Saturday, May 14, 2005
|
| 2:00pm-5:00pm |
Treasure Hunt Ice-Breaker |
| 6:30pm-9:30pm |
Opening Reception
Cambridge Hyatt |
 |
Sunday, May 15, 2005
|
| 7:30am-8:30am |
Continental Breakfast |
| 8:30am-8:45am |
Welcome |
| 8:45am-9:10am |
Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks
Jacob Scott, Trey Ideker, Richard M. Karp, Roded Sharan |
| 9:10am-9:35am |
Towards an Integrated Protein-Protein Interaction Network
Ariel Jaimovich, Gal Elidan, Hanah Margalit, Nir Friedman |
| 9:35am-10:00am |
The Factor Graph Network Model for Biological Systems
Irit Gat-Viks, Amos Tanay, Daniela Raijman, Ron Shamir |
| 10:00am-10:25am |
Pairwise Local Alignment of Protein Interaction Networks Guided by Models of Evolution
Mehmet Koyutürk, Ananth Grama, Wojciech Szpankowski |
| 10:25am-10:50am |
Coffee |
| 10:50am-11:15am |
Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate Model
Brendan J. Frey, Quaid D. Morris, Mark Robinson, Timothy R. Hughes |
| 11:15am-11:40pm |
Efficient Calculation of Interval Scores for DNA Copy Number Data Analysis
Doron Lipson, Yonatan Aumann, Amir Ben-Dor, Nathan Linial, Zohar Yakhini |
| 11:40pm-12:35pm |
Keynote: A Regulatory Network Controlling Drosophila Development
Mike Levine, University of California, Berkeley |
| 12:35pm-2:00pm |
Lunch |
| 2:00pm-2:55pm |
Keynote: Yeast Cells as a Discovery Platform for Neurodegenerative Disease
Susan Lindquist, Whitehead Institute for Biomedical Research |
| 2:55pm-3:20pm |
RIBRA - An Error-Tolerant Algorithm for the NMR Backbone Assignment Problem
Kuen-Pin Wu, Jia-Ming Chang, Jun-Bo Chen, Chi-Fon Chang, Wen-Jin Wu, Tai-Huang Huang, Ting-Yi Sung, Wen-Lian Hsu |
| 3:20pm-3:45pm |
Avoiding Local Optima in Single Particle Reconstruction
Marshall Bern, Jindong (JD) Chen, Hao Chi Wong |
| 3:45pm-4:10pm |
Coffee |
| 4:10pm-4:35pm |
A High-Throughput Approach for Associating MicroRNAs with Their Activity Conditions
Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson, Ron Y. Pinter, Zohar Yakhini |
| 4:35pm-5:00pm |
RNA-RNA Interaction Prediction and Antisense RNA Target Search
Can Alkan, Emre Karako_, Joseph H. Nadeau, S. Cenk Sahinalp, Kaizhong Zhang
|
| 5:00pm-5:25pm |
Consensus Folding of Unaligned RNA Sequences Revisited
Vineet Bafna, Haixu Tang, Shaojie Zhang
|
| 5:30pm-7:30pm |
Poster Session A |
|
Monday, May 16, 2005
|
| 7:30am-8:30am |
Continental Breakfast |
| 8:30am-9:25am |
Keynote: Discovery and Annotation of Genetic Modules
2005 Award Recipient The Stanislaw Ulam Memorial Computational Biology Lecture
Charles DeLisi, Boston University |
| 9:25am-9:50am |
Efficient
q-Gram Filters
for Finding
All ε-Matches
over a Given
Length
Kim Roland Rasmussen, Jens Stoye, Eugene W. Myers |
| 9:50am-10:15am |
A Polynomial Time Solvable Formulation of Multiple Sequence Alignment
Sing-Hoi Sze, Yue Lu, Qingwu Yang |
| 10:15am-10:40am |
Coffee |
| 10:40am-11:05am |
A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible Characters
Dan Gusfield, Vikas Bansal
|
| 11:05am-11:30am |
Reconstruction of Reticulate Networks from Gene Trees
Daniel H. Huson, Tobias Kloepper, Pete J. Lockhart, Mike A. Steel
|
| 11:30am-11:55am |
A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction
Dannie Durand, Bjarni V. Halld_rsson, Benjamin Vernot |
| 11:55am-12:20pm |
Constructing a Smallest Refining Galled Phylogenetic Network
Trinh N.D. Huynh, Jesper Jansson, Nguyen Bao Nguyen, Wing-Kin Sung |
| 12:20pm-2:00pm |
Lunch |
| 2:00pm-2:55pm |
Keynote: Mapping Molecular Landscapes Inside Cells
Wolfgang Baumeister, Max-Planck Institute of Biochemistry |
| 2:55pm-3:20pm |
Information Theoretic Approaches to Whole Genome Phylogenies
David Burstein, Igor Ulitsky, Tamir Tuller, Benny Chor |
| 3:20pm-3:45pm |
Maximum Likelihood of Evolutionary Trees is Hard
Benny Chor, Tamir Tuller |
| 3:45pm-4:10pm |
Graph Theoretical Insights into Evolution of Multidomain Proteins
Teresa Przytycka, George Davis, Nan Song, Dannie Durand |
| 4:10pm-4:35pm |
Coffee |
| 4:35pm-5:00pm |
Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry
Ari Frank, Stephen Tanner, Pavel Pevzner |
| 5:00pm-5:25pm |
A Hidden Markov Model Based Scoring Function for Mass Spectrometry Database Search
Yunhu Wan, Ting Chen |
| 5:25pm-5:50pm |
EigenMS: De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning
Marshall Bern, David Goldberg |
| 6:00pm-7:00pm |
RECOMB Business
Meeting |
|
Tuesday, May 17, 2005
|
| 7:30am-8:30am |
Continental Breakfast |
| 8:00am-4:00pm |
Registration Open |
| 8:30am-9:25am |
Keynote: Biology as Information
Eric S. Lander, Broad Institute of MIT and Harvard |
| 9:25am-9:50am |
Using Multiple Alignments to Improve Gene Prediction
Samuel S. Gross, Michael R. Brent |
| 9:50am-10:15am |
Learning Interpretable SVMs for Biological Sequence Classification
Soren Sonnenburg, Gunnar Rätsch, Christin Schäfer
|
| 10:15am-10:40am |
Coffee |
| 10:40am-11:05am |
Segmentation Conditional Random Fields (SCRFs): A New Approach for Protein Fold Recognition
Yan Liu, Jaime Carbonell, Peter Weigele, Vanathi Gopalakrishnan |
| 11:05am-11:30am |
Rapid Protein Side-Chain Packing via Tree Decomposition
Jinbo Xu |
| 11:30am-11:55am |
Recognition of Binding Patterns Common to a Set of Protein Structures
Maxim Shatsky, Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson |
| 11:55am-12:20pm |
Predicting Protein-Peptide Binding Affinity by Learning Peptide-Peptide Distance Functions
Chen Yanover, Tomer Hertz
|
| 12:20pm-2:00pm |
Lunch |
| 2:00pm-2:55pm |
Keynote: Amino Acid Sequence Control of the Folding of Parallel β-Helix, the Simplext β -Sheet Fold
2005 Award Recipient The Distinguished Biology Lecture
Jonathan King, MIT
|
| 2:55pm-3:20pm |
A Practical Approach to Significance Assessment in Alignment with Gaps
Nicholas Chia, Ralf Bundschuh
|
| 3:20pm-3:45pm |
Alignment of Optical Maps
Anton Valouev, Lei Li, Yu-Chi Liu, David C. Schwartz, Yi Yang, Yu Zhang, Michael S. Waterman
|
| 4:00pm-6:00pm |
Poster Session B |
| 6:30pm-9:30pm |
Boston Museum of Science Party |
|
Wednesday, May 18, 2005
|
| 7:30am-8:30am |
Continental Breakfast |
| 8:30am-2:00pm |
Registration
Open |
| 8:30am-9:25pm |
Keynote: Engineering Gene Regulatory Networks: A Reductionist Approach to Systems Biology
James J. Collins, Boston University |
| 9:25am-9:50am |
Modeling the Combinatorial Functions of Multiple Transcription Factors
Chen-Hsiang Yeang, Tommi Jaakkola |
| 9:50am-10:15am |
Predicting Transcription Factor Binding Sites Using Structural Knowledge
Tommy Kaplan, Nir Friedman, Hanah Margalit |
| 10:15am-10:40am |
Motif Discovery through Predictive Modeling of Gene Regulation
Manuel Middendorf, Anshul Kundaje, Mihir Shah, Yoav Freund, Chris H. Wiggins, Christina Leslie |
| 10:40am-11:05am |
Coffee |
| 11:05am-11:30am |
HAPLOFREQ - Estimating Haplotype Frequencies Efficiently
Eran Halperin, Elad Hazan |
| 11:30am-11:55am |
Improved Recombination Lower Bounds for Haplotype Data
Vineet Bafna, Vikas Bansal
|
| 11:55am-12:20pm |
A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem
Zhihong Ding, Vladimir Filkov, Dan Gusfield |
| 12:20pm-1:30pm |
Lunch |
| 1:30pm-2:25pm |
Keynote: Human Genome Sequence Variation and the Inherited Basis of Common Disease
David Altshuler, Broad Institute of MIT and Harvard/MGH
|
| 2:25pm-2:50pm |
Stability of Rearrangement Measures in the Comparison of Genome Sequences
David Sankoff, Matthew Mazowita
|
| 2:50pm-3:15pm |
On Sorting by Translocations
Anne Bergeron, Julia Mixtacki, Jens Stoye
|
| 3:15pm-3:35pm |
Awards Ceremony |
| 3:35pm |
Adjourn |
|
