mardi 3 juillet 2018

Heures événement  
12:00 - 14:00 Registration | Check-in | Welcome coffee - Accueil Enregistrement Badges Café d’accueil  
14:00 - 14:30 Welcome opening speech (Auditorium) - Christine Brun, Benoit Ballester  
14:30 - 15:30 Keynote: Ludovic Orlando (Auditorium) - Bioinformatics for Bugs, Beasts and Greens: Horses genomics  
15:30 - 16:30 Bioinformatics for Bugs, Beasts and Greens (Auditorium) - Chair: Guy Perriere  
15:30 - 15:50 › Co-option of complex molecular system in bacterial and archaeal membrane - Rémi Denise, Génomique évolutive des Microbes  
15:50 - 16:10 › The evolution of large and giant viruses and their relationships with Eukaryotes - Julien Guglielmini, Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB  
16:10 - 16:30 › Probabilistic PCA for count data in microbial ecology - Mahendra Mariadassou, Institut National de Recherche Agronomique - Centre de Jouy-en-Josas  
16:30 - 17:00 Coffee Break (Espace vieux-port)  
16:30 - 17:00 Booths in Exhibition Zone - omicX, EMBL-EBI, Cancéropôle PACA  
17:00 - 17:05 Presentation of "Groupement de Recherche en Génomique Environnementale" (Auditorium)  
17:05 - 18:05 Bioinformatics for Bugs, Beasts and Greens (Auditorium) - Chair: Guy Perriere  
17:05 - 17:25 › PPanGGOLiN: Depicting microbial diversity via a Partitioned Pangenome Graph - Guillaume Gautreau, Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme - Rémi Planel, Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme  
17:25 - 17:45 › CARNAC-LR : Clustering coefficient-based Acquisition of RNA Communities in Long Reads - Camille Marchet, Institut de Recherche en Informatique et Systèmes Aléatoires  
17:45 - 18:05 › Assembling the genome of the desert ant and uncovering structural rearrangements with instaGRAAL, a fast and scalable scaffolder based on Hi-C data - Lyam Baudry, Régulation spatiale des Génomes - Spatial Regulation of Genomes  
18:05 - 18:35 Presentations JeBIF / bioinfo-fr.net / Bioinfuse (Auditorium)  
18:35 - 22:00 Opening dinner cocktail (Espace vieux-port)  

mercredi 4 juillet 2018

Heures événement  
08:45 - 09:00 Welcome coffee (Espace vieux-port)  
09:00 - 10:00 Keynote: Pierre Antoine Gourraud (Auditorium)  
10:00 - 10:40 New challenges for bioinformatics in the personalized medicine era (Auditorium) - Chair: Emmanuel Barillot  
10:00 - 10:20 › Bayesian Genome-Wide Association Study to discover novel lifespan-associated loci - Ninon Mounier, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland, Institute of Social and Preventive Medicine (IUMSP), Lausanne University Hospital, Lausanne 1010, Switzerland  
10:20 - 10:40 › Aggregation of rare family-specific variants associated with Rheumatoid Arthritis - Maëva Veyssiere, GenHotel  
10:40 - 11:10 Booths in Exhibition Zone - omicX, EMBL-EBI, Cancéropôle PACA  
10:40 - 11:10 Coffee Break (Espace vieux-port)  
11:10 - 12:10 New challenges for bioinformatics in the personalized medicine era (Auditorium) - Chair: Nicolas Thierry-Mieg  
11:10 - 11:30 › Sarek, a portable workflow for WGS analysis of germline and somatic mutations - Maxime Garcia, The Swedish Childhood Tumor Biobank, Dept. of Oncology Pathology, National Genomics Infrastructure, Science for Life Laboratory, Karolinska Institutet  
11:30 - 11:50 › I-LowVarFreq : improving low-frequency variant detection using a new UMI-based variant calling approach for paired-end sequencing NGS libraries. - Pierre-Julien VIAILLY, Centre Henri Becquerel, 76000 Rouen, France, Normandie Univ, UNIROUEN, INSERM U1245, Team “Genomics and Biomarkers of Lymphoma and Solid Tumors”, 76000 Rouen  
11:50 - 12:10 › From individual genetic variations towards haplotype: GEMPROT, a new way of reading VCF files - Tania Cuppens, UMR1078 "Génétique, Génomique Fonctionnelle et Biotechnologies", INSERM, EFS, Université de Brest, IBSAM, CHU de Brest  
11:10 - 12:10 Bioinformatics for Bugs, Beasts and Greens (DNA room) - Chair: Eric Rivals  
11:10 - 11:30 › A new rapid, flexible and intuitive software to simulate phylogenies of infections - Gonché DANESH, Laboratoire “Maladies Infectieuses et Vecteurs, Ecologie, Evolution et Contrôle”  
11:30 - 11:50 › Combining eDNA metabarcoding and supervised machine learning for routine environmental applications: an example with marine aquaculture - Tristan Cordier, Université de Genève  
11:50 - 12:10 › On improving the approximation ratio of the r-shortest common superstring problem - Raluca Uricaru, Laboratoire Bordelais de Recherche en Informatique  
11:10 - 12:10 Structural Bioinformatics/Proteomics (Protein room) - Chair: Bianca Habermann  
11:10 - 11:30 › Assessing the functional impact of genomic alterations using proteogenomics - Georges Bedran, CEA/DRF/BIG/BGE/EDYP, UFR Sciences et Techniques - Université de Rouen, CEA/DRF/JACOB/CNRGH  
11:30 - 11:50 › Structural and dynamics studies of a potassium channel and disease-associated mutants - Charline FAGNEN, Laboratoire de Biologie et de Pharmacologie Appliquée, Institut de minéralogie, de physique des matériaux et de cosmochimie  
11:50 - 12:10 › NR-DBIND : A database dedicated to nuclear receptor binding data including negative data and pharmacological profile - Manon Réau, Laboratoire Génomique, Bioinformatique et Applications  
12:10 - 13:30 Lunch (Espace vieux-port)  
12:10 - 13:30 Booths in Exhibition Zone - omicX, EMBL-EBI, Cancéropôle PACA  
12:10 - 13:30 Cambridge 2 Marseille chat (DNA room) - Round table  
13:30 - 14:30 Keynote: Eleftheria Zeggini (Auditorium)  
14:30 - 15:10 New challenges for bioinformatics in the personalized medicine era (Auditorium) - Chair: Karyn Megy  
14:30 - 14:50 › Unravelling human preimplantation development by single-cell RNA-Seq: from experiment design to cell fate trajectories. - Dimitri Meistermann, Centre de Recherche en Transplantation et Immunologie, Laboratoire des Sciences du Numérique de Nantes  
14:50 - 15:10 › Proteomic and phosphoproteomic analysis of medulloblastoma reveals distinct activated pathways between subgroups - Loredana Martignetti, Cancer et génôme: Bioinformatique, biostatistiques et épidémiologie d'un système complexe  
15:10 - 15:30 Flash Poster presentation 4x5' (Auditorium)  
15:30 - 16:00 Pause (Espace vieux-port)  
16:00 - 17:00 Poster session - Even numbers - Even numbers  
17:00 - 18:00 Bioinformatics for Bugs, Beasts and Greens (Auditorium) - Chair: Pascal Hingamp  
17:00 - 17:20 › Comparative metagenomics highlighted a core of metabolic capabilities in multiple serpentinizing ecosystems - Eléonore Frouin, Institut méditerranéen d'océanologie  
17:20 - 17:40 › Single-cell genome study of marine protists in the framework of the Tara Oceans project - Léo d'Agata, Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob  
17:40 - 18:00 › MACADAM a user-friendly MetAboliC pAthway DAtabase for complex Microbial community function analysis - Malo Le Boulch, GenPhySE - UMR 1388  
17:00 - 18:00 New challenges for bioinformatics in the personalized medicine era (DNA room) - Chair: Anais Baudot  
17:00 - 17:20 › Fine-scale genetic population structure in western France - Christian Dina, Institut du Thorax  
17:20 - 17:40 › Identification de marques épigénétiques marqueurs de prédisposition aux maladies métaboliques - Jérémy Tournayre, Unité de Nutrition Humaine - Clermont Auvergne  
17:40 - 18:00 › Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence proteins - Andreas Zanzoni, Theories and Approaches of Genomic Complexity  
17:00 - 18:00 Systems Biology/Functional Genomics (Protein room) - Chair: Benoit Bely  
17:00 - 17:20 › Biocuration and rule-based modelling of protein interaction networks in KAMI - Sébastien Légaré  
17:20 - 17:40 › Build your own multi-omics website with BACNET - Christophe Becavin, Institut Pasteur – Hub Bioinformatique et Biostatistique – C3BI, USR 3756 IP CNRS  
17:40 - 18:00 › Gigwa - Genotype Investigator for Genome-Wide Analyses - Pierre Larmande, Institut de Biologie Computationnelle, Institut de Recherche pour le Développement  
18:00 - 19:30 Social Events  
18:00 - 19:30 Booths in Exhibition Zone - omicX, EMBL-EBI, Cancéropôle PACA  
19:30 - 20:30 Free evening  

jeudi 5 juillet 2018

Heures événement  
08:20 - 08:40 Welcome Coffee (Espace vieux-port)  
08:40 - 09:40 Keynote: Edda Klipp (Auditorium)  
09:40 - 10:40 Systems Biology/Functional Genomics (Auditorium) - Chair: Denis Thieffry  
09:40 - 10:00 › Statistical modeling of bacterial promoter sequences for regulatory motif discovery using expression data - Ibrahim Sultan, INRA-MaIAGE  
10:00 - 10:20 › A map of direct TF – DNA interactions in the human genome - Anthony Mathelier, Centre for Molecular Medicine Norway, Nordic EMBL, Norway  
10:20 - 10:40 › Multiple probabilistic models resolve the functional organization of the cryptochrome/photolyase protein family - Riccardo Vicedomini, Institut des Sciences du Calcul et des Données, Laboratoire de Biologie Computationnelle et Quantitative  
10:40 - 11:10 Coffee Break (Espace vieux-port)  
11:10 - 12:10 Systems Biology/Functional Genomics (Auditorium) - Chair: Anthony Mathelier  
11:10 - 11:30 › RSAT 2018: regulatory sequence analysis tools 20th anniversary - Morgane Thomas-Chollier, Institut de Biologie de l'Ecole Normale Superieure  
11:30 - 11:50 › ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments - Jeanne Chèneby, Aix-Marseille Université, UMR1090 TAGC  
11:50 - 12:10 › Enhancer-gene associations in complete genomes unravel ancestral vertebrate regulation and key principles of enhancer function - Yves CLEMENT, Institut de biologie de lÉNS Paris (UMR 8197/1024)  
11:10 - 12:10 Systems Biology/Functional Genomics (DNA room) - Chair: Aitor Gonzalez  
11:10 - 11:30 › Mathematical modeling of Fe-S biogenesis shows strong links between iron homeostasis and oxidative stress response - Firas Hammami, Institut de Mathématiques de Marseille, Laboratoire de chimie bactérienne  
11:30 - 11:50 › Logical modelling and analysis of cellular regulatory networks with GINsim 3.0 - Aurélien Naldi, Institut de Biologie de l'ENS - Denis Thieffry, Institut de Biologie de l'ENS  
11:50 - 12:10 › Multilevel logical modelling of the regulatory network governing dorsal-ventral axis specification in the sea urchin P. lividus. - Swann FLOC'HLAY, Institute of Biology at the Ecole Normale Superieure  
11:10 - 12:10 Systems Biology/Functional Genomics (Protein room) - Chair: Camille Berthelot  
11:10 - 11:30 › Predicting 3'UTR's regulation of protein multifunctionality - Diogo Ribeiro, Theories and Approaches of Genomic Complexity  
11:30 - 11:50 › Prediction of new multiciliogenesis genes using a fine-grained comparative genomic approach - Audrey Defosset, Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie  
11:50 - 12:10 › PhyloSofS: PHYLOgenies of Splicing isOForms Structures - Diego Javier Zea, Laboratory of Computational and Quantitative Biology  
12:10 - 13:30 Lunch (Espace vieux-port)  
12:10 - 13:30 Booths in Exhibition Zone - omicX, EMBL-EBI, Cancéropôle PACA  
13:30 - 14:30 Keynote: Emmanuel Levy (Auditorium)  
14:30 - 15:10 Structural Bioinformatics/Proteomics (Auditorium) - Chair : Anne-Claude Camproux  
14:30 - 14:50 › Protein interaction energy landscapes are shaped by functional and also non-functional partners - Hugo Schweke, Institute for Integrative Biology of the Cell (I2BC)  
14:50 - 15:10 › A hybrid combinatorial method for docking a single-stranded RNA in a protein pocket at the thermodynamic equilibrium - Isaure Chauvot de Beauchêne, LORIA  
15:10 - 15:30 Flash Poster presentation 4x5' (Auditorium)  
15:30 - 16:00 Coffee Break (Espace vieux-port)  
15:30 - 16:00 Booths in Exhibition Zone - omicX, EMBL-EBI, Cancéropôle PACA  
16:00 - 17:00 Poster session - Odd numbers - Odd numbers  
17:00 - 19:00 General Assembly of SFBI, IFB, GdR BIM (Auditorium)  
19:00 - 23:55 Gala Dinner & Concert (Espace vieux-port)  

vendredi 6 juillet 2018

Heures événement  
08:45 - 09:00 Welcome Coffee (Espace vieux-port)  
09:00 - 10:00 Keynote: Elizabeth Purdom (Auditorium)  
10:00 - 10:40 Data Science (Auditorium) - Chair: Chloé-Agathe Azencott  
10:00 - 10:20 › Protein domain sequence analyses using Long-Short Term Memory Recurrent Neural Networks - Tristan Bitard Feildel, Laboratoire de Biologie Computationnelle et Quantitative  
10:20 - 10:40 › RNA complex prediction as a constrained maximum clique problem - Audrey Legendre, IBISC, Univ Evry, Université Paris Saclay  
10:40 - 11:05 Coffee Break (Espace vieux-port)  
11:05 - 11:45 Data Science (Auditorium) - Chair: Chloé-Agathe Azencott  
11:05 - 11:25 › Latent Tree based Inference of Ecological Network using the Poisson Log-Normal Model - Raphaëlle Momal, UMR MIA-Paris, INRA, AgroParis Tech, Université Paris-Saclay, 75005, Paris, FRANCE  
11:25 - 11:45 › mmquant and mmannot: How to handle multiple-mapping reads in (s)RNA-Seq - Matthias Zytnicki, MIAT  
11:45 - 12:15 Closing speech JOBIM2018 | SFBI Awards | Presentation of JOBIM2019 (Auditorium) - Christine Brun, Benoit Ballester  
12:15 - 13:00 Lunch bags (Espace vieux-port)