The Second Sandia National Laboratories
Workshop on
Computational Molecular Biology
March 4-6, 1996
Albuquerque, New Mexico
Organized in collaboration with
DIMACS Special Year on
Mathematical Support for Molecular Biology
Funded by DOE MICS Office of Scientific Computing
Applied Mathematics Program
Dr. Fred Howes, Director
The Second Sandia National Laboratories Workshop on Computational
Molecular Biology will be held at the Albuquerque Hilton in
Albuquerque, New Mexico, March 4-6, 1996. The Workshop is organized in
collaboration with DIMACS Special Year on Mathematical Support for
Molecular Biology. The focus of the workshop is on open problems and
research directions in Computational Molecular Biology. In addition to
talks given by active researchers in this field, several plenary
lectures will be presented by speakers of highest distinction in
computational molecular biology.
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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.
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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
Approximation Algorithms in Computational Biology
R. Ravi
Department of Operations Research, Carnegie-Mellon
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
Efficient Algorithms for Inverting Evolution
Martin Farach
Department of Computer Science, Rutgers 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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List of Invited Participants
Plenary Speakers
Ken Dill is Professor of Chemistry in the Department of Pharmaceutical
Chemistry at the University of California San Francisco and the director
of the UCSF Center for Statistical Mechanics of Macromolecules. His
research revolutionized the thinking about protein folding and has
provided fundamental insight into the principles of protein folding. He has
made major contributions in the understanding of the hydrophobic effect.
Areas of interest: protein folding, statistical mechanics of biomolecules.
Richard Karp is Professor of Computer Science at University of
Washington. He is the recipient of the 1985 ACM Turing Award (the
"Nobel Prize" in Computing) and is a member of the National Academy of
Sciences and the National Academy of Engineering. Areas of interest:
combinatorial algorithms and their application in molecular biology.
Martin Karplus is Theodore William Richards Professor of Chemistry at
Harvard University and Professeur Conventionne at the Universite Louis
Pasteur. He is a member of the National Academy of Sciences, American
Academy of Arts and Sciences, International Academy of Quantum
Molecular Science and recipient of numerous awards. He is one of the top
researchers in the field of protein folding and his contributions have been
of fundamental importance to the development of protein folding research.
His recent work is concerned with molecules that play an important role
in living systems. Areas of interest: theoretical chemistry, including
electronic interpretations of NMR and ESR spectra of molecules, the
development of techniques for evaluation of molecular properties, the
formulation of detailed models for chemical reactions, and protein folding.
Jonathan King is Professor of Biology in the Department of Biology at
Massachusetts Institute of Technology and director of the MIT
Biomedical Electron Microscope Facility. He is Councillor of the
Biophysical Society and a recipient of the Antartic Service Medal of the
National Science Foundation. Areas of interest: the folding of large
proteins, the structure and assembly of virus particles, and the genetic
control of biological assembly processes.
Irwin Kuntz is professor of Chemistry and Pharmaceutical Chemistry at
the University of California, San Francisco, Director of the UCSF
Molecular Design Institute, and he is the 1996 UCSF Faculty Lecturer.
He is one of the most influential pioneers in the area of rational drug
design, the creator of the DOCK drug design program and the developer
of the distance geometry methods widely used in biochemistry. Areas of
interest: protein folding, protein structure determination, and
ligand-macromolecule interactions.
Michael Waterman is the USC Endowed Associates Chair Professor of
Mathematics and Biological Sciences at the University of Southern
California. He is a Fellow of the Institute of Mathematical Statistics, the
American Association for the Advancement of Science and the American
Academy of Arts and Sciences. His pioneering research in global
sequence alignment, predicting RNA secondary structures and inferring
evolutionary histories established rigorous foundations that fostered the
development of the field of Computational Molecular Biology. He is the
co-author of the Smith-Waterman local alignment algorithm, and the
co-author of the Lander-Waterman formulas for the analysis and design
of physical mapping experiments. Areas of interest: computational
molecular biology.
Regular Speakers
Stephen Altschul is a Senior Investigator at the National Center for
Biotechnology Information, National Institutes of Health. Areas of
interest: algorithms and scoring systems for biological sequence
comparison.
Sarina Bromberg is a Computational Scientist at Sandia National
Laboratories. Areas of interest: protein folding, stability, and cooperative
conformational changes.
Steve Bryant is a Senior Investigator at the National Center for
Biotechnology Information, National Institutes of Health. Areas of
interest: protein structure modelling, structure comparison, structure
database design.
Martin Farach is Associate Professor of Computer Science at Rutgers
University. Areas of interest: algorithmic phylogeny, string matching,
design and analysis of combinatorial algorithms.
Nat Goodman is a Senior Research Scientist at the Whitehead Institute
for Biomedical Research, Associate Director of the Whitehead/MIT
Center for Genome Research, and Senior Staff Scientist at the Jackson
Laboratory. Areas of interest: informatics systems for genomics.
Dan Gusfield is a Professor of Computer Science at the University of
California at Davis. Areas of interest: combinatorial optimization, graph
algorithms, string matching, computational molecular biology.
William Hart is a Computational Scientist at Sandia National
Laboratories. Areas of interest: computational biology, stochastic
methods for global optimization.
Tao Jiang is an Associate Professor of Computer Science at McMaster
University, and is now on sabatical at the University of Washington.
Areas of interest: multiple sequence alignment, restriction mapping,
mathematical models for sequencing, evolutionary trees.
John Kececioglu is an Assistant Professor of Computer Science at the
University of Georgia. Areas of interest: algorithms for DNA sequence
assembly, genome rearrangements, and multiple sequence alignment.
Pavel Pevzner is a Professor of Computer Science at the University of
Southern California. Areas of interest: computational molecular biology.
Cindy Phillips is a Computational Scientist at Sandia National
Laboratories. Areas of interest: combinatorial optimization, scheduling
theory, parallel computation, phylogenetic tree construction, multiple
sequence alignment.
R. Ravi is an Assistant Professor of Operations Research at
Carnegie-Mellon University. Areas of interest: approximation algorithms
in molecular biology, combinatorial optimization.
Ron Shamir is an Associate Professor of Computer Science at Tel-Aviv
University. Areas of interest: algorithms for genomic mapping,
algorithmic graph theory and optimization.
Tandy Warnow is an Assistant Professor of Computer Science at
University of Pennsylvania. Areas of interest: combinatorial optimization
problems in phylogenetic tree construction, and methodological advances
in historical linguistics.
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Registration
The workshop is open to the public and no registration fee is required to
attend the workshop. If you wish to attend the dinner banquet on
Tuesday night, please indicate this on the form. Payment for the dinner
banquet (in the form of cash or check) is required upon arrival to the
workshop.
Space is limited at the conference center so advanced registration by
workshop participants is strongly encouraged. Please mail or email the
following registration form to Susan Flores by February 15, 1996.
REGISTRATION FORM
The Second Sandia National Laboratories Workshop
on Computational Molecular Biology
Prof / Dr / Mr / Ms / Mrs (circle one)
Name ________________________________________________________________
Last First MI
I would like my name tag to read _____________________________________________
Affiliation/Business ______________________________________________________
Address ______________________________________________________
City ______________________________________________________
State ___________________ Zip ________________________
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FEES (all figures in US dollars)
Banquet Tickets for High Finance Restaurant, atop Sandia Peak.
This includes a ride to the top of Sandia Peak (10,378 feet)
on the world's longest tram, Sandia Peak Tramway.
Reservations for the banquet should be made as soon as possible.
Additional banquet tickets will not be available at the workshop.
#______ ticket(s) @ $35.50
Email Susan Flores (sjflore at cs.sandia.gov)
Mail CMB96 Registration
Sandia National Labs
Attn: Susan Flores
P.O. Box 5800
Albuquerque, NM 87185-1110
Fax (505) 845-7442
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Accomodations
Rooms have been reserved for workshop participants at the
Albuquereque Hilton, where the workshop will be held.
The hotel rates are as follows:
Albuquerque Hilton
1901 University Blvd
Albuquerque, NM 87102
(800) 274-6835
(505) 844-2500
$59.00 for a single
$69.00 for a double
$10.00 for each additional person
The workshop rates are only guaranteed to participants who make
reservations by February 15, 1996. When making the reservation please
mention the name of the workshop to obtain these rates.
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For more information see our web page at
http://cs.sandia.gov/cmb_workshop96.html
or contact Sorin Istrail:
Sorin Istrail, Workshop Chair
Sandia National Laboratories
Massively Parallel Computing Research Laboratory
Algorithms and Discrete Mathematics
Albuquerque, NM 87185-1110
Phone: (505) 845-7612
Secretary: (505) 845-7432
Fax : (505) 845-7442
Email: scistra at cs.sandia.gov
