Recomb'99 Preliminary Program

Hôtel de Lyon Métropole, Lyon, France

Saturday April 10, 1999

16:00 - 19:00

Welcome and registration

18:00

Cocktail offered by the City Hall of Lyon

Sunday April 11, 1999

8:45

Opening Remarks

Sorin Istrail
General RECOMB Vice-Chair, 1999 Program Committee Chair

Mireille Régnier
RECOMB 1999 Conference Chair

Ron Shamir
RECOMB 2000 Program Committee Chair

9:00

Distinguished New Technologies Lecture
Chair: S. Istrail

Large DNA Microarrays - the How and the Why
Ed Southern

10:00

Short break

Session on Gene Expression - Chair: S. Schbath

10:05

Algorithms for Choosing Differential Gene Expression Experiments
R. M. Karp, R. Stoughton, K. Y. Yeung

10:30

An Algorithm for Clustinering cDNAs for Gene Expression Analysis
E. Hartuv, A. Schmitt, J. Lange, S. Meirer-Ewert, H. Lehrach, R. Shamir

10:55

A Dictionary Based Approach for Gene Annotation
L. Pachter, S. Batzoglou, V. I. Spitkovsky, W. S. Beebee Jr., E. S. Lander, B. Berger, D. J. Kleitman

11:20

Break

Session on Sequencing - Chair: R. Karp

11:45

De Novo Peptide Sequencing via Tandem Mass Spectrometry: A Graph-Theoretical Approach
V. Dancik, T. Addona, K. Clauser, J. Vath, P. A. Pevzner

12:10

On the Power of Universal Bases in Sequencing by Hybridization
F. P. Preparata, A. M. Frieze, E. Upfal

12:35 - 14:00

Lunch

14:00

Distinguished Biology Lecture
Chair: P. Pevzner

Whole Genome Association Studies in Humans
Daniel Cohen

15:00

Short break

Session on Protein Structure - Chair: M. Levitt

15:05

Recognition of Remote Protein Homologies Using Three-Dimensional Information to Generate a Position Specific Scoring Matrix in the Program 3D-PSSM
L. Kelley, R. MacCullum, M. J. E. Sternberg

15:30

A Solvation Potential with Improved Contact Definitions and Optimized by Extensive Threading
A. Dombkowski, G. M. Crippen

15:55

Fast Detection of Common Geometric Substructure in Proteins
L. P. Chew, D. Huttenlocher, K. Kedem, J. Kleinberg

16:20

Break

16:45

Plenary Lecture Session
Chair: M. Levitt

The Past, Present and Future of Protein Structure Prediction
John Moult

18:00 - 20:00

Business Meeting

Monday April 12, 1999

8:30	Plenary Lecture Session Chair: R. Karp Computational Analysis of Molecular Diversity for Drug Discovery Peter Willett

9:30	Short break

Session on Genomic Rearrangements - Chair: R. Shamir

9:35	Reconstructing the Pre-Doubling Genome N. El-Mabrouk, D. Bryant, D. Sankoff
10:00	Formulations and Hardness of Multiple Sorting by Reversals A. Caprara
10:25	Probability Models for Genome Rearrangement and Linear Invariants for Phylogenetic Inference D. Sankoff, M. Blanchette
10:50	Break

Session on Trees - Chair: A. Guénoche

11:15	Modeling Protein Families Using Probabilistic Suffix Trees G. Bejerano, G. Yona
11:40	Faster Reliable Phylogenetic Analysis V. Berry, D. Bryant
12:05	Obtaining Highly Accurate Topology Estimates of Evolutionary Trees from Very Short Sequences D. H. Huson, S. Nettles, T. J. Warnow
12:30 - 14:00	Lunch

14:00

Plenary Lecture Session
Chair: D. Slonim

Progress Toward the Whole-Genome Shotgun Sequencing of Drosophilia
Gene Myers

15:00

Short break

Session on Statistics - Chair: J. Kececioglu

15:05

Searching Gene Transfers on Bacillus Subtilis Using Hidden Markov Models
L. Bize, F. Muri, F. Samson, F. Rodolphe, S. D. Ehrlich, B. Prum, P. Bessières

15:30

Significance Testing for Genomic Mismatch Scanning
G. R. Grant, R. S. Spielman, E. Manduchi, V. G. Cheung, W. J. Ewens

15:55

Break

Session on Statistics - Chair: G. Kucherov

16:20	Classifying Proteins by Family Using the Product of Correlated p-values T. L. Bailey, W. N. Grundy
16:45	Sequence Homology Detection Through Large Scale Pattern Discovery A. Floratos, I. Rigoutsos, L. Parida, G. Stolovitzky, Y. Gao

17:30 - 19:30 Poster Session

Tuesday April 13, 1999

8:30	Plenary Lecture Session Chair: D. Kahn Genome Sequences and Protein Structures Cyrus Chothia

9:30	Short break

Session on Mapping - Chair: R. Karp

9:35	Algorithms for Whole Genome Shotgun Sequencing E. Anson, G. Myers
10:00	Construction of Physical Maps from Oligonucleotide Fingerprints Data G. Mayraz, R. Shamir
10:25	Computing Physical Maps of Chromosomes with Nonoverlapping Probes by Branch-and-Cut T. Christof, J. Kececioglu
10:50	Break

Session on Threading - Chair: M. Vingron

11:15

A Method for Optimal Design of a Threading Scoring Function
J. R. Bienkowska, R. G. Rogers Jr., T. F. Smith

11:40

An Anytime Algorithm for Gapped Block Protein Threading with Pair Interactions
R. H. Lathrop

12:05

Efficient Algorithms for Protein Sequence Design and the Analysis of Certain Evolutionary Fitness Landscapes
J. M. Kleinberg

12:30 - 14:00

Lunch

14:00

Plenary Lecture Session
Chair: S. Istrail

Trends in Computational Biology
John Wooley

15:00

Short break

Session on Sequence Alignment - Chair: A. Apostolico

15:05	An Analytic Study of the Phase Transition Line in Local Sequence Alignment with Gaps R. Bundschuh, T. Hwa
15:30	Winnowing Sequences from a Database Search P. Berman, Z. Zhang, Y. I. Wolf, E. V. Koonin, W. Miller
15:55	q-gram Based Database Searching Using a Suffix Array (QUASAR) S. Burkhardt, A. Crauser, P. Ferragina, H-P. Lenhof, E. Rivals, M. Vingron

16:20

Break

16:45

Stanislaw Ulam - Computational Biology Address
Chair: M. Waterman

Comparison of Complete Genomes: Organisation and Evolution Piotr Slonimski

18:00 - 23:00 Evening program at Saint-Romain-en-Gal

18:00

Departure to Saint-Romain-en-Gal

19:00

Visit of the Museum

20:00

Cocktail offered by Conseil Général du Rhône

Wednesday April 14, 1999

9:00	Plenary Lecture Session Chair R. Shamir Comparing Genes and Genomes: From Polymorphism to Phylogeny Peer Bork

10:00

Short break

Session on Drug Design - Chair: R. Lathrop

10:05

Efficient Database Screening for Rational Drug Design Using Pharmacophore-Constrained Conformational Search
S. M. LaValle, L. E. Kavraki, P. W. Finn, J-C. Latombe

10:30

Coupled Optimization in Protein Docking
J. C. Mitchell, A. T. Phillips, J. B. Rosen, L. F. Ten Eyck

10:55

Derivation of Sensitive Discrimination Potential for Virtual Ligand Screening
M. Totrov, R. Abagyan

11:20

Break

Session on Molecular Structure - Chair: J.M. Claverie

11:45

Optimizing Combinatorial Library Construction via Split Synthesis
B. Cohen, S. Skiena

12:10

Internal Loops in RNA Secondary Structure Prediction
R. B. Lyngso, M. Zuker, C. N. S. Pedersen

12:35 - 14:00

Lunch

Session on Gene Networks - Chair: T. Lengauer

14:00	Identifying Gene Regulatory Networks from Experimental Data T. Chen, V. Filkov, S. S. Skiena
14:25	Evolution of Metabolisms: A New Method for the Comparison of Metabolic Pathways C. V. Forst, K. Schulten
14:50	Clustering Gene Expression Patterns A. Ben-Dor, Z. Yakhini

15:15	Closing session
15:30	End of the conference

16:00 - 19:00	Welcome and registration
18:00	Cocktail offered by the City Hall of Lyon

8:45	Opening Remarks
	Sorin Istrail General RECOMB Vice-Chair, 1999 Program Committee Chair
	Mireille Régnier RECOMB 1999 Conference Chair
	Ron Shamir RECOMB 2000 Program Committee Chair

10:05	Algorithms for Choosing Differential Gene Expression Experiments R. M. Karp, R. Stoughton, K. Y. Yeung
10:30	An Algorithm for Clustinering cDNAs for Gene Expression Analysis E. Hartuv, A. Schmitt, J. Lange, S. Meirer-Ewert, H. Lehrach, R. Shamir
10:55	A Dictionary Based Approach for Gene Annotation L. Pachter, S. Batzoglou, V. I. Spitkovsky, W. S. Beebee Jr., E. S. Lander, B. Berger, D. J. Kleitman
11:20	Break

11:45	De Novo Peptide Sequencing via Tandem Mass Spectrometry: A Graph-Theoretical Approach V. Dancik, T. Addona, K. Clauser, J. Vath, P. A. Pevzner
12:10	On the Power of Universal Bases in Sequencing by Hybridization F. P. Preparata, A. M. Frieze, E. Upfal
12:35 - 14:00	Lunch

15:05	Recognition of Remote Protein Homologies Using Three-Dimensional Information to Generate a Position Specific Scoring Matrix in the Program 3D-PSSM L. Kelley, R. MacCullum, M. J. E. Sternberg
15:30	A Solvation Potential with Improved Contact Definitions and Optimized by Extensive Threading A. Dombkowski, G. M. Crippen
15:55	Fast Detection of Common Geometric Substructure in Proteins L. P. Chew, D. Huttenlocher, K. Kedem, J. Kleinberg
16:20	Break

15:05	Searching Gene Transfers on Bacillus Subtilis Using Hidden Markov Models L. Bize, F. Muri, F. Samson, F. Rodolphe, S. D. Ehrlich, B. Prum, P. Bessières
15:30	Significance Testing for Genomic Mismatch Scanning G. R. Grant, R. S. Spielman, E. Manduchi, V. G. Cheung, W. J. Ewens
15:55	Break

11:15	A Method for Optimal Design of a Threading Scoring Function J. R. Bienkowska, R. G. Rogers Jr., T. F. Smith
11:40	An Anytime Algorithm for Gapped Block Protein Threading with Pair Interactions R. H. Lathrop
12:05	Efficient Algorithms for Protein Sequence Design and the Analysis of Certain Evolutionary Fitness Landscapes J. M. Kleinberg
12:30 - 14:00	Lunch

19:00	Visit of the Museum
20:00	Cocktail offered by Conseil Général du Rhône

10:05	Efficient Database Screening for Rational Drug Design Using Pharmacophore-Constrained Conformational Search S. M. LaValle, L. E. Kavraki, P. W. Finn, J-C. Latombe
10:30	Coupled Optimization in Protein Docking J. C. Mitchell, A. T. Phillips, J. B. Rosen, L. F. Ten Eyck
10:55	Derivation of Sensitive Discrimination Potential for Virtual Ligand Screening M. Totrov, R. Abagyan
11:20	Break