Program Committee

Martin Farach (Rutgers University and DIMACS)
Nathan Goodman (Whitehead Institute/MIT Center for Genome Research) 
Sorin Istrail (Sandia National Laboratories)
Pavel Pevzner (University of Southern California) 

Organizing Committee

The workshop is hosted by the members of DOE's Sandia Labs
Computational Biology Project.  Committee Members: Sarina Bromberg, 
David Greenberg, William E. Hart, Sorin Istrail and Cindy Phillips. 

                         Program 

Sunday, March 3

   7:00-9:00 Reception 

Monday, March 4

   8:00-9:00 Reception and registration 

   9:00-9:15 Introductory Remarks, Sorin Istrail 

   9:15-12:15 Session 1

          9:15-10:05 
          Plenary Lecture: Simulations of Protein Folding: From
          the Native to the Denatured State and Back Again
          Martin Karplus
          Department of Chemistry, Harvard University 

          10:20-11:10 
          Plenary Lecture: Combinatorial Aspects of Restriction
          Mapping
          Richard Karp
          Department of Computer Science, University of
          Washington 

          11:25-12:15 
          Plenary Lecture: Protein Folding: Simple Computational
          Models
          Ken Dill 
          Department of Pharmaceutical Chemistry, University of
          California San Francisco 

   12:15-2:00 Lunch Break 

    2:00-5:00 Session 2

          2:00-2:35 
          Gene Recognition: Combinatorics versus Statistics
          Pavel Pevzner 
          Department of Mathematics and Molecular Biology,
          University of Southern California 

          2:45-3:20
          Heuristics for Searching Sequence Databases
          Stephen Altschul 
          National Center for Biotechnology Information, NIH 

          3:30-4:05 
          Efficient Algorithms for Inverting Evolution
          Martin Farach 
          Department of Computer Science, Rutgers University 

          4:15-4:50 
          New Protein Folding Algorithms with Near-optimal
          Performance 
          William Hart 
          Sandia National Laboratories 

   5:00-6:00 Discussion Session
             Jonathan King, Chair 

   6:30 Dinner 

Tuesday, March 5

   9:00-12:15 Session 3

          9:00-9:50
          Plenary Lecture: TBA
          Michael Waterman
          Department of Mathematics and Molecular Biology,
          University of Southern California 

          10:05-10:55
          Plenary Lecture: Mathematical Issues in Molecular
          Recognition
          Irwin Kuntz 
          Department of Pharmaceutical Chemistry, University of
          California San Francisco 

          11:10-12:00
          Plenary Lecture: Protein Folding, Protein Misfolding, and
          Human Disease
          Jonathan King 
          Department of Biology, Massachusetts Institute of
          Technology 

   12:15-2:00 Lunch Break 

   2:00-4:15 Session 4

          2:00-2:35
          What makes protein folding cooperative?
          Sarina Bromberg
          Sandia National Laboratories 

          2:45-3:20 
          How Hard is the Integration of Physical Maps?
          Ron Shamir 
          Department of Computer Science, Tel-Aviv University 

          3:30-4:05 
          New Fast Algorithms for Finding Optimal Evolutionary
          Trees
          Tandy Warnow
          Department of Computer Science, University of
          Pennsylvania 

   6:00 Dinner Banquet and Discussion Session
   Pavel Pevzner, Chair
   High Finance Restaurant atop Sandia Peak (10,378 feet) 

Wednesday, March 6

   9:00-12:00 Session 5

          9:00-9:35
          The Data Management Systems Used to Map the
          Human and Mouse Genomes at the Whitehead
          Institute/MIT Center for Genome Research
          Nat Goodman 
          Whitehead Institute/MIT Center for Genome Research 

          9:45-10:20
          Approximation Algorithms in Computational Biology
          R. Ravi 
          Department of Operations Research, Carnegie-Mellon
          University 

          10:30-11:05
          Computing Optimal Multiple Sequence Alignments
          John Kececioglu 
          Department of Computer Science, University of Georgia 

          11:15-11:50
          Protein Structure Prediction by Threading
          Steve Bryant 
          National Center for Biotechnology Information, NIH 

   12:00-2:00 Lunch Break (on your own) 

   2:00-4:15 Session 6

          2:00-2:35 
          Constructing Evolutionary Trees in the Presence of
          Polymorphic Characters
          Cynthia Phillips
          Sandia National Laboratories 

          2:45-3:20
          Maping Clones with A Given Ordering or Interleaving
          Tao Jiang
          Department of Computer Science, University of
          Washington 

          3:30-4:05
          Graph Traversals, Genes, and Matroids; A Result On
          Sequencing by Hybridization
          Dan Gusfield
          Department of Computer Science, University of
          California at Davis 

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