BISC Seminar - 5/2


Subject: BISC Seminar - 5/2
From: Michelle T. Lin (michlin@cs.berkeley.edu)
Date: Wed Apr 26 2000 - 17:42:39 MET DST


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Berkeley Initiative in Soft Computing (BISC)
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From: L. A. Zadeh <zadeh@cs.berkeley.edu>

BISC Seminar
310 Soda Hall
Tuesday May 2, 2000
4-5 pm

Speaker: Simon Kasif
         Cambridge Research Laboratory (Compaq) and MIT Genome Center
 
Title: Steps Towards "Virtual Life": Methodologies for Computational
       Gene Identification in Biological Sequences

Abstract:

        The current mode of biological exploration is changing from
a single experiment where an individual investigator
is exploring a single conjecture to hypothesis-free generation of data
using revolutionary genomic technologies and new computatonal
representations and algorithms for an "in-silico" exploration of
the biology of living organisms.

         Computational genomic analysis has already inspired changes
in theories of evolution in low-order organisms (prokaryotes);
identified and mapped thousands of genes; provided order of magnitude
improvements in the cost and speed of experiments; helped progress
towards identifying minimal living organisms and suggested new
methodologies for accurate diagnosis of subtle forms of cancer.

        A recurring theme in this research is the need to build
perhaps initially naive models of biological sysems that allow
researchers to extract meaningful information from data. Without
exception all work on computational gene finding makes use of
assumptions about the organization of the genome and postulates basic
gene models that are used as templates to extract putative genes.
This paradigm has generated thousands of gene predictions that serve
as potential targets for treating disease or other important
bio-medical applications.

         In this talk we review three techniques for gene
identification in biological sequences and discuss the application of
learning systems and computer science algorithms to this scientific
challenge.

         On a more abstract level, computational genomics research
motivates the ambitious enterprise of building in-silico computational
models of biological systems. We envision that future "Virtual Human"
research will complement computer science efforts in Artificial
Intelligence that layed out the computational frameworks for cognitive
behavior. The "virtual life" focus of computational biology promises
to outline the computational foundation for functional genomics and
the behavior of cells and major organs in normal, pathological or
possibly newly designed conditions.
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