PUBLICATIONS

  1. Jahchan NS, Dudley JT, Mazur PK, Flores N, Yang D, Palmerton A, Zmoos A, Vaka D, Tran KQT, Zhou M, Krasinska K, Riess JW, Neal JW, Khatri P, Park KS, Butte AJ, and Sage J. A Drug Repositioning Approach Identifies Tricyclic Antidepressants as Inhibitors of Small Cell Lung Cancer and Other Neuroendocrine Tumors. Cancer Discovery (2013)
  2. Dudley JT, Sirota M, Shenoy M, Pai RK, Roedder S, Chiang AP, Morgan AA, Sarwal MM, Pasricha PJ, Butte AJ. Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Science Translational Medicine (2011)
  3. Sirota M, Dudley JT, Kim J, Chiang AP, Morgan AA, Sweet-Cordero A, Sage J, Butte AJ. Discovery and preclinical validation of drug indications using compendia of public gene expression data. Science Translational Medicine (2011)
  4. Dudley JT, Deshpande T, Butte AJ. Exploiting drug–disease relationships for computational drug repositioning. Briefings in Bioinformatics (2011)
  5. Dudley JT, Schadt E, Sirota M, Butte AJ, Ashley E. Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks. Journal of Cardiovascular Translational Research (2010)
  6. Dudley JT, Butte AJ. Biomarker and Drug Discovery for Gastroenterology through Translational Bioinformatics. Gastroenterology (2010)
  7. Suthram S, Dudley JT, Chiang AP, Chen R, Hastie TJ, Butte AJ. Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets. PLoS Computational Biology (2010)
  8. Shen-Orr SS, Tibshirani R, Khatri P, Bodian DL, Staedtler F, Perry NM, Hastie T, Sarwal MM, Davis MM, Butte AJ. Cell type-specific gene expression differences in complex tissues. Nature Methods (2010)
  9. Dudley JT, Tibshirani R, Deshpande T, Butte AJ. Disease signatures are robust across tissues and experiments. Molecular Systems Biology (2009)
  10. Chiang AP, Butte AJ. Systematic evaluation of drug-disease relationships to identify leads for novel drug uses. Clinical Pharmacology and Therapeutics (2009)
  11. Chen R, Li L, Butte A.J. AILUN: reannotating gene expression data automatically. Nature Methods (2007)
  12. Schadt EE, Friend SH, Shaywitz DA. A network view of disease and compound screening. Nature Reviews Drug Discovery (2009)
  13. Lum PY, Derry JMJ, Schadt EE. Integrative genomics and drug development. Pharmacogenomics (2009)
  14. Butte AJ and Kohane IS. Creation and implications of a phenome-genome network. Nature Biotechnology (2006)