Recomb 98 Schedule

Saturday March 21, 1998

7:00 pm - 10:00 pm

Welcome Reception Renaissance Room

Sunday March 22, 1998

8:45 am	Opening Remarks Embassy Ballroom
Pavel Pevzner	RECOMB 1998 Program Committee Chair
Gary Benson	RECOMB 1998 Conference Chair
Sorin Istrail	RECOMB 1999 Program Committee Chair

9:00 am

Distinguished New Technologies Lecture Pavel Pevzner, Chair   David Cox The Human Genetic Variation: Oligonucleotide Chips and Human Disease

10:00 am

Break

Session 1, Chair: Martin Vingron

10:10 am	Identifying Satellites in Nucleic Acid Sequences M. Sagot, G. Meyers
10:35 am	Genome Analysis Using Clusters of Orthologous Groups (COGs) E. Koonin, R. Tatusov, M. Y. Galperin, M. N. Rozanov
11:00 am	Break

Session 2, Chair: Gene Myers

11:15 am	Non-Adjoining Correlations within Signals in DNA P. Agarwal and V. Bafna
11:40 am	An Algorithm for Finding Tandem Repeats of Unspecified Pattern Size G. Benson
12:05 pm	Lunch

1:30 pm

Invited Lecture Session Sorin Istrail, Chair Charles Cantor Enhancements in Sequence Analysis with DNA Arrays

2:30 pm

Break

Session 3, Chair: Gary Benson

2:40 pm	Motif Discovery in Biological Sequences without Alignment or Enumeration I. Rigoutsos, A. Floratos
3:05 pm	An Algorithm for Finding Novel Gapped Motifs in DNA Sequences E. Rocke, M. Tompa
3:30 pm	A Polyhedral Approach to RNA Sequence Structure Alignment H. Lenhof, K. Reinert, M. Vingron
3:55 pm	Break

4:10 pm

Stanislav Ulam Computational Biology Address Michael Waterman, Chair  Joshua Lederberg

8:00 pm - 10:00 pm

Business Meeting Renaissance Room

Monday March 23, 1998

Embassy Ballroom

9:00 am

Distinguished Conference Lecture Chair: Gary Benson Ron Davis Whole Genome Analysis: Expression, Replication, Recombination, Allelic Variation, and Drug Discovery Function

10:00 am

Break

Session 4, Chair: David Searls

10:10 am	Assessment of Ab Initio Protein Structure Prediction A. M. Lesk
10:35 am	A Self-Consistent Field Optimization Approach to Build Energetically and Geometrically Correct Lattice Models of Proteins B. A. Reva, A. V. Finkelstein, J. Skolnick
11:00 am	Break
11:15 am	Modeling DNA Shuffling F. Sun
11:40 am	Multiple Genome Rearrangements D. Sankoff, M. Blanchette
12:05 pm	Lunch

1:30 pm

Invited Lecture Session Chair: Eugene Koonin Ruben Abagyan Challenges of Biomolecular Structure Prediction

2:30 pm

Break

Session 5, Chair: Martin Farach

2:40 pm	From Four-taxon Trees to Phylogenies: The Case of Mammalian Evolution A. Ben-Dor, B. Chor, D. Graur, R. Ophir, D. Pelleg
3:05 pm	On Reconstructing Species Trees From Gene Trees In Term of Duplications B. Ma, M. Li, L. Zhang
3:30 pm	The Ordinal Quartet Method P. E. Kearney
3:55 pm	Break

4:10 pm

Invited Lecture Session Bonnie Berger, Chair Michael Levitt Bridging the Gap between Sequence and Structure

6:00 pm-10:00 pm

Poster Session Renaissance Room

Tuesday March 24, 1998

Embassy Ballroom

9:00 am

Invited Lecture Session Ron Shamir, Chair David Schwartz  New Approaches to Genomic Analaysis Using Single Molecules

10:00 am

Break

Session 6, Chair: Minoru Kanehisa

10:10 am	Algorithms for Optical Mapping R. M. Karp, R. Shamir
10:35 am	Estimation for Restriction Sites Observed by Optical Mapping Using Reversible-jump Markov Chain Monte Carlo J. K. Lee, V. Dancik, M. S. Waterman
11:00 am	Break
11:15 am	Partitioning K Clones: Hardness Results and a Practical Solution to the K-Popultaion Problem L. Parida, B. Mishra
11:40 am	Constructing Maps Using the Span and Inclusion Relations D. Fasulo, T. Jiang, R. M. Karp, N. Sharma
12:05 pm	Lunch

1:30 pm

Invited Lecture Session Chair: Webb Miller John Yates  Mass Spectrometry and the Proteome

2:30 pm

Break

Session 7, Chair: Thomas Lengauer

2:40 pm	How Fast a Protein Chain Can Fold to Its Most Stable Structure? A. V. Finkelstein, A. Ya. Badretdinov
3:00 pm	Algorithmic Determination of Core Positions in the VL and VH Domains of Immunoglobulin Molecules I. Gelfand, A. Kister, C. Kulikowski, O. Stoyanov
3:30 pm	Alignments Without Low-Scoring Regions Z. Zhang, P. Berman, W. Miller
3:55 pm	Dynamic Programming Alignment Accuracy I. Holmes, R. Durbin
4:20 pm	Break

4:30 pm

Invited Lecture Session Chair: David Haussler Klaus Gubernator Evolutionary Drug Discovery

Wednesday March 25, 1998

Embassy Ballroom

Session 8, Chair: Dan Gusfield

8:30 am	Protein Folding in the Hydrophobic-Hydrophilic (HP) Model is NP-Complete B. Berger, T. Leight
8:55 am	On the Complexity of Protein Folding P. Crescenzi, D. Goldman, C. Papadimitriou, A. Piccolboni, M.Yannakakis
9:20 am	A New Method for Modeling and Solving the Protein Fold Recognition Problem Y. Xu, D. Xu, E. C. Uberbacher
9:45 am	Optimal Detection of Sequence Similarity by Local Alignment T. Hwa, M. Lassig
10:10 am	Break

Session 9, Chair: Terry Speed

10:20 am	A Formally Exact Method to Numerically Analyze Local Denaturation in Superhelical DNA R. M. Fye, C. J. Benham
10:45 am	The Theoretical Limits of DNA Sequence Discrimination of Polyamides W. L. Walker, D. S. Goodsell, E. M. Landaw
11:10 am	Maxwell Demon and Topology Simplification by Type II Topoisomerases A. Vologodskii
11:35 am	A Unified Approach to Word Statistics M. Regnier
12:00 pm	Lunch

Session 10, Chair: Phil Green

1:00 pm	Regression Analysis of Multiple Protein Structures  T. D. Wu, S. C. Schmidler, T. Hastie, D. L. Brutlag
1:25 pm	Better Methods for Solving Parsimony and Compatiblity M. Bonet, M. Steel, T. Warnow, S. Yooseph
1:50 pm	Beyond Mutation Matrices: Physical-Chemistry Based Evolutionary Models J. M. Koshi, D. P. Mindell, R. A. Goldstein
2:15 pm	A Structure Based Similarity Measure for Nucleic Acid Sequence Comparison R. Liu, T. W. Blackwell and D. J. States
2:40 pm	Break

Session 11, Chair: David Benson

2:55 pm	The Hierarchical Organization of Molecular Structure Computations C. C. Chen, J. P. Singh, R. B. Altman
3:20 pm	Estimaiton of Allele Frequencies From Color-Multiplexed Electropherograms D. G. Politte, D. R. Maffitt, D. J. States
3:45 pm	Analysis of the Position Dependent Amino Acid Probabilities and its Applicationts to the Search for Remote Homologues S. R. Sunyaev, I. V. Rodchenkov, F. Eisenhaber, E. N. Kuznetsov
4:10 pm	Family-based Homology Detection via Pairwise Sequence Comparison W. N. Grundy

End of RECOMB 98

Link to RECOMB 97