Committees ECCB

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

ACCEPTED PAPERS: long papers, short papers, flash presentations

LONG PAPERS (will be published in Bioinformatics) :
short papers, flash presentations

- Computational detection of cis-regulatory modules - S.Aerts, P.Van Loo, G.Thijs, Y.Moreau and B.De Moor
- Searching for statistically significant regulatory modules - T.L. Bailey and W.S Nobble
- Ab initio reconstruction of metabolic pathways - F. Boyer and A.Viari
- HMM sampling and applications to gene finding and alternative splicing - S. Cawley and L.Pachter
- Predicting gene function in Saccharomyces cerevisiae - A. Clare and R.D.King
- Inferring strengths of protein-protein interactions from experimental data using linear programming - M.Hayashida, N.Ueda and T. Akutsu
- Upper bounds on maximum likelihood for phylogenetic trees - M.D. Hendy and B.R.Holland
- A Rapid Method for Detection of Putative RNAi Target Genes in Genomic Data - Y.Horesh, A.Amir, S.Michaeli, and R. Unger
- A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins - T. R. Hvidsten, A.Kryhtafovych, J.Komorowski and K.Fidelis
- Discover Significant Rules for Classifying Cancer Diagnosis Data - J.Li, H.Liu, S-K.Ng and L.Wong
- Modelling Sequencing Errors\\by Combining Hidden Markov Models - C.Lottaz, C.Iseli, C.V.Jongeneel and P.Bucher
- A Suffix Tree Approach to the Interpretation of Tandem Mass Spectra: Applications to Peptides of Nonspecific Digestion and Post-translational Modifications - B. Lu and T.Chen
- Artificial gene networks for objective comparison of analysis algorithms - P.Mendès, W.Sha and K.Ye
- MCMC Genome Rearrangement - I. Miklós
- Gene networks inference using dynamic Bayesian networks - B-E.Perrin, L.Raviola, A.Mazurie, S.Bottani, J.Mallet and F.d'Alché-Buc
- Finding Subtle Motifs by Branching from Sample Strings - A. Price, S.Ramabhadran and P.A.Pevzner
- The Shortest Common Supersequence Problem in a Microarray Production Setting - S.Rahmann
- Genome Rearrangements in Tumor Cells: Reconstructing Tumor Genome Architecture - B.J. Raphael, S.Volik, C.Collins and P.A.Pevzner
- A description of dynamical graphs associated to elementary regulatory circuits - E.Remy, B.Mossé, C.Chaouiya and D.Thieffry
- Fast feature selection using a simple Estimation of Distribution Algorithm : A case study on splice site prediction - Y. Saeys, S.Degroeve, D.Aeyels, Y.Van de Peer and P.Rouzé
- Divide-and-Conquer Multiple Alignment with Segment-Based Constraints - M.Sammeth, B.Morgenstern and J.Stoye
- Biclustering Microarray Data by Gibbs Sampling - Q.Sheng, Y.Moreau and B.de Moor
- Finding Optimal Degenerate Patterns in DNA Sequences - D.Shinozaki, T.Akutsu and O. Maruyama
- Gene Prediction with a Hidden Markov Model and new Intron Submodel - M. Stanke and S.Waack
- Estimating Gene Networks from Gene Expression Data by Combining Bayesian Network Model with Promoter Element Detection - Y.Tamada, S.Y.Kim, H.Bannai, S.Imolo, K.Tashiro, S.Kuhara and S.Miyano
- A Rapid Method for Detection of Putative RNAi Target Genes in Genomic Data - Y.Horesh, A.Amir, S.Michaeli, and R. Unger
- Extracting Active Pathways from Gene Expression Data - J-P.Vert and M.Kanehisa
- Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites - C.Dieterich, R.Herwig and M. Vingron
- Flexible structure alignment by chaining aligned fragment pairs allowing twists - Y.Ye and A. Godzik

SHORT PAPERS
long papers, flash presentations

- Searching the Saccharomyces cerevisiae genome for -1 frameshifting sites - Alain Denise
- Resources for Bacterial Strain Identification Using Polymorphic Tandem Repeats - France Denoeud
- Modular Decision System and Information Integration for Improved Disease Outcome prediction - Matthias Futschik
- Using ChIP Data to Decipher Regulatory Logic of MBF and SBF during the Yeast Cell Cycle - Feng Gao
- Single step reconciliation algorithm for duplication, loss and horizontal gene transfer model - Pawel Gorecki
- Validation of noisy dynamical system models of gene regulation inferred from time-course gene expression data at arbitrary time intervals - Michiel de Hoon
Whole Genome-based Prokaryotic Phylogeny - Daniel Huson
- Rules extraction in linkage disequilibrium mapping with an adaptive genetic algorithm - Laetitia Jourdan
- Genomic distribution of short motifs involved in DNA repair in pathogenic and non pathogenic Escherichia coli - Meriem El Karoui
- Accuracy of the models for gene regulation - a comparison of two modeling methods - Kimmo Palin
- Data retrieval and handling tools for the PBIL gene family databases - Guy Perrière
- Overview of a software pipeline dedicated to automatic MS/MS data analysis - Erwan Reguer
- Detecting short inverted segments in a biological sequence David Robelin
- A Randomized Linear-time Majority Tree Algorithm - Katherine St. John
- Annotating animal mitochondrial tRNAs: an experimental evaluation of four methods - Stacia Wyman

FLASH PRESENTATIONS
short papers, long papers

F - Compositional analysis of non-coding regions in eukaryotic genomes - Emanuele Bultrini, Paolo Del Giudice, Elisabetta Pizzi
F - Structural similarity search in databases: YAKUSA - Mathilde Carpentier, Sophie Brouillet, Joël Pothier
F - ISYMOD: A Knowledge Base for integrated system modeling - Julie Chabalier, Yves Quentin, Cécile Capponi, Gwennaele Fichant
F - The Biochemical Abstract Machine BIOCHAM - Nathalie Chabrier, François Fages
F - Searching for ncRNAs in protist genomes - Lesley J. Collins, Thomas J. Macke, David Penny
F - 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
F - Design of a clinical microarray chip - Jochen Jäger, Rainer Spang
F - Computational detection of MicroRNAs in animal genomes - Matthieu Legendre, Daniel Gautheret
F - Graph theory based methodology for comparing intearction networks between genes across organisms - Gaëlle Lelandais, Pierre Vincens, Claude Jacq, Stéphane Vialette
F - 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
F - Spotting effects in cDNA experiments - T. Mary-Huard, S. Robin, J.-J. Daudin
F - Inferring site-specific evolutionary rates: Bayesian methods are superior - Itay Mayrose, Dan Graur, Tal Pupko
F - A new 3D statistical potential to predict protein-ligand interactions based on atomic interaction patterns in PDB - Ernesto Moreno, Luis A. Diego
F - Modeling the Rho dependent transcription termination sites in the bacterium Helicobacter pylori - Lisa Petersen, Anders Krogh
F - TIGERSearch attacks Proteins - Jasmin Saric, Uwe Reyle
F - 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
F - An automatic procedure for the search and identification of new unbounded docking examples - Frank Steinacker, Oliver Martin, Philipp Heuser, Dietmar Schomburg
F - Relevance of the secondary structure of messenger RNA: a statistical study - Fabrice Thalmann, Hervé Isambert
F - Classification of Fourier spectra of short protein sequences compared to their corresponding structural classification - Manoj Tyagi, Henri Ralambondranny, Frédéric Cadet, Philippe Charton, Bernard Offmann
F - PARIS: a system for 2-DE based proteomic data management - Juhui Wang, Christophe Caron, Michel-Yves Mistou, Christophe Gitton, Alain Trubuil
F - 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