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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 Kyu Kim, Chase Krumpelman, Weidong Tian, Guillaume Obozinski, Yanjun Qi, Sara Mostafavi, Guan Ning 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
Genome Biol. 2008; 9(Suppl 1): S2. Published online 2008 June 27. doi: 10.1186/gb-2008-9-s1-s2
PMCID:
PMC2447536
Abstract Full Text PDF–2.8M Supplementary Material
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 Is Cited by the Following 40 Articles in this Archive:
The Proteome Folding Project: Proteome-scale prediction of structure and function
Kevin Drew, Patrick Winters, Glenn L. Butterfoss, Viktors Berstis, Keith Uplinger, Jonathan Armstrong, Michael Riffle, Erik Schweighofer, Bill Bovermann, David R. Goodlett, Trisha N. Davis, Dennis Shasha, Lars Malmström, Richard Bonneau
Genome Res. 2011 November; 21(11): 1981–1994. doi: 10.1101/gr.121475.111
PMCID:
PMC3205581
Abstract Full Text PDF–1.1M
Predicting gene ontology from a global meta-analysis of 1-color microarray experiments
Mikhail G Dozmorov, Cory B Giles, Jonathan D Wren
BMC Bioinformatics. 2011; 12(Suppl 10): S14. Published online 2011 October 18. doi: 10.1186/1471-2105-12-S10-S14
PMCID:
PMC3236836
Abstract Full Text PDF–5.8M
Analysis of VEGF-A Regulated Gene Expression in Endothelial Cells to Identify Genes Linked to Angiogenesis
Corban G. Rivera, Sofie Mellberg, Lena Claesson-Welsh, Joel S. Bader, Aleksander S. Popel
PLoS One. 2011; 6(9): e24887. Published online 2011 September 13. doi: 10.1371/journal.pone.0024887
PMCID:
PMC3172305
Abstract Full Text PDF–655K 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
Integrative computational biology for cancer research
Kristen Fortney, Igor Jurisica
Hum Genet. 2011 October; 130(4): 465–481. Published online 2011 April 22. doi: 10.1007/s00439-011-0983-z
PMCID:
PMC3179275
Abstract Full Text PDF–2.3M Supplementary Material
The Impact of Multifunctional Genes on "Guilt by Association" Analysis
Jesse Gillis, Paul Pavlidis
PLoS One. 2011; 6(2): e17258. Published online 2011 February 18. doi: 10.1371/journal.pone.0017258
PMCID:
PMC3041792
Abstract Full Text PDF–706K Supplementary Material
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
Saccharomyces cerevisiae as a Model Organism: A Comparative Study
Hiren Karathia, Ester Vilaprinyo, Albert Sorribas, Rui Alves
PLoS One. 2011; 6(2): e16015. Published online 2011 February 2. doi: 10.1371/journal.pone.0016015
PMCID:
PMC3032731
Abstract Full Text PDF–1.2M Supplementary Material
Predicting Functions of Proteins in Mouse Based on Weighted Protein-Protein Interaction Network and Protein Hybrid Properties
Lele Hu, Tao Huang, Xiaohe Shi, Wen-Cong Lu, Yu-Dong Cai, Kuo-Chen Chou
PLoS One. 2011; 6(1): e14556. Published online 2011 January 19. doi: 10.1371/journal.pone.0014556
PMCID:
PMC3023709
Abstract Full Text PDF–193K Supplementary Material
Deciphering the Code for Retroviral Integration Target Site Selection
Federico Andrea Santoni, Oliver Hartley, Jeremy Luban
PLoS Comput Biol. 2010 November; 6(11): e1001008. Published online 2010 November 24. doi: 10.1371/journal.pcbi.1001008
PMCID:
PMC2991247
Abstract Full Text PDF–2.8M Supplementary Material
Generalized random set framework for functional enrichment analysis using primary genomics datasets
Johannes M. Freudenberg, Siva Sivaganesan, Mukta Phatak, Kaustubh Shinde, Mario Medvedovic
Bioinformatics. 2011 January 1; 27(1): 70–77. Published online 2010 October 22. doi: 10.1093/bioinformatics/btq593
PMCID:
PMC3025713
Abstract Full Text PDF–547K Supplementary Material
GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop
J. Montojo, K. Zuberi, H. Rodriguez, F. Kazi, G. Wright, S. L. Donaldson, Q. Morris, G. D. Bader
Bioinformatics. 2010 November 15; 26(22): 2927–2928. Published online 2010 October 5. doi: 10.1093/bioinformatics/btq562
PMCID:
PMC2971582
Abstract Full Text PDF–187K
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
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
Fast integration of heterogeneous data sources for predicting gene function with limited annotation
Sara Mostafavi, Quaid Morris
Bioinformatics. 2010 July 15; 26(14): 1759–1765. Published online 2010 May 27. doi: 10.1093/bioinformatics/btq262
PMCID:
PMC2894508
Abstract Full Text PDF–283K Supplementary Material
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
Bayesian approach to transforming public gene expression repositories into disease diagnosis databases
Haiyan Huang, Chun-Chi Liu, Xianghong Jasmine Zhou
Proc Natl Acad Sci U S A. 2010 April 13; 107(15): 6823–6828. Published online 2010 April 1. doi: 10.1073/pnas.0912043107
PMCID:
PMC2872390
Abstract Full Text PDF–400K 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
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
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
The planar cell polarity effector Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development
Ryan S. Gray, Philip B. Abitua, Bogdan J. Wlodarczyk, Heather L. Szabo-Rogers, Otis Blanchard, Insuk Lee, Greg S. Weiss, Karen J. Liu, Edward M. Marcotte, John B. Wallingford, Richard H. Finnell
Nat Cell Biol. Author manuscript; available in PMC 2010 April 1.
Published in final edited form as: Nat Cell Biol. 2009 October; 11(10): 1225–1232. Published online 2009 September 20. doi: 10.1038/ncb1966
PMCID:
PMC2755648
Abstract Full Text PDF–5.1M 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
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
A Computational Screen for Regulators of Oxidative Phosphorylation Implicates SLIRP in Mitochondrial RNA Homeostasis
Joshua M. Baughman, Roland Nilsson, Vishal M. Gohil, Daniel H. Arlow, Zareen Gauhar, Vamsi K. Mootha
PLoS Genet. 2009 August; 5(8): e1000590. Published online 2009 August 14. doi: 10.1371/journal.pgen.1000590
Correction in:
PLoS Genet. 2010 March; 6(3): 10.1371/annotation/36fe7624-0904-46d4-a013-4be6195245c4.
PMCID:
PMC2721412
Abstract Full Text PDF–996K Supplementary Material Correction
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
VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology
Zhenjun Hu, Jui-Hung Hung, Yan Wang, Yi-Chien Chang, Chia-Ling Huang, Matt Huyck, Charles DeLisi
Nucleic Acids Res. 2009 July 1; 37(Web Server issue): W115–W121. Published online 2009 July 1. doi: 10.1093/nar/gkp406
PMCID:
PMC2703932
Abstract Full Text PDF–7.0M 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
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
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