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Below is the list of papers accepted to ECCB 2006 for frontal presentation.
36 papers have been accepted out of 197 submitted (18% ratio).

Sequence Analysis I, Sun., January 21, 20:30-21:30

Ariel S. Schwartz and Lior Pachter. Multiple Alignment by Sequence Annealing
Dina Sokol, Gary Benson, and Justin Tojeira. Tandem Repeats over the Edit Distance

Early-Bird Session -- Late-Breaking Results, Mon., January 22, 8:15-8:55
Michael Sammeth and Sylvain Foissac. Algorithms on Splicing Graphs for Identifying and Aligning Alternative Splicing Events
Saad Sheikh, Tanya Y. Berger-Wolf, Wanpracha Chaovalitwongse, Bhaskar DasGupta, and Mary V. Ashley. Reconstructing Sibling Relationships from Microsatellite Data

Molecular Recognition and Computer Aided Drug Design, Mon., January 22, 10:00-11:30

Rafael J. Najmanovich, Abdellah Allali-Hassani, Richard J. Morris, Ludmila Dombrovsky, Patricia W. Pan, Masoud Vedadi, Alexander N. Plotnikov, Cheryl Arrowsmith, Aled Edwards, and Janet M. Thornton. Analysis of Binding Site Similarity, Small-Molecule Similarity and Experimental Binding Profiles in the Human Cytosolic Sulfotransferase Family
Andreas Hildebrandt, Ralf Blossey, Sergej Rjasanow, Oliver Kohlbacher, and Hans-Peter Lenhof. Electrostatic Potentials of Proteins in Water: A Structured Continuum Approach
Dietrich Rebholz-Schuhmann, Harald Kirsch, Miguel Arregui, Sylvain Gaudan, Mark Riethoven and Peter Stoehr. EBIMed Text Crunching to Gather Facts for Proteins from Medline

Computational Genomics I, Mon., January 22, 12:00-14:00

Doron Lipson, Zohar Yakhini, and Yonatan Aumann. Optimization of Probe Coverage for High-Resolution Oligonucleotide aCGH
Abha Singh Bais, Steffen Grossmann, and Martin Vingron. Simultaneous Alignment and Annotation of cis-Regulatory Regions
Matan Gavish, Amnon Peled, and Benny Chor. Genetic Code Symmetry and Efficient Design of GC-Constrained Coding Sequences
Chun Ye and Eleazar Eskin. Discovering Tightly Regulated and Differentially Expressed Gene Sets in Whole Genome Expression Data

Networks, Pathways and Systems, Mon., January 22, 15:30-18:00

Natasa Przulj. Biological Network Comparison Using Graphlet Degree Distribution
Eitan Hirsh and Roded Sharan. Identification of Conserved Protein Complexes Based on a Model of Protein Network Evolution
Jose C. Clemente, Kenji Satou, and Gabriel Valiente. Phylogenetic Reconstruction from Non-Genomic Data
Oleg Rokhlenko, Ydo Wexler, and Zohar Yakhini. Similarities and Differences of Gene Expression in Yeast Stress Conditions

Early-Bird Session -- Late-Breaking Results, Tue., January 23, 8:15-8:55
Kenzie D. MacIsaac and Ernest Fraenkel. Inferring Mechanistic Explanations for Transcription Factor Binding Changes
Irit Gat-Viks. Refinement and Expansion of Signaling Pathways: The Osmotic Response Network in Yeast

Structural Bioinformatics I, Tue., January 23, 10:00-11:30

Fabian Birzele, Jan Erik Gewehr, Gergely Csaba, and Ralf Zimmer. Vorolign - Fast Structural Alignment Using Voronoi Contacts
Angela Enosh, Sarel J. Fleishman, Nir Ben-Tal, and Dan Halperin. Prediction and Simulation of Motion in Pairs of Transmembrane Alpha-Helices
Barak Raveh, Ofer Rahat, Ronen Basri, and Gideon Schreiber. Rediscovering Secondary Structures as Network Motifs - An Unsupervised Learning Approach

Structural Bioinformatics II, Tue., January 23, 12:00-14:00

Etai Jacob and Ron Unger. A Tale of Two Tails: Why are Terminal Residues of Proteins Exposed?
Annalisa Marsico, Dirk Labudde, Tanuj Sapra, Daniel Muller, and Michael Schroeder. A Novel PatterR recognition Algorithm to Classify Membrane Protein Unfolding Pathways with High-Throughput Single Molecule Force Spectroscopy
Iddo Friedberg, Tim Harder, Rachel Kolodny, Einat Sitbon, Zhanwen Li, and Adam Godzik. Using an Alignment of Fragment Strings for Comparing Protein Structures
Yanay Ofran and Burkhard Rost. ISIS: Interaction Sites Identified from Sequence

Sequence Analysis II, Tue., January 23, 15:30-17:30

Huzefa Rangwala and George Karypis. Incremental Window-Based Protein Sequence Alignment Algorithms
Yanni Sun and Jeremy Buhler. Designing Patterns for Profile HMM Search
Sebastian Böcker. Simulating Multiplexed SNP Discovery Rates using Base-Specific Cleavage and Mass Spectrometry
Keith Noto and Mark Craven. Learning Probabilistic Models of cis-Regulatory Modules that Represent Logical and Spatial Aspects

Early-Bird Session -- Late-Breaking Results, Wed., January 24, 8:15-8:55
Omer Tamuz,Yaron Singer, and Roded Sharan. PROMO: A Method for Identifying Modules in Protein Interaction Networks
Sabine Dietmann, Michael Mader, Hans-Werner Mewes, and Martin Münsterkötter.
Temporal Aspects of Histone-Modifying Proteins Revealed by Sub-network Analysis

Proteomics, Wed., January 24, 10:00-11:30

Oliver Kohlbacher, Knut Reinert, Clemens Gröpl, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, and Marc Sturm. TOPP - The OpenMS Proteomics Pipeline
Jennifer Listgarten, Radford M. Neal, Sam T. Roweis, Peter Wong, and Andrew Emili. Difference Detection in LC-MS Data for Protein Biomarker Discovery
Tomer Hertz and Chen Yanover. Identifying HLA Supertypes by Learning Distance Functions

Comparative and Computational Genomics, Wed., January 24, 12:00-14:00

Thomas Faraut, Simon de Givry, Patrick Chabrier, Thomas Derrien, Francis Galibert, Christophe Hitte, and Thomas Schiex. A Comparative Genome Approach to Marker Ordering
Macha Nikolski and David James Sherman. Family Relationships: Should Consensus Reign?-Consensus Clustering for Protein Families
Filip Hermans and Elena Tsiporkova. Merging Microarray Cell Synchronization Experiments Through Curve Alignment

Nir Yosef, Zohar Yakhini, Anya Tsalenko, Vessela Kristensen, Anne-Lise Børresen-Dale, Eytan Ruppin, and Roded Sharan. A Supervised Approach for Identifying Discriminating Genotype Patterns and its Application to Breast Cancer Data


Evolution and Phylogenetics, Wed., January 24, 15:30-17:30

Pawel Gorecki and Jerzy Tiuryn. Inferring Phylogeny from Whole Genomes
Matthias Bernt, Daniel Merkle, and Martin Middendorf. Using Median Sets for Inferring Phylogenetic Trees
Guohua Jin, Luay Nakhleh, Sagi Snir, and Tamir Tuller. Efficient Parsimony-Based Methods for Phylogenetic Network Reconstruction
Matan Ninio, Eyal Privman, Tal Pupko, and Nir Friedman. Phylogeny Reconstruction: Increasing the Accuracy of Pairwise Distance Estimation Using Bayesian Inference of Evolutionary Rates