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Inferring drug-disease associations from integration of chemical, genomic and phenotype data using network propagation.

Huang YF, Yeh HY, Soo VW.

BMC Med Genomics. 2013;6 Suppl 3:S4. doi: 10.1186/1755-8794-6-S3-S4. Epub 2013 Nov 11.


Drug target prediction and repositioning using an integrated network-based approach.

Emig D, Ivliev A, Pustovalova O, Lancashire L, Bureeva S, Nikolsky Y, Bessarabova M.

PLoS One. 2013 Apr 4;8(4):e60618. doi: 10.1371/journal.pone.0060618. Print 2013.


Integration of Multiple Genomic and Phenotype Data to Infer Novel miRNA-Disease Associations.

Shi H, Zhang G, Zhou M, Cheng L, Yang H, Wang J, Sun J, Wang Z.

PLoS One. 2016 Feb 5;11(2):e0148521. doi: 10.1371/journal.pone.0148521. eCollection 2016.


Linking PharmGKB to phenotype studies and animal models of disease for drug repurposing.

Hoehndorf R, Oellrich A, Rebholz-Schuhmann D, Schofield PN, Gkoutos GV.

Pac Symp Biocomput. 2012:388-99.


Use of genome-wide association studies for cancer research and drug repositioning.

Zhang J, Jiang K, Lv L, Wang H, Shen Z, Gao Z, Wang B, Yang Y, Ye Y, Wang S.

PLoS One. 2015 Mar 24;10(3):e0116477. doi: 10.1371/journal.pone.0116477. eCollection 2015.


Inferring novel lncRNA-disease associations based on a random walk model of a lncRNA functional similarity network.

Sun J, Shi H, Wang Z, Zhang C, Liu L, Wang L, He W, Hao D, Liu S, Zhou M.

Mol Biosyst. 2014 Aug;10(8):2074-81. doi: 10.1039/c3mb70608g.


Inferring the perturbed microRNA regulatory networks from gene expression data using a network propagation based method.

Wang T, Gu J, Li Y.

BMC Bioinformatics. 2014 Jul 29;15:255. doi: 10.1186/1471-2105-15-255.


PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries.

Huang H, Wu X, Sonachalam M, Mandape SN, Pandey R, MacDorman KF, Wan P, Chen JY.

BMC Bioinformatics. 2012;13 Suppl 15:S2. doi: 10.1186/1471-2105-13-S15-S2. Epub 2012 Sep 11.


Predicting response to preoperative chemotherapy agents by identifying drug action on modeled microRNA regulation networks.

Zhu L, Liu J, Liang F, Rayner S, Xiong J.

PLoS One. 2014 May 21;9(5):e98140. doi: 10.1371/journal.pone.0098140. eCollection 2014.


Prediction of disease genes using tissue-specified gene-gene network.

Ganegoda G, Wang J, Wu FX, Li M.

BMC Syst Biol. 2014;8 Suppl 3:S3. doi: 10.1186/1752-0509-8-S3-S3. Epub 2014 Oct 22.


Integrative pathway analysis of genome-wide association studies and gene expression data in prostate cancer.

Jia P, Liu Y, Zhao Z.

BMC Syst Biol. 2012;6 Suppl 3:S13. doi: 10.1186/1752-0509-6-S3-S13. Epub 2012 Dec 17.


Inferring drug-disease associations based on known protein complexes.

Yu L, Huang J, Ma Z, Zhang J, Zou Y, Gao L.

BMC Med Genomics. 2015;8 Suppl 2:S2. doi: 10.1186/1755-8794-8-S2-S2. Epub 2015 May 29.


Cliques for the identification of gene signatures for colorectal cancer across population.

Pradhan MP, Nagulapalli K, Palakal MJ.

BMC Syst Biol. 2012;6 Suppl 3:S17. doi: 10.1186/1752-0509-6-S3-S17. Epub 2012 Dec 17.


Applications of Connectivity Map in drug discovery and development.

Qu XA, Rajpal DK.

Drug Discov Today. 2012 Dec;17(23-24):1289-98. doi: 10.1016/j.drudis.2012.07.017. Epub 2012 Aug 5. Review.


Network based approach to drug discovery: a mini review.

Li P, Fu Y, Wang Y.

Mini Rev Med Chem. 2015;15(8):687-95. Review.


Chemical genetics-based target identification in drug discovery.

Cong F, Cheung AK, Huang SM.

Annu Rev Pharmacol Toxicol. 2012;52:57-78. doi: 10.1146/annurev-pharmtox-010611-134639. Epub 2011 Aug 2. Review.


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.


IPAD: the Integrated Pathway Analysis Database for Systematic Enrichment Analysis.

Zhang F, Drabier R.

BMC Bioinformatics. 2012;13 Suppl 15:S7. doi: 10.1186/1471-2105-13-S15-S7. Epub 2012 Sep 11.


Chemical biology approaches to target validation in cancer.

Blagg J, Workman P.

Curr Opin Pharmacol. 2014 Aug;17:87-100. doi: 10.1016/j.coph.2014.07.007. Epub 2014 Aug 28. Review.

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