Saturday September 27                                        sunday 28th      monday 29th      tuesday 30th         

• 9h30 Registration opens, welcome coffee
• 12h-13h Light buffet

• 13h15-13h30 Welcoming speeches
• 13h30-14h20 Invited talk
  Chair: Shoshana Wodak
  Thomas Lengauer    Analyzing resistance phenomena in HIV with bioinformatics methods

• 14h20-14h45 A description of dynamical graphs associated to elementary regulatory circuits
  Elisabeth Rémy, Brigitte Mossé, Claudine Chaouiya, Denis Thieffry
• 14h45-15h00 Using ChIP data to decipher regulatory logic of MBF and SBF during the Yeast cell cycle
  Feng Gao, Harmen Bussemaker
• 15h00-15h15 Validation of noisy dynamical system models of gene regulation inferred from time-course gene expression data at arbitrary time intervals Michiel de Hoon, Sascha Ott, Seiya Imoto, Satoru Miyano
• 15h15-15h30 Accuracy of the models for gene regulation - a comparison of two modeling methods
  Kimmo Palin

• 15h30-16h10 Break

Contributed talks - Genetic networks and gene expression
Chair: Stéphane Robin

• 16h10-16h35 Extracting active pathways from gene expression data
  Jean-Philippe Vert, Minoru Kanehisa
• 16h35-17h00 Gene networks inference using dynamic Bayesian networks
  Bruno-Edouard Perrin, Liva Ralaivola, Florence d'Alché-Buc, Samuele Bottani, Aurélien Mazurie
• 17h00-17h25 Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection
  Yoshinori Tamada, Sunyong Kim, Hideo Bannai, Seiya Imoto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
• 17h25-17h50 Biclustering microarray data by Gibbs sampling
  Qizheng Sheng, Yves Moreau, Bart De Moor
• 17h50-18h15 Discover significant rules for classifying cancer Diagnosis Data
  Jinyan Li, Huiqing Liu, See-Kiong Ng, Limsoon Wong
  

• 19h-22h Cocktail at "Le Palais de la Découverte"
  (Avenue Franklin Roosevelt near the Champs Elysées)
  

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Sunday September 28                                       saturday 27th       monday 29th      tuesday 30th         

• 9h-9h50 Invited talk
  Chair: Satoru Miyano
  Nir Friedman    Models for identifying regulation networks

Contributed talks - Gene expression and motifs
Chair: Alvis Brazma

• 9h50-10h15 The shortest common supersequence problem in a microarray production setting
  Sven Rahmann
• 10h15-10h40 Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites
  Christoph Dieterich, Ralf Herwig, Martin Vingron

Flash presentations - Genetic networks and gene expression
Chair: Alvis Brazma

• 10h40-10h45 Graph theory based methodology for comparing interaction networks between genes across organisms
  Gaëlle Lelandais, Pierre Vincens, Claude Jacq, Stéphane Vialette
• 10h45-10h50 Spotting effects in cDNA experiments
  T. Mary-Huard, S. Robin, J.-J. Daudin
• 10h50-10h55 Design of a clinical microarray chip
  Jochen Jäger, Rainer Spang
• 10h55-11h00 Classification of cancers by gene expression profiles from peripheral blood
  Andrey Loboda, Michael Nebozhyn, Steven W. Johnson, Peter J. O'Dwyer, Calen Nichols, Linda Alila, Louise C. Showe, Michael K. Showe

• 11h00-11h45 Posters and break

Contributed talks - Gene expression and motifs
Chair: Philipp Bucher

• 11h45-12h00 Modular decision system and information integration for improved disease outcome prediction
  Matthias Futschik, Mi Sullivan, Anthony Reeve, Nikola Kasabov
• 12h00-12h15 Genomic distribution of short motifs involved in DNA repair in pathogenic and non pathogenic Escherichia coli
  Isabelle Bourgait, Hélène Chiapello, Christelle Hennequet-Antier, Stéphane Robin, Sophie Schbath, Alexandra Gruss, Meriem El Karoui
• 12h15-12h40 Searching for statistically significant regulatory modules
  Timothy Bailey, William Noble
• 12h40-13h05 Computational detection of cis-regulatory modules
  Stein Aerts, Peter Van Loo, Gert Thijs, Yves Moreau, Bart De Moor

• 13h05-14h30 Lunch

• 14h30-15h20 Invited talk
  Chair: James McInerney
  Hiroshi Akashi   Metabolic economics and microbial proteome evolution

Contributed talks - Gene expression and motifs
Chair: Michal Linial

• 15h20-15h45 Finding subtle motifs by branching from sample strings
  Alkes Price, Sriram Ramabhadran, Pavel Pevzner
• 15h45-16h10 Finding optimal degenerate patterns in DNA sequences
  Daisuke Shinozaki, Tatsuya Akutsu, Osamu Maruyama

Flash presentations - Motifs, protein-protein interactions and proteomics
Chair: Michal Linial

• 16h10-16h15 Automatic procedures for compilation of promoter sequences and their evaluation based on signal content and positional distributions Christoph S. Schmid, Viviane Praz, Mauro Delorenzi, Rouaida Perier, Philipp Bucher
• 16h15-16h20 Modeling the Rho dependent transcription termination sites in the bacterium Helicobacter pylori
  Lisa Petersen, Anders Krogh
• 16h20-16h25 GENOFRAG: A software to design primers optimized for whole genome scanning by long-range PCR amplification. Application to the study of Staphylococcus aureaus genome plasticity
  Nouri Ben Zakour, Michel Gautier, Rumen Andonov, Dominique Lavenier, Philippe Veber, Alexeï Sorokin, Yves Le Loir
• 16h25-16h30 ISYMOD: A Knowledge Base for integrated system modeling
  Julie Chabalier, Yves Quentin, Cécile Capponi, Gwennaele Fichant
• 16h30-16h35 PARIS: a system for 2-DE based proteomic data management
  Juhui Wang, Christophe Caron, Michel-Yves Mistou, Christophe Gitton, Alain Trubuil

• 16h35-17h15 Posters and break

Contributed talks - Proteomics and repeats
Chair: Graziano Pesole

• 17h15-17h40 A Suffix Tree approach to the interpretation of tandem mass spectra: Applications to peptides of nonspecific digestion and post-translational modifications Bingwen Lu, Ting Chen
• 17h40-18h05 Inferring strengths of protein-protein interactions from experimental data using linear programming
  Morihiro Hayashida, Nobuhisa Ueda, Tatsuya Akutsu
• 18h05-18h20 Overview of a software pipeline dedicated to automatic MS/MS data analysis
  Erwan Reguer, Estelle Nugues, Romain Cahuzac
• 18h20-18h35 Resources for bacterial strain identification Using polymorphic tandem repeats
  France Denoeud, Gilles Vergnaud
• 18h35-18h50 Detecting short inverted segments in a biological sequence
  David Robelin, Bernard Prum

• 19h30-dawn Gala Diner
  

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Monday September 29                                                  saturday 27th      sunday 28th      tuesday 30th         

• 9h-9h50 Invited talk
  Chair: Anna tramontano
  Janet Thornton   The proteome and the metabolome

Contributed talks - Metabolic networks and RNAs
Chair: Martin Vingron

• 9h50-10h15 Ab initio reconstruction of metabolic pathways
  Frédéric Boyer, Alain Viari
• 10h15-10h40 A rapid method for detection of putative RNAi target genes in genomic data
  Yair Horesh, Amihood Amir, Shulamit Michaeli, Ron Unger

Flash presentations - Systems biology and RNAs
Chair: Martin Vingron

• 10h40-10h45 The Biochemical Abstract Machine BIOCHAM
  Nathalie Chabrier, François Fages
• 10h45-10h50 Relevance of the secondary structure of messenger RNA: a statistical study
  Fabrice Thalmann, Hervé Isambert
• 10h50-10h55 Searching for ncRNAs in protist genomes
  Lesley J. Collins, Thomas J. Macke, David Penny
• 10h55-11h00 Computational detection of MicroRNAs in animal genomes
  Matthieu Legendre, Daniel Gautheret

• 11h-11h45 Posters and break

Contributed talks - RNAs and gene finding
Chair: SØren Brunak

• 11h45-12h00 Annotating animal mitochondrial tRNAs: an experimental evaluation of four methods
  Stacia Wyman, Jeffrey Boore
• 12h00-12h15 Searching the Saccharomyces cerevisiae genome for -1 frameshifting sites
  Michaël Bekaert, Jean-Paul Forest, Laure Bidou, Alain Denise, Guillemette Duchateau-Nguyen, Céline Fabret, Christine Froidevaux, Isabelle Hatin, Jean-Pierre Rousset, Michel Termier
• 12h15-12h40 Fast feature selection using a simple Estimation of Distribution Algorithm : A case study on splice site prediction Yvan Saeys, Sven Degroeve, Dirk Aeyels, Yves Van de Peer, Pierre Rouzé
• 12h40-13h05 HMM sampling and applications to gene finding and alternative splicing
  Simon Cawley, Lior Pachter

• 13h05-14h30 Lunch

• 14h30-15h20 Invited talk
  Chair: Daniel Gautheret
  Jürgen Brosius How significant is 98.5% "junk" in mammalian genomes ?

Contributed talks - Sequence analysis and gene finding
Chair: Roderic GuigÓ

• 15h20-15h45 Modelling sequencing errors by combining Hidden Markov Models
  Claudio Lottaz, Christian Iseli, C. Victor Jongeneel, Philipp Bucher
• 15h45-16h10 Gene prediction with a Hidden Markov Model and new intron submodel
  Mario Stanke, Stephan Waack

Flash presentations - Functional genomics
Chair: Roderic GuigÓ

• 16h10-16h15 Compositional analysis of non-coding regions in eukaryotic genomes
  Emanuele Bultrini, Paolo Del Giudice, Elisabetta Pizzi
• 16h15-16h20 Inferring site-specific evolutionary rates: Bayesian methods are superior
  Itay Mayrose, Dan Graur, Tal Pupko
• 16h20-16h25 TIGERSearch attacks Proteins
  Jasmin Saric, Uwe Reyle
• 16h25-16h30 Protein function prediction: Application of a propositional rules learning system to a set of human protein sequences  Manuel J. Gómez, Francisco Javier Guijarro, Ramón P. Otero, Lars J. Jensen, Søren Brunak, Alfonso Valencia

• 16h30-17h15 Posters and break

• 17h15-18h05 Invited talk
  Chair: Esko Ukkonen
  Pedro Mendes   Simulation meets data analysis: the development of objective tests for functional genomics data analysis algorithms

Contributed talks - Functional genomics and evolution
Chair: Alfonso Valencia

• 18h05-18h30 Predicting gene function in Saccharomyces cerevisiae
  Amanda Clare, Ross King
• 18h30-18h45 Rules extraction in linkage disequilibrium mapping with an adaptive genetic algorithm
  Laetitia Jourdan, Clarisse Dhaenens, El-Ghazali Talb

• 18h50-19h50 Business meeting at the Parc de la Villette and Poster session
  for those not wishing to attend the Business meeting
  

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  Tuesday September 30                                               saturday 27th      sunday 28th      monday 29th         
  

• 9h-9h50 Invited talk
  Chair: Mike Hendy
  Andy Waters   Comparative genomics of malaria parasites and its exploitation in a rodent malaria model

Contributed talks - Protein structure
Chair: Jerzy Tiuryn

• 9h50-10h15 A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins  Torgeir R. Hvidsten, Andriy Kryshtafovych, Jan Komorowski, Krzysztof Fidelis
• 10h15-10h40 Flexible structure alignment by chaining aligned fragment pairs allowing twists
  Yuzhen Ye, Adam Godzik

Flash presentations - Protein structure
Chair: Jerzy Tiuryn

• 10h40-10h45 Structural similarity search in databases: YAKUSA
  Mathilde Carpentier, Sophie Brouillet, Joël Pothier
• 10h45-10h50 A new 3D statistical potential to predict protein-ligand interactions based on atomic interaction patterns in PDB
  Ernesto Moreno, Luis A. Diego
• 10h50-10h55 An automatic procedure for the search and identification of new unbounded docking examples
  Frank Steinacker, Oliver Martin, Philipp Heuser, Dietmar Schomburg
• 10h55-11h00 Classification of Fourier spectra of short protein sequences compared to their corresponding structural classification
  Manoj Tyagi, Henri Ralambondranny, Frédéric Cadet, Philippe Charton, Bernard Offmann

• 11h-11h45 Posters and break

Contributed talks - Multiple alignment and phylogeny
Chair: Daniel Huson

• 11h45-12h10 Divide-and-Conquer multiple alignment with segment-Based constraints
  Michael Sammeth Burkhard Morgenstern, Jens Stoye
• 12h10-12h35 Upper bounds on maximum likelihood for phylogenetic trees
  Michael Hendy, Barbara Holland
• 12h35-12h50 A Randomized Linear-time Majority Tree Algorithm
  Nina Amenta, Fredericke Clarke, Katherine St. John
• 12h50-13h05 Whole genome-based prokaryotic phylogeny
  Stefan Henz, Alexander Auch, Daniel Huson, Kay Nieselt-Struwe, Stephan Schuster

• 13h05-14h30 Lunch

• 14h30-15h20 Invited talk
  Chair: Eduardo Rocha
  François Taddei   Sources of genetic and phenotypic variability

Contributed talks - Comparative genomics
Chair: Bernard Prum

• 15h20-15h45 Genome rearrangements in tumor cells: Reconstructing tumor genome architecture
  Pavel Pevzner, Ben Raphael
• 15h45-16h10 MCMC genome rearrangement
  István Miklós
• 16h10-16h25 Single step reconciliation algorithm for duplication, loss and horizontal gene transfer model
  Pawel Gorecki
• 16h25-16h40 Data retrieval and handling tools for the PBIL gene family databases
  Guy Perrière, Jean-François Dufayard, Simon Penel, Julien Grassot, Laurent Duret, Manolo Gouy

• 16h45-17h Closing remarks

• 17h-18h Final posters session for those not needing to catch an early train or flight