A review of validation strategies for computational drug repositioning

Adam S Brown; Chirag J Patel

doi:10.1093/bib/bbw110

journal article Open Access Nov 22, 2016

A review of validation strategies for computational drug repositioning

Adam S Brown Chirag J Patel

Briefings in Bioinformatics Vol. 19 No. 1 pp. 174-177 · Oxford University Press (OUP)

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References

22

[1]

Rodriguez-Esteban "A drug-centric view of drug development: how drugs spread from disease to disease" PLoS Comput Biol (2016) 10.1371/journal.pcbi.1004852

[2]

Li "A survey of current trends in computational drug repositioning" Brief Bioinform (2016) 10.1093/bib/bbv020

[3]

The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease

Justin Lamb, Emily D. Crawford, David Peck et al.

Science 2006 10.1126/science.1132939

[4]

Gottlieb "PREDICT: a method for inferring novel drug indications with application to personalized medicine" Mol Syst Biol (2011) 10.1038/msb.2011.26

[5]

Huang "DMAP: a connectivity map database to enable identification of novel drug repositioning candidates" BMC Bioinformatics (2015) 10.1186/1471-2105-16-s13-s4

[6]

Brown "ksRepo: a generalized platform for computational drug repositioning" BMC Bioinformatics (2016) 10.1186/s12859-016-0931-y

[7]

Qu "Inferring novel disease indications for known drugs by semantically linking drug action and disease mechanism relationships" BMC Bioinformatics (2009) 10.1186/1471-2105-10-s5-s4

[8]

Cheung "Quantitative biomedical annotation using medical subject heading over-representation profiles (MeSHOPs)" BMC Bioinformatics (2012) 10.1186/1471-2105-13-249

[9]

Kissa "Prediction of drug gene associations via ontological profile similarity with application to drug repositioning" Methods (2015) 10.1016/j.ymeth.2014.11.017

[10]

Patchala "Concept modeling-based drug repositioning" AMIA Jt Summits Transl Sci Proc (2015)

[11]

Ryan "Medication-wide association studies" CPT Pharmacometrics Syst Pharmacol (2013) 10.1038/psp.2013.52

[12]

Xu "Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality" J Am Med Inform Assoc (2015) 10.1136/amiajnl-2014-002649

[13]

Pahikkala "Toward more realistic drug–target interaction predictions" Brief Bioinform (2015) 10.1093/bib/bbu010

[14]

DrugBank: a comprehensive resource for in silico drug discovery and exploration

David S. Wishart

Nucleic Acids Research 2006 10.1093/nar/gkj067

[15]

Davis "The comparative toxicogenomics database’s 10th year anniversary: update 2015" Nucleic Acids Res (2015) 10.1093/nar/gku935

[16]

Sirota "Discovery and preclinical validation of drug indications using compendia of public gene expression data" Sci Transl Med (2011) 10.1126/scitranslmed.3001318

[17]

Jung "Inferring disease association using clinical factors in a combinatorial manner and their use in drug repositioning" Bioinformatics (2013) 10.1093/bioinformatics/btt327

[18]

Thorn "PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base" Methods Mol Biol (2005)

[19]

Zhu "Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery" Nucleic Acids Res (2012) 10.1093/nar/gkr797

[20]

Model selection and overfitting

Jake Lever, Martin Krzywinski, Naomi Altman

Nature Methods 2016 10.1038/nmeth.3968

[21]

An introduction to ROC analysis

Tom Fawcett

Pattern Recognition Letters 2006 10.1016/j.patrec.2005.10.010

[22]

Small-sample precision of ROC-related estimates

Blaise Hanczar, Jianping Hua, Chao Sima et al.

Bioinformatics 2010 10.1093/bioinformatics/btq037

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Metrics

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Citations

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References

Details

Published: Nov 22, 2016
Vol/Issue: 19(1)
Pages: 174-177
License: View

Authors

A

Adam S Brown

Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck St, Boston, MA, USA

C

Chirag J Patel

Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck St, Boston, MA, USA

Funding

National Institutes of Health

National Human Genome Research Institute Award: T32HG002295-12

Agilent Technologies

National Institute of Environmental Health Sciences Award: R00 ES023504

PhRMA fellowship

Cite This Article

Adam S Brown, Chirag J Patel (2016). A review of validation strategies for computational drug repositioning. Briefings in Bioinformatics, 19(1), 174-177. https://doi.org/10.1093/bib/bbw110

A review of validation strategies for computational drug repositioning

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