DIMACS Workshop on Whole Genome Comparison

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

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
Presented under the auspices of the Special Year on Computational Molecular Biology.

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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Document last modified on March 13, 2003.