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
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.