Overview

I am interested in the dynamics of complex biological systems. My group uses a variety of computational techniques, including machine-learning and formal methods to: i) understand the relationship between dynamics and function, ii) predict outcomes, and iii) automatically design control strategies.

My research spans two areas: Structural Biology and Systems Biology

Group Wiki

I Computational Structural Biology

Publications

We are developing novel, physics-based algorithms for modeling, analyzing, and simulating proteins at, or near, atomic resolution. Our work is relevant to structure-based drug design and synthetic biology.

II Systems Biology

II-a The Dynamics of Cancer

Collaborators: Arijit Chakravarty (Millennium), Ph.D., David Whitcomb MD, PhD. (UPMC), Randall Brand MD (UPMC), Yang Liu, Ph.D. (UPMC),

I am presently developing both mechanistic and statistical models of cancer, especially Pancreatic Cancer

II-b The Dynamics of Acute Illness

Collaborators: Gilles Clermont, M.D., U. Pittsburgh /UPMC,  David Whitcomb, M.D., Ph.D., UPMC, Georgios Papachristou, M.D., UPMC, VA

We are developing machine-learning and formal methods-based techniques for predicting patient-specific outcomes for patients with severe sepsis (Clermont), and pancreatitis (Whitcomb and Papachristou).

Current Students

Narges Sharif Razavian, Ph.D. candidate, Language Technology Institute

Subhodeep Moitra, M.S. candidate, Language Technology Institute

Sunguk Choi, M.S. candidate, Computational Biology

Alumni

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

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

Arvind Ramanathan, Ph.D. Joint CMU-Pitt Ph.D. Program in Computational Biology, 2010

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

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 Ph.D. student at Columbia

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