University of California San Francisco
Helen Diller Family Comprehensive Cancer Center
Atul Butte, MD, PhD

Atul Butte, MD, PhD

Director, Institute for Computational Health Sciences, Professor of Pediatrics, UCSF

Cancer Center Program Memberships

Cancer Genetics

Research Summary

In April 2015, I became the new Director of the Institute for Computational Health Sciences at the University of California, San Francisco, with the role of recruiting new computational-related faculty to UCSF.

My prior decade was spent at Stanford University, where I developed my career from Assistant to Full Professor and Division Chief, by developing and using bioinformatics methods to integrate, leverage, and reason over genomic, genetic, phenotypic, and other sources of molecular data to yield tools for physicians and patients. Example of this method includes work on cancer drug discovery (PNAS, 2000), type 2 diabetes (PNAS, 2003), fat cell formation (Nature Cell Biology, 2005), obesity (Bioinformatics, 2007), and transplantation (PNAS, 2009). To facilitate this, we have developed tools for indexing public genomic data sets (Nature Biotechnology, 2006), re-mapping microarray data (Nature Methods, 2007), and in cloud-computing (Nature Biotechnology, 2010). We also develop novel methods to explore human physiology using electronic health record data (Science, 2008), and in the medical risk estimation from whole genomes (Lancet, 2010).

My research lab currently has 3 graduate students, 5 post-doctoral research fellows, and 3 staff members. I have successfully administered multiple research projects, including the NIAID ImmPort data archival repository, collaborated with many other researchers around the world, and continue to produce many peer-reviewed publications from each project. As a result, I am aware of the importance of frequent collaboration and communication among project members and of constructing realistic research plans, timelines, and budgets. In summary, I have a demonstrated record of successful and productive research projects, and my expertise and experience have prepared me to participate in the proposed project.

Education

  • Brown University, Providence, RI, A.B./Honors, 1987–1991, Computer Science
  • Brown University Medical School, RI, M.D., 1991–1995, Medicine
  • Children’s Hospital and Harvard, Boston, MA, Residency, 1995–1998, Pediatrics
  • Children’s Hospital and Harvard, Boston, MA, Fellowship, 1998–2001, Pediatric Endocrinology,
  • Massachusetts Institute of Technology, MA Sc.M. 1998–2002 Medical Informatics
  • Harvard Medical School and MIT, MA Ph.D. 2002–2004 Health Sci Technology

Professional Experience

  • 1989
    Software Engineer, Excel Unit, Microsoft Corp., Redmond, Washington
  • 1990 - 1991
    System Software Engineer, Apple Computer, Inc., Cupertino, California
  • 2001
    Board certified pediatrics and pediatric endocrinology, American Board of Pediatrics
  • 2001 - 2005
    Instructor in Pediatrics (Endocrinology), Harvard Medical School
  • 2001 - 2005
    Attending in Pediatric Endocrinology, Children’s Hospital, Boston, MA
  • 2005 - 2015
    Assistant, Associate, Professor of Pediatrics, Medicine (Medical Informatics), Stanford University
  • 2011 - 2015
    Chief, Division of Systems Medicine, Stanford University School of Medicine
  • 2015 - present
    Professor of Pediatrics, University of California, San Francisco
  • 2015 - present
    Director, Institute for Computational Health Sciences, UCSF

Honors & Awards

  • 2002, 2003
    Outstanding Speaker, American Association for Clinical Chemistry (awarded twice)
  • 2006
    PhRMA Foundation Informatics Research Starter Grant
  • 2006
    Howard Hughes Medical Institute Physician-Scientist Early Career Award
  • 2007
    Genome Technology magazine “Tomorrow’s Principal Investigator” award
  • 2008
    American Medical Informatics Association New Investigator Award
  • 2009
    Elected into the American College of Medical Informatics
  • 2010
    Young Investigator Award, Society for Pediatric Research
  • 2011
    National Human Genome Research Institute (NHGRI) Genomic Advance of the Month
  • 2012
    Recognized for Outstanding Scientific Accomplishment and Lectureship by the NIH Director (Wednesday Afternoon Lecture Series, WALS)
  • 2013
    Elected into the American Society of Clinical Investigation (ASCI)
  • 2013
    Awarded White House Champion of Change in Open Science
  • 2014
    Kavli Frontiers of Science Invited Fellow for the Indonesian-American Symposium, National Academy of Science
  • 2014
    E. Mead Johnson Award, Society for Pediatrics Research
  • 2015
    Elected to the National Academy of Medicine (NAS)

Selected Publications

  1. Nolan G, Butte A. The Atacama skeleton. Genome Res. 2018 Mar 30.
    View on PubMed
  2. Bhattacharya S, Li J, Sockell A, Kan MJ, Bava FA, Chen SC, Ávila-Arcos MC, Ji X, Smith E, Asadi NB, Lachman RS, Lam HYK, Bustamante CD, Butte AJ, Nolan GP. Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia. Genome Res. 2018 Apr; 28(4):423-431.
    View on PubMed
  3. Bhattacharya S, Dunn P, Thomas CG, Smith B, Schaefer H, Chen J, Hu Z, Zalocusky KA, Shankar RD, Shen-Orr SS, Thomson E, Wiser J, Butte AJ. ImmPort, toward repurposing of open access immunological assay data for translational and clinical research. Sci Data. 2018 Feb 27; 5:180015.
    View on PubMed
  4. Kido T, Sikora-Wohlfeld W, Kawashima M, Kikuchi S, Kamatani N, Patwardhan A, Chen R, Sirota M, Kodama K, Hadley D, Butte AJ. Are minor alleles more likely to be risk alleles? BMC Med Genomics. 2018 Jan 19; 11(1):3.
    View on PubMed
  5. Rappoport N, Toung J, Hadley D, Wong RJ, Fujioka K, Reuter J, Abbott CW, Oh S, Hu D, Eng C, Huntsman S, Bodian DL, Niederhuber JE, Hong X, Zhang G, Sikora-Wohfeld W, Gignoux CR, Wang H, Oehlert J, Jelliffe-Pawlowski LL, Gould JB, Darmstadt GL, Wang X, Bustamante CD, Snyder MP, Ziv E, Patsopoulos NA, Muglia LJ, Burchard E, Shaw GM, O'Brodovich HM, Stevenson DK, Butte AJ, Sirota M. A genome-wide association study identifies only two ancestry specific variants associated with spontaneous preterm birth. Sci Rep. 2018 Jan 09; 8(1):226.
    View on PubMed
  6. Wise PH, Shaw GM, Druzin ML, Darmstadt GL, Quaintance C, Mäkinen E, Relman DA, Quake SR, Butte AJ, Angst MS, Muglia LJ, Macones G, Driscoll D, Ober C, Simpson JL, Katz M, Howse J, Stevenson DK. Risky Business: Meeting the Structural Needs of Transdisciplinary Science. J Pediatr. 2017 Dec; 191:255-258.
    View on PubMed
  7. Aran D, Hu Z, Butte AJ. xCell: digitally portraying the tissue cellular heterogeneity landscape. Genome Biol. 2017 Nov 15; 18(1):220.
    View on PubMed
  8. Mirza AN, Fry MA, Urman NM, Atwood SX, Roffey J, Ott GR, Chen B, Lee A, Brown AS, Aasi SZ, Hollmig T, Ator MA, Dorsey BD, Ruggeri BR, Zificsak CA, Sirota M, Tang JY, Butte A, Epstein E, Sarin KY, Oro AE. Combined inhibition of atypical PKC and histone deacetylase 1 is cooperative in basal cell carcinoma treatment. JCI Insight. 2017 Nov 02; 2(21).
    View on PubMed
  9. Meehan TF, Conte N, Goldstein T, Inghirami G, Murakami MA, Brabetz S, Gu Z, Wiser JA, Dunn P, Begley DA, Krupke DM, Bertotti A, Bruna A, Brush MH, Byrne AT, Caldas C, Christie AL, Clark DA, Dowst H, Dry JR, Doroshow JH, Duchamp O, Evrard YA, Ferretti S, Frese KK, Goodwin NC, Greenawalt D, Haendel MA, Hermans E, Houghton PJ, Jonkers J, Kemper K, Khor TO, Lewis MT, Lloyd KCK, Mason J, Medico E, Neuhauser SB, Olson JM, Peeper DS, Rueda OM, Seong JK, Trusolino L, Vinolo E, Wechsler-Reya RJ, Weinstock DM, Welm A, Weroha SJ, Amant F, Pfister SM, Kool M, Parkinson H, Butte AJ, Bult CJ. PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models. Cancer Res. 2017 Nov 01; 77(21):e62-e66.
    View on PubMed
  10. Jaffee EM, Dang CV, Agus DB, Alexander BM, Anderson KC, Ashworth A, Barker AD, Bastani R, Bhatia S, Bluestone JA, Brawley O, Butte AJ, Coit DG, Davidson NE, Davis M, DePinho RA, Diasio RB, Draetta G, Frazier AL, Futreal A, Gambhir SS, Ganz PA, Garraway L, Gerson S, Gupta S, Heath J, Hoffman RI, Hudis C, Hughes-Halbert C, Ibrahim R, Jadvar H, Kavanagh B, Kittles R, Le QT, Lippman SM, Mankoff D, Mardis ER, Mayer DK, McMasters K, Meropol NJ, Mitchell B, Naredi P, Ornish D, Pawlik TM, Peppercorn J, Pomper MG, Raghavan D, Ritchie C, Schwarz SW, Sullivan R, Wahl R, Wolchok JD, Wong SL, Yung A. Future cancer research priorities in the USA: a Lancet Oncology Commission. Lancet Oncol. 2017 Nov; 18(11):e653-e706.
    View on PubMed
  11. Aran D, Camarda R, Odegaard J, Paik H, Oskotsky B, Krings G, Goga A, Sirota M, Butte AJ. Comprehensive analysis of normal adjacent to tumor transcriptomes. Nat Commun. 2017 10 20; 8(1):1077.
    View on PubMed
  12. Hadley D, Pan J, El-Sayed O, Aljabban J, Aljabban I, Azad TD, Hadied MO, Raza S, Rayikanti BA, Chen B, Paik H, Aran D, Spatz J, Himmelstein D, Panahiazar M, Bhattacharya S, Sirota M, Musen MA, Butte AJ. Precision annotation of digital samples in NCBI's gene expression omnibus. Sci Data. 2017 09 19; 4:170125.
    View on PubMed
  13. Butte AJ. Big data opens a window onto wellness. Nat Biotechnol. 2017 Aug 08; 35(8):720-721.
    View on PubMed
  14. Chen B, Ma L, Paik H, Sirota M, Wei W, Chua MS, So S, Butte AJ. Reversal of cancer gene expression correlates with drug efficacy and reveals therapeutic targets. Nat Commun. 2017 Jul 12; 8:16022.
    View on PubMed
  15. Lasry A, Aran D, Butte AJ, Ben-Neriah Y. Cancer Cell-Autonomous Parainflammation Mimics Immune Cell Infiltration. Cancer Res. 2017 07 15; 77(14):3740-3744.
    View on PubMed
  16. Shankar RD, Bhattacharya S, Jujjavarapu C, Andorf S, Wiser JA, Butte AJ. RImmPort: an R/Bioconductor package that enables ready-for-analysis immunology research data. Bioinformatics. 2017 04 01; 33(7):1101-1103.
    View on PubMed
  17. Chen B, Wei W, Ma L, Yang B, Gill RM, Chua MS, Butte AJ, So S. Computational Discovery of Niclosamide Ethanolamine, a Repurposed Drug Candidate That Reduces Growth of Hepatocellular Carcinoma Cells In Vitro and in Mice by Inhibiting Cell Division Cycle 37 Signaling. Gastroenterology. 2017 06; 152(8):2022-2036.
    View on PubMed
  18. Geifman N, Brinton RD, Kennedy RE, Schneider LS, Butte AJ. Evidence for benefit of statins to modify cognitive decline and risk in Alzheimer's disease. Alzheimers Res Ther. 2017 Feb 17; 9(1):10.
    View on PubMed
  19. Pessetto ZY, Chen B, Alturkmani H, Hyter S, Flynn CA, Baltezor M, Ma Y, Rosenthal HG, Neville KA, Weir SJ, Butte AJ, Godwin AK. In silico and in vitro drug screening identifies new therapeutic approaches for Ewing sarcoma. Oncotarget. 2017 Jan 17; 8(3):4079-4095.
    View on PubMed
  20. Vodovotz Y, Xia A, Read EL, Bassaganya-Riera J, Hafler DA, Sontag E, Wang J, Tsang JS, Day JD, Kleinstein SH, Butte AJ, Altman MC, Hammond R, Sealfon SC. Solving Immunology? Trends Immunol. 2017 02; 38(2):116-127.
    View on PubMed

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