Bio Info SIG: Towards a Programming Language for Genomics (G)






    Sorin Istrail, Senior Director, Informatics Research, Celera/Applied Biosystems

    Presentation Overview

    There is no such thing as the Post-Genomics Era. Genomics is forever. The above cliché captures, sub-optimally terminology-wise, the fact that bioinformatics behavior experienced recently a phase transition. Its critical region was powered by Smith-Waterman and BLAST, reaching the phase-transition point in 2000 when the First Assemblers and Assemblies of the Human Genome were constructed. Since then, in the Post-Dynamic Programming Era, bioinformatics behavior focuses on the Genomics Integration of Biology. Our company, Applied Biosystems, calls this program iScience.

    In this talk I will present computational challenges in computational biology and bioinformatics as well as reflections towards programming language frameworks to meet them. I will exemplify the emerging challenges by presenting our work on two projects: (1) assembly-to-assembly comparison, automatic annotation and navigation, and (2) genomics regulatory systems, and the industrial strength acceleration of the discovery of the cis-regulatory code.


    About the Presenter

    Sorin Istrail

    Sorin 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. Currently he is Senior Director and Head of the Informatics Research Division at Celera/Applied Biosystems. In 2003 he also became Applied Biosystems Science Fellow.

    Istrail’s work has been focused on combinatorial algorithms, computational complexity, programming languages, and on applications of computer science to biology, physics and chemistry. In 2000, he resolved a longstanding 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/Applied Biosystems 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, mass spec based proteomics and biomarkers, compu/combichem and protein structure, BLAST-replacement tools, genomic regulatory systems, literature datamining and machine learning, DNA array design and gene expression analysis, and game theory and pharma economic behavior. 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.


    Event Logistics:



    Hanson Bridgett

    333 Market Street, 21st Floor

    San Francisco, CA, 94105

    Note: Location provided courtesy of Hanson, Bridgett, Marcus, Vlahos, Rudy, LLP.


    6:30 - 7:00 p.m. Registration and Networking

    7:00 - 9:00 p.m. Presentation



    $15 at the door for non-SDForum members
    No charge for SDForum members
    Please call 408.494.8378 for student memberships
    Registration NOT required