Our Publications

We share our lab’s findings and the results of our cutting-edge research with the scientific community and with the public

Disease Meta-Analysis

Genetics and Environment

  • Ashley EA, Butte AJ, Wheeler MT, Chen R, Klein TE, Dewey FE, Dudley JT, Ormond KE, Pavlovic A, Morgan AA, Pushkarev D, Neff NF, Hudgins L, Gong L, Hodges LM, Berlin DS, Thorn CF, Sangkuhl K, Hebert JM, Woon M, Sagreiya H, Whaley R, Knowles JW, Chou MF, Thakuria JV, Rosenbaum AM, Zaranek AW, Church GM, Greely HT, Quake SR, Altman RB.(2010). Clinical assessment incorporating a personal genome. Lancet. 2010 May 1;375(9725):1525-35. doi: 10.1016/S0140-6736(10)60452-7. Full Text
  • Sirota M, Schaub MA, Batzoglou S, Robinson WH, Butte AJ.(2009) Autoimmune disease classification by inverse association with SNP alleles. PLoS Genet. 2009 Dec;5(12):e1000792. doi: 10.1371/journal.pgen.1000792. Epub 2009 Dec 24.Full Text
  • Corona E1, Chen R, Sikora M, Morgan AA, Patel CJ, Ramesh A, Bustamante CD, Butte AJ.(2013). Analysis of the genetic basis of disease in the context of worldwide human relationships and migration. PLoS Genet.2013 May;9(5):e1003447. doi: 10.1371/journal.pgen.1003447. Epub 2013 May 23. Full Text
  • Ruau D, Dudley JT, Chen R, Phillips NG, Swan GE, Lazzeroni LC, Clark JD, Butte AJ, Angst MS.(2012). Integrative approach to pain genetics identifies pain sensitivity loci across diseases. PLoS Comput Biol. 2012;8(6):e1002538. doi: 10.1371/journal.pcbi.1002538. Epub 2012 Jun 7. Full Text
  • Chen R, Corona E, Sikora M, Dudley JT, Morgan AA, Moreno-Estrada A, Nilsen GB, Ruau D, Lincoln SE, Bustamante CD, Butte AJ.(2012). Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases. PLoS Genet. 2012;8(4):e1002621. doi: 10.1371/journal.pgen.1002621. Epub 2012 Apr 12.Full Text
  • Patel CJ, Bhattacharya J, Butte AJ.(2010). An Environment-Wide Association Study (EWAS) on type 2 diabetes mellitus.PLoS One. 2010 May 20;5(5):e10746. doi: 10.1371/journal.pone.0010746. Full Text


  • Paik H, Chung AY, Park HC, Park RW, Suk K, Kim J, Kim H, Lee K, Butte AJ.(2015) Repurpose terbutaline sulfate for amyotrophic lateral sclerosis using electronic medical records. Sci Rep. 2015 Mar 5;5:8580. doi: 10.1038/srep08580.Full Text
  • Sirota M, Dudley JT, Kim J, Chiang AP, Morgan AA, Sweet-Cordero A, Sage J, Butte AJ.(2011) Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci Transl Med. 2011 Aug 17;3(96):96ra77. doi: 10.1126/scitranslmed.3001318.Full Text
  • Dudley JT, Sirota M, Shenoy M, Pai RK, Roedder S, Chiang AP, Morgan AA, Sarwal MM, Pasricha PJ, Butte AJ.(2011) Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease.Sci Transl Med. Full Text
  • Jahchan NS, Dudley JT, Mazur PK, Flores N, Yang D, Palmerton A, Zmoos AF, Vaka D, Tran KQ, Zhou M, Krasinska K, Riess JW, Neal JW, Khatri P, Park KS, Butte AJ, Sage J.(2013) A drug repositioning approach identifies tricyclic antidepressants as inhibitors of small cell lung cancer and other neuroendocrine tumors. Cancer Discov.2013 Dec;3(12):1364-77. doi: 10.1158/2159-8290.CD-13-0183. Epub 2013 Sep 26. Full Text


  • Li L, Ruau DJ, Patel CJ, Weber SC, Chen R, Tatonetti NP, Dudley JT, Butte AJ.(2014) Disease risk factors identified through shared genetic architecture and electronic medical records.Sci Transl Med.2014 Apr 30;6(234):234ra57. doi: 10.1126/scitranslmed.3007191. Full Text

Immune Informatics

  • Geifman N, Bhattacharya S, Butte AJ.(2015) Immune modulators in disease: integrating knowledge from the biomedical literature and gene expression.J Am Med Inform Assoc.2015 Dec 11. pii: ocv166. doi: 10.1093/jamia/ocv166. Full Text
  • Nasrallah M, Pouliot Y, Hartmann B, Dunn P, Thomson E, Wiser J, Butte AJ.(2014) Reanalysis of the Rituximab in ANCA-Associated Vasculitis trial identifies granulocyte subsets as a novel early marker of successful treatment. Res Ther. 2015 Sep 21;17:262. doi: 10.1186/s13075-015-0778-z. PubMed PMID: 24791905. Full Text
  • Bhattacharya S, Andorf S, Gomes L, Dunn P, Schaefer H, Pontius J, Berger P, Desborough V, Smith T, Campbell J, Thomson E, Monteiro R, Guimaraes P, Walters B, Wiser J, Butte AJ.(2014) ImmPort: disseminating data to the public for the future of immunology. Immunol Res. 2014 May;58(2-3):234-9. doi: 10.1007/s12026-014-8516-1. PubMed PMID: 24791905. Full Text
  • Shen-Orr SS, Goldberger O, Garten Y, Rosenberg-Hasson Y, Lovelace PA, Hirschberg DL, Altman RB, Davis MM, Butte AJ.(2009) Towards a cytokine-cell interaction knowledgebase of the adaptive immune system.Pac Symp Biocomput.2009:439-50. Full Text
  • Shen-Orr SS, Tibshirani R, Khatri P, Bodian DL, Staedtler F, Perry NM, Hastie T, Sarwal MM, Davis MM, Butte AJ.(2010) Cell type-specific gene expression differences in complex tissues. Nat Methods.2010 Apr;7(4):287-9. doi: 10.1038/nmeth.1439. Epub 2010 Mar 7. Full Text

Cancer Informatics

  • Kosti I, Jain N, Aran D, Butte AJ, Sirota M.(2016) Cross-tissue Analysis of Gene and Protein Expression in Normal and Cancer Tissues.Sci Rep.2016 May 4;6:24799. doi: 10.1038/srep24799. PubMed PMID: 27142790.
  • Aran D Sirota M, Butte AJ.(2015) Systematic pan-cancer analysis of tumour purity.Nat Commun.2015 Dec 4;6:8971. doi: 10.1038/ncomms9971. Full Text
  • Chen B, Sirota M, Fan-Minogue H, Hadley D, Butte AJ.(2015) Relating hepatocellular carcinoma tumor samples and cell lines using gene expression data in translational research. BMC Med Genomics.2015;8 Suppl 2:S5. doi: 10.1186/1755-8794-8-S2-S5. Epub 2015 May 29. Full Text