People

We’re a diverse team of scientists, physicians, and students at the UCSF Institute for Computational Health Sciences (ICHS).

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.
Marina Sirota, PhD Assistant Professor
Marina is currently an Assistant Professor at the Institute for Computational Health Sciences at UCSF. Prior to that she was the Lead Research Scientist in the Division of Systems Medicine at Stanford University and has worked as a Senior Research Scientist at Pfizer where she focused on developing Precision Medicine strategies in drug discovery. She completed her PhD in Biomedical Informatics at Stanford University, where her graduate work focused on predicting drug-disease relationships based on gene expression to identify novel therapeutic indications for known drugs. Her research interests lie in developing computational integrative methods and applying these approaches in the context of disease diagnostics and therapeutics. Her primary focus is on leveraging and integrating different types of omics and clinical data to better understand the role of the immune system in disease.
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.
Keiichi Kodama, MD, PhD Assistant Professor
Keiichi Kodama MD, PhD is Assistant Professor of the Pediatric Department at UCSF School of Medicine. Dr. Kodama’s research interests focus on integrating genomics (bioinformatics) to identify diagnostics biomarkers, disease mechanisms and therapeutical drugs for diabetes and other metabolic diseases.
Boris Oskotsky, PhD Bioinformatics Systems Admin
Boris Oskotsky studied at Saint Petersburg Technical University where he earned a M.S. in Computers Science and a Ph.D. 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.
Idit Kosti, PhD Postdoctoral Fellow
Idit has a PhD in computational biology from the Technion, Haifa, Israel, where she studied epigenetics, trancription and splicing co-regulation in the human gene expression pathway. Her current focus is in meta anaylsis and computational integrative methods of human microbiome towards better understanding of pre term births patients microenvironment. This work is done in collaboration with the march Of Dimes project at Stanford university.
Thomas A. Peterson, Ph.D. Postdoctoral Fellow
Tom Peterson earned his Ph.D. In Biology with a specialization in Bioinformatics & Computational Biology from the University of Maryland, Baltimore County. He developed statistical models and used machine learning techniques for analyzing the functional impact of genetic variants in human diseases such as cancer.
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 Executive Administrator
Andrew is the executive administrator 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.

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