Final Program

Saturday April 21, 2001
Sunday April 22, 2001

Monday April 23, 2001
Tuesday April 24, 2001
Wednesday April 25, 2001
Saturday April 21, 2001
18:00-20:00 Welcome Reception and Registration

Sunday April 22, 2001
8:45 Opening
Program Chair
Conference Chair

Intro: Thomas Lengauer
The Distinguished Biology Lecture
RNA Biology and the Genome
Phillip Sharp

Protein Structure
Isidore Rigoutsos
Guang Song, Nancy M. Amato
Using Motion Planning to Study Protein Folding Pathways
10:15 Coffee Break
10:50 Giuseppe Lancia, Robert Carr, Brian Walenz, Sorin Istrail
101 Optimal PDB Structure Alignments: a Branch-and-Cut Algorithm for the Maximum Contact Map Overlap Problem
11:15 Ting Chen, Jacob D. Jaffe, George M. Church
Algorithms for Identifying Protein Cross-links Via Tandem Mass Spectrometry
11:40 Phil Bradley, Lenore Cowen, Matthew Menke, Jonathan King, Bonnie Berger
Predicting The Beta-Helix Fold From Protein Sequence Data
12:05 Christopher James Langmead, Bruce Randall Donald
Extracting Structural Information Using Time-Frequency Analysis of Protein NMR Data
12:30 Lunch Break

Intro: Thomas Lengauer
The Role of Computational Chemistry in Translating Genomic Information into Bioactive Small Molecules 
Yvonne Martin

Molecular Interactions
Satoru Miyano
14:50   Mona Singh, Peter S. Kim
Towards Predicting Coiled-Coil Protein Interactions
15:15 O. Kohlbacher, A. Burchardt, A. Moll, A. Hildebrandt, P. Bayer, H.-P. Lenhof
A NMR-spectra-based Scoring Function for Protein Docking
15:40 Coffee Break
16:15 Poster Session
18:15 RECOMB business meeting (open for all attendees)
20:00 End of Day

Monday April 23, 2001
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Intro: Ron Shamir
The Stanislav Ulam Memorial Computational Biology Address
Hunger for new technologies, metrics, and spatiotemporal models in functional genomic
George M. Church

Expression Patterns
Ron Shamir
Amir Ben-Dor, Nir Friedman, Zohar Yakhini
Class Discovery in Gene Expression Data
10:15 Coffee Break
10:50 Harmen J. Bussemaker, Hao Li, Eric D. Siggia
Regulatory Element Detection Using Correlation with Expression
11:15 Paul Pavlidis, Jason Weston, Jinsong Cai, William Noble Grundy
Gene Functional Classification From Heterogenous Data
11:40 Yoseph Barash, Nir Friedman
Context-Specific Bayesian Clustering for Gene Expression Data
12:05 Vladimir Filkov, Steven Skiena, Jizu Zhi
Analysis Techniques for Microarray Time-Series Data
12:30 Lunch Break

Intro: Pavel Pevzner
Information processing by cells and biologists
Roger Brent

Sequencing by Hybridization
Michal Linial
Ron Shamir, Dekel Tsur
Large Scale Sequencing By Hybridization
15:00 Alan Frieze, Bjarni V. Halldórsson
Optimal Sequencing by Hybridization in Rounds
15:25 Coffee Break
Sequence Analysis I
Pavel Pevzner
16:00 Gonzalo Navarro, Mathieu Raffinot
Fast and Simple Character Classes and Bounded Gaps Pattern Matching, With Application to Protein Searching
16:25 Lior Pachter, Marina Alexandersson, Simon Cawley
Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems
16:50 Gert Thijs, Kathleen Marchal, Magali Lescot, Stéphane Rombauts, Bart De Moor, P. Rouze, Y. Moreau
A Gibbs Sampling Method to Detect Over-represented Motifs in the Upstream Regions of Co-expressed Genes
17:15 Yonathan Bilu, Michal Linial
On the Predictive Power of Sequence Similarity in Yeast
17:40 Wentian Li
DNA Segmentation as A Model Selection Process

Intro: Thomas Lengauer
Genetics and Genomics: Impact on Drug Discovery and Development
Klaus Lindpaintner
20:00 Conference Banquet

Tuesday April 24, 2001 back to front

Intro: David Sankoff
Comparative analysis of organelle genomes, a biologist's view of computational challenges
Franz Lang

Phylogeny and Gene Duplications
Tandy Warnow
9:50   Nir Friedman, Matan Ninio, Itsik Pe'er, Tal Pupko
A Structural EM Algorithm for Phylogenetic Inference
10:15 Coffee Break
10:50 Mathieu Blanchette
Algorithms for Phylogenetic Footprinting
11.15 Miklós Csürös
Fast Recovery of Evolutionary Trees With Thousands of Nodes
11:40 Michael T. Hallett, Jens Lagergren
Efficient Algorithms for Lateral Gene Transfer Problems
12:05 Mengxiang Tang, Michael S. Waterman, Shibu Yooseph
Zinc Finger Gene Clusters and Tandem Gene Duplication
12:30 Lunch Break

Intro: Martin Vingron
Imposing Specificity by Regulated Localization
Mark Ptashne

Sequence Analysis II
Michael Watermann
Abdullah N. Arslan, Ömer Egecioglu, Pavel A. Pevzner
A New Approach to Sequence Comparison: Normalized Sequence Alignment
15:15 Ralf Bundschuh
Rapid Significance Estimation in Local Sequence Alignment With Gaps
15:40 Jeremy Buhler, Martin Tompa
Finding Motifs Using Random Projections
16:15 Coffee Break
16:50 Poster Session
18:50 End of Day

Wednesday April 25, 2001 back to front

Intro: Sorin Istrail
The Distinguished New Technologies Lecture
The Sequence of the Human Genome 
Mark Adams
Martin Vingron
Pavel A. Pevzner, Haixu Tang, Michael S. Waterman
A New Approach to Fragment Assembly in DNA Sequencing
10:15 Coffee Break
10:50 John Kececioglu, Jun Yu
Separating Repeats in DNA Sequence Assembly
11:15 Gene Myers
Comparing Sequence Scaffolds
11:40 Daniel H. Huson, Knut Reinert, Gene Myers
The Greedy Path-Merging Algorithm for Sequence Assembly
12:05 Richard Beigel, Noga Alon, Mehmet Serkan Apaydin, Lance Fortnow, Simon Kasif
An Optimal Procedure for Gap Closing in Whole Genome Shotgun Sequencing
12:30 Lunch Break
14:00 Intro: Ralf Zimmer
Creating the Backbone for the Virtual Cell: Cell Mapping Projects on the Run
Matthias Wilm

Proteomics, RNA Structure
François Major
14:50   Alon Efrat, Frank Hoffmann, Klaus Kriegel, Christof Schultz, Carola Wenk
Geometric Algorithms for the Analysis of 2D-Electrophoresis Gels
15:15 Ting Chen
Gene-Finding Via Tandem Mass Spectrometry
15:40 Guo-Hui Lin, Bin Ma, Kaizhong Zhang
Edit Distance Between Two RNA Structures
16:15 Award Ceremony and Close of Conference
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