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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 Biol. 2008; 9(Suppl 1): S3. Published online 2008 June 27. doi: 10.1186/gb-2008-9-s1-s3
PMCID:
PMC2447537
Abstract Full Text PDF–1.9M
 Is Cited by the Following 20 Articles in this Archive:
Using Interpolation to Estimate System Uncertainty in Gene Expression Experiments
Lee J. Falin, Brett M. Tyler
PLoS One. 2011; 6(7): e22071. Published online 2011 July 22. doi: 10.1371/journal.pone.0022071
PMCID:
PMC3142119
Abstract Full Text PDF–473K 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
Enriching for correct prediction of biological processes using a combination of diverse classifiers
Daijin Ko, Brad Windle
BMC Bioinformatics. 2011; 12: 189. Published online 2011 May 23. doi: 10.1186/1471-2105-12-189
PMCID:
PMC3121646
Abstract Full Text PDF–414K
A Gene-Phenotype Network for the Laboratory Mouse and Its Implications for Systematic Phenotyping
Octavio Espinosa, John M. Hancock
PLoS One. 2011; 6(5): e19693. Published online 2011 May 19. doi: 10.1371/journal.pone.0019693
PMCID:
PMC3098258
Abstract Full Text PDF–926K Supplementary Material
SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells
Huilei Xu, Ihor R Lemischka, Avi Ma'ayan
BMC Syst Biol. 2010; 4: 173. Published online 2010 December 21. doi: 10.1186/1752-0509-4-173
PMCID:
PMC3019180
Abstract Full Text PDF–627K 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
Predicting gene function using few positive examples and unlabeled ones
Yiming Chen, Zhoujun Li, Xiaofeng Wang, Jiali Feng, Xiaohua Hu
BMC Genomics. 2010; 11(Suppl 2): S11. Published online 2010 November 2. doi: 10.1186/1471-2164-11-S2-S11
PMCID:
PMC2975410
Abstract Full Text PDF–844K
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
Bayesian Markov Random Field Analysis for Protein Function Prediction Based on Network Data
Yiannis A. I. Kourmpetis, Aalt D. J. van Dijk, Marco C. A. M. Bink, Roeland C. H. J. van Ham, Cajo J. F. ter Braak
PLoS One. 2010; 5(2): e9293. Published online 2010 February 24. doi: 10.1371/journal.pone.0009293
PMCID:
PMC2827541
Abstract Full Text PDF–1.1M 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
Identification of protein functions using a machine-learning approach based on sequence-derived properties
Bum Ju Lee, Moon Sun Shin, Young Joon Oh, Hae Seok Oh, Keun Ho Ryu
Proteome Sci. 2009; 7: 27. Published online 2009 August 9. doi: 10.1186/1477-5956-7-27
PMCID:
PMC2731080
Abstract Full Text PDF–1.5M
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
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
Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge
Martin Krallinger, Alexander Morgan, Larry Smith, Florian Leitner, Lorraine Tanabe, John Wilbur, Lynette Hirschman, Alfonso Valencia
Genome Biol. 2008; 9(Suppl 2): S1. Published online 2008 September 1. doi: 10.1186/gb-2008-9-s2-s1
PMCID:
PMC2559980
Abstract Full Text PDF–848K
Automating curation using a natural language processing pipeline
Beatrice Alex, Claire Grover, Barry Haddow, Mijail Kabadjov, Ewan Klein, Michael Matthews, Richard Tobin, Xinglong Wang
Genome Biol. 2008; 9(Suppl 2): S10. Published online 2008 September 1. doi: 10.1186/gb-2008-9-s2-s10
PMCID:
PMC2559981
Abstract Full Text PDF–478K
OntoGene in BioCreative II
Fabio Rinaldi, Thomas Kappeler, Kaarel Kaljurand, Gerold Schneider, Manfred Klenner, Simon Clematide, Michael Hess, Jean-Marc von Allmen, Pierre Parisot, Martin Romacker, Therese Vachon
Genome Biol. 2008; 9(Suppl 2): S13. Published online 2008 September 1. doi: 10.1186/gb-2008-9-s2-s13
PMCID:
PMC2559984
Abstract Full Text PDF–702K
Gene mention normalization and interaction extraction with context models and sentence motifs
Jörg Hakenberg, Conrad Plake, Loic Royer, Hendrik Strobelt, Ulf Leser, Michael Schroeder
Genome Biol. 2008; 9(Suppl 2): S14. Published online 2008 September 1. doi: 10.1186/gb-2008-9-s2-s14
PMCID:
PMC2559985
Abstract Full Text PDF–779K Supplementary Material
Introducing meta-services for biomedical information extraction
Florian Leitner, Martin Krallinger, Carlos Rodriguez-Penagos, Jörg Hakenberg, Conrad Plake, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tzong-Han Tsai, Hsi-Chuan Hung, William W Lau, Calvin A Johnson, Rune Sætre, Kazuhiro Yoshida, Yan Hua Chen, Sun Kim, Soo-Yong Shin, Byoung-Tak Zhang, William A Baumgartner, Jr, Lawrence Hunter, Barry Haddow, Michael Matthews, Xinglong Wang, Patrick Ruch, Frédéric Ehrler, Arzucan Özgür, Güneş Erkan, Dragomir R Radev, Michael Krauthammer, ThaiBinh Luong, Robert Hoffmann, Chris Sander, Alfonso Valencia
Genome Biol. 2008; 9(Suppl 2): S6. Published online 2008 September 1. doi: 10.1186/gb-2008-9-s2-s6
PMCID:
PMC2559990
Abstract Full Text PDF–1.7M
Concept recognition for extracting protein interaction relations from biomedical text
William A Baumgartner, Jr, Zhiyong Lu, Helen L Johnson, J Gregory Caporaso, Jesse Paquette, Anna Lindemann, Elizabeth K White, Olga Medvedeva, K Bretonnel Cohen, Lawrence Hunter
Genome Biol. 2008; 9(Suppl 2): S9. Published online 2008 September 1. doi: 10.1186/gb-2008-9-s2-s9
PMCID:
PMC2559993
Abstract Full Text PDF–270K
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