Accepted oral communications are the following:
Proceedings:
Tuesday July 5th
Exploring variability of machine learning methods : first step towards biomarker consensus signatures
Elsa Claude, Mickaël Leclercq, Arnaud Droit, Patricia Thébault and Raluca Uricaru
Optimal Scaffolding for Chloroplasts’ Inverted Repeats
Victor Epain, Rumen Andonov and Dominique Lavenier
Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence
Nina Guérin, Quentin Carradec and Patrick Wincker
Adaptive splines-based logistic regression with a ReLU neural network
Marie Guyomard, Susana Barbosa and Lionel Fillatre
Detection and correction of non-conformities and redundancies in complexes of molecules in BioPAX
Camille Juigné, Olivier Dameron, François Moreews, Florence Gondret and Emmanuelle Becker
Gene Expression prediction using Deep Learning
Camille Kergal, Christophe Hitte, Marie-Dominique Galibert, Catherine Andre, Doga Consortium and Thomas Derrien
VOCAL: An early warning system to detect concerning new SARS-CoV-2 variants from sequencing data
Kunaphas Kongkitimanon, Martin Hölzer and Hugues Richard
Wednesday July 6th
kmtricks: creating bloom filters for indexing large sequencing data collections
Téo Lemane, Paul Medvedev, Rayan Chikhi and Pierre Peterlongo
Analysis of SARS-CoV-2 and human protein interactions: a CAPRI-COVID Round
Théo Mauri, Guillaume Brysbaert, Paul A. Bates, Shoshana J. Wodak and Marc F. Lensink
Comprehensive multi-omics integration of major depressive disorder
Amazigh Mokhtari, El Chérif Ibrahim, Arnaud Gloaguen, David Cohen, Margot Derouin, Cynthia Marie-Claire, Bruno Etain, Raoul Belzeaux, Andrée Delahaye-Duriez and Pierre-Eric Lutz
Thursday July 7th
Single-cell RNA sequencing reveals aberrant megakaryocyte-erythroid progenitor and megakaryocyte populations in thrombocytopenic ETV6 variant carriers
Timothée Bigot, Laurent Hannouche, Elisa Gabinaud, Véronique Sbarra, Dominique Payet-Bornet, Marie Loosveld, Delphine Potier, Marie-Christine Alessi and Poggi Marjorie
Condition-specific and recurrent perturbation-communities in multiple differential co-expression networks
Galadriel Brière, Agnès Nadjar, Raluca Uricaru and Patricia Thébault
Improving the accuracy of small variant calling with ensemble machine learning methods
Jennifer Del Giudice and Gavin Parnaby
LowKi: Efficient estimation of kinship and fraternity coefficients from low-depth sequencing data
Anthony Herzig, Marina Ciullo, Francegenref Consortium, Anne-Louise Leutenegger and Hervé Perdry
Uncovering specific alterations of ribosomal RNA 2'O-ribose methylation in glioma subtypes using the latest improvements of RiboMethSeq technology
Hermes Paraqindes, Nour-El-Houda Mourksi, Samantha Ballesta, Emilie Thomas, Janice Kielbassa, Jessie Perrossier, Marjorie Carrere, Valéry Attignon, Alain Viari, Jean-Jacques Diaz, David Meyronet, Mathieu Gabut, François Ducray, Virginie Marcel and Sébastien Durand
Friday July 8th
Insertion of Alu elements impacts sequence-mediated nucleosome positioning
Jeremy Barbier, Fabien Sassolas, Cédric Vaillant, Jean-Nicolas Volff, Frédéric G. Brunet and Benjamin Audit
Overcoming small and incomplete datasets limitations in multi-omic integration
Pauline Brochet, Edecio Cunha-Neto, Christophe Chevillard and Lionel Spinelli
Interaction between gene expression and chromatin environment: application to the study of H3K79me2 and its methyltransferase DOT1L during spermatogenesis
Manon Coulee, Julie Cocquet and Laila El Khattabi
Discovery of potential functional paths by integration of phospho-proteomics data in the PPI network using a RWR framework
Jérémie Perrin, Olivier Destaing and Christine Brun
KinDock 2.0: A robust protein-kinases virtual screening tool enhanced by machine learning predictors.
Victor Reys and Gilles Labesse
Highlights:
Tuesday July 5th
GraphGONet: a self-explaining neural network encapsulating the Gene Ontology graph for phenotype prediction on gene expression (link)
Victoria Bourgeais, Farida Zehraoui and Blaise Hanczar
FORUM: Knowledge Graph (KG) for semantic representation and inference of relations between chemicals and biomedical concepts (link)
Maxime Delmas, Olivier Filangi, Nils Paulhe, Florence Vinson, Christophe Duperier, William Garrier, Paul-Emeric Saunier, Yoann Pitarch, Fabien Jourdan, Franck Giacomoni and Clément Frainay
GC content but not nucleosome positioning directly contributes to intron-splicing efficiency in Paramecium (link)
Stefano Gnan, Mélody Matelot, Marion Weiman, Olivier Arnaiz, Frédéric Guérin, Linda Sperling, Mireille Bétermier, Claude Thermes, Sandra Duharcourt and Chun-Long Chen
TopoFun: a machine learning method to improve the functional similarity of gene co-expression modules (link)
Ali Janbain, Christelle Reynès, Zainab Assaghir, Hassan Zeineddine, Robert Sabatier and Laurent Journot
Biosynthetic potential of the global ocean microbiome (link)
Lucas Paoli, Hans-Joachim Ruscheweyh, Clarissa C. Forneris, Florian Hubrich, Satria Kautsar, Agneya Bhushan, Quentin Clayssen, Guillem Salazar, Alessio Milanese, Charlotte I. Carlström, Chrysa Papadopoulou, Daniel Gehrig, Mikhail Karasikov, Harun Mustafa, Alessandro Lotti, Martin Larralde, Laura M. Carroll, Pablo Sánchez, Ahmed A. Zayed, Dylan R. Cronin, Silvia G. Acinas, Peer Bork, Chris Bowler, Tom O. Delmont, Josep M. Gasol, Alvar D. Gossert, Andre Kahles, Matthew B. Sullivan, Patrick Wincker, Georg Zeller, Serina L. Robinson, Jörn Piel and Shinichi Sunagawa
findere: fast and precise approximate membership query (link)
Lucas Robidou and Pierre Peterlongo
Wednesday July 6th
Genotyping multiscale variation with genome graphs (link)
Brice Letcher, Martin Hunt and Zamin Iqbal
Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics (link)
Bertrand Marchand, Yann Ponty and Laurent Bulteau
Inference of an Integrative, Executable Network for Rheumatoid Arthritis Combining Data-Driven Machine Learning Approaches and a State-of-the-Art Mechanistic Disease Map (link)
Quentin Miagoux, Vidisha Singh, Dereck de Mézquita, Valérie Chaudru, Mohamed Elati, Elisabeth Petit-Teixeira and Anna Niarakis
Conformational variability in proteins bound to single-stranded DNA: A new benchmark for new docking perspectives (link)
Dominique Mias-Lucquin and Isaure Chauvot de Beauchene
Calcium signaling is impaired in PTEN-deficient T cell acute lymphoblastic leukemia (link)
Saran Pankaew, Delphine Potier, Clémence Grosjean, Mathis Nozais, Julie Quessada, Marie Loosveld, Élisabeth Remy and Dominique Payet-Borne
Assessing conservation of alternative splicing with evolutionary splicing graphs (link)
Diego Zea, Elodie Laine and Hugues Richard
Thursday July 7th
Computing disease progression scores using multimodal variational autoencoders trained with neuroimaging and microRNA data (link)
Virgilio Kmetzsch, Emmanuelle Becker, Dario Saracino, Vincent Anquetil, Daisy Rinaldi, Agnès Camuzat, Thomas Gareau, Isabelle Le Ber and Olivier Colliot
Friday July 8th
Pseudoquantifying hundreds of proteins in millions of single cells (link)
Etienne Becht, Evan Newell, Raphael Gottardo and Mark B. Headley
Investigating ADR mechanisms with Explainable AI: a feasibility study with knowledge graph mining (link)
Emmanuel Bresso, Pierre Monnin, Cédric Bousquet, François-Elie Calvier, Ndeye-Coumba Ndiaye, Nadine Petitpain, Malika Smail-Tabbone and Adrien Coulet
Effect of quercetin on lipid membrane rigidity: assessment by atomic force microscopy and molecular dynamics simulations (link)
Jad Eid, Alia Jraij, Luca Monticelli and Helene Greige-Gerges
Semantic Web technologies are effective to remove redundancies from protein-protein interaction databases and define reproducible interactomes (link)
Marc Melkonian, Camille Juigné, Olivier Dameron, Gwenaël Rabut and Emmanuelle Becker
Platforms:
Tuesday July 5th
UseGalaxy.fr: a Galaxy server for the French bioinformatics community
Anthony Bretaudeau, Thomas Chaussepied, Lain Pavot, Julien Seiler and Gildas Le Corguillé
EMERGEN-BioInfo : The digital platform for the French SARS-CoV-2 genomic surveillance and research program
Thomas Denecker, Imane Messak, Anliat Mohamed, Chiara Antoinat, Arthur Le Bars, Arianna Tonazzolli, Benjamin Demaille, Olivier Sand, François Gerbes, Thomas Rosnet, Laurent Bouri, Julien Seiler, Nicole Charrière, Christophe Antoniewski, Anne Bozorgan, Javier Castro Alvarez, Jeanne Sudour, Yann Le Strat, Bruno Coignard, Abdelkader Amzert, Nebras Gharbi, Franck Lethimonier, Hélène Chiapello, Naira Naouar, Claudine Médigue, Gildas Le Corguillé, David Salgado and Jacques van Helden
Thursday July 7th
Bioinformatics platforms and data management : the GenOuest experience
Olivier Collin and Konogan Bourhy
Linda: an interactive framework for experimental design and management of metadata
Benjamin Dartigues, Alexis Groppi, Sylvain Prigent, Yves Gibon, Cécile Cabasson and Macha Nikolski
Improving clinical diagnosis using Nanopore Adaptive Sampling and NanoCliD
Eleonore Frouin, Kevin Merchadou, Mathilde Filser, Abderaouf Hamza, Elodie Girard, Nicolas Servant, Julien Masliah-Planchon and Victor Renault
