Research Summary

In April 2015, I became the inaugural Director of the Bakar Computational Health Sciences Institute 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 advanced from Assistant to Full Professor and Division Chief by developing and using bioinformatics methods to integrate, leverage, and reason over genomic and other molecular and clinical data sets to yield tools for physicians and patients. Example of this method includes work on cancer drug discovery (PNAS, 2000), type 2 diabetes (PNAS, 2003, 2012), fat cell formation (Nature Cell Biology, 2005), obesity (Bioinformatics, 2007), and transplantation (PNAS, 2009). To facilitate this, we developed tools to index public genomic data sets (Nature Biotechnology, 2006), reuse gene expression data (Nature Methods, 2007, 2010; Nature Communications 2015), and for cloud-computing (Nature Biotechnology, 2010). With these methods, we explore human physiology using electronic health record data (Science, 2008; Science Translational Medicine, 2014), estimate medical risk with whole genomes (Lancet, 2010), computationally reposition drugs (Science Translational Medicine, 2011). In newer work, we are studying entire medical systems through real-world clinical data (Journal of Clinical Investigation, 2020).

My research lab currently has 3 graduate students, 7 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. I have been heavily invested in teaching and mentoring. I am currently training or have trained 30 post-doctoral scholars in my research lab, with many obtaining prestigious research positions after departing. Twelve graduate students are completing, or have completed their PhD work in the lab, including two members of underrepresented minorities.

Research Funding

  • April 1, 2020 - March 31, 2025 - Computational models of naturally acquired immunity to falciparum malaria, Co-Principal Investigator. Sponsor: NIH/NIAID, Sponsor Award ID: U01AI150741
  • September 26, 2016 - April 30, 2021 - Integrative Analysis of Genomic, Epigenomic and Phenotypic Data for Disease Stratification of Endometriosis, Co-Principal Investigator. Sponsor: NIH/NICHD, Sponsor Award ID: R01HD089511
  • September 1, 2015 - August 31, 2020 - Stanford and Northrop Grumman proposal for the Oncology Models Forum, Principal Investigator. Sponsor: NIH/NCI, Sponsor Award ID: U24CA195858
  • April 15, 2014 - March 31, 2019 - Biorepository of Human iPSCs for Studying Dilated and Hypertrophic Cardiomyopathy, Co-Principal Investigator. Sponsor: NIH/NHLBI, Sponsor Award ID: R24HL117756

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

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. Mahendra M, Luo Y, Mills H, Schenk G, Butte AJ, Dudley RA. Impact of Different Approaches to Preparing Notes for Analysis With Natural Language Processing on the Performance of Prediction Models in Intensive Care. Crit Care Explor. 2021 Jun; 3(6):e0450.  View on PubMed
  2. Liu X, Anstey J, Li R, Sarabu C, Sono R, Butte AJ. Rethinking PICO in the Machine Learning Era: ML-PICO. Appl Clin Inform. 2021 Mar; 12(2):407-416.  View on PubMed
  3. Rudrapatna VA, Glicksberg BS, Butte AJ. Utility of routinely collected electronic health records data to support effectiveness evaluations in inflammatory bowel disease: a pilot study of tofacitinib. BMJ Health Care Inform. 2021 May; 28(1).  View on PubMed
  4. Bhattacharya S, Hu Z, Butte AJ. Opportunities and Challenges in Democratizing Immunology Datasets. Front Immunol. 2021; 12:647536.  View on PubMed
  5. Madhavan S, Bastarache L, Brown JS, Butte AJ, Dorr DA, Embi PJ, Friedman CP, Johnson KB, Moore JH, Kohane IS, Payne PRO, Tenenbaum JD, Weiner MG, Wilcox AB, Ohno-Machado L. Use of electronic health records to support a public health response to the COVID-19 pandemic in the United States: a perspective from 15 academic medical centers. J Am Med Inform Assoc. 2021 02 15; 28(2):393-401.  View on PubMed
  6. Eaneff S, Obermeyer Z, Butte AJ. Algorithmic Stewardship in Health Care-Reply. JAMA. 2021 02 09; 325(6):588-589.  View on PubMed
  7. Kwon DH, Vashisht R, Borno HT, Aggarwal RR, Small EJ, Butte AJ, Huang FW. Androgen-deprivation therapy and SARS-CoV-2 in men with prostate cancer: findings from the University of California Health System registry. Ann Oncol. 2021 05; 32(5):678-679.  View on PubMed
  8. Peterson TA, Fontil V, Koliwad SK, Patel A, Butte AJ. Quantifying Variation in Treatment Utilization for Type 2 Diabetes Across Five Major University of California Health Systems. Diabetes Care. 2021 Apr; 44(4):908-914.  View on PubMed
  9. Vashisht R, Patel A, Crews BO, Garner OB, Dahm L, Wilson C, Butte AJ. Age- and Sex-Associated Variations in the Sensitivity of Serological Tests Among Individuals Infected With SARS-CoV-2. JAMA Netw Open. 2021 02 01; 4(2):e210337.  View on PubMed
  10. Nelson CA, Acuna AU, Paul AM, Scott RT, Butte AJ, Cekanaviciute E, Baranzini SE, Costes SV. Knowledge Network Embedding of Transcriptomic Data from Spaceflown Mice Uncovers Signs and Symptoms Associated with Terrestrial Diseases. Life (Basel). 2021 Jan 12; 11(1).  View on PubMed
  11. Butte AJ. Trials and Tribulations-11 Reasons Why We Need to Promote Clinical Trials Data Sharing. JAMA Netw Open. 2021 01 04; 4(1):e2035043.  View on PubMed
  12. Patel NA, Butte AJ. Characteristics and challenges of the clinical pipeline of digital therapeutics. NPJ Digit Med. 2020 Dec 11; 3(1):159.  View on PubMed
  13. Reznikov LR, Norris MH, Vashisht R, Bluhm AP, Li D, Liao YJ, Brown A, Butte AJ, Ostrov DA. Identification of antiviral antihistamines for COVID-19 repurposing. Biochem Biophys Res Commun. 2021 01 29; 538:173-179.  View on PubMed
  14. Moron-Lopez S, Telwatte S, Sarabia I, Battivelli E, Montano M, Macedo AB, Aran D, Butte AJ, Jones RB, Bosque A, Verdin E, Greene WC, Wong JK, Yukl SA. Human splice factors contribute to latent HIV infection in primary cell models and blood CD4+ T cells from ART-treated individuals. PLoS Pathog. 2020 11; 16(11):e1009060.  View on PubMed
  15. Arneson D, Elliott M, Mosenia A, Oskotsky B, Solodar S, Vashisht R, Zack T, Bleicher P, Butte AJ, Rudrapatna VA. CovidCounties is an interactive real time tracker of the COVID19 pandemic at the level of US counties. Sci Data. 2020 11 16; 7(1):405.  View on PubMed
  16. Eaneff S, Obermeyer Z, Butte AJ. The Case for Algorithmic Stewardship for Artificial Intelligence and Machine Learning Technologies. JAMA. 2020 Oct 13; 324(14):1397-1398.  View on PubMed
  17. Norgeot B, Quer G, Beaulieu-Jones BK, Torkamani A, Dias R, Gianfrancesco M, Arnaout R, Kohane IS, Saria S, Topol E, Obermeyer Z, Yu B, Butte AJ. Minimum information about clinical artificial intelligence modeling: the MI-CLAIM checklist. Nat Med. 2020 09; 26(9):1320-1324.  View on PubMed
  18. Hu Z, Tang A, Singh J, Bhattacharya S, Butte AJ. A robust and interpretable end-to-end deep learning model for cytometry data. Proc Natl Acad Sci U S A. 2020 09 01; 117(35):21373-21380.  View on PubMed
  19. Arneson D, Elliott M, Mosenia A, Oskotsky B, Vashisht R, Zack T, Bleicher P, Butte AJ, Rudrapatna VA. CovidCounties - an interactive, real-time tracker of the COVID-19 pandemic at the level of US counties. medRxiv. 2020 May 02.  View on PubMed
  20. Norgeot B, Muenzen K, Peterson TA, Fan X, Glicksberg BS, Schenk G, Rutenberg E, Oskotsky B, Sirota M, Yazdany J, Schmajuk G, Ludwig D, Goldstein T, Butte AJ. Protected Health Information filter (Philter): accurately and securely de-identifying free-text clinical notes. NPJ Digit Med. 2020; 3:57.  View on PubMed

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