› Co-option of complex molecular system in bacterial and archaeal membrane - Rémi Denise, Génomique évolutive des Microbes
15:30-15:50 (20min)
› The evolution of large and giant viruses and their relationships with Eukaryotes - Julien Guglielmini, Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB
15:50-16:10 (20min)
› Probabilistic PCA for count data in microbial ecology - Mahendra Mariadassou, Institut National de Recherche Agronomique - Centre de Jouy-en-Josas
16:10-16:30 (20min)
› 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
17:05-17:25 (20min)
› CARNAC-LR : Clustering coefficient-based Acquisition of RNA Communities in Long Reads - Camille Marchet, Institut de Recherche en Informatique et Systèmes Aléatoires
17:25-17:45 (20min)
› 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
17:45-18:05 (20min)
New challenges for bioinformatics in the personalized medicine era
Auditorium
Chair: Emmanuel Barillot
› 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
10:00-10:20 (20min)
› Aggregation of rare family-specific variants associated with Rheumatoid Arthritis - Maëva Veyssiere, GenHotel
10:20-10:40 (20min)
New challenges for bioinformatics in the personalized medicine era
Auditorium
Chair: Nicolas Thierry-Mieg
› 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
11:10-11:30 (20min)
› 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
11:30-11:50 (20min)
› 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
11:50-12:10 (20min)
11:10 - 12:10 (1h)
Bioinformatics for Bugs, Beasts and Greens
DNA room
Chair: Eric Rivals
› A new rapid, flexible and intuitive software to simulate phylogenies of infections - Gonché DANESH, Laboratoire “Maladies Infectieuses et Vecteurs, Ecologie, Evolution et Contrôle”
11:10-11:30 (20min)
› Combining eDNA metabarcoding and supervised machine learning for routine environmental applications: an example with marine aquaculture - Tristan Cordier, Université de Genève
11:30-11:50 (20min)
› On improving the approximation ratio of the r-shortest common superstring problem - Raluca Uricaru, Laboratoire Bordelais de Recherche en Informatique
11:50-12:10 (20min)
11:10 - 12:10 (1h)
Structural Bioinformatics/Proteomics
Protein room
Chair: Bianca Habermann
› 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
11:10-11:30 (20min)
› 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
11:30-11:50 (20min)
› NR-DBIND : A database dedicated to nuclear receptor binding data including negative data and pharmacological profile - Manon Réau, Laboratoire Génomique, Bioinformatique et Applications
11:50-12:10 (20min)
New challenges for bioinformatics in the personalized medicine era
Auditorium
Chair: Karyn Megy
› 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
14:30-14:50 (20min)
› 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
14:50-15:10 (20min)
› Comparative metagenomics highlighted a core of metabolic capabilities in multiple serpentinizing ecosystems - Eléonore Frouin, Institut méditerranéen d'océanologie
17:00-17:20 (20min)
› 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
17:20-17:40 (20min)
› MACADAM a user-friendly MetAboliC pAthway DAtabase for complex Microbial community function analysis - Malo Le Boulch, GenPhySE - UMR 1388
17:40-18:00 (20min)
17:00 - 18:00 (1h)
New challenges for bioinformatics in the personalized medicine era
DNA room
Chair: Anais Baudot
› Fine-scale genetic population structure in western France - Christian Dina, Institut du Thorax
17:00-17:20 (20min)
› Identification de marques épigénétiques marqueurs de prédisposition aux maladies métaboliques - Jérémy Tournayre, Unité de Nutrition Humaine - Clermont Auvergne
17:20-17:40 (20min)
› Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence proteins - Andreas Zanzoni, Theories and Approaches of Genomic Complexity
17:40-18:00 (20min)
17:00 - 18:00 (1h)
Systems Biology/Functional Genomics
Protein room
Chair: Benoit Bely
› Biocuration and rule-based modelling of protein interaction networks in KAMI - Sébastien Légaré
17:00-17:20 (20min)
› Build your own multi-omics website with BACNET - Christophe Becavin, Institut Pasteur – Hub Bioinformatique et Biostatistique – C3BI, USR 3756 IP CNRS
17:20-17:40 (20min)
› Gigwa - Genotype Investigator for Genome-Wide Analyses - Pierre Larmande, Institut de Biologie Computationnelle, Institut de Recherche pour le Développement
17:40-18:00 (20min)
› Statistical modeling of bacterial promoter sequences for regulatory motif discovery using expression data - Ibrahim Sultan, INRA-MaIAGE
09:40-10:00 (20min)
› A map of direct TF – DNA interactions in the human genome - Anthony Mathelier, Centre for Molecular Medicine Norway, Nordic EMBL, Norway
10:00-10:20 (20min)
› 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
10:20-10:40 (20min)
› 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
11:30-11:50 (20min)
› 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)
11:50-12:10 (20min)
11:10 - 12:10 (1h)
Systems Biology/Functional Genomics
DNA room
Chair: Aitor Gonzalez
› 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
11:10-11:30 (20min)
› 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
11:30-11:50 (20min)
› 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
11:50-12:10 (20min)
11:10 - 12:10 (1h)
Systems Biology/Functional Genomics
Protein room
Chair: Camille Berthelot
› Predicting 3'UTR's regulation of protein multifunctionality - Diogo Ribeiro, Theories and Approaches of Genomic Complexity
11:10-11:30 (20min)
› 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
11:30-11:50 (20min)
› PhyloSofS: PHYLOgenies of Splicing isOForms Structures - Diego Javier Zea, Laboratory of Computational and Quantitative Biology
11:50-12:10 (20min)
› Protein interaction energy landscapes are shaped by functional and also non-functional partners - Hugo Schweke, Institute for Integrative Biology of the Cell (I2BC)
14:30-14:50 (20min)
› A hybrid combinatorial method for docking a single-stranded RNA in a protein pocket at the thermodynamic equilibrium - Isaure Chauvot de Beauchêne, LORIA
14:50-15:10 (20min)
› Protein domain sequence analyses using Long-Short Term Memory Recurrent Neural Networks - Tristan Bitard Feildel, Laboratoire de Biologie Computationnelle et Quantitative
10:00-10:20 (20min)
› RNA complex prediction as a constrained maximum clique problem - Audrey Legendre, IBISC, Univ Evry, Université Paris Saclay
10:20-10:40 (20min)
› 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
11:05-11:25 (20min)
› mmquant and mmannot: How to handle multiple-mapping reads in (s)RNA-Seq - Matthias Zytnicki, MIAT
11:25-11:45 (20min)
Auditorium
