Detailed Agenda

Saturday, March 27, 2004
5:00pm - 8:00pm
2nd Floor Foyer
Registration Open
6:00pm - 8:00pm
TBA
Opening Reception
Sunday, March 28, 2004
7:30am - 5:30pm
2nd Floor Foyer
Registration
7:30am - 8:30am Continental Breakfast
8:30am - 8:45am
California Ballroom
 Welcome
8:45am - 9:40am
California Ballroom
SNPing in the Human Genome
Deborah Nickerson Keynote
Abstract (pdf)
9:40am - 10:05am
California Ballroom
Maximum Likelihood Resolution of Multi-block Genotypes
Gad Kimmel, Ron Shamir
10:05am - 10:30am
California Ballroom
Perfect Phylogeny and Haplotype Assignment
Eran Halperin, Richard M. Karp
10:30am - 10:55am Coffee
10:55am - 11:20am
California Ballroom
An exact solution for finding minimum recombinant haplotype configurations on pedigrees with missing data by integer linear programming
Jing Li, Tao Jiang
11:20am - 11:45am
California Ballroom
Chromosomal breakpoint re-use in the inference of genome sequence rearrangement
David Sankoff, Phil Trinh
11:45am - 12:10pm
California Ballroom
Learning Multiple Evolutionary Pathways from Cross-sectional Data
Niko Beerenwinkel, Jorg Rahnenfuhrer, Martin Daumer, Daniel Hoffmann, Rolf Kaiser, Joachim Selbig, Thomas Lengauer
12:10pm - 2:00pm
Harbor Terrace,
4th floor
Lunch at hotel
2:00pm - 2:55pm
California Ballroom

Algorithms for Inferring Cis-Regulatory Structures and Protein Interaction Networks
Richard Karp Keynote
Fred Howes Distinguished Service Award
Abstract (pdf)

2:55pm - 3:20pm
California Ballroom
A Novel Ensemble-Based Scoring and Search Algorithm for Protein Redesign, and its Application to Modify the Substrate Specificity of the Gramicidin Synthetase A Phenylalanine Adenylation Enzyme
Ryan H. Lilien, Brian W. Stevens, Amy C. Anderson, Bruce R. Donald
3:20pm - 3:45pm
California Ballroom
A Random Graph Approach to NMR Sequential Assignment
Chris Bailey-Kellogg, Sheetal Chainraj, Gopal Pandurangan
3:45pm - 4:10pm Coffee
4:10pm - 4:35pm
California Ballroom
Finding Short DNA Motifs Using Permuted Markov Models
Xiaoyue Zhao, Haiyan Huang, Terence P. Speed

4:35pm - 5:00pm
California Ballroom

Designing multiple simultaneous seeds for DNA similarity search
Yanni Sun and Jeremy Buhler
5:00pm - 5:25pm
California Ballroom
Aligning alignments exactly
John Kececioglu, Dean Starrett
5:30pm - 7:30pm
Garden Pavillion,
4th floor
Poster Session Group A authors present
7:30pm - 9:00pm Program Committee and Steering Committee dinner (by invitation)
Monday, March 29, 2004
7:30am - 5:30pm
2nd Floor Foyer
Registration
7:30am - 8:30am Continental Breakfast
8:30am - 9:25am
California Ballroom
Systems Biology and Malaria
Elizabeth Winzeler Keynote
Abstract (pdf)
9:25am - 9:50am
California Ballroom
Stochastic Models Based on Molecular Hybridization Theory for Short Oligonucleotide Microarrays
Zhijin Wu, Rafael A. Irizarry
9:50am - 10:15am
California Ballroom
Checking homogeneity of motifs distribution in heterogenous sequences
Sabrina Ledent and Stephane Robin
10:15am - 10:40am Coffee
10:40am - 11:05am
California Ballroom
From Profiles to Patterns and Back Again: A Branch and Bound Algorithm for Finding Optimal Motif Profiles
Eleazar Eskin
11:05am - 11:30am
California Ballroom
Finding Motifs for Insufficient Number of Sequences with Strong Binding to Transcription Factor
Francis Y.L. Chin, Henry C.M. Leung, S.M. Yiu, T.W. Lam, Roni Rosenfeld, W.W. Tsang, David K. Smith, Y.Jiang
11:30am - 11:55am
California Ballroom
Structured Motifs Search
Michele Morgante, Alberto Policriti, Nicola Vitacolonna, Andrea Zuccolo
11:55am - 2:00pm BOF lunch off site restaurants
2:00pm - 2:55pm
California Ballroom
Evolutionary Change in Developmental Genetic Networks
William McGinnis Keynote
Abstract (pdf)
2:55pm - 3:20pm
California Ballroom
A Discriminative Model for Identifying Spatial Cis-Regulatory Modules
Eran Segal and Roded Sharan
3:20pm - 3:45pm
California Ballroom
Discovering temporal relations in molecular pathways using protein-protein interactions
Martin Farach-Colton, Yang Huang, John L. Woolford
3:45pm - 4:10pm Coffee
4:10pm - 4:35pm
California Ballroom
Hybrid-GMM-Matching toward Comparing Embryogenesis-Staining-Pattern- Images of Drosophila melanogaster and Finding Co-Regulated Genes
Hanchuan Peng, Eugene Myers
4:35pm - 5:00pm
California Ballroom
Probabilistic Discovery of Overlapping Cellular Processes and Their Regulation
Alexis Battle, Eran Segal, Daphne Koller
5:00pm - 5:25pm
California Ballroom
Computational identification of evolutionarily conserved exons
A. Siepel, D. Haussler
5:25pm - 5:50pm
California Ballroom
Multiple Organism Gene Finding by Collapsed Gibbs Sampling
Sourav Chatterji, Lior Pachter
6:00pm - 7:00pm
California Ballroom
RECOMB Business Meeting
Tuesday, March 30, 2004
7:30am
2nd Floor Foyer
Registration
7:30am - 8:30am Continental Breakfast
8:30am - 9:25am
California Ballroom
Somatic Evolution of Cancer
Martin Nowak Keynote
9:25am - 9:50am
California Ballroom
Protein Similarity from Knot Theory and Geometric Convolution
Michael Erdmann
9:50am - 10:15am
California Ballroom
Interface Surfaces for Protein-Protein Complexes
Yih-En Andrew Ban, Herbert Edelsbrunner, Johannes Rudolph
10:15am - 10:40am Coffee
10:40am - 11:05am
California Ballroom
De novo Repeat Classification and Fragment Assembly
Pavel A. Pevzner, Haixu Tang, Glenn Tesler
11:05am - 11:30am
California Ballroom
Finding Approximate Tandem Repeats in Genomic Sequences
Ydo Wexler, Zohar Yakhini, Yechezkel Kashi, Dan Geiger
11:30am - 11:55am
California Ballroom
Finding anchors for genomic sequence comparison
Ross A. Lippert, Xiaoyue Zhao, Liliana Florea, Clark Mobarry, Sorin Istrail
11:55am - 2:00pm Lunch on own
2:00pm - 2:55pm
California Ballroom
RNAi, Genome Ultrastructure, and Other Unexpected Tales from the Analysis of Genetic Silencing
Andrew Fire Keynote
The Distinguished Biology Lecture
Abstract (pdf)
2:55pm - 3:20pm
California Ballroom
Faster genome annotation of non-coding RNA families without loss of accuracy
Zasha Weinberg, Walter L. Ruzzo
3:20pm - 3:45pm
California Ballroom
Using Motion Planning to Study RNA Folding Kinetics
Xinyu Tang, Bonnie Kirkpatrick, Shawna Thomas, Guang Song, Nancy M. Amato
3:45pm - 4:10pm Coffee
4:10pm - 4:35pm
California Ballroom
A Class of Edit Kernels for SVMs to Predict Translation Initiation Sites in Eukaryotic mRNAs
Haifeng Li, Tao Jiang
4:35pm - 5:00pm
California Ballroom
Identifying Conserved Gene Clusters in the Presence of Orthologous Groups
Xin He, Michael H. Goldwasser
5:00pm - 7:00pm
Garden Pavillion,
4th floor
Poster Session Group B authors present
5:00pm - 7:00pm
California Ballroom
PDB talk
7:00pm - 7:30pm Buses to Dinner at Aquarium
7:30pm - 10:00pm Dinner at Aquarium (optional)
Wednesday, March 31, 2004
7:30am - 8:30am Continental Breakfast
8:30am - 9:25am
California Ballroom
Fifty Years of Sequence Analysis: What Have We Learned?
Russell Doolittle Keynote
The Stanislaw Ulam Memorial Computational Biology Lecture
Abstract (pdf)
9:25am - 9:50am
California Ballroom
Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data
Roded Sharan, Trey Ideker, Brian Kelley, Ron Shamir, Richard Karp
9:50am - 10:15am
California Ballroom
The Evolutionary Capacity of Protein Structures
Leonid Meyerguz, David Kempe, Jon Kleinberg, Ron Elber
10:15am - 10:40am
California Ballroom
Wrap-and-Pack: A New Paradigm for Beta Structural Motif Recognition with Application to Recognizing Beta Trefoils
Matthew Menke, Eben Scanlon, Jonathan King, Bonnie Berger, Lenore Cowen
10:40am - 11:05am Coffee
11:05am - 11:30am
California Ballroom
Mining spatial motifs from protein structure graphs
Jun Huan, Wei Wang, Deepak Bandyopadhyay, Jack Snoeyink, Jan Prins, Alex Tropsha
11:30am - 11:55am
California Ballroom
Reconciliation problems for duplication, loss and horizontal gene transfer
Pawel Gorecki
11:55am - 12:20pm
California Ballroom
Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution
Lars Arvestad, Ann-Charlotte Berglund, Jens Lagergren and Bengt Sennblad
12:20pm-2:00pm
Harbor Terrace,
4th floor
Lunch at hotel
2:00pm - 2:55pm
California Ballroom
A Structural Perspective on Genome Evolution
Christine Orengo Keynote
Abstract (pdf)
2:55pm - 3:20pm
California Ballroom
Reconstructing Reticulate Evolution in Species - Theory and Practice
Luay Nakhleh, Tandy Warnow and C. Randal Linder
3:20pm - 3:45pm
California Ballroom
Simultaneous Identification of Duplications and Lateral Transfers
M. Hallett, J. Lagergren, A. Tofigh
3:45pm - 4:10pm Coffee
4:10pm - 5:00pm
California Ballroom
Recent Advances on the Manipulation of Single Biomolecules
Carlos Bustamante Keynote
The Distinguished New Technologies Lecture
Abstract
(pdf)
5:00pm-5:15pm
California Ballroom
Awards Ceremony
5:15pm Adjourn