Scalable Algorithms for Analysis of Gene and Metabolic Networks

April 18, 2007
Time: 11:00am-12:00pm
Room 414 CEPSR Schapiro
Speaker: Calin Belta, Boston University

Abstract

Bacteria continuously respond to environmental changes through a complicated mechanism consisting of an interplay between metabolic and gene networks. Through hundreds of chemical reactions, the metabolic network converts nutrients from the environment to elements necessary for growth and survival of the cell. Most of these chemical reactions are regulated by enzymes produced by a gene network. In turn, the expression of the genes from the gene network is regulated by its own products and metabolites produced by the metabolic network.

In the first part of the talk, I will show how a quasi-steady state assumption on the dynamics of the metabolic network, combined with tools from convex analysis and in vivo survivability data, can lead to predictions such as essentiality of metabolites, nutrients, and chemical reactions. In the second part of the talk, I will focus on gene networks. I will show how a particular approach to modelling, together with discrete abstractions and model checking, can be used to tune and analyze gene networks from qualitative specifications given as arbitrary temporal and logic statements over species concentrations. I will exemplify the methods on the metabolism of E.coli and on a four-gene synthetic transcriptional cascade.


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