DIMACS Workshop on Whole Genome Comparison

February 28 - March 2, 2001
DIMACS Center, Rutgers University, Piscataway, NJ

Organizer:

Dannie Durand, Carnegie Mellon University, durand@cmu.edu

Program Committee

Joseph H. Nadeau, Case Western Reserve University School of Medicine, jhn4@po.cwru.edu

Steven L. Salzberg, The Institute for Genomic Research, salzberg@tigr.org

David Sankoff, University of Montreal, sankoff@ere.umontreal.ca

Preliminary Program:

Wednesday, February 28, 2001

8:15-9:00   Breakfast and Registration

9:00-9:05   Welcome and Greeting:
            Fred S. Roberts, DIMACS Director

9:05-9:15   Welcome and Greeting:
            Dannie Durand, Carnegie Mellon University

9:15-10:00  Overview of Current Sequencing Efforts
            Richard Mural, Celera Genomics
            
10:00-10:30 Break

Whole Genome Sequence Comparison III:

10:30-11:15 Human and Mouse Gene Structure: Finding Genes by
            Cross-Species Sequence Comparison
            Serafim Batzoglou, Whitehead Institute

11:15-11:45 Large-scale Sequence Comparison by Locality-Sensitive Hashing
            Jeremy Buhler, University of Washington

11:45-1:15  Lunch

Whole Genome Sequence Comparison II:

1:15-2:00   Structure and Dynamics of Transcriptional
	    Regulatory Networks in the Yeast S. cerevisiae
	    Saeed Tavazoie, Princeton University

2:00-2:30   Assignment-like optimization on bipartite graphs with ordered 
            nodes as an approach to the analysis of comparative genomic data
            Ilya Muchnik, Alair Pereira do Lago, Victor Llaca, Eric Linton,
            Casimir A. Kulikowski, Joachim Messing

2:30-3:00   Optimal Spliced Alignment
            Wei Zhu, Iowa State university

3:00-3:30   Break

3:30-4:15   Large-scale genome duplications in the model plant Arabidopsis
            and in the human genome
            Steven L. Salzberg, The Institute for Genomic Research

4:15-5:00   Comparative Genome Analysis and Molecular Evolution
            Elizabeth Tillier, Centre for Clinical Genomics
            
5:00-5:30   Strategy for the Multiple Whole Genome
            Alignment of four strains of E.coli using modified suffix arrays
            Bob Mau, Nicole T. Perna, Aaron Darling, Jason Christensen, 
            Jacob Milhans, Brian Gettler, and Frederick R. Blattner


Thursday, March 1, 2001

8:15-9:00   Breakfast and Registration 

Gene and Genome Duplication:

9:00-9:45   Computational, Spatial Analysis of Gene Duplication in the Mouse Genome
            Dannie Durand, Carnegie Mellon University            

9:45-10:15  Analysis of large-scale genome rearrangement and duplication in real
            sequence data: experience with Arabidopsis thaliana and the draft 
            human sequence
            Dan Brown, Cornell University

10:15-10:45 Determination of vertebrate gene families
            Antje Krause, Deutsches Krebsforschungszentrum, Theoretische 
            Bioinformatik; Steffen Hennig, Max-Planck Institut fuer 
            Molekulare Genetik; Georgia Panopoulou, Max-Planck Institut 
            fuer Molekulare Genetik and Martin Vingron, Deutsches 
            Krebsforschungszentrum, Theoretische Bioinformatik and 
            Max-Planck Institut fuer Molekulare Genetik	

10:45-11:15 Break

Evolution of Gene Function:


11:15-12:00 Gene Duplication and the Origin of Evolutionary Novelties
            Michael Lynch, University of Oregon

12:00-12:30 Detecting And Characterizing Functional Change In Proteins: 
            A Genomic Perspective
            David A. Liberles, Stockholm University	

12:30-2:00  Lunch

Comparative Mapping:


2:00-2:45   Conserved Clusters Versus Conserved Segments
            David Sankoff, University of Montreal 

2:45-3:15   Automating Comparative Map Construction
            Debra Goldberg, Susan McCouch, Jon Kleinberg 	

3:15-3:45   Break

Gene Order Phylogeny

3:45-4:15   High-Performance Algorithm Engineering for Gene-Order Phylogenies
            David A. Bader, Bernard M.E. Moret, Tandy Warnow, Stacia K. Wyman,
            and Mi Yan

4:15-4:45   A Gossip-Based Approach to Syntenic Distance
            David Liben-Nowell, MIT

4:45-5:15   New polynomial time methods for whole genome phylogeny reconstruction
            Li-San Wang and Tandy Warnow, University of Texas at Austin

Wine and Cheese Reception


Friday, March 2, 2001

8:15-9:00   Breakfast and Registration

Molecular Evolution:

9:00-9:15   DIMACS - Celera Genomics/Applied Biosystems Graduate Student Award Presentation:
            Winner:  Barry Cohen, State University of New York, Stony Brook.
            Award Presenters: Fred S. Roberts, DIMACS Director
            Sorin Istrail, Celera Genomics            

9:15-9:45   The Space of RNA Encodings of a Target Protein
            Barry Cohen, State University of New York at Stony Brook

9:45-10:15  Amino Acid Substitution Matrices for Compositionally 
            Biased Bacterial Genomes
            Susan Abramski and Marek Kimmel, Rice University; George Weinstock, 
            University of Texas at Houston and Baylor College of Medicine, Texas

10:15-10:45 Have Functional Nucleic Acid Sequences Evolved Characteristic Base
            Composition Biases: A Comparative Study of Genes and Genomes
            Rob Knight, Princeton University and Erik Schultes, MIT

10:45-11:00 Break

Genomic Regulation:

11:00-11:45 Computational Identification of Distal Regulatory
            Elements in the Human Genome
            David J. States, Washington University School of Medicine

11:45-12:15 The Central Role of DNA Structural Properties in Genomic Regulation
            Craig Benham, Mount Sinai School of Medicine

12:15-1:30  Lunch

Inferring Gene Function from Genomic Context:

1:30-2:15   Computational Functional Genomics
            Matteo Pellegrini, Protein Pathways, Inc.
            
2:15-2:45   Detection of related genes in prokaryotes using syntenic regions 
            Nalvo F. de Almeida Jr., Federal University of Mato Grosso do Sul,
            Brazil and Joao Carlos Setubal, Institute of Computing, 
            University of Campinas, Brazil
     
2:45-3:15   Computational Comparative Genomics
            Clemens Suter-Crazzolara, Guenther Kurapkat & Deborah Riley  

3:15-3:30   Break

Conclusion - Genomic Analysis from Sequence to Pathways:

3:30-4:15   Comparing Genomic DNA Sequences: Solved and Unsolved Problems
            Webb Miller, The Pennsylvania State University

4:15-5:00   Genetic, expression and evolutionary mapping of a physiological pathway
            Joseph H. Nadeau, Case Western Reserve University School of Medicine

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