Sunday, April 2, 2006
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| 8:00am-4:00pm | Registration open |
| 8:30am-8:45am | Welcome |
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SESSION 1
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| 8:45am-9:10am | Integrated Protein Interaction Networks for 11 Microbes. |
| Balaji Srinivasan, Antal Novak, Jason Flannick, Serafim
Batzoglou and Harley McAdams. |
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9:10am-9:35am
| Hypergraph Model of Multi-residue Interactions in Proteins: Sequentially-constrained Partitioning Algorithms for Optimization of Site-directed Protein Recombination. |
| Xiaoduan Ye, Chris Bailey-Kellogg and Alan Friedman. |
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9:35am-10:00am
| Biological Networks: Comparison, Conservation, and Evolutionary Trees. |
| Benny Chor and Tamir Tuller. |
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10:00am-10:25am
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Assessing Significance of Connectivity and Conservation
in Protein Interaction Networks.
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| Mehmet Koyuturk, Ananth Grama and Wojciech Szpankowski. |
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| 10:25am-10:50am | Coffee |
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SESSION 2
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| 10:50am-11:15am |
Clustering Short Gene Expression Profiles. |
| Ling Wang, Marco Ramoni and Paola Sebastiani. |
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11:15am-11:40pm
| A Patient-Gene Model for Temporal Expression Profiles in
Clinical Studies.
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| Naftali Kaminski and Ziv Bar-Joseph. |
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| 11:40pm-12:35pm | Keynote: Anne-Claude Gavin, EMBL Heidelberg - Germany |
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| 12:35pm-2:00pm | Lunch |
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SESSION 3
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| 2:00pm-2:55pm | Keynote: David Sankoff, University of Ottawa - Canada |
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2:55pm-3:20pm
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An Improved Statistic for Detecting Over-represented Gene
Ontology Annotations in Gene Sets.
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Steffen Grossmann, Sebastian Bauer, Peter N. Robinson and Martin Vingron.
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3:20pm-3:45pm
| Protein Function Annotation Based on Ortholog Clusters Extracted
from Incomplete Genomes Using Combinatorial Optimization.
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| Akshaya Vashist, Casimir Kulikowski and Ilya Muchnik. |
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| 3:45pm-4:10pm | Coffee |
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SESSION 4
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4:10pm-4:35pm
| Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression Data. |
| Jim Huang, Quaid Morris and Brendan Frey. |
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4:35pm-5:00pm
| RNA Secondary Structure Prediction via Energy Density Minimization. |
| Can Alkan, Emre Karakoc, Süleyman Cenk Sahinalp, Peter Unrau, Holger Alex Ebhardt, Kaizhong Zhang and Jeremy Buhler. |
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| 5:00pm-5:25pm | Structural Alignment of Pseudoknotted RNA. |
| Banu Dost, Buhm Han, Shaojie Zhang and Vineet Bafna. |
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SESSION 5
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| 5:30pm-7:30pm | Poster Session A |
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Monday, April 3, 2006
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SESSION 6
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8:30am-9:25am
| Keynote: Michael S. Waterman, University of Southern California - USA |
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| 9:25am-9.50am | CONTRAlign: Discriminative Training for Protein Sequence Alignment |
| Chuong Do, Samuel Gross and Serafim Batzoglou. |
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| 9:50am-10:15am | Clustering Near-Identical Sequences for Fast Homology Search. |
| Michael Cameron, Yaniv Bernstein and Hugh E. Williams. |
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| 10:15am-10:40am | Coffee |
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SESSION 7
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| 10:40am-11:05am | New Methods for Detecting Lineage-specific Selection. |
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Adam Siepel, Katherine Pollard and David Haussler. |
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11:05am-11:30am
| A Probabilistic Model for Gene Content Evolution with Duplication, Loss, and Horizontal Transfer. |
| Miklos Csuros and Istvan Miklos. |
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11:30m-11:55am
| A Sublinear-Time Randomized Approximation Scheme for the Robinson-Foulds Metric. |
| Nicholas Pattengale and Bernard Moret. |
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11:55am-12:20pm
| Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations. |
| Yun Song, Zhihong Ding, Dan Gusfield, Charles Langley and Yufeng Wu. |
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| 12:20pm-2:00pm | Lunch |
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SESSION 8
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| 2:00pm-2:55pm | Keynote: Ajay K Royyuru, IBM T.J. Watson Research Center - USA |
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| 2:55pm-3:20pm |
Efficient Enumeration of Phylogenetically Informative Substrings. |
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Stanislav Angelov, Boulos Harb, Sampath Kannan, Sanjeev Khanna and Junhyong Kim. |
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| 3:20pm-3:45pm |
Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes. |
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Sagi Snir and Lior Pachter. |
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| 3:45pm-4:10pm | Maximal Accurate Forest from Distance Matrices. |
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Constantinos Daskalakis, Cameron Hill, Alexander Jaffe, Radu Mihaescu, Elchanan Mossel and Satish Rao
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| 4:10pm-4:35pm |
Coffee |
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| SESSION 9 |
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| 4:35pm-5:00pm | Leveraging Information Across MHC Alleles/Supertypes Improves MHC-Specific Epitope Prediction. |
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David Heckerman, Carl Kadie and Jennifer Listgarten. |
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| 5:00pm-5:25pm | Improving Prediction of Zinc Binding Sites by Modeling the Linkage between Residues Close in Sequence. |
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Sauro Menchetti, Andrea Passerini, Paolo Frasconi, Claudia Andreini and Antonio Rosato. |
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| 5:25pm-5:50pm |
An Important Connection Between Network Motifs and Parsimony Models.
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| Teresa Przytycka. |
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RECOMB Business Meeting
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| 6:00pm-6:10pm | RECOMB 06 Report |
| Alberto Apostolico |
| 6:10pm-6:20pm | RECOMB 10th Anniversary Presentation |
| Sarah J. Aerni and Eleazar Eskin |
| 6:20pm-6:25pm | RECOMB 07 Announcement |
| Terry Speed |
| 6:25pm-6:35pm | Short Break |
| 6:35pm-7:25pm | Panel: ``Computational Biology: Past Glories / Past Failures / Future
Directions" |
| Alberto Apostolico, David Haussler, Sorin Istrail, Thomas Lengauer, Michal Linial,
Pavel Pevzner, David Sankoff, Ron Shamir, Terry Speed, Michael Waterman |
| 7:25pm-7:40pm | Questions from the Audience |
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Tuesday, April 4, 2006
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| SESSION 10 |
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| 8:30am-9:25am | Keynote: David Haussler, University of California, Santa Cruz - USA |
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| 9:25am-9:50am |
Permutation Filtering: A Novel Concept for Significance Analysis of Large-scale Genomic Data. |
| Stefanie Scheid and Rainer Spang. |
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| 9:50am-10:15am |
Genome-wide Discovery of Modulators of Transcriptional
Interactions in Human B Lymphocytes. |
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Kai Wang, Ilya Nemenman, Nilanjana Banerjee and Andrea Califano.
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| 10:15am-10:40am |
Coffee |
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SESSION 11 |
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| 10:40am-11:05am | A New Approach to Protein Identification.
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Nuno Bandeira, Dekel Tsur, Ari Frank and Pavel Pevzner. |
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| 11:05am-11:30am | Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics. |
| Chakra Chennubhotla and Ivet Bahar. |
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| 11:30am-11:55am |
Simulating Protein Motions with Rigidity Analysis. |
| Shawna Thomas, Xinyu Tang, Lidia Tapia, Nancy M. Amato. |
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| 11:55am-12:20pm | Predicting Experimental Quantities in Protein Folding Kinetics using Stochastic Roadmap Simulation. |
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Tsung-Han Chiang, David Hsu, Mehmet Serkan Apaydin, Douglas L. Brutlag, Jean-Claude Latombe. |
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| 12:20pm-2:00pm | Lunch |
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SESSION 12
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| 2:00pm-2:55pm | Keynote: Carl Zimmer, Science Writer - USA |
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| 2:55pm-3:20pm | Alignment Statistics for Long-Range Correlated Genomic Sequences.
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| Philipp W. Messer, Ralf Bundschuh, Martin Vingron and Peter F. Arndt. |
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| 3:20pm-3:45pm | Simple and Fast Inverse Alignment.
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| John Kececioglu and Eagu Kim. |
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| SESSION 13 |
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| 4:00pm-6:00pm | Poster Session B |
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| 6:30pm-9:30pm | Social Dinner |
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| Wednesday, April 5, 2006 |
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| SESSION 14 |
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| 8:30am-9:25pm | Keynote: Roman Zubarev, Uppsala University - Sweden |
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| 9:25am-9:50am | Motif Yggdrasil: Sampling from a Tree Mixture Model.
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| Samuel A. Andersson and Jens Lagergren. |
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9:50am-10:15am | A Study of Accessible Motifs and RNA Folding Complexity.
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| Ydo Wexler, Chaya Zilberstein and Michal Ziv-Ukelson.
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| 10:15am-10:40am | Coffee |
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| SESSION 15 |
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| 10:40am-11:05am | A Parameterized Algorithm for Protein Structure Alignment.
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| Jinbo Xu, Feng Jiao and Bonnie Berger. |
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| 11:05am-11:30am | Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction.
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Brian Y. Chen, Viacheslav Y. Fofanov, Drew H. Bryant, Bradley D. Dodson, David M. Kristensen, Andreas M. Lisewski, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki.
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| 11:30am-11:55am | A Branch-and-reduce Algorithm for the Contact Map Overlap Problem.
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| Wei Xie and Nikolaos Sahinidis. |
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| 11:55am-12:20pm | A Novel Minimized Dead-End Elimination Criterion and Its Application to Protein Redesign in a Hybrid Scoring and Search Algorithm for Computing Partition Functions over Molecular Ensembles.
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| Ivelin Georgiev, Ryan Lilien and Bruce Donald.
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| 12:20pm-1:45pm |
Lunch |
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SESSION 16
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| 1:45pm-2:25pm |
RECOMB Satellite Panel |
| Genome Technologies, Serafim Batzoglou |
| Computational Proteomics, Vineet Bafna |
| Regulatory Genomics, Eleazar Eskin |
| Genetic Variations, Sorin Istrail |
| Comparative Genomics, David Sankoff and Jens Lagergren |
| System Biology, Ron Shamir |
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| 2:25pm-2:50pm | Sorting by Weighted Reversals, Transpositions, and Inverted Transpositions.
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| Martin Bader and Enno Ohlebusch. |
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| 2:50pm-3:15pm | A Parsimony Approach to Genome-Wide Ortholog Assignment.
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| Zheng Fu, Xin Chen, Vladimir Vacic, Peng Nan, Yang Zhong and Tao Jiang. |
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| 3:15pm-3:40pm | Detecting the Dependent Evolution of Biosequences.
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| Chen-Hsiang Yeang, Jeremy Darot and David Haussler.
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| 3:40pm-3:45pm | Best Poster Award |
| 3:45pm-4:00pm | Sponsor Presentation |
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| 4:00pm | Adjourn |
