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. Binvignat M, Emond P, Mifsud F, Miao B, Courties A, Lef?vre 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 Apr 25.  View on PubMed
  2. 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
  3. 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
  4. 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 Mar 21.  View on PubMed
  5. 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
  6. Bauchner H, McDermott MM, Butte AJ. Data Sharing Enters a New Era. Ann Intern Med. 2023 03; 176(3):400-401.  View on PubMed
  7. 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
  8. 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
  9. 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
  10. Aras MA, Abreau S, Mills H, Radhakrishnan L, Klein L, Mantri N, Rubin B, Barrios J, Chehoud C, Kogan E, Gitton X, Nnewihe A, Quinn D, Bridges C, Butte AJ, Olgin JE, Tison GH. Electrocardiogram Detection of Pulmonary Hypertension Using Deep Learning. J Card Fail. 2023 Jan 24.  View on PubMed
  11. Radtke KK, Butte AJ. Advancing evidence-based treatment of infectious diseases in children with real-world data: Opportunities and challenges. Front Pharmacol. 2022; 13:1054688.  View on PubMed
  12. Huie JR, Vashisht R, Galivanche A, Hadjadj C, Morshed S, Butte AJ, Ferguson AR, O'Neill C. Toward a causal model of chronic back pain: Challenges and opportunities. Front Comput Neurosci. 2022; 16:1017412.  View on PubMed
  13. Arvisais-Anhalt S, Ravi A, Weia B, Aarts J, Ahmad HB, Araj E, Bauml JA, Benham-Hutchins M, Boyd AD, Brecht-Doscher A, Butler-Henderson K, Butte AJ, Cardilo AB, Chilukuri N, Cho MK, Cohen JK, Craven CK, Crusco S, Dadabhoy F, Dash D, DeBolt C, Elkin PL, Fayanju OA, Fochtmann LJ, Graham JV, Hanna JJ, Hersh W, Hofford MR, Hron JD, Huang SS, Jackson BR, Kaplan B, Kelly W, Ko K, Koppel R, Kurapati N, Labbad G, Lee JJ, Lehmann CU, Leitner S, Liao ZC, Medford RJ, Melnick ER, Muniyappa AN, Murray SG, Neinstein AB, Nichols-Johnson V, Novak LL, Ogan WS, Ozeran L, Pageler NM, Pandita D, Perumbeti A, Petersen C, Pierce L, Puttagunta R, Ramaswamy P, Rogers KM, Rosenbloom ST, Ryan A, Saleh S, Sarabu C, Schreiber R, Shaw KA, Sim I, Sirintrapun SJ, Solomonides A, Spector JD, Starren JB, Stoffel M, Subbian V, Swanson K, Tomes A, Trang K, Unertl KM, Weon JL, Whooley MA, Wiley K, Williamson DFK, Winkelstein P, Wong J, Xie J, Yarahuan JKW, Yung N, Zera C, Ratanawongsa N, Sadasivaiah S. Paging the Clinical Informatics Community: Respond STAT to Dobbs v. Jackson's Women's Health Organization. Appl Clin Inform. 2023 01; 14(1):164-171.  View on PubMed
  14. Arora A, Lituiev D, Jain D, Hadley D, Butte AJ, Berven S, Peterson TA. Predictive Models for Length of Stay and Discharge Disposition in Elective Spine Surgery: Development, Validation, and Comparison to the ACS NSQIP Risk Calculator. Spine (Phila Pa 1976). 2022 Nov 21.  View on PubMed
  15. Binvignat M, Pires G, Tchitchek N, Costantino F, Courties A, Klatzmann D, Butte AJ, Combe B, Dougados M, Richette P, Mariotti-Ferrandiz E, Berenbaum F, Sellam J. Identification of Symptoms Phenotypes of Hand Osteoarthritis using Hierarchical Clustering: Results from the DIGICOD Cohort. Arthritis Care Res (Hoboken). 2022 Oct 20.  View on PubMed
  16. Hu Z, van der Ploeg K, Chakraborty S, Arunachalam PS, Mori DAM, Jacobson KB, Bonilla H, Parsonnet J, Andrews JR, Holubar M, Subramanian A, Khosla C, Maldonado Y, Hedlin H, de la Parte L, Press K, Ty M, Tan GS, Blish C, Takahashi S, Rodriguez-Barraquer I, Greenhouse B, Butte AJ, Singh U, Pulendran B, Wang TT, Jagannathan P. Early immune markers of clinical, virological, and immunological outcomes in patients with COVID-19: a multi-omics study. Elife. 2022 10 14; 11.  View on PubMed
  17. Davidson J, Vashisht R, Butte AJ. From Genes to Geography, from Cells to Community, from Biomolecules to Behaviors: The Importance of Social Determinants of Health. Biomolecules. 2022 10 09; 12(10).  View on PubMed
  18. Kornblith AE, Singh C, Devlin G, Addo N, Streck CJ, Holmes JF, Kuppermann N, Grupp-Phelan J, Fineman J, Butte AJ, Yu B. Predictability and stability testing to assess clinical decision instrument performance for children after blunt torso trauma. PLOS Digit Health. 2022 Aug; 1(8):e0000076.  View on PubMed
  19. Padula WV, Kreif N, Vanness DJ, Adamson B, Rueda JD, Felizzi F, Jonsson P, IJzerman MJ, Butte A, Crown W. Machine Learning Methods in Health Economics and Outcomes Research-The PALISADE Checklist: A Good Practices Report of an ISPOR Task Force. Value Health. 2022 07; 25(7):1063-1080.  View on PubMed
  20. Abernethy A, Adams L, Barrett M, Bechtel C, Brennan P, Butte A, Faulkner J, Fontaine E, Friedhoff S, Halamka J, Howell M, Johnson K, Long P, McGraw D, Miller R, Lee P, Perlin J, Rucker D, Sandy L, Savage L, Stump L, Tang P, Topol E, Tuckson R, Valdes K. The Promise of Digital Health: Then, Now, and the Future. NAM Perspect. 2022; 2022.  View on PubMed

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