Atul Butte, MD, PhD

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
Atul Butte, MD, PhD

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

Atul.Butte@ucsf.edu

Box 0110, UCSF
San Francisco, CA 94158

UCSF Profiles

Cancer Center Membership

Program Member » Developmental Therapeutics» 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. 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 CDC37 Signaling. Gastroenterology. 2017 Mar 08.
    View on PubMed
  2. 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 Jan 05.
    View on PubMed
  3. 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. 2016 Dec 13.
    View on PubMed
  4. 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. 2016 Nov 16.
    View on PubMed
  5. Paik H, Chen B, Sirota M, Hadley D, Butte AJ. Integrating Clinical Phenotype and Gene Expression Data to Prioritize Novel Drug Uses. CPT Pharmacometrics Syst Pharmacol. 2016 Nov 14.
    View on PubMed
  6. Butte AJ. It takes a genome to understand a village: Population scale precision medicine. Proc Natl Acad Sci U S A. 2016 Nov 1; 113(44):12344-12346.
    View on PubMed
  7. Shen-Orr SS, Furman D, Kidd BA, Hadad F, Lovelace P, Huang YW, Rosenberg-Hasson Y, Mackey S, Grisar FA, Pickman Y, Maecker HT, Chien YH, Dekker CL, Wu JC, Butte AJ, Davis MM. Defective Signaling in the JAK-STAT Pathway Tracks with Chronic Inflammation and Cardiovascular Risk in Aging Humans. Cell Syst. 2016 Oct 26; 3(4):374-384.e4.
    View on PubMed
  8. Hughey JJ, Butte AJ. Differential Phasing between Circadian Clocks in the Brain and Peripheral Organs in Humans. J Biol Rhythms. 2016 Oct 4.
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  9. Aran D, Butte AJ. Digitally deconvolving the tumor microenvironment. Genome Biol. 2016; 17(1):175.
    View on PubMed
  10. Aran D, Lasry A, Zinger A, Biton M, Pikarsky E, Hellman A, Butte AJ, Ben-Neriah Y. Widespread parainflammation in human cancer. Genome Biol. 2016; 17(1):145.
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  11. Amor M, Moreno-Viedma V, Sarabi A, Grün NG, Itariu B, Leitner L, Steiner I, Bilban M, Kodama K, Butte AJ, Staffler G, Zeyda M, Stulnig TM. Identification of matrix metalloproteinase-12 as a candidate molecule for prevention and treatment of cardiometabolic disease. Mol Med. 2016 Jun 30; 22.
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  12. Rennert RC, Januszyk M, Sorkin M, Rodrigues M, Maan ZN, Duscher D, Whittam AJ, Kosaraju R, Chung MT, Paik K, Li AY, Findlay M, Glotzbach JP, Butte AJ, Gurtner GC. Microfluidic single-cell transcriptional analysis rationally identifies novel surface marker profiles to enhance cell-based therapies. Nat Commun. 2016; 7:11945.
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  13. Geifman N, Butte AJ. A patient-level data meta-analysis of standard-of-care treatments from eight prostate cancer clinical trials. Sci Data. 2016; 3:160027.
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  14. Kosti I, Jain N, Aran D, Butte AJ, Sirota M. Cross-tissue Analysis of Gene and Protein Expression in Normal and Cancer Tissues. Sci Rep. 2016; 6:24799.
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  15. Bagley SC, Sirota M, Chen R, Butte AJ, Altman RB. Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants. PLoS Comput Biol. 2016 Apr; 12(4):e1004885.
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  16. Kodama K, Zhao Z, Toda K, Yip L, Fuhlbrigge R, Miao D, Fathman CG, Yamada S, Butte AJ, Yu L. Expression-Based Genome-Wide Association Study Links Vitamin D-Binding Protein With Autoantigenicity in Type 1 Diabetes. Diabetes. 2016 May; 65(5):1341-9.
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  17. Chen B, Butte AJ. Leveraging big data to transform target selection and drug discovery. Clin Pharmacol Ther. 2016 Mar; 99(3):285-97.
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  18. Aran D, Sirota M, Butte AJ. Corrigendum: Systematic pan-cancer analysis of tumour purity. Nat Commun. 2016; 7:10707.
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  19. Hughey JJ, Hastie T, Butte AJ. ZeitZeiger: supervised learning for high-dimensional data from an oscillatory system. Nucleic Acids Res. 2016 May 5; 44(8):e80.
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  20. Godec J, Tan Y, Liberzon A, Tamayo P, Bhattacharya S, Butte AJ, Mesirov JP, Haining WN. Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation. Immunity. 2016 Jan 19; 44(1):194-206.
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