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. Sim I, Stebbins M, Bierer BE, Butte AJ, Drazen J, Dzau V, Hernandez AF, Krumholz HM, Lo B, Munos B, Perakslis E, Rockhold F, Ross JS, Terry SF, Yamamoto KR, Zarin DA, Li R. Time for NIH to lead on data sharing. Science. 2020 03 20; 367(6484):1308-1309.
    View on PubMed
  2. Rough K, Dai AM, Zhang K, Xue Y, Vardoulakis LM, Cui C, Butte AJ, Howell MD, Rajkomar A. Predicting inpatient medication orders from electronic health record data. Clin Pharmacol Ther. 2020 Mar 05.
    View on PubMed
  3. Rudrapatna VA, Glicksberg BS, Avila P, Harding-Theobald E, Wang C, Butte AJ. Accuracy of medical billing data against the electronic health record in the measurement of colorectal cancer screening rates. BMJ Open Qual. 2020 Mar; 9(1).
    View on PubMed
  4. Nam SM, Peterson TA, Butte AJ, Seo KY, Han HW. Explanatory Model of Dry Eye Disease Using Health and Nutrition Examinations: Machine Learning and Network-Based Factor Analysis From a National Survey. JMIR Med Inform. 2020 Feb 20; 8(2):e16153.
    View on PubMed
  5. Rudrapatna VA, Butte AJ. Opportunities and challenges in using real-world data for health care. J Clin Invest. 2020 Feb 03; 130(2):565-574.
    View on PubMed
  6. Farrand E, Vittinghoff E, Ley B, Butte AJ, Collard HR. Corticosteroid use is not associated with improved outcomes in acute exacerbation of IPF. Respirology. 2019 Dec 17.
    View on PubMed
  7. Telwatte S, Morón-López S, Aran D, Kim P, Hsieh C, Joshi S, Montano M, Greene WC, Butte AJ, Wong JK, Yukl SA. Heterogeneity in HIV and cellular transcription profiles in cell line models of latent and productive infection: implications for HIV latency. Retrovirology. 2019 11 11; 16(1):32.
    View on PubMed
  8. Glicksberg BS, Oskotsky B, Thangaraj PM, Giangreco N, Badgeley MA, Johnson KW, Datta D, Rudrapatna VA, Rappoport N, Shervey MM, Miotto R, Goldstein TC, Rutenberg E, Frazier R, Lee N, Israni S, Larsen R, Percha B, Li L, Dudley JT, Tatonetti NP, Butte AJ. PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model. Bioinformatics. 2019 Nov 01; 35(21):4515-4518.
    View on PubMed
  9. Paik H, Kan MJ, Rappoport N, Hadley D, Sirota M, Chen B, Manber U, Cho SB, Butte AJ. Tracing diagnosis trajectories over millions of patients reveal an unexpected risk in schizophrenia. Sci Data. 2019 10 15; 6(1):201.
    View on PubMed
  10. Yu K, Chen B, Aran D, Charalel J, Yau C, Wolf DM, van 't Veer LJ, Butte AJ, Goldstein T, Sirota M. Comprehensive transcriptomic analysis of cell lines as models of primary tumors across 22 tumor types. Nat Commun. 2019 08 08; 10(1):3574.
    View on PubMed
  11. Nelson CA, Butte AJ, Baranzini SE. Integrating biomedical research and electronic health records to create knowledge-based biologically meaningful machine-readable embeddings. Nat Commun. 2019 07 10; 10(1):3045.
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  12. Schüssler-Fiorenza Rose SM, Contrepois K, Moneghetti KJ, Zhou W, Mishra T, Mataraso S, Dagan-Rosenfeld O, Ganz AB, Dunn J, Hornburg D, Rego S, Perelman D, Ahadi S, Sailani MR, Zhou Y, Leopold SR, Chen J, Ashland M, Christle JW, Avina M, Limcaoco P, Ruiz C, Tan M, Butte AJ, Weinstock GM, Slavich GM, Sodergren E, McLaughlin TL, Haddad F, Snyder MP. A longitudinal big data approach for precision health. Nat Med. 2019 05; 25(5):792-804.
    View on PubMed
  13. Farrand E, Anstrom KJ, Bernard G, Butte AJ, Iribarren C, Ley B, Martinez FJ, Collard HR. Closing the Evidence Gap in Interstitial Lung Disease. The Promise of Real-World Data. Am J Respir Crit Care Med. 2019 05 01; 199(9):1061-1065.
    View on PubMed
  14. Chen J, Bhattacharya S, Sirota M, Laiudompitak S, Schaefer H, Thomson E, Wiser J, Sarwal MM, Butte AJ. Assessment of Postdonation Outcomes in US Living Kidney Donors Using Publicly Available Data Sets. JAMA Netw Open. 2019 04 05; 2(4):e191851.
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  15. Hu Z, Glicksberg BS, Butte AJ. Robust prediction of clinical outcomes using cytometry data. Bioinformatics. 2019 04 01; 35(7):1197-1203.
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  16. Norgeot B, Glicksberg BS, Trupin L, Lituiev D, Gianfrancesco M, Oskotsky B, Schmajuk G, Yazdany J, Butte AJ. Assessment of a Deep Learning Model Based on Electronic Health Record Data to Forecast Clinical Outcomes in Patients With Rheumatoid Arthritis. JAMA Netw Open. 2019 03 01; 2(3):e190606.
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  17. Andorf S, Bhattacharya S, Gaudilliere B, Shaw GM, Stevenson DK, Butte AJ, Sirota M. A pilot study showing a stronger H1N1 influenza vaccination response during pregnancy in women who subsequently deliver preterm. J Reprod Immunol. 2019 04; 132:16-20.
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  18. Wong DR, Bhattacharya S, Butte AJ. Prototype of running clinical trials in an untrustworthy environment using blockchain. Nat Commun. 2019 02 22; 10(1):917.
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  19. Aran D, Looney AP, Liu L, Wu E, Fong V, Hsu A, Chak S, Naikawadi RP, Wolters PJ, Abate AR, Butte AJ, Bhattacharya M. Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Nat Immunol. 2019 02; 20(2):163-172.
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  20. Glicksberg BS, Oskotsky B, Giangreco N, Thangaraj PM, Rudrapatna V, Datta D, Frazier R, Lee N, Larsen R, Tatonetti NP, Butte AJ. ROMOP: a light-weight R package for interfacing with OMOP-formatted electronic health record data. JAMIA Open. 2019 Apr; 2(1):10-14.
    View on PubMed

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