2002-2003 AbstractsComputer Science Distinguished Lecturer Series:Inferring Gene Transcription Networks: The Davidson ModelSorin Istrail, Celera Genomics4:10pm, Monday September 23, 2002
AbstractIn 2001 Eric Davidson published his "Genomic Regulatory Systems" book where he reports on 30 years of work, together with his colleagues, on purple sea urchin. Their work provided a general experimental framework for the study of a gene's cis-regulatory region (an upstream DNA sequence containing a series of consecutive binding sites). Their approach consisted of systematic, almost exhaustive, series of mutations of individual binding sites, together with the associated measurements of the transcription rates. By quantitative analysis, they were able to infer a complete set of minimal functional units of regulation and their interrelations. They proceeded hierarchically to uncover "modularity" and "hardwired information processing logic" of a gene's cis-region. Most of their work was focused on the endo16 gene. Their extraordinary technology and the inference of the underlying "network" for this gene resulted in the most completely understood transcriptional system to date.It is quite remarkable how combinatorial and robust their approach is. We present an analysis and a mathematical formalism for the Davidson transcriptional network inference framework together with combinatorial challenges and algorithms related to it. We will also provide a glance at our ongoing collaborative work with Eric Davidson towards the quest for the cis-regulatory "programming language." This is joint work with Eric Davidson and Vladimir Filkov.
BiographySorin Istrail has a Ph.D. in computer science from University of Bucharest, Romania. After his immigration to the US, he was a visiting scientist at MIT and also taught at Wesleyan University. He joined Sandia National Labs in 1992 where he held several positions, including Principal Senior Member of the Technical Staff. From 1992 to 2000, he led the Sandia National Labs research in genomics and structural proteomics within the Computational Biology Project, part of the DOE Applied Mathematics Program -- program started at DOE by John von Neumann. In April 2000, he joined Celera Genomics, where he is Senior Director and COO of Informatics Research.Istrail's work has been focused on combinatorial algorithms, computational complexity, programming languages, and on applications of computer science to biology, physics, chemistry and economics. In 2000, he resolved a 50-year old open problem in statistical mechanics, the Three-Dimensional Ising Model Problem; the negative solution shows the "impossibility" (computational intractability) of deriving closed forms explicit partition functions for every three-dimensional model. Recent work of Istrail's research group at Celera has been devoted to algorithmic design and software development for the following areas: genetics of SNPs and haplotypes, high-throughput EST mapping, genomic vaccine design and comparative peptidomics, compu/combichem and protein structure, BLAST-replacement tools, genomic regulatory systems, literature datamining, DNA array design and expression analysis, and game theory and pharma economic behavior. He is Co-Editor-in-Chief of the Journal of Computational Biology, and Co-Founder of the RECOMB Conference Series. Faculty Contact: Nancy Amato (amato@cs.tamu.edu)
Computer Science Distinguished Lecturer Series:Greatest Common Measure: The Last 2500 YearsAlexander Stepanov, Adobe Systems, Inc.
4:10pm, Wednesday April 2, 2003 AbstractThe talk describes development of Euclid's algorithm from early Pythagoreans to modern times. This development shows gradual evolution of a notion of abstract (or generic) algorithm. We maintain that while the term "generic programming" was introduced by Musser and Stepanov in 1988, the notion of algorithmic genericity goes back to remote centuries and is one of the main driving forces of mathematical progress. We will encounter some remarkable men and one great woman.BiographyAlexander Stepanov is now a Principal Scientist at Adobe Systems. Alex is responsible for the architecture of a new core UI system for use in Adobe products. Prior to joining Adobe, Alex was Vice President and Chief Scientist at Compaq Computer Corporation. He led the development of the top-level corporate technology roadmap and was also responsible for initiating strategic relationships with some major software partners. Before Compaq, Alex was working on technology directions as VP and Chief Architect at AT&T Laboratories and as CTO of Server and Supercomputer Business Unit of SGI.Before his five year stint as an executive, Alex spent 25 years doing research at Hewlett-Packard Laboratories, AT&T Bell Laboratories, General Electric Corporate R&D, Polytechnic University, Institute of Control Problems (IPU) and Institute of Complex Automation (TzNIIKA). His work was in the areas of generic programming, programming language design, storage systems, path-planning algorithms, and real-time operating systems. In 1995 for his work on Standard Template Library he shared (with Linus Torvalds) the first Dr. Dobb's Excellence in Programming Award. From 1967 to 1972 Alex studied Mathematics at the Moscow State University and received a diploma of teacher of Mathematics from Moscow District Pedagogical Institute in 1973. Faculty Contact: Bjarne Stroustrup (bs@cs.tamu.edu)
Computer Science Distinguished Lecturer Series:Intelligent Software SystemsKeshav Pingali, Cornell University
4:10pm, Monday April 7, 2003 AbstractIntelligence can be defined as the ability of an organism to adapt to a changing environment with the goal of improving its efficiency or its odds of survival. By this definition, most existing software systems are not very intelligent.In this talk, we will argue that computational environments are changing rapidly, and that to keep up with these changes, software must become more intelligent - that is, it must be able to adapt to improve its efficiency and its odds of survival. We will describe two ongoing projects at Cornell towards these goals. BiographyKeshav Pingali is a professor in the Computer Science department of Cornell University where he has taught since 1986. He received the B.Tech. degree in Electrical Engineering from the Indian Institute of Technology, Kanpur, India, and the S.M., E.E. and Sc.D. degrees from M.I.T.Faculty Contact: Lawrence Rauchwerger (rwerger@cs.tamu.edu)
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