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, Sponsor Award ID: U01AI150741
  • September 1, 2015 - August 31, 2021 - Stanford and Northrop Grumman proposal for the Oncology Models Forum , Principal Investigator . Sponsor: NIH, Sponsor Award ID: U24CA195858
  • September 26, 2016 - April 30, 2021 - Integrative Analysis of Genomic, Epigenomic and Phenotypic Data for Disease Stratification of Endometriosis , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01HD089511
  • April 15, 2014 - August 31, 2020 - Biorepository of Human iPSCs for Studying Dilated and Hypertrophic Cardiomyopathy , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: R24HL117756


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. Silverman AL, Sushil M, Bhasuran B, Ludwig D, Buchanan J, Racz R, Parakala M, El-Kamary S, Ahima O, Belov A, Choi L, Billings M, Li Y, Habal N, Liu Q, Tiwari J, Butte AJ, Rudrapatna VA. Algorithmic identification of treatment-emergent adverse events from clinical notes using large language models: a pilot study in inflammatory bowel disease. medRxiv. 2023 Sep 08.  View on PubMed
  2. Khera R, Butte AJ, Berkwits M, Hswen Y, Flanagin A, Park H, Curfman G, Bibbins-Domingo K. AI in Medicine-JAMA's Focus on Clinical Outcomes, Patient-Centered Care, Quality, and Equity. JAMA. 2023 09 05; 330(9):818-820.  View on PubMed
  3. Butte AJ. Artificial Intelligence-From Starting Pilots to Scalable Privilege. JAMA Oncol. 2023 Aug 24.  View on PubMed
  4. Zamirpour S, Hubbard AE, Feng J, Butte AJ, Pirracchio R, Bishara A. Development of a Machine Learning Model of Postoperative Acute Kidney Injury Using Non-Invasive Time-Sensitive Intraoperative Predictors. Bioengineering (Basel). 2023 Aug 05; 10(8).  View on PubMed
  5. Patel S, Sparman NZR, Arneson D, Alvarsson A, Santos LC, Duesman SJ, Centonze A, Hathaway E, Ahn IS, Diamante G, Cely I, Cho CH, Talari NK, Rajbhandari AK, Goedeke L, Wang P, Butte AJ, Blanpain C, Chella Krishnan K, Lusis AJ, Stanley SA, Yang X, Rajbhandari P. Mammary duct luminal epithelium controls adipocyte thermogenic programme. Nature. 2023 Aug; 620(7972):192-199.  View on PubMed
  6. Radhakrishnan L, Schenk G, Muenzen K, Oskotsky B, Ashouri Choshali H, Plunkett T, Israni S, Butte AJ. A certified de-identification system for all clinical text documents for information extraction at scale. JAMIA Open. 2023 Oct; 6(3):ooad045.  View on PubMed
  7. Wang M, Slatter S, Sussell J, Lin CW, Ogale S, Datta D, Butte AJ, Bazhenova L, Rudrapatna VA. ALK Inhibitor Treatment Patterns and Outcomes in Real-World Patients with ALK-Positive Non-Small-Cell Lung Cancer: A Retrospective Cohort Study. Target Oncol. 2023 Jul; 18(4):571-583.  View on PubMed
  8. Wang M, Sushil M, Miao BY, Butte AJ. Bottom-up and top-down paradigms of artificial intelligence research approaches to healthcare data science using growing real-world big data. J Am Med Inform Assoc. 2023 06 20; 30(7):1323-1332.  View on PubMed
  9. Wang M, Goldgof GM, Patel A, Whitaker B, Belov A, Chan B, Phelps E, Rubin B, Anderson S, Butte AJ. Novel computational methods on electronic health record yields new estimates of transfusion-associated circulatory overload in populations enriched with high-risk patients. Transfusion. 2023 07; 63(7):1298-1309.  View on PubMed
  10. Farrand E, Gologorskaya O, Mills H, Radhakrishnan L, Collard HR, Butte AJ. Machine-Learning Algorithm to Improve Cohort Identification in Interstitial Lung Disease. Am J Respir Crit Care Med. 2023 05 15; 207(10):1398-1401.  View on PubMed
  11. Kany S, Rämö JT, Hou C, Jurgens SJ, Nauffal V, Cunningham J, Lau ES, Butte AJ, Ho JE, Olgin JE, Elmariah S, Lindsay ME, Ellinor PT, Pirruccello JP. Assessment of valvular function in over 47,000 people using deep learning-based flow measurements. medRxiv. 2023 May 01.  View on PubMed
  12. Binvignat M, Emond P, Mifsud F, Miao B, Courties A, Lefèvre A, Maheu E, Crema MD, Klatzmann D, Kloppenburg M, Richette P, Butte AJ, Mariotti-Ferrandiz E, Berenbaum F, Sokol H, Sellam J. Serum tryptophan metabolites are associated with erosive hand osteoarthritis and pain: results from the DIGICOD cohort. Osteoarthritis Cartilage. 2023 08; 31(8):1132-1143.  View on PubMed
  13. Loy CJ, Sotomayor-Gonzalez A, Servellita V, Nguyen J, Lenz J, Bhattacharya S, Williams ME, Cheng AP, Bliss A, Saldhi P, Brazer N, Streithorst J, Suslovic W, Hsieh CJ, Bahar B, Wood N, Foresythe A, Gliwa A, Bhakta K, Perez MA, Hussaini L, Anderson EJ, Chahroudi A, Delaney M, Butte AJ, DeBiasi RL, Rostad CA, De Vlaminck I, Chiu CY. Nucleic acid biomarkers of immune response and cell and tissue damage in children with COVID-19 and MIS-C. Cell Rep Med. 2023 06 20; 4(6):101034.  View on PubMed
  14. Voss EA, Shoaibi A, Yin Hui Lai L, Blacketer C, Alshammari T, Makadia R, Haynes K, Sena AG, Rao G, van Sandijk S, Fraboulet C, Boyer L, Le Carrour T, Horban S, Morales DR, Martínez Roldán J, Ramírez-Anguita JM, Mayer MA, de Wilde M, John LH, Duarte-Salles T, Roel E, Pistillo A, Kolde R, Maljkovic F, Denaxas S, Papez V, Kahn MG, Natarajan K, Reich C, Secora A, Minty EP, Shah NH, Posada JD, Garcia Morales MT, Bosca D, Cadenas Juanino H, Diaz Holgado A, Pedrera Jiménez M, Serrano Balazote P, García Barrio N, Sen S, Üresin AY, Erdogan B, Belmans L, Byttebier G, Malbrain MLNG, Dedman DJ, Cuccu Z, Vashisht R, Butte AJ, Patel A, Dahm L, Han C, Bu F, Arshad F, Ostropolets A, Nyberg F, Hripcsak G, Suchard MA, Prieto-Alhambra D, Rijnbeek PR, Schuemie MJ, Ryan PB. Contextualising adverse events of special interest to characterise the baseline incidence rates in 24 million patients with COVID-19 across 26 databases: a multinational retrospective cohort study. EClinicalMedicine. 2023 Apr; 58:101932.  View on PubMed
  15. Zack T, Losert KP, Maisel SM, Wild J, Yaqubie A, Herman M, Knox JJ, Mayer RJ, Venook AP, Butte A, O'Neill AF, Abou-Alfa GK, Gordan JD. Defining incidence and complications of fibrolamellar liver cancer through tiered computational analysis of clinical data. NPJ Precis Oncol. 2023 Mar 23; 7(1):29.  View on PubMed
  16. Rudrapatna VA, Cheng YW, Feuille C, Mosenia A, Shih J, Shi Y, Roberson O, Rubin B, Butte AJ, Mahadevan U, Skomrock N, Erondu N, Chehoud C, Rahim S, Apfel D, Curran M, Khan NS, O'Brien C, Terry N, Martini BD. Creation of an ustekinumab external control arm for Crohn's disease using electronic health records data: A pilot study. PLoS One. 2023; 18(3):e0282267.  View on PubMed
  17. Bauchner H, McDermott MM, Butte AJ. Data Sharing Enters a New Era. Ann Intern Med. 2023 03; 176(3):400-401.  View on PubMed
  18. Goldgof GM, Sun S, Van Cleave J, Wang L, Lucas F, Brown L, Spector JD, Boiocchi L, Baik J, Zhu M, Ardon O, Lu CM, Dogan A, Goldgof DB, Carmichael I, Prakash S, Butte AJ. DeepHeme: A generalizable, bone marrow classifier with hematopathologist-level performance. bioRxiv. 2023 Feb 21.  View on PubMed
  19. Rodriguez-Watson CV, Sheils NE, Louder AM, Eldridge EH, Lin ND, Pollock BD, Gatz JL, Grannis SJ, Vashisht R, Ghauri K, Valo G, Chakravarty AG, Lasky T, Jung M, Lovell SL, Major JM, Kabelac C, Knepper C, Leonard S, Embi PJ, Jenkinson WG, Klesh R, Garner OB, Patel A, Dahm L, Barin A, Cooper DM, Andriola T, Byington CL, Crews BO, Butte AJ, Allen J. Real-world utilization of SARS-CoV-2 serological testing in RNA positive patients across the United States. PLoS One. 2023; 18(2):e0281365.  View on PubMed
  20. Rodriguez-Watson CV, Louder AM, Kabelac C, Frederick CM, Sheils NE, Eldridge EH, Lin ND, Pollock BD, Gatz JL, Grannis SJ, Vashisht R, Ghauri K, Knepper C, Leonard S, Embi PJ, Jenkinson G, Klesh R, Garner OB, Patel A, Dahm L, Barin A, Cooper DM, Andriola T, Byington CL, Crews BO, Butte AJ, Allen J. Real-world performance of SARS-Cov-2 serology tests in the United States, 2020. PLoS One. 2023; 18(2):e0279956.  View on PubMed

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