RECOMB 2001

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

9:00		 Intro: Thomas Lengauer
The Distinguished Biology Lecture
RNA Biology and the Genome
Phillip Sharp

 		 Protein Structure
Isidore Rigoutsos
9:50
 		 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

14:00		 Intro: Thomas Lengauer
Keynote
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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9:00		 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
9:50
 		 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

13:45		 Intro: Pavel Pevzner
Keynote
Information processing by cells and biologists
Roger Brent

 		 Sequencing by Hybridization
Michal Linial
14:35
 		 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

18:45		 Intro: Thomas Lengauer
Keynote
Genetics and Genomics: Impact on Drug Discovery and Development
Klaus Lindpaintner
20:00 Conference Banquet
Tuesday April 24, 2001 back to front

9:00		 Intro: David Sankoff
Keynote
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

14:00		 Intro: Martin Vingron
Keynote
Imposing Specificity by Regulated Localization
Mark Ptashne

 		 Sequence Analysis II
Michael Watermann
14:50
 		 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

9:00		 Intro: Sorin Istrail
The Distinguished New Technologies Lecture
The Sequence of the Human Genome 
Mark Adams
  Sequencing
Martin Vingron
9:50
 		 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
Keynote
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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