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
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