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Click here for schedule-at-a-glance
The schedule may be modified as a result of the change in the conference dates
Sunday, 21 January
08:30
Registration opens (8:30-10:00: workshop and tutorial participants only)
10:00
Workshop 1:

Distributed, High-Performance, and Grid Computing

Workshop 2:

BioSapiens - Genome Annotation

Tutorial 1:

Discovering and Interpreting Regulatory DNA Sequence Motifs

12:00
Coffee
12:30
Workshop 1:

Distributed, High-Performance, and Grid Computing

Workshop 2:

BioSapiens - Genome Annotation
Tutorial 1:

Discovering and Interpreting Regulatory DNA Sequence Motifs

14:00
Lunch
15:00
Workshop 1:

Distributed, High-Performance, and Grid Computing
Workshop 2:

BioSapiens - Genome Annotation
Tutorial 3:

Gene and Protein Networks
Tutorial 4:

Immunological Bioinformatics, Epitope Discovery, and Vaccine Design

17:00
Coffee
17:30
Workshop 1:

Distributed, High-Performance, and Grid Computing
Workshop 2:

BioSapiens - Genome Annotation
Tutorial 3:

Gene and Protein Networks
Tutorial 4:

Immunological Bioinformatics, Epitope Discovery, and Vaccine Design

19:00
Conference opening
19:30
Keynote:
Structural Bioinformatics, Cancer and Drug Discovery

Tom Blundell


20:30
Multiple Alignment by Sequence Annealing

Ariel S. Schwartz and Lior Pachter

21:00

Tandem Repeats over the Edit Distance

Dina Sokol, Gary Benson, and Justin Tojeira

21:30
Opening reception

Perle bleue
The best product on the market!
https://www.e-odchudzanie.com.pl/nl/perle-bleue-opinies.html
Monday, 22 January
07:45
Registration opens
08:15
Algorithms on Splicing Graphs for Identifying and Aligning Alternative Splicing Events

Michael Sammeth and Sylvain Foissac

08:35
Reconstructing Sibling Relationships from Microsatellite Data

Saad Sheikh, Tanya Y. Berger-Wolf, Wanpracha Chaovalitwongse, Bhaskar DasGupta, and Mary V. Ashley

09:00
Keynote:
Combinatorial Algorithms for Regulatory Network Analysis and Pathway Reconstruction

Richard Karp


10:00
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

Software Demo:
Advanced Micro Devices

10:30
Electrostatic Potentials of Proteins in Water: A Structured Continuum Approach

Andreas Hildebrandt, Ralf Blossey, Sergej Rjasanow, Oliver Kohlbacher, and Hans-Peter Lenhof

11:00

EBIMed - Text Crunching to Gather Facts for Proteins from Medline

Dietrich Rebholz-Schuhmann, Harald Kirsch, Miguel Arregui, Sylvain Gaudan, Mark Riethoven, and Peter Stoehr

Software Demo:
Large Scale Pedigree Haplotyper (LSPH)
11:30
Coffee
12:00
Optimization of Probe Coverage for High-Resolution Oligonucleotide aCGH

Doron Lipson, Zohar Yakhini, and Yonatan Aumann

Software Demo:
Grid Computing for Bioinformatics
12:30
Simultaneous Alignment and Annotation of cis-Regulatory Regions

Abha Singh Bais, Steffen Grossmann, and Martin Vingron

13:00
Genetic Code Symmetry and Efficient Design of GC-Constrained Coding Sequences

Matan Gavish, Amnon Peled, and Benny Chor

Software Demo:
Text Mining as Web Services Provided from the EBI
13:30
Discovering Tightly Regulated and Differentially Expressed Gene Sets in Whole Genome Expression Data

Chun Ye and Eleazar Eskin

14:00
Lunch
15:30
Biological Network Comparison using Graphlet Degree Distribution

Natasa Przulj

Software Demo:
Selecton: A Web Server for the Detection of Site-Specific Positive Darwinian Selection and Purifying Selection
16:00
Identification of Conserved Protein Complexes Based on a Model of Protein Network Evolution

Eitan Hirsh and Roded Sharan

16:30
Phylogenetic Reconstruction from Non-Genomic Data

Jose C. Clemente, Kenji Satou, and Gabriel Valiente

Software Demo:
DeltaProt: Molecular Comparison of Proteins based on Sequence Alignments
17:00
Similarities and Differences of Gene Expression in Yeast Stress Conditions

Oleg Rokhlenko, Ydo Wexler, and Zohar Yakhini

Software Demo:
EVEREST: A Collection of Evolutionary Conserved Protein Domains
17:30
Coffee
18:00
Keynote:
Principles of Gene Expression Evolution

Naama Barkai

19:00
Poster session & reception
21:30

Tuesday, 23 January
07:45
Registration opens
08:15
Inferring Mechanistic Explanations for Transcription Factor Binding Changes

Kenzie D. MacIsaac and Ernest Fraenkel

08:35
Refinement and Expansion of Signaling Pathways: The Osmotic Response Network in Yeast

Irit Gat-Viks

09:00
Keynote:
Prediction of Protein Structure, Function and Druggability on a Proteomic Scale

Jeffrey Skolnick


10:00
Vorolign - Fast Structural Alignment using Voronoi Contacts

Fabian Birzele, Jan Erik Gewehr, Gergely Csaba, and Ralf Zimmer

Software Demo:
Sun Microsystems, Inc.

10:30
Prediction and Simulation of Motion in Pairs of Transmembrane Alpha-Helices

Angela Enosh, Sarel J. Fleishman, Nir Ben-Tal, and Dan Halperin

11:00
Rediscovering Secondary Structures as Network Motifs - An Unsupervised Learning Approach

Barak Raveh, Ofer Rahat, Ronen Basri, and Gideon Schreiber

Software Demo:
Blast2GO v2
11:30
Coffee
12:00
A Tale of Two Tails: Why are Terminal Residues of Proteins Exposed?

Etai Jacob and Ron Unger


12:30
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


13:00
Using an Alignment of Fragment Strings for Comparing Protein Structures

Iddo Friedberg, Tim Harder, Rachel Kolodny, Einat Sitbon, Zhanwen Li, and Adam Godzik

Software Demo:
Agilent CGH Analytics Solution for Comparative Genomic Hybridization Studies
13:30
ISIS: Interaction Sites Identified from Sequence

Yanay Ofran and Burkhard Rost

14:00
Lunch
15:30
Incremental Window-Based Protein Sequence Alignment Algorithms

Huzefa Rangwala and George Karypis

Software Demo:
CFinder: Locating Cliques and Overlapping Modules in Biological Networks

16:00
Designing Patterns for Profile HMM Search

Yanni Sun and Jeremy Buhler

16:30
Simulating Multiplexed SNP Discovery Rates using Base-Specific Cleavage and Mass Spectrometry

Sebastian Böcker

Software Demo:
SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics)
17:00
Learning Probabilistic Models of cis-Regulatory Modules that Represent Logical and Spatial Aspects

Keith Noto and Mark Craven

17:30
Festive dinner
(Buses leave hotel lobbies at 18:30)
23:00

Wednesday, 24 January
07:45
Registration opens
08:15
PROMO: A Method for Identifying Modules in Protein Interaction Networks

Omer Tamuz,Yaron Singer, and Roded Sharan

08:35
Temporal Aspects of Histone-Modifying Proteins Revealed by Sub-network Analysis

Sabine Dietmann, Michael Mader, Hans-Werner Mewes, and Martin Münsterkötter

09:00
Keynote:
Evolution Teaches Protein Function Prediction

Burkhard Rost


10:00
TOPP - The OpenMS Proteomics Pipeline

Oliver Kohlbacher, Knut Reinert, Clemens Gröpl, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, and Marc Sturm

Software Demo:
The SimpAT Package: Integrating SIMAP into its own Applications
10:30
Difference Detection in LC-MS Data for Protein Biomarker Discovery

Jennifer Listgarten, Radford M. Neal, Sam T. Roweis, Peter Wong, and Andrew Emili

11:00
Identifying HLA Supertypes by Learning Distance Functions

Tomer Hertz and Chen Yanover

Software Demo:
COLOMBO/SIGI-HMM: Prediction of Genomic Islands in Procaryotic Genomes using HMMs
11:30
Coffee
12:00
A Comparative Genome Approach to Marker Ordering

Thomas Faraut, Simon de Givry, Patrick Chabrier, Thomas Derrien, Francis Galibert, Christophe Hitte, and Thomas Schiex

Software Demo:
The Scriptome: Protocols for Manipulating Biological Data
12:30
Family Relationships: Should Consensus Reign?-Consensus Clustering for Protein Families

Macha Nikolski and David James Sherman

13:00
Merging Microarray Cell Synchronization Experiments through Curve Alignment

Filip Hermans and Elena Tsiporkova


13:30
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

14:00
Lunch
15:30
Inferring Phylogeny from Whole Genomes

Pawel Gorecki and Jerzy Tiuryn

Software Demo:
Agilent's "Gene Spring" Platform for Gene Expression Studies

16:00
Using Median Sets for Inferring Phylogenetic Trees

Matthias Bernt, Daniel Merkle, and Martin Middendorf

16:30
Efficient Parsimony-Based Methods for Phylogenetic Network Reconstruction

Guohua Jin, Luay Nakhleh, Sagi Snir, and Tamir Tuller

Software Demo:
CoryneRegNet:
An Integrative Bioinformatics Platform for the Analysis of Transcription Factors and Regulatory Networks

17:00
Phylogeny Reconstruction: Increasing the Accuracy of Pairwise Distance Estimation using Bayesian Inference of Evolutionary Rates

Matan Ninio, Eyal Privman, Tal Pupko, and Nir Friedman

17:30
Coffee
18:00
Keynote:
Markov Models in Protein Evolution: The Resolvent Method and Family-Specific Rates

Martin Vingron

19:00
Closing ceremony & awards