The International Computer Science Institute
is pleased to present a talk:

Network bioinformatics: From effect detection to comparative network analysis

Adam P. Arkin University of California, Berkeley

aparkin		lbl.gov

http://genomics.lbl.gov

Wednesday, December 5, 2001 ICSI, Rm 607 4:00-5:00 pm

Biological regulatory networks are the circuitry that control cellular function and malfunction. The chemistry underlying the function of these networks is extraordinarily complex and difficult, if not impossible, to understand, knowing only a list of the parts (genes, proteins, and other chemicals) and a list of which parts react with which other parts. Just as when analyzing and diagnosing complex electronic circuits, mathematical models and computational tools for analysis and simulation are necessary if we are to understand, control and even design our own biological and genetic reaction networks. Mathematical methods for analyzing these multiscale systems with mixed levels of abstraction are just becoming available.

In this talk, we will describe our efforts at modeling bacterial genetic systems from the stochastic processes of gene expression to comparative dynamics in signal transduction pathways and the mathematical and computational challenges of doing so accurately. We will show how concepts of necessity and sufficiency from control theory can be used to deduce mechanistic details about less well studied systems demonstrated through analyses of various microbial systems from phage to Bacillus subtilis. These will underline the challenge faced in understanding the "engineering principles" of control in these systems. We will also describe our efforts at creating a framework for biological data analysis and simulation to aid in these efforts.

web		icsi.berkeley.edu