Accepted papers

Oral Presentations

Scientific Workflows for Computational Reproducibility in the Life Sciences: Status, Challenges and Opportunities
Sarah Cohen-Boulakia and Christophe Blanchet

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

Probing factor-dependent long-range contacts using regression with higher-order interaction terms
Raphaël Mourad, Lang Li and Olivier Cuvier

Simka: large scale de novo comparative metagenomics
Gaëtan Benoit, Pierre Peterlongo, Mahendra Mariadassou, Erwan Drezen, Sophie Schbath, Dominique Lavenier and Claire Lemaitre

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, Enrico Petretto and Michael R. Johnson

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

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

Network Inference of Dynamic Models by the Combination of Spanning Arborescences
Anthony Coutant and Céline Rouveirol

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

Reconstruction of full-length 16S rRNA sequences for taxonomic assignment in metagenomics
Pierre Pericard, Yoann Dufresne, Samuel Blanquart and Hélène Touzet

Origin and evolution of multiple haem copper oxidases in Archaea
Anne Oudart, Simonetta Gribaldo and Céline Brochier-Armanet

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

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

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

HG-CoLoR: A new method for the production of synthetic long reads
Pierre Morisse, Thierry Lecroq and Arnaud Lefebvre

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

NCboost: a meta-classifier of pathogenic non-coding variants integrating multiple sequence conservation and unsupervised functional scores
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

Assembly of heterozygous genomes using high-order de Bruijn graphs
Antoine Limasset, Camille Marchet, Pierre Peterlongo and Jean-Francois Flot

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

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

Software Demonstrations

Dynamix: Dynamic visualization by automatic selection of informative tracks from hundreds of genomic data sets
Matthias Monfort, Eileen Furlong and Charles Girardot

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

GeneSpy, a simple tool to explore genomic context
Pierre Simon Garcia, Frédéric Jauffrit, Christophe Grangeasse and Céline Brochier-Armanet

MCXpress: An R Package for functional interpretation of single cell RNA-Seq data using multivariate analysis.
Akira Cortal and Antonio Rausell

New Generation Refactoring for Innovative Phylogenetic Services
Damien Correia, Vincent Lefort, Olivia Doppelt-Azeroual, Fabien Mareuil, Sarah Cohen-Boulakia and Olivier Gascuel

Genomicus – New tools for comparative genomics and evolution in eukaryotes
Alexandra Louis, Nga Thi Thuy Nguyen and Hugues Roest Crollius

Deciphering The Functional Effects of Genetic Variation With UniProt Annotations.
Benoit Bely, Andrew Nightingale and Maria Martin

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

Sequanix: A Dynamic Graphical Interface for Snakemake Workflows
Dimitri Desvillechabrol, Rachel Legendre, Christiane Bouchier, Sean Kennedy and Thomas Cokelaer

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

Biodjango, an open framework for bioinformatics publishing
Ennys Gheyouche and Stéphane Téletchéa

PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies
Ludovic Mallet, Tristan Bitard-Feildel, Franck Cerutti and Hélène Chiapello

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

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