DIMACS Workshop on Combinatorial Methods for DNA Mapping and Sequencing

October 6, 1994 thru October 9, 1994
DIMACS Center, CoRE Building, Rutgers University

Pavel Pevzner (CS Dept., Penn State) [pevzner@cse.pesu.edu]
Charles Cantor (Center for Advanced Biotechnology, Boston U.)

Program Committee:
Pat Gillevet (National Center for Human Genome Research)
Richard Karp (CS, U.C. Berkeley)
Maynard Olson (Molecular Biotechnology, Washington)
Gene Myers (CS, Arizona)
Mihalis Yannakakis (AT&T Bell Labs)
Presented under the auspices of the Special Year in Mathematical Support for Molecular Biology.

Workshop Program:

Thursday, October, 6
8:15 a.m. Registration and Coffee In Room 401
8:45 a.m. Opening Session
Fred Roberts, Department of Mathematics and DIMACS, Chair of Special Year
Joachim Messing, Director, Wakeman Institute for Molecular Genetics and Chair of Special Year
Andras Hajnal Director, DIMACS
Joseph Seneca, Vice President for Academic Affairs, Rutgers University
Session DNA MAPPING I (chair: P.Pevzner)
9:00 a.m. Richard Karp, Department of Computer Science, University of California at Berkeley
A Survey of Algorithmic Problems in Physical Mapping
10:20 a.m. Coffee Break
10:50 a.m. Maynard Olson, Department of Molecular Biotechnology, University of Washington
Computing High-resolution Restriction-site Maps: Past, Present, and Future.
11:40 a.m. Ron Shamir, Computer Science Department, Tel Aviv University
Graph-theoretic Support for Physical Mapping of DNA
12:30 a.m. Lunch
Session DNA MAPPING II (chair: M.Olson)
2:00 p.m. Michael Waterman, Department of Math. and Mol. Biol., University of Southern California
Statistical Models of Physical Mapping
2:50 p.m. Jim Orlin, MIT and Whitehead Institute
Creating a Physical Map of the Human Genome
3:40 p.m. Coffee Break
4:10 p.m. Contributed talks
6:00 p.m. Reception at CoRE Building (4th Floor)
Friday, October, 7
9:00 a.m. Charles Cantor, Center for Advanced Biotechnology, Boston University
Parallel Processing in Genome Mapping and Sequencing
9:50 a.m. Coffee Break
10:05 a.m. Robert Lipshutz, Affymetrix
Oligonucleotide Arrays and Sequence Analysis by Hybridization: a Survey
11:25 a.m. Coffee Break
11:40 a.m. Steven Skiena, Department of Computer Science, State University of New York at Stony Brook
Reconstructing Strings from Substrings
12:30 a.m. Lunch
2:00 p.m. Radoje Drmanac, Argonne National Laboratory
Informatics of DNA Screening, Mapping, and Sequencing by Hybridization with 30-3000 Oligomers
2:50 p.m. Pavel Pevzner, Dept. of Computer Science and Engineering, Pennsylvania State University
Rearrangements of Maps, Sequences and Genomes
3:40 p.m. Coffee Break
4:10 p.m. Ming Li, Department of Computer Science, University of Waterloo
DNA Sequencing and Learning
5:00 p.m. Open Problems Sesion and Software Demonstration
Saturday, October, 8
Session DNA SEQUENCING I (chair: M.Yannakakis)
9:00 a.m. Leroy Hood, Department of Molecular Biotechnology, University of Washington
Computational Challenges in the Human Genome Project
9:50 a.m. Gene Myers, Department of Computer Science, University of Arizona
An Alternative Formulation of Sequence Assembly
10:40 Coffee Break
11:10 a.m. S. Rao Kosaraju, Department of Computer Science, The Johns Hopkins University
Experiments on Large Scale DNA Sequence Assembly
12:00 a.m. Contributed talks
12:30 a.m. Lunch
Session: DNA SEQUENCING II (chair: E.Myers)
2:00 p.m. Richard Wilson, Dept. of Genetics, Washington University School of Medicine
The C. elegans Genome Sequencing Project
2:50 p.m. John Kececioglu, Department of Computer Science, University of California at Davis
DNA sequencing in the Presence of Errors
3:40 p.m. Coffee Break
4:10 p.m. Pat Gillevet, National Center for Human Genome Research
Automatic Analysis and Annotation of Data from Mycoplasma capricolum Project
5:00 p.m. Contributed talks
Sunday, October, 9
Session DNA MAPPING III (chair. P.Gillevet)
9:00 a.m. Richard Mott, Genome Analysis Laboratory, Imperial Cancer Research Fund
Oligonucleotide Fingerprinting of Clone Libraries
9:50 a.m. Alan Frieze, Dept. of Mathematics, Carnegie Mellon University
Ordering Clone Libraries in Computational Biology
10:40 a.m. Coffee Break
11:10 a.m. Phil Green, Department of Molecular Biotechnology, University of Washington
Methods for Assembly and Error Identification in Mapping and Sequencing
12:00 am. Contributed talks
12:30 a.m. Lunch
Session DNA MAPPING IV (chair: P.Pevzner)
2:00 p.m. Tom Marr, Cold Spring Harbor Laboratory
Genome Topographer: Computer Science, System and Software Engineering, and the Study of Complex Genetic Diseases
2:50 p.m. Sorin Istrail, Sandia National Laboratories
Algorithmic strategies for handling errors in physical mapping: Chimerism and Deletions
3:40 p.m. Coffee Break
4:00 p.m. Contributed talks

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Document last modified on March 28, 2000.