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
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
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).
Narges Sharif Razavian, Ph.D. candidate, Language Technology Institute
Subhodeep Moitra, M.S. candidate, Language Technology Institute
Sunguk Choi, M.S. candidate, Computational Biology
Xin Gao, Ph.D., Post-doc, 2010, Currently an assistant professor of computer science at KAUST
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