08:30
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Registration opens (8:30-10:00: workshop and tutorial participants only)
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10:00
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Workshop 1:
Distributed, High-Performance, and Grid Computing
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Workshop 2:
BioSapiens - Genome Annotation
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Tutorial 1:
Discovering and Interpreting Regulatory DNA Sequence Motifs
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12:00
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Coffee
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12:30
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Workshop 1:
Distributed, High-Performance, and Grid Computing
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Workshop 2:
BioSapiens - Genome Annotation
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Tutorial 1:
Discovering and Interpreting Regulatory DNA Sequence Motifs
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14:00
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Lunch
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15:00
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Workshop 1:
Distributed, High-Performance, and Grid Computing
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Workshop 2:
BioSapiens - Genome Annotation
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Tutorial 3:
Gene and Protein Networks
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Tutorial 4:
Immunological Bioinformatics, Epitope Discovery, and Vaccine Design
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17:00
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Coffee
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17:30
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Workshop 1:
Distributed, High-Performance, and Grid Computing
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Workshop 2:
BioSapiens - Genome Annotation
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Tutorial 3:
Gene and Protein Networks
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Tutorial 4:
Immunological Bioinformatics, Epitope Discovery, and Vaccine Design
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19:00
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Conference opening
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19:30
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Keynote:
Structural Bioinformatics, Cancer and Drug Discovery
Tom Blundell
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20:30
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Multiple Alignment by Sequence Annealing
Ariel S. Schwartz and Lior Pachter
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21:00
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Tandem Repeats over the Edit Distance
Dina Sokol, Gary Benson, and Justin Tojeira
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21:30
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Opening reception
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Monday, 22 January
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07:45
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Registration opens
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08:15
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Algorithms on Splicing Graphs for Identifying and Aligning Alternative Splicing Events
Michael Sammeth and Sylvain Foissac
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08:35
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Reconstructing Sibling Relationships from Microsatellite Data
Saad Sheikh, Tanya Y. Berger-Wolf, Wanpracha Chaovalitwongse, Bhaskar DasGupta, and Mary V. Ashley
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09:00
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Keynote:
Combinatorial Algorithms for Regulatory Network Analysis and Pathway Reconstruction
Richard Karp
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10:00
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Analysis of Binding Site Similarity, Small-Molecule Similarity and Experimental Binding Profiles in the Human Cytosolic Sulfotransferase Family
Rafael J. Najmanovich, Abdellah Allali-Hassani, Richard J. Morris, Ludmila Dombrovsky, Patricia W. Pan, Masoud Vedadi, Alexander N. Plotnikov, Aled Edwards, Cheryl Arrowsmith, and Janet M. Thornton
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Software Demo:
Advanced Micro Devices |
10:30
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Electrostatic Potentials of Proteins in Water: A Structured Continuum Approach
Andreas Hildebrandt, Ralf Blossey, Sergej Rjasanow, Oliver Kohlbacher, and Hans-Peter Lenhof
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11:00
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EBIMed - Text Crunching to Gather Facts for Proteins from Medline
Dietrich Rebholz-Schuhmann, Harald Kirsch, Miguel Arregui, Sylvain Gaudan, Mark Riethoven, and Peter Stoehr
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Software Demo:
Large Scale Pedigree Haplotyper (LSPH)
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11:30
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Coffee
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12:00
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Optimization of Probe Coverage for High-Resolution Oligonucleotide aCGH
Doron Lipson, Zohar Yakhini, and Yonatan Aumann
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Software Demo:
Grid Computing for Bioinformatics
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12:30
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Simultaneous Alignment and Annotation of cis-Regulatory Regions
Abha Singh Bais, Steffen Grossmann, and Martin Vingron
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13:00
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Genetic Code Symmetry and Efficient Design of GC-Constrained Coding Sequences
Matan Gavish, Amnon Peled, and Benny Chor
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Software Demo:
Text Mining as Web Services Provided from the EBI
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13:30
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Discovering Tightly Regulated and Differentially Expressed Gene Sets in Whole Genome Expression Data
Chun Ye and Eleazar Eskin
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14:00
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Lunch
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15:30
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Biological Network Comparison using Graphlet Degree Distribution
Natasa Przulj
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Software Demo:
Selecton: A Web Server for the Detection of Site-Specific Positive Darwinian Selection and Purifying Selection |
16:00
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Identification of Conserved Protein Complexes Based on a Model of Protein Network Evolution
Eitan Hirsh and Roded Sharan
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16:30
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Phylogenetic Reconstruction from Non-Genomic Data
Jose C. Clemente, Kenji Satou, and Gabriel Valiente
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Software Demo:
DeltaProt: Molecular Comparison of Proteins based on Sequence Alignments
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17:00
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Similarities and Differences of Gene Expression in Yeast Stress Conditions
Oleg Rokhlenko, Ydo Wexler, and Zohar Yakhini
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Software Demo:
EVEREST: A Collection of Evolutionary Conserved Protein Domains
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17:30
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Coffee
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18:00
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Keynote:
Principles of Gene Expression Evolution
Naama Barkai
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19:00
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Poster session & reception
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21:30
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Tuesday, 23 January
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07:45
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Registration opens
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08:15
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Inferring Mechanistic Explanations for Transcription Factor Binding Changes
Kenzie D. MacIsaac and Ernest Fraenkel
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08:35
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Refinement and Expansion of Signaling Pathways: The Osmotic Response Network in Yeast
Irit Gat-Viks
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09:00
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Keynote:
Prediction of Protein Structure, Function and Druggability on a Proteomic Scale
Jeffrey Skolnick
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10:00
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Vorolign - Fast Structural Alignment using Voronoi Contacts
Fabian Birzele, Jan Erik Gewehr, Gergely Csaba, and Ralf Zimmer
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Software Demo:
Sun Microsystems, Inc.
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10:30
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Prediction and Simulation of Motion in Pairs of Transmembrane Alpha-Helices
Angela Enosh, Sarel J. Fleishman, Nir Ben-Tal, and Dan Halperin
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11:00
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Rediscovering Secondary Structures as Network Motifs - An Unsupervised Learning Approach
Barak Raveh, Ofer Rahat, Ronen Basri, and Gideon Schreiber
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Software Demo:
Blast2GO v2
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11:30
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Coffee
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12:00
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A Tale of Two Tails: Why are Terminal Residues of Proteins Exposed?
Etai Jacob and Ron Unger
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12:30
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A Novel Pattern Recognition Algorithm to Classify Membrane Protein Unfolding Pathways with High-Throughput Single Molecule Force Spectroscopy
Annalisa Marsico, Dirk Labudde, Tanuj Sapra, Daniel Muller, and Michael Schroeder
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13:00
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Using an Alignment of Fragment Strings for Comparing Protein Structures
Iddo Friedberg, Tim Harder, Rachel Kolodny, Einat Sitbon, Zhanwen Li, and Adam Godzik
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Software Demo:
Agilent CGH Analytics Solution for Comparative Genomic Hybridization Studies
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13:30
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ISIS: Interaction Sites Identified from Sequence
Yanay Ofran and Burkhard Rost
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14:00
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Lunch
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15:30
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Incremental Window-Based Protein Sequence Alignment Algorithms
Huzefa Rangwala and George Karypis
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Software Demo:
CFinder: Locating Cliques and Overlapping Modules in Biological Networks
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16:00
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Designing Patterns for Profile HMM Search
Yanni Sun and Jeremy Buhler
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16:30
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Simulating Multiplexed SNP Discovery Rates using Base-Specific Cleavage and Mass Spectrometry
Sebastian Böcker
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Software Demo:
SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics)
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17:00
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Learning Probabilistic Models of cis-Regulatory Modules that Represent Logical and Spatial Aspects
Keith Noto and Mark Craven
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17:30
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Festive dinner
(Buses leave hotel lobbies at 18:30) |
23:00
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Wednesday, 24 January
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07:45
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Registration opens
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08:15
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PROMO: A Method for Identifying Modules in Protein Interaction Networks
Omer Tamuz,Yaron Singer, and Roded Sharan
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08:35
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Temporal Aspects of Histone-Modifying Proteins Revealed by Sub-network Analysis
Sabine Dietmann, Michael Mader, Hans-Werner Mewes, and Martin Münsterkötter
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09:00
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Keynote:
Evolution Teaches Protein Function Prediction
Burkhard Rost
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10:00
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TOPP - The OpenMS Proteomics Pipeline
Oliver Kohlbacher, Knut Reinert, Clemens Gröpl, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, and Marc Sturm
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Software Demo:
The SimpAT Package: Integrating SIMAP into its own Applications
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10:30
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Difference Detection in LC-MS Data for Protein Biomarker Discovery
Jennifer Listgarten, Radford M. Neal, Sam T. Roweis, Peter Wong, and Andrew Emili
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11:00
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Identifying HLA Supertypes by Learning Distance Functions
Tomer Hertz and Chen Yanover
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Software Demo:
COLOMBO/SIGI-HMM: Prediction of Genomic Islands in Procaryotic Genomes using HMMs
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11:30
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Coffee
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12:00
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A Comparative Genome Approach to Marker Ordering
Thomas Faraut, Simon de Givry, Patrick Chabrier, Thomas Derrien, Francis Galibert, Christophe Hitte, and Thomas Schiex
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Software Demo:
The Scriptome: Protocols for Manipulating Biological Data
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12:30
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Family Relationships: Should Consensus Reign?-Consensus Clustering for Protein Families
Macha Nikolski and David James Sherman
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13:00
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Merging Microarray Cell Synchronization Experiments through Curve Alignment
Filip Hermans and Elena Tsiporkova
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13:30
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A Supervised Approach for Identifying Discriminating Genotype Patterns and its Application to Breast Cancer Data
Nir Yosef, Zohar Yakhini, Anya Tsalenko, Vessela Kristensen, Anne-Lise Børresen-Dale, Eytan Ruppin, and Roded Sharan
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14:00
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Lunch
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15:30
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Inferring Phylogeny from Whole Genomes
Pawel Gorecki and Jerzy Tiuryn
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Software Demo:
Agilent's "Gene Spring" Platform for Gene Expression Studies
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16:00
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Using Median Sets for Inferring Phylogenetic Trees
Matthias Bernt, Daniel Merkle, and Martin Middendorf
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16:30
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Efficient Parsimony-Based Methods for Phylogenetic Network Reconstruction
Guohua Jin, Luay Nakhleh, Sagi Snir, and Tamir Tuller
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Software Demo:
CoryneRegNet:
An Integrative Bioinformatics Platform for the Analysis of Transcription Factors and Regulatory Networks
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17:00
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Phylogeny Reconstruction: Increasing the Accuracy of Pairwise Distance Estimation using Bayesian Inference of Evolutionary Rates
Matan Ninio, Eyal Privman, Tal Pupko, and Nir Friedman
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17:30
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Coffee
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18:00
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Keynote:
Markov Models in Protein Evolution: The Resolvent Method and Family-Specific Rates
Martin Vingron
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19:00
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Closing ceremony & awards
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