Journées Ouvertes en Biologie, Informatique et Mathématiques 2021

Keynote : Thomas Schiex
Chairwoman: Gwenaelle André-Leroux
Salle principale

Main room - https://us02web.zoom.us/s/85223524848

Computer-aided protein design

Algorithmes & structure de données de séquence I

Room 1 - https://us02web.zoom.us/s/85935915598

Raluca Uricaru
Room 1

› UMI-Gen: a UMI-based read simulator for variant calling evaluation - Vincent Sater 10:00-10:20 (20min)

› QUARTIC: QUick pArallel algoRithms for high- Throughput sequencIng data proCessing - Frédéric Jarlier 10:20-10:40 (20min)

› GraphUnzip: unzipping assembly graphs with long reads and Hi-C - Roland Faure 10:40-11:00 (20min)

Meta-omiques & génomique microbienne

Room 2 - https://us02web.zoom.us/s/87021240668

Damien Éveillard
Room 2

› No microbe is an island: metabolic complementarity in the microbiota and identification of key players - Clémence Frioux 10:00-10:20 (20min)

› Shallow Shotgun Metagenomics as a cost- effective and accurate alternative to WGS for taxonomic profiling and clinical diagnosis - Benoit Goutorbe 10:20-10:40 (20min)

› panRGP: a pangenome-based method to predict genomic islands and explore their diversity - Adelme Bazin 10:40-11:00 (20min)

Services et activités de plateforme

Room 3 - https://us02web.zoom.us/j/82493854546

Erwan Corre
Room 3

› Best practices of software development with Nextflow to support daily production in oncology - Fabrice Allain 10:00-10:20 (20min)

› ToulligQC 2: fast and comprehensive quality controlfor Oxford Nanoporesequencing data - Laurent Jourdren 10:20-10:40 (20min)

› Galaxy Genome Annotation (GGA) environment in the cloud - Romain Dallet 10:40-10:50 (10min)

› A digital space for EMERGEN, the French plan for SARS-CoV-2 genomic surveillance and research - Jacques van Helden 10:50-11:00 (10min)

Pause café
Gather town

Gather Town

Association des Jeunes Bioinformaticiens de France (JeBiF)
Salle principale

Main room - https://us02web.zoom.us/s/85223524848

Assemblée Générale de la Société Française de Bioinformatique (SFBI)
Salle principale

Main room - https://us02web.zoom.us/s/85223524848

Déjeuner
Gather town

Gather Town

Keynote : Carole Goble
Chairwoman: Sarah Cohen-Boulaka
Salle principale

Main room - https://us02web.zoom.us/s/85223524848

FAIR Computational Workflows

Sponsor - Genopole d’Evry
Salle principale

Main room - https://us02web.zoom.us/s/85223524848

Pause café
Gather town

Gather Town

Symposium: Open Science and Interoperability in Bioinformatics
Salle 1 - https://us02web.zoom.us/s/85935915598

Sarah Cohen-Boulakia Introduction aux concepts de la Science Ouverte et de l'Interopérabilité appliqués à la Bioinformatique
Frank Michel Annoter les pages web liées à la biodiversité avec des informations structurées pour les rendre plus découvrables et réutilisables
Philippe Rocca-Serra Operating Fair principles: the FAIR cookbook project
Cyril Pommier Standards d'échanges et concepts FAIR pour la Communauté Plantes
Laura Furlong The DisGeNET knowledge platform: facilitating the access and use of disease genomics data
Oliver Collin & Konogan Bouhry maDMP: vers un écosystème intégré pour la gestion des données de la Recherche
Pause
Flash presentations: T.Rosnet, J. Seiler, P.Poulain, H. Chiapello
Table ronde

Where are we in the search for DNA motifs involved in transcriptional regulation?
Salle 2 - https://us02web.zoom.us/s/87021240668

François Parcy Confronting in vitro genomics to real life data reveals properties of floral transcription factors
Morgane Thomas-Chollier Motif discovery in epigenomics datasets with RSAT peak-motifs2
Anthony Mathelier Combining TF binding profiles with ChIP-seq data to predict high quality direct TF-DNA interaction
Pause
Laurent Brehelin Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes
Julien Rozière Genome-wide de novo detection of preferentially located motifs in 5’- and 3’-proximal regions from Arabidopsis and maize

Symposium: Integrative structural modeling in the era of big data and artificial intelligence
Salle 3 - https://us02web.zoom.us/s/82493854546

Introduction: Current challenges in 3D modeling of proteins and complexes
Riccardo Pellarin Bayesian modeling in integrative structural biology
Ezgi Karaca Dynamic Integrative Modeling of Molecular Machines
Pause
Sergei Grudinin Entering the post-protein structure prediction era
Slavica Jonic Cryo-EM studies of continuous conformational variability of biomolecules in vitro and in situ based on image analysis, simulation and deep learning

	Mar. 06	Mer. 07	Jeu. 08	Ven. 09
09:00 10:00 11:00 12:00 13:00 14:00 15:00 16:00 17:00 18:00	Test de connexion Salle 1 9:00 - 10:00 (1h) Test de connexion Salle 1 Room 1 - https://us02web.zoom.us/s/85935915598 Ouverture Salle principale 10:00 - 11:00 (1h) Ouverture Salle principale Main room - https://us02web.zoom.us/s/85223524848 Keynote: Sarah Teichman Chaiwoman: Emmanuelle Becker Salle principale 11:00 - 11:55 (55min) Keynote: Sarah Teichman Chaiwoman: Emmanuelle Becker Salle principale Main room - https://us02web.zoom.us/s/85223524848 TBAMultiMAP: Dimensionality Reduction of Multiple Datasets by Manifold Approximation and Projection Plan France Médecine Génomique Salle principale 12:00 - 12:15 (15min) Plan France Médecine Génomique Salle principale Main room - https://us02web.zoom.us/s/85223524848 Déjeuner Gather town 12:15 - 13:30 (1h15) Déjeuner Gather town Gather Town GDR BIM Salle principale 13:30 - 14:00 (30min) GDR BIM Salle principale Main room - https://us02web.zoom.us/s/85223524848 Bioinformatique structurale I Statistiques, machine learning & intelligence artificielle I Genomique fonctionnelle 14:00 - 15:20 (1h20) Bioinformatique structurale I Room 1 - https://us02web.zoom.us/s/85935915598 Christine Gaspin Room 1 › Flexible protein structural alignment for non trivial comparisons - Jean-Christophe Gelly 14:00-14:20 (20min) › MEDUSA: deep learning based protein flexibility prediction - Tatiana Galochkina 14:20-14:40 (20min) › A Graph-based Similarity Approach to Classify Recurrent Complex Motifs from their Context in RNA Structures - Coline Gianfrotta 14:40-15:00 (20min) › Feature extraction for the clustering of small 3D structures: application to RNA fragments - Alix Delannoy 15:00-15:20 (20min) 14:00 - 15:20 (1h20) Statistiques, machine learning & intelligence artificielle I Room 2 - https://us02web.zoom.us/s/87021240668 Laura Cantini Room 2 › Spliceator: A new strategy for genome annotation using deep learning algorithm - Nicolas Scalzitti 14:00-14:20 (20min) › MISTIC: A prediction tool to reveal disease- relevant deleterious missense variants - Thomas Weber 14:20-14:40 (20min) › Discovery of widespread transcription initiation at microsatellites predictable by sequence- based deep neural network - Mathys Grapotte 14:40-15:00 (20min) › Processing of Proton Transfer Reaction Time- of Flight Mass Spectrometry (PTR-TOF-MS) data for untargeted biomarker discovery in exhaled breath: application to COVID-19 intubated ventilated patient - Camille Roquencourt 15:00-15:20 (20min) 14:00 - 15:20 (1h20) Genomique fonctionnelle Room 3 - https://us02web.zoom.us/j/82493854546 Nicolas Thierry-Mieg Room 3 › Dissection of intercellular communication using the transcriptome-based framework ICELLNET - Lucile Massenet-Regad 14:00-14:20 (20min) › Topoisomerase I prevents transcription- replication conflicts at transcription termination sites - Yaqun Liu 14:20-14:40 (20min) › Automated Quality Control of NGS Data using Machine Learning - Jean-Fred Fontaine 14:40-15:00 (20min) › PenDA, a rank-based method for personalized differential analysis: application to lung cancer - Clémentine Decamps 15:00-15:20 (20min) Pause café Gather town 15:20 - 15:30 (10min) Pause café Gather town Gather Town Session posters 1 (nombres pairs) gather town 15:30 - 17:00 (1h30) Session posters 1 (nombres pairs) gather town Session posters 1 (nombres pairs) gather town IFB Salle principale 17:00 - 17:30 (30min) IFB Salle principale Main room - https://us02web.zoom.us/s/85223524848	Keynote : Jean-Philippe Vert Chairman: Mahendra Mariadassou Salle principale 9:00 - 9:55 (55min) Keynote : Jean-Philippe Vert Chairman: Mahendra Mariadassou Salle principale Main room - https://us02web.zoom.us/s/85223524848 Deep learning for biological sequences Base de données & visualisation de données Évolution & phylogenetique Biologie computationnelle des systèmes 10:00 - 10:40 (40min) Base de données & visualisation de données Room 1 - https://us02web.zoom.us/s/85935915598 Sophie Schbath Room 1 › CALR-ETdb, the database of calreticulin variants diversity in essential thrombocythemia - Alexandre de Brevern 10:00-10:20 (20min) › Genoscapist: online exploration of quantitative profiles along genomes via interactively customized graphical representations - Sandra Dérozier 10:20-10:40 (20min) 10:00 - 10:40 (40min) Évolution & phylogenetique Room 2 - https://us02web.zoom.us/s/87021240668 Étienne Danchin Room 2 › AvP: a software package for automatic phylogenetic detection of candidate horizontal gene transfers. - Georgios Koutsovoulos 10:00-10:20 (20min) › ConDor: Site-wise convergence detector in large protein alignments - Morel Marie 10:20-10:40 (20min) 10:00 - 10:40 (40min) Biologie computationnelle des systèmes Room 3 - https://us02web.zoom.us/j/82493854546 Elisabeth Remy Room 3 › Automatic Synthesis of Boolean Networks from Biological Knowledge and Data - Athénaïs Vaginay 10:00-10:20 (20min) › Distinguishing Context Dependent Events in Quotients of Causal Stories - Sebastien Legare 10:20-10:40 (20min) Pause café Gather town 10:40 - 11:00 (20min) Pause café Gather town Gather Town Session posters 2 (nombres impairs) Gather town 11:00 - 12:30 (1h30) Session posters 2 (nombres impairs) Gather town Session posters 2 (nombres impairs) Gather town Déjeuner Gather town 12:30 - 14:00 (1h30) Déjeuner Gather town Gather Town Keynote: Julie Reveillaud Chairwoman: Claudine Médigue Salle principale 14:00 - 14:55 (55min) Keynote: Julie Reveillaud Chairwoman: Claudine Médigue Salle principale Main room - https://us02web.zoom.us/s/85223524848 Wolbachia population genomes from individual Culex pipiens ovaries reveal a plasmid-like extrachromosomal circular element Sponsor - Illumina Salle principale 15:00 - 15:15 (15min) Sponsor - Illumina Salle principale Main room - https://us02web.zoom.us/s/85223524848 Pause café Gather town 15:15 - 15:30 (15min) Pause café Gather town Gather Town Symposium: Bioinformatics for microbiomes Salle 1 Symposium Post selection inference: valid double-dipping Salle 2 15:30 - 18:00 (2h30) Symposium: Bioinformatics for microbiomes Salle 1 Rob Fin : Translating microbiome research outputs into main stream services in MGnify Lisa Röttjers Development of computational approaches for the prediction and analysis of species interaction networks from metagenomics data Raffaele Siano Sedimentary ancient DNA revealed irreversible plankton shifts and toxic microalgae species invasion in relation to human impact in the Bay of Brest Pause Table Ronde 15:30 - 18:00 (2h30) Symposium Post selection inference: valid double-dipping Salle 2 Yuval Benjamini Selective inference for region detection with high- throughput genomic assays Mitra Ebrahimpoor Inflated False Discovery Rate due to Volcano Plots: Problem and Solutions Pause Antoine Villié Post-Selection Inference for Sequence Motifs Lucy Gao Valid DifferentialAnalysis for Groups Defined via Clustering	Keynote : Thomas Schiex Chairwoman: Gwenaelle André-Leroux Salle principale 9:00 - 9:55 (55min) Keynote : Thomas Schiex Chairwoman: Gwenaelle André-Leroux Salle principale Main room - https://us02web.zoom.us/s/85223524848 Computer-aided protein design Algorithmes & structure de données de séquence I Meta-omiques & génomique microbienne Services et activités de plateforme 10:00 - 11:00 (1h) Algorithmes & structure de données de séquence I Room 1 - https://us02web.zoom.us/s/85935915598 Raluca Uricaru Room 1 › UMI-Gen: a UMI-based read simulator for variant calling evaluation - Vincent Sater 10:00-10:20 (20min) › QUARTIC: QUick pArallel algoRithms for high- Throughput sequencIng data proCessing - Frédéric Jarlier 10:20-10:40 (20min) › GraphUnzip: unzipping assembly graphs with long reads and Hi-C - Roland Faure 10:40-11:00 (20min) 10:00 - 11:00 (1h) Meta-omiques & génomique microbienne Room 2 - https://us02web.zoom.us/s/87021240668 Damien Éveillard Room 2 › No microbe is an island: metabolic complementarity in the microbiota and identification of key players - Clémence Frioux 10:00-10:20 (20min) › Shallow Shotgun Metagenomics as a cost- effective and accurate alternative to WGS for taxonomic profiling and clinical diagnosis - Benoit Goutorbe 10:20-10:40 (20min) › panRGP: a pangenome-based method to predict genomic islands and explore their diversity - Adelme Bazin 10:40-11:00 (20min) 10:00 - 11:00 (1h) Services et activités de plateforme Room 3 - https://us02web.zoom.us/j/82493854546 Erwan Corre Room 3 › Best practices of software development with Nextflow to support daily production in oncology - Fabrice Allain 10:00-10:20 (20min) › ToulligQC 2: fast and comprehensive quality controlfor Oxford Nanoporesequencing data - Laurent Jourdren 10:20-10:40 (20min) › Galaxy Genome Annotation (GGA) environment in the cloud - Romain Dallet 10:40-10:50 (10min) › A digital space for EMERGEN, the French plan for SARS-CoV-2 genomic surveillance and research - Jacques van Helden 10:50-11:00 (10min) Pause café Gather town 11:00 - 11:15 (15min) Pause café Gather town Gather Town Association des Jeunes Bioinformaticiens de France (JeBiF) Salle principale 11:15 - 11:30 (15min) Association des Jeunes Bioinformaticiens de France (JeBiF) Salle principale Main room - https://us02web.zoom.us/s/85223524848 Assemblée Générale de la Société Française de Bioinformatique (SFBI) Salle principale 11:30 - 12:30 (1h) Assemblée Générale de la Société Française de Bioinformatique (SFBI) Salle principale Main room - https://us02web.zoom.us/s/85223524848 Déjeuner Gather town 12:30 - 14:00 (1h30) Déjeuner Gather town Gather Town Keynote : Carole Goble Chairwoman: Sarah Cohen-Boulaka Salle principale 14:00 - 14:55 (55min) Keynote : Carole Goble Chairwoman: Sarah Cohen-Boulaka Salle principale Main room - https://us02web.zoom.us/s/85223524848 FAIR Computational Workflows Sponsor - Genopole d’Evry Salle principale 15:00 - 15:15 (15min) Sponsor - Genopole d’Evry Salle principale Main room - https://us02web.zoom.us/s/85223524848 Pause café Gather town 15:15 - 15:30 (15min) Pause café Gather town Gather Town Symposium: Open Science and Interoperability in Bioinformatics Salle 1 - https://us02web.zoom.us/s/85935915598 Where are we in the search for DNA motifs involved in transcriptional regulation? Salle 2 - https://us02web.zoom.us/s/87021240668 Symposium: Integrative structural modeling in the era of big data and artificial intelligence Salle 3 - https://us02web.zoom.us/s/82493854546 15:30 - 18:00 (2h30) Symposium: Open Science and Interoperability in Bioinformatics Salle 1 - https://us02web.zoom.us/s/85935915598 Sarah Cohen-Boulakia Introduction aux concepts de la Science Ouverte et de l'Interopérabilité appliqués à la Bioinformatique Frank Michel Annoter les pages web liées à la biodiversité avec des informations structurées pour les rendre plus découvrables et réutilisables Philippe Rocca-Serra Operating Fair principles: the FAIR cookbook project Cyril Pommier Standards d'échanges et concepts FAIR pour la Communauté Plantes Laura Furlong The DisGeNET knowledge platform: facilitating the access and use of disease genomics data Oliver Collin & Konogan Bouhry maDMP: vers un écosystème intégré pour la gestion des données de la Recherche Pause Flash presentations: T.Rosnet, J. Seiler, P.Poulain, H. Chiapello Table ronde 15:30 - 18:00 (2h30) Where are we in the search for DNA motifs involved in transcriptional regulation? Salle 2 - https://us02web.zoom.us/s/87021240668 François Parcy Confronting in vitro genomics to real life data reveals properties of floral transcription factors Morgane Thomas-Chollier Motif discovery in epigenomics datasets with RSAT peak-motifs2 Anthony Mathelier Combining TF binding profiles with ChIP-seq data to predict high quality direct TF-DNA interaction Pause Laurent Brehelin Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes Julien Rozière Genome-wide de novo detection of preferentially located motifs in 5’- and 3’-proximal regions from Arabidopsis and maize 15:30 - 18:00 (2h30) Symposium: Integrative structural modeling in the era of big data and artificial intelligence Salle 3 - https://us02web.zoom.us/s/82493854546 Introduction: Current challenges in 3D modeling of proteins and complexes Riccardo Pellarin Bayesian modeling in integrative structural biology Ezgi Karaca Dynamic Integrative Modeling of Molecular Machines Pause Sergei Grudinin Entering the post-protein structure prediction era Slavica Jonic Cryo-EM studies of continuous conformational variability of biomolecules in vitro and in situ based on image analysis, simulation and deep learning	Keynote : Roderic Guigó Serra Chairman: Charles Lecellier Salle principale 9:00 - 9:55 (55min) Keynote : Roderic Guigó Serra Chairman: Charles Lecellier Salle principale Main room - https://us02web.zoom.us/s/85223524848 The epigenetic logic of gene activation Sponsor - France Génomique Salle principale 10:00 - 10:15 (15min) Sponsor - France Génomique Salle principale Main room - https://us02web.zoom.us/s/85223524848 Pause café Gather town 10:15 - 10:30 (15min) Pause café Gather town Gather Town Bioinformatique structurale II Statistiques, machine learning & intelligence artificielle II Algorithmes & structure de données de séquence II 10:30 - 11:50 (1h20) Bioinformatique structurale II Room 1 - https://us02web.zoom.us/s/85935915598 Benjamin Bardiaux Room 1 › SLiMAN - a webserver to analyze protein- protein interaction mediated by short linear motifs - Victoria Reys 10:30-10:50 (20min) › Discovery of macrocyclic inhibitors of ALK using Frags2Drugs, a fragment-based drug design in silico tool - Gautier Peyrat 10:50-11:10 (20min) › Structural analysis of interaction between SARS-CoV-2 spike protein and the human ACE2 receptor - Sarah Nacéri 11:10-11:30 (20min) › Cyclodipeptide synthases of the NYH subfamily recognize tRNA using an α-helix enriched with positive residues - Anastasia Croitoru 11:30-11:50 (20min) 10:30 - 11:50 (1h20) Statistiques, machine learning & intelligence artificielle II Room 2 - https://us02web.zoom.us/s/87021240668 Nicolas Vergne Room 2 › IIDEA: Interactive Inference for Differential Expression Analyses - Nicolas Enjalbert Courrech 10:30-10:50 (20min) › Benchmarking joint multi-omics dimensionalityreduction approaches for the study of cancer - Laura Cantini 10:50-11:10 (20min) › The SgenoLasso and its cousins for selective genotyping and extreme sampling - Charles-Elie Rabier 11:10-11:30 (20min) › A systematic analysis of the genomic features involved in cellular specificities of transcription factor binding - Raphaël Romero 11:30-11:50 (20min) 10:30 - 11:50 (1h20) Algorithmes & structure de données de séquence II Room 3 - https://us02web.zoom.us/j/82493854546 Rayan Chiki Room 3 › MTG-Link: filling gaps in draft genome assemblies with linked read data - Anne Guichard 10:30-10:50 (20min) › LEVIATHAN: efficient discovery of large structural variants by leveraging long-range information from Linked-Reads data - Pierre Morisse 10:50-11:10 (20min) › Freddie: annotation-independent detection and Ddscovery of transcriptomic alternative splicing isoforms using long-read sequencing - Cedric Chauve 11:10-11:30 (20min) Présentation JOBIM 2022 Prix SFBI Clôture de JOBIM 2021 Salle principale 11:50 - 12:30 (40min) Présentation JOBIM 2022 Prix SFBI Clôture de JOBIM 2021 Salle principale Main room - https://us02web.zoom.us/s/85223524848