

{"id":375,"date":"2017-05-12T15:28:28","date_gmt":"2017-05-12T13:28:28","guid":{"rendered":"http:\/\/project.inria.fr\/jobim2017\/?page_id=375"},"modified":"2017-07-03T11:18:11","modified_gmt":"2017-07-03T09:18:11","slug":"accepted-papers","status":"publish","type":"page","link":"https:\/\/project.inria.fr\/jobim2017\/accepted-papers\/","title":{"rendered":"Accepted papers"},"content":{"rendered":"<p><\/p>\n<ul>\n<li><a href=\"#oral\">Oral Presentations<\/a><\/li>\n<li><a href=\"#demos\">Software Demonstrations<\/a><\/li>\n<li><a href=\"http:\/\/project.inria.fr\/jobim2017\/files\/2017\/06\/posters.pdf\">Posters<\/a><\/li>\n<li><a href=\"http:\/\/cristal.univ-lille.fr\/~salson\/actes_jobim_2017.pdf\">Proceedings<\/a><\/li>\n<\/ul>\n<p><a name=\"oral\"><\/p>\n<h3>Oral Presentations<\/h3>\n<p><\/a><\/p>\n<p>Scientific Workflows for Computational Reproducibility in the Life Sciences: Status, Challenges and Opportunities<br \/>\nSarah Cohen-Boulakia and Christophe Blanchet<\/p>\n<p>FEELnc: an alignment-free tool for long non-coding RNAs annotation<br \/>\nValentin Wucher, Fabrice Legeai, Beno\u00eet H\u00e9dan, Guillaume Rizk, Laetitia Lagoutte, Edouard Cadieu, Audrey David, Nadine Botherel, C\u00e9line Le B\u00e9guec, Catherine Andr\u00e9, Christophe Hitte and Thomas Derrien<\/p>\n<p>Probing factor-dependent long-range contacts using regression with higher-order interaction terms<br \/>\nRapha\u00ebl Mourad, Lang Li and Olivier Cuvier<\/p>\n<p>Simka: large scale de novo comparative metagenomics<br \/>\nGa\u00ebtan Benoit, Pierre Peterlongo, Mahendra Mariadassou, Erwan Drezen, Sophie Schbath, Dominique Lavenier and Claire Lemaitre<\/p>\n<p>Rare and common epilepsies converge on a shared gene regulatory network providing opportunities for novel antiepileptic drug discovery<br \/>\nAndr\u00e9e Delahaye-Duriez, Prashant Srivastava, Kirill Shkura, Sarah R. Langley, Enrico Petretto and Michael R. Johnson<\/p>\n<p>Rapid spectra comparison with data-mining algorithms: accessing post translational modification profiles on a sample scale<br \/>\nMatthieu David, Guillaume Fertin, H\u00e9l\u00e8ne Rogniaux and Dominique Tessier<\/p>\n<p>Analysis, Integration and Modeling of Cell Clustering Results in High-Dimensional Cytometry Data<br \/>\nGuillaume Gautreau, David Pejoski, Roger Le Grand, Antonio Cosma, Anne-Sophie Beignon and Nicolas Tchitchek<\/p>\n<p>Network Inference of Dynamic Models by the Combination of Spanning Arborescences<br \/>\nAnthony Coutant and C\u00e9line Rouveirol<\/p>\n<p>Extreme halophilic archaea derive from two distinct methanogen Class II ancestors<br \/>\nMonique Aouad, Najwa Taib, Anne Oudart, Michel Lecocq, Manolo Gouy and C\u00e9line Brochier-Armanet<\/p>\n<p>Reconstruction of full-length 16S rRNA sequences for taxonomic assignment in metagenomics<br \/>\nPierre Pericard, Yoann Dufresne, Samuel Blanquart and H\u00e9l\u00e8ne Touzet<\/p>\n<p>Origin and evolution of multiple haem copper oxidases in Archaea<br \/>\nAnne Oudart, Simonetta Gribaldo and C\u00e9line Brochier-Armanet<\/p>\n<p>Analyse int\u00e9grative des ARN longs non-codant (lncRNAs) du g\u00e9nome canin<br \/>\nC\u00e9line Le B\u00e9guec, Valentin Wucher, Laetitia Lagoutte, Edouard Cadieu, Beno\u00eet H\u00e9dan, Catherine Andr\u00e9, Christophe Hitte and Thomas Derrien<\/p>\n<p>Prediction of Disease-associated Genes by advanced Random Walk with Restart on Multiplex and Heterogeneous Biological Networks<br \/>\nAlberto Valdeolivas, Elisabeth Remy, Laurent Tichit, Ga\u00eblle Odelin, Claire Navarro, Sophie Perrin, Pierre Cau, Nicolas Levy and Ana\u00efs Baudot<\/p>\n<p>Food-Microbiomes Transfert, a shotgun metagenomic tool and a database to analyze cheese ecosystems<br \/>\nThibaut Guirimand, Anne-Laure Abraham, Sandra Derozier, Charlie Pauvert, Mahendra Mariadassou, Valentin Loux and Pierre Renault<\/p>\n<p>HG-CoLoR: A new method for the production of synthetic long reads<br \/>\nPierre Morisse, Thierry Lecroq and Arnaud Lefebvre<\/p>\n<p>GenomeOnRails: depicting microbial species diversity via a pangenome graph<br \/>\nGuillaume Gautreau, R\u00e9mi Planel, Amandine Perrin, Marie Touchon, Eduardo Rocha, Christophe Ambroise, Catherine Matias, St\u00e9phane Cruveiller, Claudine M\u00e9digue and David Vallenet<\/p>\n<p>NCboost: a meta-classifier of pathogenic non-coding variants integrating multiple sequence conservation and unsupervised functional scores<br \/>\nBarthelemy Caron and Antonio Rausell<\/p>\n<p>Context-specific prioritization of non-coding variants implicated in human diseases<br \/>\nLambert Moyon, Yves Cl\u00e9ment, Camille Berthelot and Hugues Roest Crollius<\/p>\n<p>Assembly of heterozygous genomes using high-order de Bruijn graphs<br \/>\nAntoine Limasset, Camille Marchet, Pierre Peterlongo and Jean-Francois Flot<\/p>\n<p>Use of cross-docking simulations for identification of protein-protein interactions sites: the case of proteins with multiple binding sites<br \/>\nNathalie Lagarde, Lydie Vamparys, Benoist Laurent, Alessandra Carbone and Sophie Sacquin-Mora<\/p>\n<p>In silico developments for the study of glycosylation applied to extracellular matrix proteins<br \/>\nCamille Besan\u00e7on, Alexandre Guillot, S\u00e9bastien Blaise, Manuel Dauchez, Jessica Jonquet, Nicolas Belloy and St\u00e9phanie Baud<\/p>\n<p>An integrative approach for predicting the RNA secondary structure for the HIV&#8211;1 Gag UTR using probing data<br \/>\nAfaf Saaidi, Yann Ponty and Bruno Sargueil<\/p>\n<p><a name=\"demos\"><\/p>\n<h3>Software Demonstrations<\/h3>\n<p><\/a><\/p>\n<p>Dynamix: Dynamic visualization by automatic selection of informative tracks from hundreds of genomic data sets<br \/>\nMatthias Monfort, Eileen Furlong and Charles Girardot<\/p>\n<p>Long-term Tracking of Budding Yeast Cells with CellStar<br \/>\nCristian Versari, Szymon Stoma, Kirill Batmanov, Art\u00e9mis Llamosi, Filip Mroz, Adam Kaczmarek, Matt Deyell, C\u00e9dric Lhoussaine, Pascal Hersen and Gregory Batt<\/p>\n<p>GeneSpy, a simple tool to explore genomic context<br \/>\nPierre Simon Garcia, Fr\u00e9d\u00e9ric Jauffrit, Christophe Grangeasse and C\u00e9line Brochier-Armanet<\/p>\n<p>MCXpress: An R Package for functional interpretation of single cell RNA-Seq data using multivariate analysis.<br \/>\nAkira Cortal and Antonio Rausell<\/p>\n<p>New Generation Phylogeny.fr: Refactoring Phylogeny.fr for Innovative Phylogenetic Services<br \/>\nDamien Correia, Vincent Lefort, Olivia Doppelt-Azeroual, Fabien Mareuil, Sarah Cohen-Boulakia and Olivier Gascuel<\/p>\n<p>Genomicus \u2013 New tools for comparative genomics and evolution in eukaryotes<br \/>\nAlexandra Louis, Nga Thi Thuy Nguyen and Hugues Roest Crollius<\/p>\n<p>Deciphering The Functional Effects of Genetic Variation With UniProt Annotations.<br \/>\nBenoit Bely, Andrew Nightingale and Maria Martin<\/p>\n<p>Biosphere Web : un portail haut niveau pour une utilisation bioinformatique des clouds<br \/>\nBryan Brancotte, Mohamed Bedri, Jonathan Lorenzo, Sandrine Perrin, Fr\u00e9d\u00e9ric S\u00e9n\u00e9, Awa Sepou Nga\u00eflo, Christophe Blanchet and Jean-Fran\u00e7ois Gibrat<\/p>\n<p>Sequanix: A Dynamic Graphical Interface for Snakemake Workflows<br \/>\nDimitri Desvillechabrol, Rachel Legendre, Christiane Bouchier, Sean Kennedy and Thomas Cokelaer<\/p>\n<p>CRCmapper: models of core transcriptional regulatory circuitries<br \/>\nViolaine Saint-Andr\u00e9, Alexender J. Federation, Charles Y. Lin, Brian J. Abraham, Jessica Reddy, Tong Ihn Lee, James E. Bradner and Richard A. Young<\/p>\n<p>Biodjango, an open framework for bioinformatics publishing<br \/>\nEnnys Gheyouche and St\u00e9phane T\u00e9letch\u00e9a<\/p>\n<p><!--REGOVAR, logiciel libre pour l\u2019analyse de donn\u00e9es de s\u00e9quen\u00e7age haut d\u00e9bit pour les maladies g\u00e9n\u00e9tiques rares\nAnne-Sophie Denomm\u00e9-Pichon, Olivier Gueudelot, J\u00e9r\u00e9mie Roquet, June Sallou, Sacha Schutz and David Gouden\u00e8ge--><\/p>\n<p>PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies<br \/>\nLudovic Mallet, Tristan Bitard-Feildel, Franck Cerutti and H\u00e9l\u00e8ne Chiapello<\/p>\n<p>Listeriomics: A Multi-Omics Interactive Web Platform for Systems Biology of the Model Pathogen Listeria<br \/>\nChristophe Becavin, Mikael Koutero, Nicolas Tchitchek, Franck Cerutti, Pierre Lechat, Nicolas Maillet, Claire Hoede, H\u00e9l\u00e8ne Chiapello, Christine Gaspin and Pascale Cossart<\/p>\n<p>AskOmics, a web tool to integrate and query biological data using semantic web technologies<br \/>\nXavier Garnier, Anthony Bretaudeau, Olivier Filangi, Fabrice Legeai, Anne Siegel and Olivier Dameron<\/p>\n<p>Regulatory and signaling network assembly through Linked Open Data<br \/>\nMarie Lefebvre, J\u00e9r\u00e9mie Bourdon, Carito Guziolowski and Alban Gaignard<\/p>","protected":false},"excerpt":{"rendered":"<p>Oral Presentations Software Demonstrations Posters Proceedings 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, Beno\u00eet H\u00e9dan, Guillaume Rizk, Laetitia Lagoutte, Edouard Cadieu, Audrey David, Nadine\u2026<\/p>\n<p> <a class=\"continue-reading-link\" href=\"https:\/\/project.inria.fr\/jobim2017\/accepted-papers\/\"><span>Continue reading<\/span><i class=\"crycon-right-dir\"><\/i><\/a> <\/p>\n","protected":false},"author":991,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-375","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/project.inria.fr\/jobim2017\/wp-json\/wp\/v2\/pages\/375","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/project.inria.fr\/jobim2017\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/project.inria.fr\/jobim2017\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/project.inria.fr\/jobim2017\/wp-json\/wp\/v2\/users\/991"}],"replies":[{"embeddable":true,"href":"https:\/\/project.inria.fr\/jobim2017\/wp-json\/wp\/v2\/comments?post=375"}],"version-history":[{"count":11,"href":"https:\/\/project.inria.fr\/jobim2017\/wp-json\/wp\/v2\/pages\/375\/revisions"}],"predecessor-version":[{"id":555,"href":"https:\/\/project.inria.fr\/jobim2017\/wp-json\/wp\/v2\/pages\/375\/revisions\/555"}],"wp:attachment":[{"href":"https:\/\/project.inria.fr\/jobim2017\/wp-json\/wp\/v2\/media?parent=375"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}