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Research |
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
Students:
Hetu Kamisetty, Arvind
Ramanathan , Gerald Nora Collaborators: Pratul
Agarwal, Ph.D. ORNL; Maria Kurnikova,
Ph.D., CMU; Patricia Opresko,
Ph.D., U. Pittsburgh (Gerald Nora is one of Dr. Opresko’s
M.D.-Ph.D. students) 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 and dynamic simulations, 2)
tensor-based analysis of molecular dynamics simulation trajectories, and 3)
predicting the structure of telomeric DNA.
II Systems Biology
II-a Formal
Methods in Systems Biology
Students: Sumit
Kumar Jha Collaborators: Ed Clarke, Ph.D., CMU (Sumit Jha is one of Dr.
Clarke’s students); 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. We
are developing machine-learning and formal methods-based techniques for predicting
patient-specific outcomes for patients with severe sepsis (Clermont), and pancreatitis (Whitcomb). II-c The Dynamics of Cancer
Students: Cordelia Ziraldo 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 Cordelia Ziraldo, Ph.D.
candidate, Joint CMU-Pitt Ph.D. Program
in Computational Biology Arvind Ramanathan, Ph.D.
candidate, Joint CMU-Pitt Ph.D. Program
in Computational Biology Alumni
K. Arun: Ph.D., Department of Biological Sciences , 2007. Aly Azeem Khan: M.S.,
Computational Biology, 2005. Currently a Ph.D. student at 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 |