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Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy
Wan Kyu Kim, Chase Krumpelman, Edward M Marcotte
Genome Biol. 2008; 9(Suppl 1): S5. Published online 2008 June 27. doi: 10.1186/gb-2008-9-s1-s5
PMCID:
PMC2447539
Abstract Full Text PDF–393K Supplementary Material
 Is Cited by the Following 19 Articles in this Archive:
Systematic Search for Recipes to Generate Induced Pluripotent Stem Cells
Rui Chang, Robert Shoemaker, Wei Wang
PLoS Comput Biol. 2011 December; 7(12): e1002300. Published online 2011 December 22. doi: 10.1371/journal.pcbi.1002300
PMCID:
PMC3245295
Abstract Full Text PDF–765K Supplementary Material
Genetic dissection of the biotic stress response using a genome-scale gene network for rice
Insuk Lee, Young-Su Seo, Dusica Coltrane, Sohyun Hwang, Taeyun Oh, Edward M. Marcotte, Pamela C. Ronald
Proc Natl Acad Sci U S A. 2011 November 8; 108(45): 18548–18553. Published online 2011 October 31. doi: 10.1073/pnas.1110384108
PMCID:
PMC3215029
Abstract Full Text PDF–1.2M Supplementary Material
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
A novel method to identify cooperative functional modules: study of module coordination in the Saccharomyces cerevisiae cell cycle
Jeh-Ting Hsu, Chien-Hua Peng, Wen-Ping Hsieh, Chung-Yu Lan, Chuan Yi Tang
BMC Bioinformatics. 2011; 12: 281. Published online 2011 July 12. doi: 10.1186/1471-2105-12-281
PMCID:
PMC3143111
Abstract Full Text PDF–5.2M Supplementary Material
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
Prediction of quantitative phenotypes based on genetic networks: a case study in yeast sporulation
Li Shen, Iouri Chepelev, Jie Liu, Wei Wang
BMC Syst Biol. 2010; 4: 128. Published online 2010 September 10. doi: 10.1186/1752-0509-4-128
PMCID:
PMC2944141
Abstract Full Text PDF–558K 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
Computational analysis of tissue-specific gene networks: application to murine retinal functional studies
Jianfei Hu, Jun Wan, Laszlo Hackler, Jr., Donald J. Zack, Jiang Qian
Bioinformatics. 2010 September 15; 26(18): 2289–2297. Published online 2010 July 8. doi: 10.1093/bioinformatics/btq408
PMCID:
PMC2935398
Abstract Full Text PDF–483K Supplementary Material
Clustering phenotype populations by genome-wide RNAi and multiparametric imaging
Florian Fuchs, Gregoire Pau, Dominique Kranz, Oleg Sklyar, Christoph Budjan, Sandra Steinbrink, Thomas Horn, Angelika Pedal, Wolfgang Huber, Michael Boutros
Mol Syst Biol. 2010; 6: 370. Published online 2010 June 8. doi: 10.1038/msb.2010.25
PMCID:
PMC2913390
Abstract Full Text PDF–2.5M 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
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
Ontological Discovery Environment: A system for integrating gene-phenotype associations
Erich J. Baker, Jeremy J. Jay, Vivek M. Philip, Yun Zhang, Zuopan Li, Roumyana Kirova, Michael A. Langston, Elissa J. Chesler
Genomics. Author manuscript; available in PMC 2010 December 1.
Published in final edited form as: Genomics. 2009 December; 94(6): 377–387. Published online 2009 September 3. doi: 10.1016/j.ygeno.2009.08.016
PMCID:
PMC2783409
Abstract Full Text PDF–3.8M
Mining gene functional networks to improve mass-spectrometry-based protein identification
Smriti R. Ramakrishnan, Christine Vogel, Taejoon Kwon, Luiz O. Penalva, Edward M. Marcotte, Daniel P. Miranker
Bioinformatics. 2009 November 15; 25(22): 2955–2961. Published online 2009 July 24. doi: 10.1093/bioinformatics/btp461
PMCID:
PMC2773251
Abstract Full Text PDF–302K
Global Prediction of Tissue-Specific Gene Expression and Context-Dependent Gene Networks in Caenorhabditis elegans
Maria D. Chikina, Curtis Huttenhower, Coleen T. Murphy, Olga G. Troyanskaya
PLoS Comput Biol. 2009 June; 5(6): e1000417. Published online 2009 June 19. doi: 10.1371/journal.pcbi.1000417
PMCID:
PMC2692103
Abstract Full Text PDF–1.7M Supplementary Material
Comparative systems biology of human and mouse as a tool to guide the modeling of human placental pathology
Brian Cox, Max Kotlyar, Andreas I Evangelou, Vladimir Ignatchenko, Alex Ignatchenko, Kathie Whiteley, Igor Jurisica, S Lee Adamson, Janet Rossant, Thomas Kislinger
Mol Syst Biol. 2009; 5: 279. Published online 2009 June 16. doi: 10.1038/msb.2009.37
PMCID:
PMC2710868
Abstract Full Text PDF–1.2M 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
Text mining for biology - the way forward: opinions from leading scientists
Russ B Altman, Casey M Bergman, Judith Blake, Christian Blaschke, Aaron Cohen, Frank Gannon, Les Grivell, Udo Hahn, William Hersh, Lynette Hirschman, Lars Juhl Jensen, Martin Krallinger, Barend Mons, Seán I O'Donoghue, Manuel C Peitsch, Dietrich Rebholz-Schuhmann, Hagit Shatkay, Alfonso Valencia
Genome Biol. 2008; 9(Suppl 2): S7. Published online 2008 September 1. doi: 10.1186/gb-2008-9-s2-s7
PMCID:
PMC2559991
Abstract Full Text PDF–231K
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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