Tuesday, June 30, 2020

Time Event  
11:00 - 12:30 Initial connection test (Salle 2: User Connection Test) - jobim2020-contact@lirmm.fr  
13:00 - 14:00 Welcome & Opening remarks (Salle 1: Opening, Keynote Flora Jay)  
13:00 - 13:10 › ouverture de JOBIM 2020 - -  
13:10 - 13:50 › discours des invités d'honneur et créateurs de JOBIM Marie-France Sagot et Olivier Gascuel - -  
13:50 - 13:55 › le mot de la SFBI - -  
14:00 - 15:00 Keynote: Flora Jay (Salle 1: Opening, Keynote Flora Jay) - Creating Artificial Genomes using Generative Networks  
15:00 - 15:10 Break  
15:10 - 16:10 Evolution and Phylogeny (Salle 2: Evolution and Phylogeny)  
15:10 - 15:30 › A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios - Anna Zhukova  
15:30 - 15:50 › Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data - Gonché Danesh  
15:50 - 16:10 › Evolution of replication origins in vertebrate genomes: rapid turnover despite selective constraints - Florian Massip  
15:10 - 16:10 Networks and Systems (Salle 3: Network and Systems)  
15:10 - 15:30 › Inferring ligand-receptor interactions from single-cell and bulk transcriptomic data - Jacques Colinge  
15:30 - 15:50 › Formalizing and enriching phenotype signatures using Boolean networks - Meline Wery  
15:50 - 16:10 › Inferring biochemical reactions and metabolite structures using a molecular transformation approach - Gabriel Markov  
16:10 - 16:30 Break  
16:30 - 17:30 Posters & demos (Salle virtuelle des posters) - 1  

Wednesday, July 1, 2020

Time Event  
09:00 - 10:00 Keynote: Kjell Petersen (Salle 1: Keynote Kjell Petersen) - E-infrastructure, platforms and services provided by Elixir Norway  
10:00 - 11:00 Posters & demos (Salle virtuelle des posters) - 2  
11:00 - 12:40 IFB Session (Salle 2: Platforms and Services in Bioinformatics)  
11:00 - 11:20 › Ensembl 2020, data growth - Species Quick Release Processing - Marc Chakiachvili  
11:20 - 11:40 › nf-core, a community effort for collaborative, peer-reviewed analysis pipelines - Maxime Garcia  
11:40 - 12:00 › Fostering Open Science and FAIR practices among the IFB infrastructures : the OpenLink and maDMP4LS projects - Julien Seiler / Olivier Collin  
12:00 - 12:20 › What's new on IFB NNCR Cluster(s) ? - Gildas Le Corguillé / Julien Seiler  
12:20 - 12:40 › Bio2M platform: find everything in your RNA-Seq data - Anthony Boureux  
11:00 - 12:20 Statistics & Machine Learning (Salle 3: Statistics and Machine Learning)  
11:00 - 11:20 › Consensus clustering applied to multi-omic disease subtyping - Marie-Galadriel Briere  
11:20 - 11:40 › Bringing ABC inference to the machine learning realm : AbcRanger,an optimized random forests library for ABC - François-David Collin  
11:40 - 12:00 › On the accuracy in high‐dimensional linear models and its application to genomic selection - Charles-Elie Rabier  
12:00 - 12:20 › Towards CNNs Representations for Small Data Classification - Khawla Seddiki  
12:40 - 14:00 Break  
14:00 - 15:00 Keynote: Martin Weigt (Salle 1: Keynote Martin Weigt, Mini-symposium Long Reads) - Protein sequence landscapes: from data-driven models to evolution-guided sequence design  
15:00 - 15:10 Break  
15:10 - 17:40 Mini Symp. Long reads (Salle 1: Keynote Martin Weigt, Mini-symposium Long Reads) - Programme  
15:10 - 17:40 › Long reads in the wide - Jean-Marc Aury, Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob - Vincent Lacroix, ERABLE, Laboratoire de Biométrie et Biologie Evolutive UMR5558 - Hélène Touzet, 2. Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, bilille, F-59000 Lille, France., 3. Univ. Lille, CNRS, Centrale Lille, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France.  
15:10 - 17:40 Mini Symp. Deep learning (Salle 2: Mini-symposium Deep Learning for Omics) - Programme  
15:10 - 17:40 › Deep learning for omics - Laurent Jacob, Laboratoire de Biométrie et Biologie Evolutive - Raphaël Mourad, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération - Vera Pancaldi, Centre de Recherche en Cancérologie de Toulouse - Elissar Nasseredine, CBI, Toulouse - Vincent Rocher, Syndicat interdépartemental pour l'assainissement de l'agglomération parisienne - Mathys Grapotte, Sanofi-Aventis R&D, Institut de Génétique Moléculaire de Montpellier, Laboratoire dÍnformatique de Robotique et de Microélectronique de Montpellier - Arnaud Abreu, Laboratoire des sciences de língénieur, de línformatique et de límagerie  
15:10 - 17:40 Mini Symp. RNA structure (Salle 3: Mini-symposium RNA Structure) - Programme  
15:10 - 17:40 › RNA structure, design and interaction with proteins - Petr Sulc, Rockefeller University - Samuela Pasquali, Cibles Thérapeutiques et conception de médicaments - Fabrice Leclerc, Institut de Biologie Intégrative de la Cellule - Sebastian Will, Laboratoire dínformatique de l\'École polytechnique [Palaiseau]  

Thursday, July 2, 2020

Time Event  
09:00 - 10:00 Keynote: Johannes Söding (Salle 1: Keynote Johannes Söding) - Methods for the analysis of big data in metagenomics and systems medicine  
10:00 - 11:00 Posters & demos (Salle virtuelle des posters) - 3  
11:00 - 12:00 Functional Genomics (Salle 2: Functional Genomics)  
11:00 - 11:20 › Automated Inference of Gene Regulatory Networks Using Explicit Regulatory Modules - Clemence Reda  
11:20 - 11:40 › Chromosight: a computer vision based program for pattern recognition in chromosome contact maps - Cyril Matthey-Doret  
11:40 - 12:00 › Reproducibility first: mining CLIP-seq data to understand the Exon Junction Complex - Toni Paternina  
11:00 - 12:40 NGS & Algorithmics (Salle 3: NGS and Algorithmics)  
11:00 - 11:20 › Long-read error correction: a survey and qualitative comparison - Pierre Morisse  
11:20 - 11:40 › UMI-VarCal: a new UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries - Vincent SATER  
11:40 - 12:00 › Towards a better understanding of the low discovery rate of short-read based insertion variant callers - Wesley Delage  
12:00 - 12:20 › Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms - Nadège Guiglielmoni  
12:20 - 12:40 › REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets - Camille Marchet  
12:40 - 14:00 Break  
14:00 - 15:00 Keynote: Andrea Rau (Salle 1: Keynote Andrea Rau) - Integrative and interactive analyses of multi-omics data  
15:00 - 15:10 Break  
15:10 - 16:30 AG SFBI (Salle 2: SFBI Meeting, GDR-BIM, IFB, JeBIF)  
16:30 - 16:55 GDR-BIM presentation (Salle 2: SFBI Meeting, GDR-BIM, IFB, JeBIF)  
16:55 - 17:20 IFB presentation (Salle 2: SFBI Meeting, GDR-BIM, IFB, JeBIF)  
17:20 - 17:30 JeBIF presentation (Salle 2: SFBI Meeting, GDR-BIM, IFB, JeBIF)  

Friday, July 3, 2020

Time Event  
09:00 - 10:20 Computational Medicine (Salle 1: Computational Medicine)  
09:00 - 09:20 › Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software - Clémentine Decamps  
09:20 - 09:40 › Designing a statistical and user friendly application to analyse cell imaging - Rachel Torchet  
09:40 - 10:00 › PRECISE: A domain adaptation approach to transfer predictors of drug response from pre-clinical models to tumors - Soufiane Mourragui  
10:00 - 10:20 › Using the Human Cell Atlas for tracking SARS-CoV-2 entry factors - Christophe Becavin  
09:00 - 11:00 Proteins & Structure (Salle 2: Proteins and Structure)  
09:00 - 09:20 › Local conformations in ordered and intrinsically disordered proteins - Alexandre G. de Brevern  
09:20 - 09:40 › A new mechanism of glucose transport by GluT1 discovered in molecular dynamics simulations - Tatiana Galochkina  
09:40 - 10:00 › ComPotts: Optimal alignment of coevolutionary models for protein sequences - Hugo Talibart  
10:00 - 10:20 › Docking of RNA Hairpin on Protein Using a Fragment-Based Method - Antoine Moniot  
10:20 - 10:40 › Computational methods for RNA complexes secondary structure prediction - Fariza Tahi  
10:40 - 11:00 › InterPro: the protein classification database - Typhaine Paysan-Lafosse  
11:00 - 11:15 Break  
11:15 - 12:15 Keynote: Nuria Lopez-Bigas (Salle 3: Keynote Nuria Lopez-Bigas, Closing) - Computational analysis of cancer genomes  
12:15 - 12:30 Closing (Salle 3: Keynote Nuria Lopez-Bigas, Closing)