The Ninth Annual International Conference on Research in Computational Molecular Biology

RECOMB 2005 Detailed Agenda

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
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