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Monday, July 3
13:00 Registration  
14:00-14:30 Welcome  
14:30-15:30 Patrick Wincker Keynote – Pasteur
  Holistic metagenomics in marine plankton communities
15:30-16:30 Metagenomics Plenary – Pasteur
  Simka: Large Scale De Novo Comparative Metagenomics
  Gaëtan Benoit, Pierre Peterlongo, Mahendra Mariadassou, Erwan Drezen, Sophie Schbath, Dominique Lavenier and Claire Lemaitre
  Food-Microbiomes Transfert, a Shotgun Metagenomic Tool and a Database to Analyze Cheese Ecosystems
  Thibaut Guirimand, Anne-Laure Abraham, Sandra Derozier, Charlie Pauvert, Mahendra Mariadassou, Valentin Loux and Pierre Renault
  Reconstruction of Full-Length 16S rRNA Sequences for Taxonomic Assignment in Metagenomics
  Pierre Pericard, Yoann Dufresne, Samuel Blanquart and Hélène Touzet
16:30-17:00 Break  
17:00-18:00 Integrative Biology Plenary – Pasteur
  FEELnc: an Alignment-Free Tool for Long Non-Coding RNAs Annotation
  Valentin Wucher, Fabrice Legeai, Benoît Hédan, Guillaume Rizk, Laetitia Lagoutte, Edouard Cadieu, Audrey David, Nadine Botherel, Céline Le Béguec, Catherine André, Christophe Hitte and Thomas Derrien
  Analyse intégrative des ARN longs non-codant (lncRNAs) du génome canin
  Céline Le Béguec, Valentin Wucher, Laetitia Lagoutte, Edouard Cadieu, Benoît Hédan, Catherine André, Christophe Hitte and Thomas Derrien
  Analysis, Integration and Modeling of Cell Clustering Results in High-Dimensional Cytometry Data
  Guillaume Gautreau, David Pejoski, Roger Le Grand, Antonio Cosma, Anne-Sophie Beignon and Nicolas Tchitchek
18:00-18:30 JeBiF / / Bioinfuse  
Tuesday, July 4
9:00-10:00 Tobias Marschall [abstract] Keynote – Pasteur
  A Guided Tour to Computational Haplotyping
10:00-10:40 High Throughput Sequencing Plenary – Pasteur
  GenomeOnRails: Depicting Microbial Species Diversity Via a Pangenome Graph
  Guillaume Gautreau, Rémi Planel, Amandine Perrin, Marie Touchon, Eduardo Rocha, Christophe Ambroise, Catherine Matias, Stéphane Cruveiller, Claudine Médigue and David Vallenet
  Assembly of Heterozygous Genomes Using High-Order de Bruijn Graphs
  Antoine Limasset, Camille Marchet, Pierre Peterlongo and Jean-Francois Flot
10:40-11:05 Break  
11:05-11:25 Proteomics Plenary – Pasteur
  Rapid Spectra Comparison with Data-Mining Algorithms: Accessing Post-Translational Modification Profiles on a sample scale
  Matthieu David, Guillaume Fertin, Hélène Rogniaux and Dominique Tessier
11:25-12:40 Posters (odd numbers)  
12:40-13:40 Lunch  
13:40-14:40 Julio Saez-Rodriguez [abstract] Keynote – Pasteur
  Network Models to Understand and Combat Cancer: from Clinical Genomics to Biochemical Modelling
14:40-15:40 Systems biology Plenary – Pasteur
  Rare and Common Epilepsies Converge on a Shared Gene Regulatory Network Providing Opportunities for Novel Antiepileptic Drug Discovery
  Andrée Delahaye-Duriez, Prashant Srivastava, Kirill Shkura, Sarah R. Langley, Liisi Laaniste, Aida Moreno-Moral, Bénédicte Danis, Manuela Mazzuferi, Patrik Foerch, Elena Gazina, Kay Richards, Steven Petrou, Rafal Kaminski, Enrico Petretto and Michael R. Johnson
  Prediction of Disease-associated Genes by advanced Random Walk with Restart on Multiplex and Heterogeneous Biological Networks
  Alberto Valdeolivas, Elisabeth Remy, Laurent Tichit, Gaëlle Odelin, Claire Navarro, Sophie Perrin, Pierre Cau, Nicolas Levy and Anaïs Baudot
💻 CRCmapper: Models of Core Transcriptional Regulatory Circuitries
  Violaine Saint-André, Alexender J. Federation, Charles Y. Lin, Brian J. Abraham, Jessica Reddy, Tong Ihn Lee, James E. Bradner and Richard A. Young
15:40-16:05 Break  
16:05-17:45 Systems biology Parallel 1/2 – Matisse
  Network Inference of Dynamic Models by the Combination of Spanning Arborescences
  Anthony Coutant and Céline Rouveirol
💻  Long-term Tracking of Budding Yeast Cells with CellStar
  Cristian Versari, Szymon Stoma, Kirill Batmanov, Artémis Llamosi, Filip Mroz, Adam Kaczmarek, Matt Deyell, Cédric Lhoussaine, Pascal Hersen and Gregory Batt
 💻 Listeriomics: A Multi-Omics Interactive Web Platform for Systems Biology of the Model Pathogen Listeria
  Christophe Becavin, Mikael Koutero, Nicolas Tchitchek, Franck Cerutti, Pierre Lechat, Nicolas Maillet, Claire Hoede, Hélène Chiapello, Christine Gaspin and Pascale Cossart
💻  AskOmics, a Web Tool to Integrate and Query Biological Data Using Semantic Web Technologies
  Xavier Garnier, Anthony Bretaudeau, Olivier Filangi, Fabrice Legeai, Anne Siegel and Olivier Dameron
 💻 Regulatory and Signaling Network Assembly through Linked Open Data
  Marie Lefebvre, Jérémie Bourdon, Carito Guziolowski and Alban Gaignard
16:05-17:45 Software Development and Workflows Parallel 2/2 – Pasteur
  Scientific Workflows for Computational Reproducibility in the Life Sciences: Status, Challenges and Opportunities
  Sarah Cohen-Boulakia, Khalid Belhajjame, Olivier Collin, Jérôme Chopard, Christine Froidevaux, Alban Gaignard, Konrad Hinsen, Pierre Larmande, Yvan Le Bras, Frédéric Lemoine, Fabien Mareuil, Hervé Ménager, Christophe Pradal and Christophe Blanchet
 💻 Sequanix: A Dynamic Graphical Interface for Snakemake Workflows
  Dimitri Desvillechabrol, Rachel Legendre, Christiane Bouchier, Sean Kennedy and Thomas Cokelaer
 💻 Biosphere Web : un portail haut niveau pour une utilisation bioinformatique des clouds
  Bryan Brancotte, Mohamed Bedri, Jonathan Lorenzo, Sandrine Perrin, Frédéric Séné, Awa Sepou Ngaïlo, Christophe Blanchet and Jean-François Gibrat
💻  Biodjango, an Open Framework for Bioinformatics Publishing
  Ennys Gheyouche and Stéphane Téletchéa
💻  New Generation Refactoring for Innovative Phylogenetic Services
  Damien Correia, Vincent Lefort, Olivia Doppelt-Azeroual, Fabien Mareuil, Sarah Cohen-Boulakia and OlivierGascuel
18:00 Social events  
Wednesday, July 5
9:00-10:00 Franca Fraternali [abstract] Keynote – Pasteur
  Unraveling the Good and the Bad in Protein Networks: Functional versus Dysfunctional Interactions
10:00-10:40 High Throughput Sequencing Parallel 1/2 – Matisse
  HG-CoLoR: Hybrid Graph for the error Correction of Long Reads
  Pierre Morisse, Thierry Lecroq and Arnaud Lefebvre
💻  PhylOligo: a Package to Identify Contaminant or Untargeted Organism Sequences in Genome Assemblies
  Ludovic Mallet, Tristan Bitard-Feildel, Franck Cerutti and Hélène Chiapello
10:00-10:40 Proteins Parallel 2/2 – Pasteur
  Use of Cross-Docking Simulations for Identification of Protein-Protein Interactions Sites: The Case of Proteins with Multiple Binding Sites
  Nathalie Lagarde, Lydie Vamparys, Benoist Laurent, Alessandra Carbone and Sophie Sacquin-Mora
  In silico developments for the study of glycosylation applied to extracellular matrix proteins
  Camille Besançon, Alexandre Guillot, Sébastien Blaise, Manuel Dauchez, Jessica Jonquet, Nicolas Belloy and Stéphanie Baud
10:40-11:05 Break  
11:05-11:45 Genome visualization Parallel 1/2 – Matisse
💻  Dynamix: Dynamic Visualization by Automatic Selection of Informative Tracks from Hundreds of Genomic Data Sets
  Matthias Monfort, Eileen Furlong and Charles Girardot
💻  GeneSpy, a Simple Tool to Explore Genomic Context
  Pierre Simon Garcia, Frédéric Jauffrit, Christophe Grangeasse and Céline Brochier-Armanet
11:05-11:45 High Throughput Sequencing Parallel 2/2 – Pasteur
💻  MCXpress: An R Package for Functional Interpretation of Single Cell RNA-Seq Data Using Multivariate Analysis
  Akira Cortal and Antonio Rausell
💻  Deciphering the Functional Effects of Genetic Variation with UniProt Annotations
  Benoit Bely, Andrew Nightingale and Maria Martin
11:45-12:50 Posters (even numbers)  
12:50-13:50 Lunch  
13:50-14:50 John Huelsenbeck [abstract] Keynote – Pasteur
  Bayesian inference in phylogeny for genome-scale data
14:50-15:50 Phylogeny Plenary – Pasteur
  Extreme Halophilic Archaea Derive from Two Distinct Methanogen Class II Ancestors
  Monique Aouad, Najwa Taib, Anne Oudart, Michel Lecocq, Manolo Gouy and Céline Brochier-Armanet
  Origin and Evolution of Multiple Haem Copper Oxidases in Archaea
  Anne Oudart, Simonetta Gribaldo and Céline Brochier-Armanet
💻  Genomicus – New tools for Comparative Genomics and Evolution in Eukaryotes
  Alexandra Louis, Nga Thi Thuy Nguyen and Hugues Roest Crollius
15:50-16:15 Break  
16:15-17:15 SFBI – assemblée générale  
17:15-17:45 GdR BIM (BioInformatique Moléculaire) – assemblée générale
17:45-18:15 IFB (Institut Français de Bioinformatique)  
18:30 Bus departure for the Gala Dinner  
19:00-23:55 Gala Dinner  
Thursday, July 6
9:00-10:00 Céline Brochier [abstract] Keynote – Pasteur
  The growing tree of Archaea: changing perspectives on the diversity and evolution of the third domain of life
10:00-10:40 Integrative Biology Plenary – Pasteur
  Probing Factor-Dependent Long-Range Contacts Using Regression with Higher-Order Interaction Terms
  Raphaël Mourad, Lang Li and Olivier Cuvier
  An Integrative Approach for Predicting the RNA Secondary Structure for the HIV–1 Gag UTR Using Probing Data
  Afaf Saaidi, Yann Ponty and Bruno Sargueil.
10:40-11:10 Break  
11:10-11:50 Integrative Biology Plenary – Pasteur
  NCBoost: a machine-learning method to detect disease-causing non-coding variants
  Barthelemy Caron and Antonio Rausell
  Context-Specific Prioritization of Non-Coding Variants Implicated in Human Diseases
  Lambert Moyon, Yves Clément, Camille Berthelot and Hugues Roest Crollius
11:50-12:30 Annonce RECOMB 2018 (Paris) Plenary – Pasteur
Prix SFBI  
  Annonce JOBIM 2018  

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