Translational bioinformatics: Data-driven drug discovery and development

Clinical Pharmacology and Therapeutics

Volumn 91, Issue 6, 2012, Pages 949-952

  Butte, A J ^a,b   Ito, S ^c  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b LUCILE PACKARD CHILDREN S HOSPITAL   (United States)

^c HOSPITAL FOR SICK CHILDREN   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; DRUG DEVELOPMENT; DRUG RESEARCH; DRUG SAFETY; DRUG SURVEILLANCE PROGRAM; PREDICTION; PRIORITY JOURNAL; REVIEW; TRANSLATIONAL BIOINFORMATICS;

ANIMALS; COMPUTATIONAL BIOLOGY; COMPUTERS; DATABASES, FACTUAL; DATABASES, GENETIC; DRUG DISCOVERY; HUMANS; PHARMACOLOGY; TRANSLATIONAL MEDICAL RESEARCH;

EID: 84861410191     PISSN: 00099236     EISSN: 15326535     Source Type: Journal    
DOI: 10.1038/clpt.2012.55     Document Type: Review

References (27)

1. Leiter, J., Bourke, A.R., Fitzgerald, D.B., Schepartz, S.A. & Wodinsky, I. Screening data from the Cancer Chemotherapy National Service Center screening laboratories. VII. Cancer Res. 22 (Suppl), 221-353 (1962).
2. IBM. 1401 Data processing system http://www-03. ibm.com/ibm/history/ exhibits/mainframe/mainframe-PP1401.html (1959).
3. Dudley, J.T., Pouliot, Y., Chen, R., Morgan, A.A. & Butte, A.J. Translational bioinformatics in the cloud: an affordable alternative. Genome Med. 2, 51 (2010).
4. Galperin, M.Y. & Fernandez-Suarez, X.M. The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. Nucleic Acids Res. 40, D1-D8 (2012).
5. Wang, Y. et al. PubChem's BioAssay Database. Nucleic Acids Res. 40, D400-D412 (2012).
6. Butte, A.J. Translational bioinformatics: coming of age. J. Am. Med. Inform. Assoc. 15, 709-714 (2008).
7. Altman, R.B. Translational bioinformatics: linking the molecular world to the clinical world. Clin. Pharmacol. Ther. 91, 994-1000 (2012).
8. Cordero, P. & Ashley, E. Whole-genome sequencing in personalized therapeutics. Clin. Pharmacol. Ther. 91, 1001-1009 (2012).
9. Harpaz, R., DuMouchel, W., Shah, N.H., Madigan, D., Ryan, P. & Friedman, C. Novel data-mining methodologies for adverse drug event discovery and analysis. Clin. Pharmacol. Ther. 91, 1010-1021(2012).
10. Weinstein, J.N. et al. An information-intensive approach to the molecular pharmacology of cancer. Science 275, 343-349 (1997). (Pubitemid 27051604)
11. Barker, A.D., Sigman, C.C., Kelloff, G.J., Hylton, N.M., Berry, D.A. & Esserman, L.J. I-SPY 2: an adaptive breast cancer trial design in the setting of neoadjuvant chemotherapy. Clin. Pharmacol. Ther. 86, 97-100 (2009).
12. Harris, P.A., Taylor, R., Thielke, R., Payne, J., Gonzalez, N. & Conde, J.G. Research electronic data capture (REDCap)-a metadata-driven methodology and workflow process for providing translational research informatics support. J. Biomed. Inform. 42, 377-381 (2009).
13. Lehman, H.P. et al. An evaluation of computer-aided disproportionality analysis for post-marketing signal detection. Clin. Pharmacol. Ther. 82, 173-180 (2007). (Pubitemid 47075337)
14. Pouliot, Y., Chiang, A.P. & Butte, A.J. Predicting adverse drug reactions using publicly available PubChem BioAssay data. Clin. Pharmacol. Ther. 90, 90-99 (2011).
15. Harpaz, R., Perez, H., Chase, H.S., Rabadan, R., Hripcsak, G. & Friedman, C. Biclustering of adverse drug events in the FDA's spontaneous reporting system. Clin. Pharmacol. Ther. 89, 243-250 (2011).
16. Linder, J.A. et al. Secondary use of electronic health record data: spontaneous triggered adverse drug event reporting. Pharmacoepidemiol. Drug Saf. 19, 1211-1215 (2010).
17. Dudley, J.T., Deshpande, T. & Butte, A.J. Exploiting drug-disease relationships for computational drug repositioning. Brief. Bioinform. 12, 303-311 (2011).
18. Tatonetti, N.P. et al. Detecting drug interactions from adverse-event reports: interaction between paroxetine and pravastatin increases blood glucose levels. Clin. Pharmacol. Ther. 90, 133-142 (2011).
19. Ioannidis, J.P. et al. Repeatability of published microarray gene expression analyses. Nat. Genet. 41, 149-155 (2009).
20. Mailman, M.D. et al. The NCBI dbGaP database of genotypes and phenotypes. Nat. Genet. 39, 1181-1186 (2007). (Pubitemid 47482671)
21. Wiley, H.S. & Michaels, G.S. Should software hold data hostage? Nat. Biotechnol. 22, 1037-1038 (2004). (Pubitemid 39014485)
22. Guha, R. et al. The Blue Obelisk-interoperability in chemical informatics. J. Chem. Inf. Model. 46, 991-998 (2006).
23. Wagner, J.A. et al. The Biomarkers Consortium: practice and pitfalls of open-source precompetitive collaboration. Clin. Pharmacol. Ther. 87, 539-542 (2010).
24. Joly, Y. Open biotechnology: licenses needed. Nat. Biotechnol. 28, 417-419 (2010).
25. Wild, D.J. & Wiggins, G.D. Challenges for chemoinformatics education in drug discovery. Drug Discov. Today 11, 436-439 (2006).
26. Kaitin, K.I. Deconstructing the drug development process: the new face of innovation. Clin. Pharmacol. Ther. 87, 356-361 (2010).
27. Qureshi, Z.P., Seoane-Vazquez, E., Rodriguez-Monguio, R., Stevenson, K.B. & Szeinbach, S.L. Market withdrawal of new molecular entities approved in the United States from 1980 to 2009. Pharmacoepidemiol. Drug Saf. 20, 772-777 (2011).