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ECCB'2003 European Conference on Computational Biology
September 27-30, 2003, Paris, FRANCE


Invited papers (abstracts),
Selected papers (long papers, short papers and flash): click here,

ECCB'2003: posters abstracts
Final program in PDF

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
Contributed talks - Genetic networks
Chair: David Gilbert
  • 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)

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

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

    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

  saturday 27th      sunday 28th      monday 29th      tuesday 30th         

Welcome to ECCB'2003, see you soon in Paris!
Catherine Christophe