Bud Mishra Professor of Computer Science, Mathematics, Cell Biology, and Human Genetics (Courant Institute, NYU Medical School, Mt. Sinai School of Medicine & TIFR)

What's Next? Challenges from Systems Biology

Abstract:

Motivated by the need for scalable symbolic reasoning methodologies aimed at systems biology, as well as the novel opportunities made possible by powerful hybrid automata models of biochemical networks, we have embarked upon the Algorithmic Algebraic Model Checking (AAMC) project that combines symbolic computation with model checking to analyze biochemical systems. Briefly, AAMC aims to identify a decidable (ultimately, practical) component of a theory for systems biology by examining the connections between semi-algebraic hybrid automata, modal logic, computability and systems biology, starting with a characterization based on Semi-Algebraic Hybrid Automata.

In Semi-Algebraic Hybrid Automata, the continuous dynamics and discrete jump conditions are defined by first-order formulæ whose terms are polynomials over the reals. Consequently, they can exploit a series of real algebraic techniques, based on Tarski's result on the decidability of real quantifier elimination, to study the possible evolutions of the system entirely symbolically. Beyond decidability of Timed Computation Tree Logic (TCTL), we studied Semi-Algebraic Constant Reset Automata and Independent Dynamics Automata whose resets were constrained to be constant or identity, thus providing a suitable generalization of O-minimal systems without sacrificing decidability.

Short Bio:

Prof. Bud Mishra is a professor of computer science and mathematics at NYU's Courant Institute of Mathematical Sciences and a professor of cell biology at NYU School of Medicine. He founded the NYU/Courant Bioinformatics Group, a multi-disciplinary group working on research at the interface of computer science and biology. He has developed several sophisticated technologies, algorithms, and statistical analysis tools to attack biological problems that range from deciphering the structure of a genome to understanding chromosomal aberrations and their relation to cancer genetics. Prof. Mishra has a degree in Physics from Utkal University, in Electronics and Communication Engineering from IIT, Kharagpur, and MS and PhD degrees in Computer Science from Carnegie-Mellon University. He has industrial experience in Computer Science (Tartan Laboratories, and ATTAP), Finance (Tudor Investment and PRF, LLC), Robotics and Biotechnology (OpGen, and Bioarrays). His research has ranged from compilers, algorithms and complexity, logic, and algebra to robotics, finance, internet, and biology. He also holds adjunct professorships at Tata Institute of Fundamental Research and Mt. Sinai School of Medicine. From 2001-04, he was a professor at the Watson School of Biological Sciences, Cold Spring Harbor Lab.