My research spans two areas: Personalized Medicine and Computational Structural Biology.

Personalized Medicine

My group uses a combination of Machine Learning and Mechanistic Modeling (ODEs, Agent Based Models) to built predictive models for individual patients. This research is in collaboration with David Whitcomb, MD Ph.D, Randy Brand, MD, Geogios Papachrisou, MD. and Ahmad Tarhini, MD Ph.D. We focus on diseases of the pancreas, including:
  • Acute Pancreatitis
  • Chronic Pancreatitis
  • Pancreatic Cancer
  • Diabetes
  • Melanoma

Computational Structural Biology

My group has developed a number of computational methods, primarily built on probabilistic graphical models for simulating and designing molecules. Our current work focuses on:
  • non-parametric graphical models of protein dynamics
  • graphical models of allosteric regulation
  • graphical models for simulating the emergence of drug resistance-causing mutations
  • graphical models for designing resistance-evading drugs

Current Students

Trevor Frisby, Ph.D. candidate, Computational Biology

Nikhila Vembu, B.S. candidate, Biomedical Engineering



Manaswitha Edupalli, B.S. Computational Biology 2018

Basit Adebiyi, B.S. Computer Science, Lincoln University 2018

Jiachen Ning, B.S. Machine Learning 2017

Nghia Le, B.S. Computer Science 2017

Jingzhi Pan, M.S. Computational Biology 2017, Currently an engineer at Petuum

Benjamin Kaufman , M.S. Computational Biology 2017

Qingyuan (Diana) Song , M.S. Computational Biology 2017, Currently a Ph.D. student at Dartmouth

Jack Paparian, M.S. Computer Science 2016, Currently an engineer at Verily

Christine Baek, M.S. Computational Biology 2015

Zhishen Cao, M.S. Computational Biology 2016, Currently a bioinformaticist at UPMC

Yanyu Liang, M.S. Computational Biology 2016, Currently a Ph.D. student at U. Chicago

Chensu Xie Computational Biology, 2015 Currently a Ph.D. student at Cornell

Michael Gregory, B.S. Chemical Engineering and Biomedical Engineering

Subhodeep Moitra, Ph.D. Language Technology Institute, 2015. Currently Engineer at Google

Ji Oh Yoo, M.S. Computer Science, 2015

Adam Scarlat, M.S. Computational Biology 2016

Naina Thangaraj, M.S. Computational Biology 2015

Preeti Singh, M.S. Computational Biology 2014

Nikita Roy, M.S. Computational Biology 2014

John Krill-Burger, M.S. Computational Biology 2014 Currently at the Broad Institute

Sunguk Choi, M.S.Computational Biology, 2013. Currently VP, Senior Data Scientist at BNY Mellon

Jiayue (Amy) Li , B.S. Computational Biology, 2013 (now a Ph.D student at Boston University)

Yue Yu , M.S. Computational Biology, 2012

Hetu Kamisetty, Ph.D., Department of Computer Science, 2011, Post-doc in David Baker’s Lab (2011) Currently Engineer at Facebook

Xin Gao, Ph.D., Post-doc, 2010, Currently an assistant professor of computer science at KAUST

Sumit Jha, Ph.D. Department of Computer Science, 2010, Currently an assistant professor of computer science at the University of Central Florida

Philip Davidson, M.S., Computational Biology

James Dang, M.S., Computational Biology, 2010

David Nicholson, B.S., Computer Science

Md. Ahaduzzaman Munna, M.S., Language Technologies

Deepa Sathaye, B.S., Computer Science

Vardhan Dharnidharka, M.S., Computational Biology , 2010

Rupinder P. Khandpur,  M.S., Computational Biology, 2010

K. Arun: Ph.D., Department of Biological Sciences , 2007

Aly Azeem Khan: M.S., Computational Biology, 2005. Currently a research fellow at U. Chicago

Ka-Young An:  M.S., Computational Biology, 2005. Currently a Ph.D. student at the New Jersey Institute of Technology

Tal Blum: M.S. Language Technology Institute, 2005.

Ruben Valas: B.S. Department of Computer Science. Currently a Ph.D. student at UCSD