Material
Predicting gene function using hierarchical multi-label decision tree ensembles
Leander Schietgat, Celine Vens, Jan Struyf, Hendrik Blockeel, Dragi Kocev, Sašo Džeroski
BMC Bioinformatics. 2010; 11: 2. Published online 2010 January 2. doi: 10.1186/1471-2105-11-2
PMCID:
PMC2824675
Abstract Full Text PDF–2.1M
Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns
Karen R. Christie, Eurie L. Hong, J. Michael Cherry
Trends Microbiol. Author manuscript; available in PMC 2011 March 15.
Published in final edited form as: Trends Microbiol. 2009 July; 17(7): 286–294. Published online 2009 July 2. doi: 10.1016/j.tim.2009.04.005
PMCID:
PMC3057094
Abstract Full Text PDF–273K
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