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Systematic integration of biomedical knowledge prioritizes drugs for repurposing.

Himmelstein DS, Lizee A, Hessler C, Brueggeman L, Chen SL, Hadley D, Green A, Khankhanian P, Baranzini SE.

Elife. 2017 Sep 22;6. pii: e26726. doi: 10.7554/eLife.26726.


Integrative approach in the era of failing drug discovery and development.

Earm K, Earm YE.

Integr Med Res. 2014 Dec;3(4):211-216. doi: 10.1016/j.imr.2014.09.002. Epub 2014 Sep 10. Review.


Efficient Drug-Pathway Association Analysis via Integrative Penalized Matrix Decomposition.

Li C, Yang C, Hather G, Liu R, Zhao H.

IEEE/ACM Trans Comput Biol Bioinform. 2016 May-Jun;13(3):531-40. doi: 10.1109/TCBB.2015.2462344.


CART-a chemical annotation retrieval toolkit.

Deghou S, Zeller G, Iskar M, Driessen M, Castillo M, van Noort V, Bork P.

Bioinformatics. 2016 Sep 15;32(18):2869-71. doi: 10.1093/bioinformatics/btw233. Epub 2016 Jun 2.


QSAR-Driven Discovery of Novel Chemical Scaffolds Active against Schistosoma mansoni.

Melo-Filho CC, Dantas RF, Braga RC, Neves BJ, Senger MR, Valente WC, Rezende-Neto JM, Chaves WT, Muratov EN, Paveley RA, Furnham N, Kamentsky L, Carpenter AE, Silva-Junior FP, Andrade CH.

J Chem Inf Model. 2016 Jul 25;56(7):1357-72. doi: 10.1021/acs.jcim.6b00055. Epub 2016 Jun 16.


Mining integrated semantic networks for drug repositioning opportunities.

Mullen J, Cockell SJ, Tipney H, Woollard PM, Wipat A.

PeerJ. 2016 Jan 19;4:e1558. doi: 10.7717/peerj.1558. eCollection 2016.


An automated real-time integration and interoperability framework for bioinformatics.

Lopes P, Oliveira JL.

BMC Bioinformatics. 2015 Oct 13;16:328. doi: 10.1186/s12859-015-0761-3.


A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case.

Huang LC, Soysal E, Zheng W, Zhao Z, Xu H, Sun J.

BMC Syst Biol. 2015;9 Suppl 4:S2. doi: 10.1186/1752-0509-9-S4-S2. Epub 2015 Jun 11.


Systems Pharmacology Links GPCRs with Retinal Degenerative Disorders.

Chen Y, Palczewski K.

Annu Rev Pharmacol Toxicol. 2016;56:273-98. doi: 10.1146/annurev-pharmtox-010715-103033. Epub 2015 Mar 23. Review.


Multi-omic landscape of rheumatoid arthritis: re-evaluation of drug adverse effects.

Tieri P, Zhou X, Zhu L, Nardini C.

Front Cell Dev Biol. 2014 Nov 4;2:59. doi: 10.3389/fcell.2014.00059. eCollection 2014.


Systematic analysis of new drug indications by drug-gene-disease coherent subnetworks.

Wang L, Wang Y, Hu Q, Li S.

CPT Pharmacometrics Syst Pharmacol. 2014 Nov 12;3:e146. doi: 10.1038/psp.2014.44.


Identification of structural features in chemicals associated with cancer drug response: a systematic data-driven analysis.

Khan SA, Virtanen S, Kallioniemi OP, Wennerberg K, Poso A, Kaski S.

Bioinformatics. 2014 Sep 1;30(17):i497-504. doi: 10.1093/bioinformatics/btu456.


A testing strategy to predict risk for drug-induced liver injury in humans using high-content screen assays and the 'rule-of-two' model.

Chen M, Tung CW, Shi Q, Guo L, Shi L, Fang H, Borlak J, Tong W.

Arch Toxicol. 2014 Jul;88(7):1439-49. doi: 10.1007/s00204-014-1276-9. Epub 2014 Jun 11.


Constructing and characterizing a bioactive small molecule and microRNA association network for Alzheimer's disease.

Meng F, Dai E, Yu X, Zhang Y, Chen X, Liu X, Wang S, Wang L, Jiang W.

J R Soc Interface. 2013 Dec 18;11(92):20131057. doi: 10.1098/rsif.2013.1057. Print 2014 Mar 6.


Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding.

Iskar M, Zeller G, Blattmann P, Campillos M, Kuhn M, Kaminska KH, Runz H, Gavin AC, Pepperkok R, van Noort V, Bork P.

Mol Syst Biol. 2013;9:662. doi: 10.1038/msb.2013.20.


Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review.

Csermely P, Korcsmáros T, Kiss HJ, London G, Nussinov R.

Pharmacol Ther. 2013 Jun;138(3):333-408. doi: 10.1016/j.pharmthera.2013.01.016. Epub 2013 Feb 4. Review.


Drug target inference through pathway analysis of genomics data.

Ma H, Zhao H.

Adv Drug Deliv Rev. 2013 Jun 30;65(7):966-72. doi: 10.1016/j.addr.2012.12.004. Epub 2013 Jan 28. Review.


Transcriptional data: a new gateway to drug repositioning?

Iorio F, Rittman T, Ge H, Menden M, Saez-Rodriguez J.

Drug Discov Today. 2013 Apr;18(7-8):350-7. doi: 10.1016/j.drudis.2012.07.014. Epub 2012 Aug 7.

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