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

I Computational Structural Biology

Publications

Students: Hetu Kamisetty, Arvind Ramanathan

Collaborators: Pratul Agarwal, Ph.D. ORNL; Chris Bailey-Kellogg, Ph.D., Dartmouth

We are developing novel, physics-based algorithms for modeling, analyzing, and simulating proteins and nucleic acids at, or near, atomic resolution. Our work is relevant to structure-based drug design and synthetic biology. Current projects include: 1) Markov Random Field-based techniques for fast free-energy calculations, protein design, and dynamic simulations, and 2) the analysis of molecular dynamics simulations data.

II Systems Biology

II-a Formal Methods in Systems Biology

          Publications

Students: Sumit Kumar Jha

Collaborators: James Faeder, Ph.D., U. Pittsburgh

We are developing novel techniques for formally reasoning about the dynamics of complex biological systems. Current projects include: 1) model-checking based analysis of protein folding pathways; 2) the design of control policies for engineered biological systems; and 3) formal verification of in the context of rule-based modeling.

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).

II-c The Dynamics of Cancer

Collaborators: Arijit Chakravarty, Ph.D.

We are interested in applying a systems biology perspective to the study of the causes and consequences of chromosomal instability (CIN) in cancer.

Current Students

Hetu Kamisetty, Ph.D. candidate, Department of Computer Science

Sumit Jha, Ph.D. candidate, Department of Computer Science

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

Armaghan (Rumi) Naik, Ph.D. candidate, Joint CMU-Pitt Ph.D. Program in Computational Biology

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

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

Alumni

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