Friday April 7
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16:00 -19:00    Welcome and  Registration

(at: Tokyo Bay Ariake Washington Hotel, 3F "Iris")

(at: Tokyo Bay Ariake Washington Hotel, 3F "Iris")

Saturday April 8
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8:30 -           Registration at: Tokyo Big Sight Conference Tour Building 6F

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 Generationof 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

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

Session Chair : Steve Skiena

11:40-12:05

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

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

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

Session Chair : Thomas Lengaur

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

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

Session Chair : David Sankoff

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

Sunday April 9
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Session Chair : Andrea Califano

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

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

Session Chair : Jadwiga Bienkowska

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

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

Session Chair : Satoru Miyano

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

R. Desper, M. Vingron :
Tree Fitting: an Algebraic Approach Using Profile Distances

Session Chair : John Kececioglu

17:25-17:50

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

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

Session Chair : Pavel Pevzner

18:30-21:30    banquet and Distinguished Biology Lecture: Walter Gilbert

Introns and Modules in Ancient Conserved Genes

Monday April 10
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Session Chair : Ron Shamir

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

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

Session Chair : Lushheng Wang

11:25-11:50

R. B. Lyngso, C. N. S. Pederson :
Pseudonknots in RNA Secondary Structures

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

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

12:40-14:00    lunch
 

Session Chair : Nir Friedman

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

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

Session Chair : Dannie Durand

16:25-16:50

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

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

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

Tuesday April 11
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Session Chair : Donna Slonim

9:00 - 9:25

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

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

S. Heber, J. Stoye, J. Hoheisel, M. Vingron :
Contig Selection in Physical Mapping

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

Session Chair : Alberto Apostolico

11:15-11:40

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

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

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

Session Chair : Tatsuya Akutsu

14:00-14:25

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

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

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

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