People

We’re a diverse team of scientists, physicians, and students at the Bakar Computational Health Sciences Institute(BCHSI)

Atul Butte, PhD
Atul Butte, MD, PhD Professor
Atul Butte, MD, PhD, Professor, Director of UCSF’s Institute for Computational Health Sciences (ICHS). Former Professor of Pediatrics and Genetics, and by courtesy, Medicine, Pathology, and Computer Science, at Stanford University and Lucile Packard Children’s Hospital. Dr. Butte trained in Computer Science at Brown University, worked as a software engineer at Apple and Microsoft, received his MD at Brown University, trained in Pediatrics and Pediatric Endocrinology at Children’s Hospital Boston, then received his PhD in Health Sciences and Technology from Harvard Medical School and MIT. Dr. Butte is Chief of the new Division of Systems Medicine at Stanford. Dr. Butte is also a founder of three investor-backed companies: Personalis, providing clinical interpretation of whole genome sequences, Carmenta, discovering diagnostics for pregnancy complications, and NuMedii, finding new uses for drugs through open molecular data. Dr. Butte has authored more than 160 publications, with research repeatedly featured in Wired Magazine, and in the New York Times Science Times and the International Herald Tribune (2008), Wall Street Journal (2010 -2012), San Jose Mercury News (2010), and the San Francisco Chronicle (2013). In 2013, Dr. Butte was recognized by the White House as an Open Science Champion of Change for promoting science through publicly available data. Other recent awards include the 2013 induction into the American Society for Clinical Investigation, the 2012 FierceBiotech IT “Top 10 Biotech Techies”, 2011 National Human Genome Research Institute Genomic Advance of the Month, 2010 Society for Pediatric Research Young Investigator Award, and the 2008 AMIA New Investigator Award.
Sanchita Bhattacharya Bioinformatics Project Leader
Sanchita Bhattacharya is currently leading the efforts to leverage open-access clinical trials and research data from ImmPort, a National Institute of Allergy and Infectious Diseases Division of Allergy, Immunology, and Transplantation (NIAID-DAIT) sponsored shared data repository for subject-level human immunology study data and protocols. Her projects involve “The 10,000 Immunomes Project”, a diverse human immunology reference derived from over 44,000 individuals across 291 studies. Sanchita comes with over sixteen years of work experience as a data scientist at various academic institutions such as Stanford School of Medicine, Lawrence Berkeley National Laboratory, and MIT. Her formal training in bioinformatics coupled with expertise in computational modeling and immunology has led to a number of publications demonstrating the repurposing of big data in Immunology and other research areas to facilitate translational research.
Boris Oskotsky, PhD Bioinformatics Systems Admin
Boris Oskotsky studied at Saint Petersburg Technical University where he earned a MS in Computers Science and a PhD in Solid State Physics. Previously worked at Stanford University in different departments within the School of Medicine including IRT, BMIR and Neurobiology. He loves tea and everything tea-related (e.g. teapots and teakettles). His favorite way to spend time is traveling with his wife.
Thomas A. Peterson, Ph.D. Assistant Professor
Thomas is currently an Assistant Professor in the Bakar Computational Health Sciences Institute and the Department of Orthopaedic Surgery at UCSF. In addition, he is the Director of the Informatics Core for the UCSF REACH Center for Chronic Low Back Pain. After completing his PhD in Biology with focus on Biomedical Informatics and Computational Biology, Thomas continued his research in the Butte lab as a postdoctoral research scholar at UCSF. His current research interests include creating translational models and tools for clinicians using Electronic Health Records and other large datasets like nationwide surveys and claims databases while innovating using network-based risk factor analyses and machine / deep learning to create predictive models.
Zicheng Hu, PhD Research Scientist
Zicheng completed his undergraduate degree at the Hong Kong University of Science and Technology. After that, he moved to The University of Texas at Austin, where he earned his Master’s degree in Statistics and Ph.D. in Cell and Molecular Biology from Lauren Ehrlich’s lab. He used knock-out mouse models to study the roles chemokine receptors play in the autoimmune diseases. Currently, he is focused on characterizing dynamics of the human immune system using high through-put data.
Navchetan Kaur, PhD Postdoctoral Fellow
Navchetan is a postdoctoral scholar in Butte Lab. She has earned her PhD in Immunopathology from PostGraduate Institute of Medical Research, Chandigarh, India, where she explored the immune and genetic basis of co-existence of autoimmune diseases. She learned bioinformatics skills while working on solid organ transplantation projects at Tulane University in New Orleans. Navchetan also has experience in supervising histocompotbility lab at a tertiary referral center. Currently, her research is focused on understanding big data related to Immunology.
Andrew Bishara, MD Postdoctoral Fellow and Clinical Instructor
Andrew completed his undergraduate degree at Massachusetts Institute of Technology in the department of mechanical engineering. He then received his MD from Harvard Medical School. He completed residency in anesthesia and perioperative Care at University of California, San Francisco and is a board certified anesthesiologist. Andrew is an NIH T32 post-doctoral research fellowship recipient and a clinical instructor in the department of anesthesia and perioperative care at UCSF. He spends part of his week as a clinical anesthesiologist and the rest of his time applying artificial intelligence to medicine through machine/deep learning techniques for time series analysis, imaging, language processing, and decision support.
Daniel Wong BMI PhD Student
Daniel graduated from UC Berkeley in 2017 with degrees in Computer Science and Molecular and Cellular Biology. He is an aspiring PhD student who focuses on deep learning applied to medicine, computer vision, and blockchain technologies.
Michelle Wang, DPharm PSPG PhD Student
Michelle is currently a PhD student with the Pharmaceutical Sciences and Pharmacogenomics program. Michelle completed her undergraduate degree in chemistry at University of Washington and received her PharmD degree from the Ohio State University. Subsequently, she was involved in regulatory science development at the FDA before coming to UCSF. In the Butte Lab, she is very interested in clinical informatics and hopes to develop novel methods to use real-world data to help improve healthcare and drug development.
Andrew Jan, MA Chief of Staff
Andrew is chief of staff to Atul Butte. Andrew holds a Master’s degree in History from UCLA; a master’s degree in Middle Eastern Studies from UT Austin; and Bachelor’s degrees from UC San Diego. In that capacity, he participated in studied in Cairo, Egypt; Salalah, Oman; and Istanbul, Ankara, and Cunda, Turkey. Andrew spends all of his free time with dogs, including wrangling his Pomeranian mix named Toby and volunteering at Oakland Animal Services.
Douglas Arneson, PhD Postdoctoral Fellow
Doug earned his B.S. in Bioengineering and PhD in Bioinformatics from the University of California, Los Angeles. He used single cell sequencing to tease apart the underlying mechanisms of traumatic brain injury and developed computational methods for network construction using single cell data.
Gregory Goldgof, MD, PhD Postdoctoral Fellow
Greg is currently a postdoctoral fellow in the Butte lab and a resident in the Physician Scientist Pathway in the department of Laboratory Medicine, where he is developing artificial intelligence and deep learning applications with a focus on laboratory medicine, hematopathology, and diseases of the blood, bone marrow, and immune system. Greg previously double-majored in Computer Science and Biological Sciences at Stanford University. He then received a Masters in Bioengineering at Stanford, followed by a Whitaker International Bioengineering research fellowship at Imperial College London. Next, Greg received an MD/PhD from the Medical Scientist Training Program at UC San Diego. During his PhD, he combined computational and wet-lab approaches to discover and characterize novel drug targets with applications in parasitology, mycology and cancer, for which he was the recipient of three Bill and Melinda Grand Challenge Exploration grants.

Collaborators

  • Jeff Wiser, Patrick Dunn, Mike AtassiNorthrop Grumman
  • Ashley Xia and Quan ChenNIAID
  • Takashi Kadowaki, Momoko Horikoshi, Kazuo Hara, Hiroshi Ohtsu U Tokyo
  • Kyoko Toda, Satoru Yamada, Junichiro IrieKitasato Univ and Hospital
  • Shiro MaedaRIKEN
  • Alejandro Sweet-Cordero, Julien SagePediatric Oncology
  • Mark Davis, C. Garrison FathmanImmunology
  • Russ Altman, Steve QuakeBioengineering
  • Euan Ashley, Joseph Wu, Tom Quertermous Cardiology
  • Mike Snyder, Carlos Bustamante, Anne Brunet Genetics
  • Jay Pasricha Gastroenterology
  • Rob Tibshirani, Brad Efron Statistics
  • Hannah Valantine, Kiran Khush Cardiology
  • Ken Weinberg Pediatric Stem Cell Therapeutics
  • Mark Musen, Nigam Shah National Center for Biomedical Ontology
  • Minnie Sarwal Nephrology
  • David Miklos Oncology

Alumni