VALIS or VANISH: a survivor's guide to computational and systems biology

Bud Mishra

Professor of Computer Science & Mathematics
Courant Institute of Mathematical Sciences, NYU
Watson School of Biological Sciences, CSHL
Tata Institute of Fundamental Research, Mumbai


I will discuss several computational tools within our Valis environment that have been developed to answer questions arising in computational and systems biology. I will illustrate power of these tools through examples based on models of genome evolution and biochemical networks. In particular, I will focus on the challenges in systems biology, algorithm design and mathematical modeling that make these problems interesting to biologists, computer scientists and applied mathematicians.

I will also introduce the concept of algebraic model checking systems to reason about biological processes, and how we use them to interpret experimental data modulated by regulatory, metabolic and inter-cellular signaling processes.


Prof. Bud Mishra is a professor of computer science and mathematics at NYU's Courant Institute and a Professor at Cold Spring Harbor Laboratory. His most recent research work is at the interface of computer science and biology. He has developed several sophisticated algorithms and statistical analysis tools to attack biological problems that range from deciphering the genome of pathogens (E. coli, P. falciparum, etc.) to understanding chromosomal aberrations that are implicated in cancer. This work will eventually lead to diagnostics, therapy, vaccines and drugs for various infectious and genetic diseases. His most recent focus has been on a bioinformatics environment that will make it easier for biologists to develop their own computational tools. This environment, dubbed Valis, includes tools for sophisticated visualization of biological information, design and simulation of in silico experiments and storage and communication of biological information.

Prof. Mishra has a degree in Physics from Utkal University, in Electronics and Communication Engineering from IIT, Kharagpur, MS and PhD degrees in Computer Science from Carnegie-Mellon University. He has industrial experience in Computer Science (Tartan Laboratories) and Finance (Tudor Investment and PRF, LLC) and is a founder of a biotechnology company, Opgen, Madison, Wisconsin. His research has ranged from compilers, algorithms and complexity, logic, and algebra to robotics, finance and biology.