Colloquia, Seminars and Conference News
Title : The regulatory Genome and the Computer
Date : November 7, 2008. (2:00 pm) Tea starts half an hour before each seminar
Location: ITEB 336
Speaker : Sorin Istrail
Abstract:
The definitive feature of the many thousand cis-regulatory control modules in an animal genome is their information processing capability. These modules are “wired” together in large networks that control major processes such as development; they constitute “genomic computers.” Each control module receives multiple inputs in the form of the incident transcription factors which bind to them. The functions they execute upon these inputs can be reduced to basic AND, OR and NOT logic functions, which are also the unit logic functions of electronic computers. Here we consider the operating principles of the genomic computer, the product of evolution, in comparison to those of electronic computers. For example, in the genomic computer intra-machine communication occurs by means of diffusion (of transcription factors), while in electronic computers it occurs by electron transit along pre-organized wires. There follow fundamental differences in design principle in respect to the meaning of time, speed, multiplicity of processors, memory, robustness of computation and hardware and software. The genomic computer controls spatial gene expression in the development of the body plan, and its appearance in remote evolutionary time must be considered to have been a founding requirement for animal grade life.
Bio:Sorin Istrail is Julie Nguyen Brown Professor of Computational and Mathematical Sciences, Professor of Computer Science, and Director of the Center for Computational Biology at Brown University. He has a Ph.D. in computer science from University of Bucharest, Romania. After being a visiting scientist at MIT, he joined Sandia National Laboratories, where he founded in 1992 the Computational Biology Project, within the DOE Applied Mathematics Program, started at DOE by John von Neumann. In April 2000, he joined Celera Genomics as Senior Director of the Informatics Research Group. In 2003 he was elected Celera/Applied Biosystems Science Fellow, position recognizing individual technical contributions (one of the five Science Fellows in a company of 800 scientists). Since 2004, he is a Visiting Associate in the Division of Biology at California Institute of Technology.
Istrail’s work has been focused on computational molecular biology – genomic regulatory systems and networks, genetic patterns of inheritance of complex disease, protein folding, and comparative and integrative genomics. His research interests also include combinatorial algorithms, mathematical logic, computational complexity, and applications of computer science to biology, physics, economics and chemistry. In 2000, he resolved a longstanding open problem in statistical mechanics, the Three-Dimensional Ising Model Problem; his proof uses computational complexity methods to provide the negative “solution” to the problem. His “impossibility” (computational intractability) theorem shows that “complexity,” in the analytical rigorous NP-completeness framework, unifies the sources of difficulty intrinsic to deriving explicit partition function closed forms, for every three-dimensional Ising model.
He is Co-Editor-in-Chief of the Journal of Computational Biology, Co-Founder of the RECOMB Conference Series, Co-Editor of the MIT Press Computational Molecular Biology Book Series, and Co-Editor of the Springer-Verlag Lecture Notes in Bioinformatics Book Series.
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