Recomb98: Deadlines & Preliminary Program

Eugene Kolker eugene at genome.biotech.washington.edu
Mon Feb 9 14:12:20 EST 1998

Early registration    ends  February 20, 1998!
Hotel conference rate ends  February 24, 1998!

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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 
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 
Richard Karp, Chair 

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 
Eugene Koonin, Chair 

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 
Webb Miller, Chair 
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 Programmimg Alignment Accuracy
I. Holmes and R. Durbin  

4:20 pm Break  

4:30 pm  	Invited Lecture Session 
David Haussler, Chair 

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. Leighton 

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 
C. C. Chen, J. P. Singh, R. B. Altman 

3:20 pm 	Estimaiton of Allele Frequencies From Color-Multiplexed 
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 
W. N. Grundy 

End of RECOMB 98

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