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An integrated approach to inferring gene-disease associations in humans.

Radivojac P, Peng K, Clark WT, Peters BJ, Mohan A, Boyle SM, Mooney SD.

Proteins. 2008 Aug 15;72(3):1030-7. doi: 10.1002/prot.21989.


Detecting disease genes based on semi-supervised learning and protein-protein interaction networks.

Nguyen TP, Ho TB.

Artif Intell Med. 2012 Jan;54(1):63-71. doi: 10.1016/j.artmed.2011.09.003. Epub 2011 Oct 14.


Co-clustering phenome-genome for phenotype classification and disease gene discovery.

Hwang T, Atluri G, Xie M, Dey S, Hong C, Kumar V, Kuang R.

Nucleic Acids Res. 2012 Oct;40(19):e146. doi: 10.1093/nar/gks615. Epub 2012 Jun 26.


Disease candidate gene identification and prioritization using protein interaction networks.

Chen J, Aronow BJ, Jegga AG.

BMC Bioinformatics. 2009 Feb 27;10:73. doi: 10.1186/1471-2105-10-73. Erratum in: BMC Bioinformatics. 2009;10:406.


Associating genes and protein complexes with disease via network propagation.

Vanunu O, Magger O, Ruppin E, Shlomi T, Sharan R.

PLoS Comput Biol. 2010 Jan 15;6(1):e1000641. doi: 10.1371/journal.pcbi.1000641.


Information-theoretic evaluation of predicted ontological annotations.

Clark WT, Radivojac P.

Bioinformatics. 2013 Jul 1;29(13):i53-61. doi: 10.1093/bioinformatics/btt228.


Global risk transformative prioritization for prostate cancer candidate genes in molecular networks.

Chen L, Tai J, Zhang L, Shang Y, Li X, Qu X, Li W, Miao Z, Jia X, Wang H, Li W, He W.

Mol Biosyst. 2011 Sep;7(9):2547-53. doi: 10.1039/c1mb05134b. Epub 2011 Jul 7.


Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: case study of primary immunodeficiencies.

Ortutay C, Vihinen M.

Nucleic Acids Res. 2009 Feb;37(2):622-8. doi: 10.1093/nar/gkn982. Epub 2008 Dec 10.


ToppGene Suite for gene list enrichment analysis and candidate gene prioritization.

Chen J, Bardes EE, Aronow BJ, Jegga AG.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W305-11. doi: 10.1093/nar/gkp427. Epub 2009 May 22.


Inferring gene-phenotype associations via global protein complex network propagation.

Yang P, Li X, Wu M, Kwoh CK, Ng SK.

PLoS One. 2011;6(7):e21502. doi: 10.1371/journal.pone.0021502. Epub 2011 Jul 25.


Discovering cancer genes by integrating network and functional properties.

Li L, Zhang K, Lee J, Cordes S, Davis DP, Tang Z.

BMC Med Genomics. 2009 Sep 19;2:61. doi: 10.1186/1755-8794-2-61.


Information theory applied to the sparse gene ontology annotation network to predict novel gene function.

Tao Y, Sam L, Li J, Friedman C, Lussier YA.

Bioinformatics. 2007 Jul 1;23(13):i529-38.


Identifying gene-disease associations using centrality on a literature mined gene-interaction network.

Ozg├╝r A, Vu T, Erkan G, Radev DR.

Bioinformatics. 2008 Jul 1;24(13):i277-85. doi: 10.1093/bioinformatics/btn182.


Inferring disease and gene set associations with rank coherence in networks.

Hwang T, Zhang W, Xie M, Liu J, Kuang R.

Bioinformatics. 2011 Oct 1;27(19):2692-9. doi: 10.1093/bioinformatics/btr463. Epub 2011 Aug 8.


EnrichNet: network-based gene set enrichment analysis.

Glaab E, Baudot A, Krasnogor N, Schneider R, Valencia A.

Bioinformatics. 2012 Sep 15;28(18):i451-i457. doi: 10.1093/bioinformatics/bts389.


Disease gene identification by random walk on multigraphs merging heterogeneous genomic and phenotype data.

Li Y, Li J.

BMC Genomics. 2012;13 Suppl 7:S27. doi: 10.1186/1471-2164-13-S7-S27. Epub 2012 Dec 13.


GPEC: a Cytoscape plug-in for random walk-based gene prioritization and biomedical evidence collection.

Le DH, Kwon YK.

Comput Biol Chem. 2012 Apr;37:17-23. doi: 10.1016/j.compbiolchem.2012.02.004. Epub 2012 Mar 3.


PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium.

Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, Thomas PD.

Nucleic Acids Res. 2010 Jan;38(Database issue):D204-10. doi: 10.1093/nar/gkp1019. Epub 2009 Dec 16.


WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation.

Capriotti E, Calabrese R, Fariselli P, Martelli PL, Altman RB, Casadio R.

BMC Genomics. 2013;14 Suppl 3:S6. doi: 10.1186/1471-2164-14-S3-S6. Epub 2013 May 28.

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