RECOMB97 NEWS
December 6, 1996
****************
recomb97 at hto.usc.eduhttp://www.cs.sandia.gov/recomb97http://www.eldoradohotel.com
Reminder: Early registration deadline (extended to Dec 20, 1996)
is approaching fast!!
THE ELDORADO HOTEL IS FULL!!!
However, there are a few extra rooms available
at the RECOMB 97 rate. Please hurry up.
The overflow will go to the Hilton of Santa Fe Hotel
(1-800-336-3676 or fax 505-986-6439 ask for the
"RECOMB97 Conference") where we have a block of rooms
reserved at identical rates.
1. RECOMB'97 Final Program
2. Available Financial support for students/graduate
students/postdocs. Thanks to the generous help from
the Sloan Foundation and the U.S. Department of Energy.
3. Babysitting and Recreational Activities
4. Travel to Santa Fe
---------------------------------------------------------
1. RECOMB'97 Final Program
FIRST ANNUAL INTERNATIONAL CONFERENCE ON
COMPUTATIONAL MOLECULAR BIOLOGY
January 20-23, 1997
Eldorado Hotel
Santa Fe, New Mexico
Sponsored by
ACM SIGACT
with support from
SLOAN Foundation
US Department of Energy
recomb97 at hto.usc.eduhttp://www.cs.sandia.gov/recomb97
RECOMB 97 SCHEDULE
******************
***************************************
Sunday January 19, 1996
***************************************
7:00-10:00 p.m. Reception Eldorado Hotel
Anasazi South
***************************************
Monday January 20, 1996
***************************************
9:00 a.m.- 5:00 p.m. Poster Session, Zia B&C
General Session, Anasazi Ballroom
8:45 a.m. Opening Remarks:
Michael Waterman, General RECOMB Chair
1997 Program Committee Chair
Sorin Istrail, General RECOMB Vice-Chair
1997 Conference Chair
Pavel Pevzner, General RECOMB Chair
1998 Program Committee Chair
---------------------------------------
9:00 Distinguished Conference Lecture Session
Pavel Pevzner, Chair
Rich Roberts
Hunting for new restriction enzymes in GeneBank
---------------------------------------
10:00 Break
Session on Mapping
Chair: Phil Green
10:15 Shili Lin, Terence P. Speed
An Algorithm for Haplotype Analysis
10:40 Donna Slonim, L. Kruglyak, L. Stein, E. Lander
Building Human Genome Maps with Radiation Hybrids
Break 11:05
Session on Genomic Rearrangements
Chair: Richard Karp
11:15 Haim Kaplan, Ron Shamir, Robert Tarjan
Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals
11:40 David Sankoff, V. Ferretti, Joe Nadeau
Conserved segment identification
12:05 Lunch, Eldorado Court
---------------------------------------
1:30 Invited Lecture Session
Pavel Pevzner, Chair
Rob Lipshutz
DNA Probe Arrays - Accessing the Genome
---------------------------------------
2:30 Break
Session on New Technologies
Chair: Gene Myers
2:45 J. Richard Bradley, Steven Skiena
Fabricating Arrays of Strings
3:10 Dan Fasulo, Tao Jiang, Richard M. Karp, R. Settergren, E. C. Thayer
An Algorithmic Approach to Multiple Complete Digest Mapping
3:45 S. Muthukrishnan, Laxmi Parida
A highly effective simple combinatorial approach for constructing physical
maps by optical mapping
4:10 Break
---------------------------------------
4:25 Invited Lecture Session
Sam Karlin, Chair
Terry Speed
Variations on a theme of Lander and Waterman
---------------------------------------
8:00-10:00 p.m. Business Meeting, Anasazi Ballroom
***************************************
Tuesday January 21, 1996
***************************************
9:00 a.m.- 5:00 p.m. Poster Session, Zia B&C
General Session, Anasazi Ballroom
---------------------------------------
8:30 Invited Lecture Session
Rich Roberts, Chair
David Botstein
Expression Arrays: An Open Problem for Mathematicians in
Post-Genome Sequence Biology
---------------------------------------
9:30 Break
Session on Sequence Alignment
Chair: Steven Altschul
9:45 Gene Myers, Sanford Selznick, Zheng Zhang, Webb Miller
Progressive Multiple Alignment with Constrains
10:10 George A. Komatsoulis, Michael Waterman
Chimeric alignment by dynamic programming: Algorithm and biological uses
10:35 Break
Session on Sequence Alignment
Chair: Temple Smith
10:45 Gary Benson
Sequence Alignment with Tandem Duplication
11:10 K. Reinert, Hans-Peter Lenhof, P. Mutzel, K. Mehlhorn, J. D. Kececioglu
A Branch-and-Cut Algorithm for Multiple Sequence Alignment
11:35 Ralf Zimmer, Tom Lengauer
Fast and Numerically Stable Parametric Alignment of Biosequences
12:00 Lunch, Eldorado Court
---------------------------------------
1:30 Invited Lecture Session
Mike Waterman, Chair
Sam Karlin
Assesing Inhomogeneities in Bacterial Long Genomic Sequences
---------------------------------------
2:30 Break
Session on Gene Recognition
Chair: Gary Stormo
2:45 Ying Xu, Edward Uberbacher
Reference-based Gene Model Prediction on DNA Contigs
3:10 Sing-Hoi Sze, Pavel Pevzner
Las Vegas Algorithms for Gene Recognition:
Suboptimal and Error-Tolerant Spliced Alignment
3:35 Break
Session on Protein Folding
Chair: Martin Karplus
3:45 Ken Dill, Andrew T. Phillips, J. Ben Rosen,
Protein Structure Prediction and Potential Energy
Landscape Analysis using Continuous Global Minimization
4:10 William Hart, S. Istrail
Lattice and Off-Lattice Side Chain Models of Protein Folding:
Linear Time Structure Prediction Better than 86% of Optimal
4:10 Break
---------------------------------------
4:25 Invited Lecture Session
Martin Karplus, Chair
Temple Smith
The threading approach to the inverse protein folding problem
---------------------------------------
7:00 p.m. Cocktails, Anasazi Ballroom
7:30-10:00 Banquet, Anasazi Ballroom
---------------------------------------
7:30 Stanislaw Ulam Computational Biology Address Session
Mike Waterman, Chair
Eric Lander
The Human Genome and Beyond
---------------------------------------
***************************************
Wednesday January 22, 1996
***************************************
9:00 a.m.- 5:00 p.m. Poster Session, Zia B&C
General Session, Anasazi Ballroom
---------------------------------------
8:30 Invited Lecture Session
Sorin Istrail, Chair
Martin Karplus
Protein Dynamics: From the Native to the Unfolded State and Back Again
---------------------------------------
9:30 Break
Session on Protein Folding
Chair: Bonnie Berger
9:45 William Hart
On the Computational Complexity of Sequence Design Problems
10:10 Tatsuya Akutsu, S. Miyano
On the Approximation of Protein Threading
10:45 Break
Session on Mapping
Chair: Ron Shamir
10:55 Amir Ben-Dor, Benny Chor
On Constructing Radiation Hybrid Maps
11:20 Fengzhu Sun, Gary Benson, Mike Waterman
Pooling Strategies for Establishing Physical Genome Maps Using FISH
11:45 Mutida Jain, Gene Myers
Algorithm for Computing and Integrating Physical Maps Using Unique Probes
12:10 Lunch, Eldorado Court
---------------------------------------
1:30 Invited Lecture Session
Sorin Istrail, Chair
Jonathan King
Problems in Understanding the Structure and Assembly of Viruses
---------------------------------------
2:30 Break
Session on Protein Folding
Chair: Bonnie Berger
2:45 Richa Agarwala, Serafim Batzogloa, V. Dancik,
Scott E. Decatur, M. Farach, S. Hannenhalli,
S. Muthukrishnan, S. Skiena
Local Rules for Protein Folding on Triangular Lattice
and generalized Hydrophobicity in the HP Model
3:10 Hans-Peter Lenhof
New Contact Measures for the Protein Docking Problem
3:35 Break
Session on Proteins
Chair: Thomas Lengauer
3:45 Bonnie Berger, Mona Singh
An Iterative Method for Improved Protein Structural Motif Recognition
4:10 Erich Bornberg-Bauer
Chain Growth Algorithms for HP-Type Lattice Proteins
4:35 Hiroshi Mamitsuka
Supervised Learning of Hidden Markov Models for Sequence Discrimination
***************************************
Thursday January 23, 1996
***************************************
General Session, Sweeney Convention Center
Session on Sequence Alignment
Chair: Martin Farach
8:30 Zheng Zhang, William R. Pearson, Webb Miller
Aligning a DNA Sequence with a Protein Sequence
8:55 Eric L. Anson, Gene Myers
ReAligner: A Program for Refining DNA Sequence Multi-Alignments
9:20 Lusheng Wang, Tao Jiang, Dan Gasfield
A More Efficient Approximation Scheme for Tree Alignment
9:20 Break
Session on Genomic Rearrangements
Chair: David Sankoff
9:35 B. DasGupta, T. Jiang, S. Kannan, M. Li, Z. Sweekyk
On the Complexity and Approximation of Syntenic Distance
10:00 Alberto Caprara
Sorting by Reversals is Difficult
10:25 Break
Session on Statistics
Chair: Bruce Weir
10:40 Simon Heath
The application of Markov Monte Carlo Methods to Radiation Hybrid Mapping
11:05 M. G. Reese, F. H. Eeckman, D. Kulp, D. Haussler
Improved Splice Site Detection in Genie
11:30 Gary A. Churchill
Monte Carlo Sequence Alignment
11:55 Lunch, Sweeney Convention Center
Session on Sequence Alignment
Chair: Webb Miller
1:30 Benno Schwikowski, Martin Vingron
The Deferred Path Heuristic for the Generalized Tree Alignment Problem
1:55 Tetsuo Shibuya, Hiroshi Imai
New Flexible Approaches for Multiple Sequence Alignment
1:55 Break
Session on Mapping
Chair: Maynard Olson
2:05 T. Christof, M. J\"unger, John Kececioglu, P. Mutzel, G. Reinel
A Branch-and-cut Approach to physical mapping with end-probes
2:30 David Wilson, David Greenberg, Cynthia Phillips
Beyond Islands: Runs in Clone-Probe Matrices
2:55 Break
Session on Evolutionary Trees and DNA Computing
Chair: Martin Vingron
3:05 Jamie Cohen, Martin Farach
Numerical Taxonomy on Data: Experimental Results
3:30 W. Cai, Anne Condon, R.Mm Corn, E Glasser, Z. Fei, T. Frutos,
Z. Guo, MG Lagally, Q. Lui, L.M. Smith, A. Theil
The Power of Surface-Based DNA Computing
3:55 M. Ogihara, A. Ray
Simulating Boolean Circuits on a DNA Computer
End of RECOMB 97
--------------------------------------------------
2. Financial support for students/graduate students/postdocs
Limited support for students is available. We anticipate
being able to make about 22 financial awards of $400 each
for 22 students.
Please send us a one-page request to via email to
scistra at cs.sandia.gov
including your affiliation, the name of your Ph.D. adviser
(if appropriate) and the area of research that you are
working on. We would like to select for support
the students that will benefit the most from our meeting
as well as those that will be able to make valuable
contributions to the conference.
3. Babysitting and Recreational Activities
"Santa Fe Destinations" is a company located in the
Eldorado Hotel. They provide professional services
for: babysitting, airport transportation, entertainment,
recreational activities, spouse programs etc.
Please call Tom Williams the Director of the company for
services related to your visit in Santa Fe.
4. Travel to Santa Fe
http://www.eldoradohotel.com/getting_there.html
By plane to the Albuquerque International Airport.
All major airlines use the airport. From there
"Shuttlejack" ((505) 988-2441; $20 one-way trip;
about one hour long) buses pick people up
and drop them directly at the Eldorado Hotel nine
times a day. Please call Shuttlejack and make
reservations.
The complete information about arriving at the Eldorado
Hotel is available from their web page
http://www.eldoradohotel.com/getting_there.html
We hope to see you soon in Santa Fe.
-- Sorin Istrail
Conference Chair
