RECOMB 2000: preliminary program and updates

Tatsuya Akutsu takutsu at ims.u-tokyo.ac.jp
Sun Feb 13 21:14:55 EST 2000


Dear colleague:

Enclosed is the preliminary program of RECOMB 2000.
We are looking forward to an exciting program, including
nine keynote presentations by distinguished scientists, 
36 contributed talks selected by the Program Committee, 
and 120 accepted posters.

Please note: the early registration deadline is February 20, 2000.
The deadline for hotel reservation is March 1, 2000.

The list of accepted posters, as well as resigration and hotel
information, is available at http://recomb2000.ims.u-tokyo.ac.jp.
Further updates will be posted on the website.

See you in Tokyo,

Ron Shamir
RECOMB 2000 Program Chair 

----------------------------------------------------------------


       FOURTH ANNUAL INTERNATIONAL CONFERENCE ON
             COMPUTATIONAL MOLECULAR BIOLOGY

                  (RECOMB 2000)

                 April 8-11, 2000
                   Tokyo, Japan

                   Organized by
    Human Genome Center, Institute of Medical Science,
        University of Tokyo

                     Sponsored by
    ACM (Association for Computing Machinery)  - SIGACT

                  with support from
    Agilent Laboratories
                       Compugen
                   IBM Corporation
      International Society for Computational Biology
                  SmithKline Beecham
             US National Science Foundation
                 US Department of Energy

             http://recomb2000.ims.u-tokyo.ac.jp 
 
  Preliminary Program
  -------------------


Friday April 7
***************
16-19 Welcome and  Registration
18:00 Reception

Saturday April 8
****************
9:00 opening remarks
   Ron Shamir, RECOMB 2000 Program Chair
   Satoru Miyano, RECOMB 2000 Organizing Committee Chair
   Thomas Lengauer, RECOMB 2001 Program Chair

9:15-10:15 The Stanislaw Ulam Computational Biology Address.
Minoru Kanehisa : 
Sequence Comparison to Graph Comparison-A New Generation
of Algorithms for Network Analysis of Interacting Molecules

10:20-10:45  S. Batzoglou, L. Pachter, J. P. Mesirov, B. Berger,
E. S. Lander: 
Comparative Analysis of Mouse and Human DNA and Applications to 
Exon Prediction

10:45-11:10  P. Pevzner, V. Dancik, C. L. Tang:
Mutation-Tolerant Protein Identification by Mass-Spectrometry

11:10-11:40    break

11:40-12:05   N. Friedman, M. Linial, I. Nachman, D. Pe'er:
Using Bayesian Networks to Analyze Expression Data

12:05-12:30  A. Ben-Dor, L. Bruhn, N. Friedman, I. Nachman, 
M. Schummer, Z. Yakhini:
Tissue classification with gene expression profiles

12:30-12:55  D. K. Slonim, P. Tamayo, J. P. Mesirov, T. R. Golub, 
E. S. Lander:
Class prediction and discovery using gene expression data

12:55-14:15    lunch (poster setup period)

14:15-15:15 Keynote Lecture: Hans Lehrach
A Data-Analysis Pipeline for Large-Scale Gene Expression Analysis

15:20-15:45    C. Bailey-Kellogg, A. Widge, J. J. Kelley, M. J. 
Berardi, J. H. Bushweller, B. R. Donald:
The NOESY Jigsaw: automated protein secondary structure and 
main-chain assignment from sparse, unassigned NMR data

15:45-16:10  J. M. Sorenson, T. Head-Gordon:
Matching simulation and experiment: a new simplified model for 
simulating protein folding

16:10-16:40    break

16:40-17:40 Keynote Lecture: Svante Paabo
DNA Sequence Variation among Humans and Apes

17:45-18:10   A. Zien, R. Zimmer, T. Lengauer:
A simple iterative approach to parameter optimization

18:20-20:00  business meeting



Sunday April 9
**************
9:00-10:00 Keynote Lecture: Eric Davidson
Computational Analyses of Developmental cis-Regulatory Control Systems

10:05-10:30    T. Akutsu, S. Miyano, S. Kuhara :
Algorithms for Identifying Boolean Networks and Related Biological
Networks Based on Matrix Multiplication and Fingerprint Function

10:30-10:55    M. Tomita, K. Hashimoto, K. Takahashi, Y. Matsuzaki, 
R. Matsushima, K. Yugi, F. Miyoshi, H. Nakano, Y. Saito, S. Shimizu, 
Y. Nakayama :
The E-CELL project: towards integrative simulation of cellular processes

10:55-11:25    break

11:25-11:50    A. Liwo, J. Pillardy, C. Czaplewski, J. Lee, D. R. 
Ripoll, M. Groth, S. Rodziewicz-Motowidlo, R. Kazmierkiewicz, R. J. 
Wawak, S. Oldziej,  H. A. Scheraga :
UNRES -- a united-residue force field for energy-based prediction 
of protein structure - origin and significance of multibody terms

11:50-12:15 Y. Z. Ohkubo, G. M. Crippen :
Determining Contact Energy Function for Continuous State Models of 
Globular Protein Conformations

12:15-15:00    poster session and lunch

15:00-16:00 Keynote Lecture: Takashi Gojobori
Evolutionary Features of Genomes as Disclosed by Comparative 
Analysis of Complete Genome Sequences

16:05-16:30    B. Chor, M. D. Hendy, B. R. Holland, D. Penny :
Multiple Maxima of Likelihood in Phylogenetic Trees: An Analytic 
Approach

16:30-16:55  R. Desper, M. Vingron :
Tree Fitting: an Algebraic Approach Using Profile Distances

16:55-17:25   break

17:25-17:50   D. Sankoff, D. Bryant, M. Deneault, B. F. Lang, G. Burger :
Early Eukaryote Evolution Based on Mitochondrial Gene Order Breakpoints

17:50-18:15   K. Chen, D. Durand, M. Farach-Colton :
Notung: Dating gene duplications using gene family trees

18:30-21:30 banquet and Distinguished Biology Lecture: Walter Gilbert
Introns and Modules in Ancient Conserved Genes



Monday April 10
***************
9:00-10:00 Distinguished New Technologies Lecture: Leroy Hood
Computing Life and Global Technologies

10:05-10:30    A. Ben-Dor, R. M. Karp, B. Schwikowski, Z. Yakhini :
Universal DNA tag systems: a combinatorial design scheme

10:30-10:55   F. P. Preparata, E. Upfal :
Sequencing-by-hybridization at the information-theory bound: an 
optimal algorithm

10:55-11:25   break

11:25-11:50    R. B. Lyngso, C. N. S. Pederson :
Pseudonknots in RNA Secondary Structures

11:50-12:15   Y. Xu, D. Xu, O. H. Crawford, J. R. Einstein, E. Serpersu :
Protein Structure Determination using Protein Threading and Sparse  
NMR Data

12:15-12:40   E. Althaus, O. Kohlbacher, H. P. Lenhof, P. Mueller :
A combinatorial approach to protein docking with flexible side-chains

12:40-14:00    lunch

14:00-15:00 Keynote Lecture: Yusuke Nakamura
Human Genome Analysis and Medicine in the 21st Century

15:05-15:30    R. Bundschuh :
An Analytic Approach to Significance Assessment in Local Sequence  
Alignment with Gaps

15:30-15:55   T. Akutsu, H. Arimura, S. Shimozono
On Approximation Algorithms for Local Multiple Alignment

15:55-16:25    break

16:25-16:50     M. Kann, R. A. Goldstein :
Optimizing for Success: A New Score Function For Distantly Related 
Protein Sequence Comparison

16:50-17:15   S. A. Teichmann, C. Chothia, G. M. Church, J. Park :
PDB-ISL: an intermediate sequence library for fast assignment of 
protein structures to sequences

17:15-17:40   J. R. Bienkowska, L. Yu, S. Zarakhovich, R. G. Rogers, 
T. F. Smith :
Comprehensive statistical method for protein fold recognition

17:40-19:40 poster session



Tuesday April 11
****************

9:00-10:00 Keynote Lecture: Yvonne Martin
Molecular Diversity: Strategies and Concerns

10:05-10:30     S. Heber, J. Stoye, J. Hoheisel, M. Vingron :
Contig Selection in Physical Mapping

10:30-10:55    J. Kececioglu, S. Shete, J. Arnold :
Reconstructing distances in physical maps of chromosomes with 
nonoverlapping probes

10:55-11:25    break

11:25-11:50    L. Marsan, M.-F. Sagot :
Extracting structured motifs using a suffix tree - Algorithms and 
application to promoter consensus identification

11:50-12:15   X. Chen, S. Kwong, M. Li :
A Compression Algorithm for DNA Sequences and Its Applications 
in Genome Comparison

12:15-12:40   R. Hart, A. K. Royyuru, G. Stolovitzky, A. Califano :
Systematic and Automated Discovery of Patterns in PROSITE Families

12:40-14:00    lunch

14:00-14:25  M. Linial, E. Portugaly :
Probabilities for having a new fold on the basis of a map of all 
protein sequences

14:25-14:50   G. Yona, M. Levitt :
A unified sequence-structure classification of protein sequences: 
combining sequence and structure in a map of the protein space

14:50-15:15   A. Apostolico, G. Bejerano :
Optimal Amnesic Probabilistic Automata or How to Learn and Classify 
Proteins in Linear Time and Space

15:15-15:45    break

15:45-16:35     S. Batzoglou, B. Berger, J. P. Mesirov, E. S. Lander :
Sequencing a Genome by Walking with Clone-end Sequences: A Mathematical 
Analysis

16:10-16:35   M. T. Hallett, J. Lagergren :
New Algorithms for the Duplication-Loss Model

16:35 End of Conference 

17:00    sightseeing tour: boat ride and dinner (optional)








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