This message contains a preliminary program of
The Third Annual Conference on Research in
Computational Molecular Biology (RECOMB 99)
that will take place in Lyon (France) on April 11-14, 1999.
Those who would like to attend the Conference are invited to register
before
March 12, 1999
You will find a registration form as well as further information about
the conference on the web site
http://www.inria.fr/RECOMB99/
Warning: Future participants are suggested to make their hotel
reservation as soon as possible. Please be aware that there are other
congresses held in Lyon at that time and the hotel availability might
be limited.
=================================
PRELIMINARY PROGRAM OF RECOMB'99
=================================
April 11-14,
Hotel de Lyon Metropole, Lyon, France
------------------------
Saturday, April 10, 1999
------------------------
16:00 - 19:00 - Welcome and registration at Lyon Metropole Hotel
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 Regnier, 1999 Conference Chair
Ron Shamir, 2000 Program Committee Chair
Distinguished New Technologies Lecture - Chair: S. Istrail
----------------------------------------------------------
9:00 Large DNA Microarrays - the How and the Why
Ed Southern
10:00 Break
Session on Gene Expression - Chair: S. Schbath
----------------------------------------------
10:15 Algorithms for Choosing Differential Gene Expression Experiments
R. M. Karp, R. Stoughton, K. Y. Yeung
10:40 An Algorithm for Clustinering cDNAs for Gene Expression Analysis
E. Hartuv, A. Schmitt, J. Lange, S. Meirer-Ewert, H. Lehrach, R. Shamir
11:05 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
11:30 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
Lunch: 12:35 - 14:00
--------------------
Distinguished Biology Lecture - Chair: P. Pevzner
-------------------------------------------------
14:00 Whole Genome Association Studies in Humans
Daniel Cohen
15:00 Break
Session on Protein Structure - Chair: M. Levitt
-----------------------------------------------
15:15 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
15:40 A Solvation Potential with Improved Contact Definitions and
Optimized by Extensive Threading
A. Dombkowski, G. M. Crippen
16:05 Fast Detection of Common Geometric Substructure in Proteins
L. P. Chew, D. Huttenlocher, K. Kedem, J. Kleinberg
16:30 Break
Plenary Lecture Session - Chair: M. Levitt
------------------------------------------
16:45 The Past, Present and Future of Protein Structure Prediction
John Moult
18:00 - 20:00 Business Meeting
----------------------
Monday, April 12, 1999
----------------------
Plenary Lecture Session - Chair: R. Karp
----------------------------------------
8:30 Computational Analysis of Molecular Diversity for Drug Discovery
Peter Willett
9:30 Break
Session on Genomic Rearrangements - Chair: R. Shamir
----------------------------------------------------
9:45 Reconstructing the Pre-Doubling Genome
N. El-Mabrouk, D. Bryant, D. Sankoff
10:10 Formulations and Hardness of Multiple Sorting by Reversals
A. Caprara
10:35 Probability Models for Genome Rearrangement and Linear Invariants
for Phylogenetic Inference
D. Sankoff, M. Blanchette
11:00 Break
Session on Trees - Chair: A. Guenoche
-------------------------------------
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
Lunch: 12:30 - 14:00
--------------------
Plenary Lecture Session - Chair: D. Slonim
------------------------------------------
14:00 Progress Toward the Whole-Genome Shotgun Sequencing of Drosophilia
Gene Myers
15:00 Break
Session on Statistics - Chair: J. Kececioglu
--------------------------------------------
15:15 Searching Gene Transfers on Bacillus Subtilis Using Hidden Markov Models
L. Bize, F. Muri, F. Samson, F. Rodolphe, S. D. Ehrlich,
B. Prum, P. Bessieres
15:40 Significance Testing for Genomic Mismatch Scanning
G. R. Grant, R. S. Spielman, E. Manduchi, V. G. Cheung, W. J. Ewens
16h05 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
-----------------------
Plenary Lecture Session - Chair: M. Regnier
-------------------------------------------
8:30 Genome Sequences and Protein Structures
Cyrus Chothia
9:30 Break
Session on Mapping - Chair: R. Karp
-----------------------------------
9:45 Algorithms for Whole Genome Shotgun Sequencing
E. Anson, G. Myers
10:10 Construction of Physical Maps from Oligonucleotide Fingerprints Data
G. Mayraz, R. Shamir
10:35 Computing Physical Maps of Chromosomes with Nonoverlapping Probes
by Branch-and-Cut
T. Christof, J. Kececioglu
11:00 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
-------------------
Lecture Session - Chair: S. Istrail
-----------------------------------
14:00 Trends in Computational Biology
John Wooley
15:00 Break
Session on Sequence Alignment - Chair: A. Apostolico
----------------------------------------------------
15:15 An Analytic Study of the Phase Transition Line in Local Sequence
Alignment with Gaps
R. Bundschuh, T. Hwa
15:40 Winnowing Sequences from a Database Search
P. Berman, Z. Zhang, Y. I. Wolf, E. V. Koonin, W. Miller
16:05 q-gram Based Database Searching Using a Suffix Array (QUASAR)
S. Burkhardt, A. Crauser, P. Ferragina, H-P. Lenhof, E. Rivals,
M. Vingron
17:00 - 23:00 Evening program at Saint-Romain-en-Gal
----------------------------------------------------
17:00 Departure to Saint-Romain-en-Gal
18:00 Stanislaw Ulam - Computational Biology Address - Chair: M. Waterman
Comparison of Complete Genomes: Organisation and Evolution
Piotr Slonimski
19:00 Visit of the Museum
21:00 Cocktail
-------------------------
Wednesday, April 14, 1999
-------------------------
Plenary Lecture Session: Chair R. Shamir
----------------------------------------
9:00 Comparing Genes and Genomes: From Polymorphism to Phylogeny
Peer Bork
10:00 Break
Session on Drug Design - Chair: R. Lathrop
------------------------------------------
10:15 Efficient Database Screening for Rational Drug Design Using
Pharmacophore-Constrained Conformational Search
S. M. LaValle, L. E. Kavraki, P. W. Finn, J-C. Latombe
10:40 Coupled Optimization in Protein Docking
J. C. Mitchell, A. T. Phillips, J. B. Rosen, L. F. Ten Eyck
11:05 Derivation of Sensitive Discrimination Potential for Virtual
Ligand Screening
M. Totrov, R. Abagyan
11:30 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
