My NCBISign In
GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function
Sara Mostafavi, Debajyoti Ray, David Warde-Farley, Chris Grouios, Quaid Morris
Genome Biol. 2008; 9(Suppl 1): S4. Published online 2008 June 27. doi: 10.1186/gb-2008-9-s1-s4
PMCID:
PMC2447538
Abstract Full Text PDF–332K Supplementary Material

Is Cited by the Following 25 Articles in this Archive:

Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations
Brian J. O’Roak, Laura Vives, Santhosh Girirajan, Emre Karakoc, Nik Krumm, Bradley P. Coe, Roie Levy, Arthur Ko, Choli Lee, Joshua D. Smith, Emily H. Turner, Ian B. Stanaway, Benjamin Vernot, Maika Malig, Carl Baker, Beau Reilly, Joshua M. Akey, Elhanan Borenstein, Mark J. Rieder, Deborah A. Nickerson, Raphael Bernier, Jay Shendure, Evan E. Eichler
Nature. Author manuscript; available in PMC 2012 October 4.
Published in final edited form as: Nature. 2012 April 4; 485(7397): 246–250. doi: 10.1038/nature10989
PMCID:
PMC3350576
Free in PMC on 2012/10/04
“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
Predicting the lethal phenotype of the knockout mouse by integrating comprehensive genomic data
Yuan Yuan, Yanxun Xu, Jianfeng Xu, Robyn L. Ball, Han Liang
Bioinformatics. 2012 May 1; 28(9): 1246–1252. Published online 2012 March 13. doi: 10.1093/bioinformatics/bts120
PMCID:
PMC3338016
Free in PMC on 2013/05/01
Uncovering the Molecular Machinery of the Human Spindle—An Integration of Wet and Dry Systems Biology
Ana M. Rojas, Anna Santamaria, Rainer Malik, Thomas Skøt Jensen, Roman Körner, Ian Morilla, David de Juan, Martin Krallinger, Daniel Aaen Hansen, Robert Hoffmann, Jonathan Lees, Adam Reid, Corin Yeats, Anja Wehner, Sabine Elowe, Andrew B. Clegg, Søren Brunak, Erich A. Nigg, Christine Orengo, Alfonso Valencia, Juan A. G. Ranea
PLoS One. 2012; 7(3): e31813. Published online 2012 March 9. doi: 10.1371/journal.pone.0031813
PMCID:
PMC3302876
Abstract Full Text PDF–803K Supplementary Material
Methods, Challenges, and Promise of Next-Generation Sequencing in Cancer Biology
Adrian D. Haimovich
Yale J Biol Med. 2011 December; 84(4): 439–446. Published online 2011 December.
PMCID:
PMC3238319
Abstract Full Text PDF–259K
Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks
Benjamin Haibe-Kains, Catharina Olsen, Amira Djebbari, Gianluca Bontempi, Mick Correll, Christopher Bouton, John Quackenbush
Nucleic Acids Res. 2012 January; 40(D1): D866–D875. Published online 2011 November 16. doi: 10.1093/nar/gkr1050
PMCID:
PMC3245161
Abstract Full Text PDF–3.7M
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
The influence of scaffold elasticity on germ layer specification of human embryonic stem cells
Janet Zoldan, Emmanouil D. Karagiannis, Christopher Y. Lee, Daniel G. Anderson, Robert Langer, Shulamit Levenberg
Biomaterials. Author manuscript; available in PMC 2012 December 1.
Published in final edited form as: Biomaterials. 2011 December; 32(36): 9612–9621. Published online 2011 October 1. doi: 10.1016/j.biomaterials.2011.09.012
PMCID:
PMC3313669
Free in PMC on 2012/12/01
Proceedings of the Tenth Annual UT-ORNL-KBRIN Bioinformatics Summit 2011
Eric C Rouchka, Robert M Flight, Ramin Homayouni
BMC Bioinformatics. 2011; 12(Suppl 7): A1. Published online 2011 August 5. doi: 10.1186/1471-2105-12-S7-A1
PMCID:
PMC3194199
Full Text PDF–221K
The role of indirect connections in gene networks in predicting function
Jesse Gillis, Paul Pavlidis
Bioinformatics. 2011 July 1; 27(13): 1860–1866. Published online 2011 May 6. doi: 10.1093/bioinformatics/btr288
PMCID:
PMC3117376
Free in PMC on 2012/07/01
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
ePlant and the 3D Data Display Initiative: Integrative Systems Biology on the World Wide Web
Geoffrey Fucile, David Di Biase, Hardeep Nahal, Garon La, Shokoufeh Khodabandeh, Yani Chen, Kante Easley, Dinesh Christendat, Lawrence Kelley, Nicholas J. Provart
PLoS One. 2011; 6(1): e15237. Published online 2011 January 10. doi: 10.1371/journal.pone.0015237
PMCID:
PMC3018417
Abstract Full Text PDF–1.1M 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
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
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
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 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
A methodology for the analysis of differential coexpression across the human lifespan
Jesse Gillis, Paul Pavlidis
BMC Bioinformatics. 2009; 10: 306. Published online 2009 September 22. doi: 10.1186/1471-2105-10-306
PMCID:
PMC2761903
Abstract Full Text PDF–384K Supplementary Material
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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