RECOMB'99: Program and Call for Participation

Gregory Kucherov Gregory.Kucherov at
Sat Feb 20 18:31:45 EST 1999

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

                   March 12, 1999

You will find a registration form as well as further information about
the conference on the web site 


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.


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

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