Poster de conférence
BioInfo
Publications
All the team’s scientific publications can be found on HAL: https://hal.universite-paris-saclay.fr/LISN-BIOINFO
You will find below the latest submissions.
Recent publications
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Communication dans un congrès
Arnaud Quelin, Frederic Austerlitz, Flora Jay. Using supervised machine learning methods to infer demographic history from genomic data. Machine Learning for Evolutionary Genomics Data, May 2024, Heraklion, Greece. ⟨hal-05570974⟩
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Poster de conférence
Arnaud Quelin, Jazeps Medina Tretmanis, Emilia Huerta-Sanchez, Frederic Austerlitz, Flora Jay. Assessing the contribution of ancient genomic data to the inference of historical demographic parameters. JOBIM 2025 – Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2025, Bordeaux, France. ⟨hal-05570966⟩
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Communication dans un congrès
Jean Cury, Théophile Sanchez, Erik Madison Bray, Jazeps Medina-Tretmanis, María Ávila-Arcos, et al.. Inferring effective population sizes of bacterial populations while accounting for unknown recombination and selection: a deep learning approach. ECML PKDD 2022 – Machine Learning for Microbial Genomics workshop, Sep 2022, Grenoble, France. ⟨hal-05554282⟩
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Communication dans un congrès
George Marchment, Sarah Cohen-Boulakia, Frédéric Lemoine. Computational Reproducibility With Scientific Workflows: Analysing viral genomes with Nextflow. ACM REP’25 ACM Conference on Reproducibility and Replicability, Jul 2025, Vancouver, Canada. ⟨hal-05525260⟩
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Logiciel
Marie Schmit, Ulysse Le Clanche, George Marchment, Sarah Cohen-Boulakia, Olivier Dameron, et al.. ShareFAIR-KG. 2025, ⟨swh:1:rev:a96c28345857df13aafbc85461df2ab0cf259ef8;origin=https://gitlab.liris.cnrs.fr/sharefair/knowledge_base_workflow_annotations/ShareFAIR-KG.git;visit=swh:1:snp:e53f57ef45e971e1b9b76477d1f39f4fbe3de77f⟩. ⟨hal-05517690⟩
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Poster de conférence
Louis Ollivier, Gilles Fischer, Fanny Pouyet. A Robust Computational Framework to Characterize the Genetic Diversity Across 3,570 Strains in S. cerevisiae. JOBIM 2025, Jul 2025, Bordeaux, France. ⟨hal-05484804⟩
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Poster de conférence
Louis Ollivier, Gilles Fischer, Fanny Pouyet. A Robust Computational Framework to Characterize the Genetic Diversity Across 3,570 Strains in Saccharomyces cerevisiae. Yeast 2025, Jul 2025, Paris, France. ⟨hal-05484807⟩
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Thèse
Antoine Szatkownik. Modélisation générative dans un espace latent et évaluation de données synthétiques en génomique des populations. Informatique [cs]. Université Paris-Saclay, 2025. Français. ⟨NNT : 2025UPASG109⟩. ⟨tel-05475569v2⟩
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Communication dans un congrès
Burak Yelmen, Merve Nur Güler, Tõnu Kollo, Märt Möls, Guillaume Charpiat, et al.. Bias in genome-wide association testDéfinition courte Lorem ipsum statistics due to omitted interactions. RECOMB 2026 – 30th Annual International Conference on Research in Computational Molecular Biology, May 2026, Thessaloniki, Greece. ⟨10.1101/2025.11.21.689603⟩. ⟨hal-05474710⟩
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Article dans une revue
Fernando A Villanea, David Peede, Eli J Kaufman, Valeria Añorve-Garibay, Elizabeth T Chevy, et al.. The MUC19 gene: An evolutionary history of recurrent introgression and natural selection. Science, 2025, 389 (6762), pp.eadl0882. ⟨10.1126/science.adl0882⟩. ⟨hal-05410793⟩
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Article dans une revue, Article dans une revue
Nina Vittorelli, Cintia Gómez-Muñoz, Irina Andriushchenko, Louis Ollivier, Nicolas Agier, et al.. Repeated losses of self-fertility shaped heterozygosity and polyploidy in yeast evolution. Proceedings of the National Academy of Sciences of the United States of America, 2025, 123 (2), pp.e2525679123. ⟨10.1073/pnas.2525679123⟩. ⟨hal-05404528v2⟩
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Pré-publication, Document de travail
Miriam Bravo-Lopez, Eduardo Arrieta-Donato, Viridiana Villa-Islas, Åshild Joanne Vågene, Ana Villaseñor-Altamirano, et al.. Ancient genomic insights into Salmonella enterica Paratyphi C from Central Mexico. 2025. ⟨hal-05407381⟩
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Article dans une revue
Louis Ollivier, Brian Charlesworth, Fanny Pouyet. Beyond recombination: Exploring the impact of meiotic frequency on genome-wide genetic diversity. PLoS Genetics, 2025, 21 (8), pp.e1011798. ⟨10.1371/journal.pgen.1011798⟩. ⟨hal-05405132⟩
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Communication dans un congrès
Onofrio Semeraro, Michele Alessandro Bucci, Lionel Mathelin, Luigi Marra, Amine Saibi. From robotics to fluid dynamics: opportunities and pitfalls of Reinforcement Learning in flow control. iTi Workshop on Structure and control of wall-bounded turbulent flows, Jul 2025, Bertinoro, Italy. ⟨hal-05379587⟩
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Article dans une revue
Nicolas Bousquet, Quentin Chuet, Victor Falgas-Ravry, Amaury Jacques, Laure Morelle. A note on locating-dominating sets in twin-free graphs. Discrete Mathematics, 2025, 348 (2), pp.114297. ⟨10.1016/j.disc.2024.114297⟩. ⟨hal-05369304⟩
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Article dans une revue
Nicolas Agier, Nina Vittorelli, Louis Ollivier, Frédéric Chaux, Alexandre Gillet-Markowska, et al.. A transient mutational burst occurs during yeast colony development. Molecular Systems Biology, 2025, 21 (9), pp.1214-1236. ⟨10.1038/s44320-025-00117-1⟩. ⟨hal-05389997⟩
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Pré-publication, Document de travail
Fanny Pouyet, Ferdinand Petit, Jérémy Guez, Léo Planche, Evelyne Heyer, et al.. Methods for inferring coalescent tree topologies from genomic data: a comparison based on the transmission of reproductive success. 2025. ⟨hal-05347078⟩
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Pré-publication, Document de travail
Elsa Denakpo, Nicolas Dias, Johann Pitout, Thierry Naas, Dylan Pillai, et al.. Imputing missing minimum inhibitory concentration (MIC) values for Pseudomonas aeruginosa strains with a Denoising AutoEncoder. 2025. ⟨hal-05361361⟩
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Article dans une revue
Qiaomei Fu, Heng Li, Priya Moorjani, Flora Jay, Sergey Slepchenko, et al.. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature, 2014, 514 (7523), pp.445-449. ⟨10.1038/nature13810⟩. ⟨hal-05361150⟩
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Article dans une revue
Arnaud Quelin, Frédéric Austerlitz, Flora Jay. Assessing simulation-based supervised machine learning for demographic parameter inference from genomic data. Heredity, 2025, 134 (7), pp.417-426. ⟨10.1038/s41437-025-00773-x⟩. ⟨hal-05335745⟩
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Communication dans un congrès
Anca Dobrescu, Sarah Cohen-Boulakia, Nona Naderi. Attempt to rerun, reproduce and replicate Clinical Trials Sentence Classification Studies: lessons learnt. ACM REP ’25: ACM Conference on Reproducibility and Replicability, Jul 2025, Vancouver, Canada. pp.243-244, ⟨10.1145/3736731.3746133⟩. ⟨hal-05326886⟩
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Pré-publication, Document de travail
Antoine Szatkownik, Aurélien Decelle, Beatriz Seoane, Nicolas Béreux, Léo Planche, et al.. PRIVET: Privacy Metric Based On Extreme Value Theory. 2025. ⟨hal-05326013⟩
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Communication dans un congrès
Camille de Amorim, Alain Denise. Searching for variable structural motifs in RNA graphs using simple descriptors. JOBIM 2025 – Journées Ouvertes en Biologie, Informatique et Mathématiques, Université de Bordeaux, Jul 2025, Bordeaux, France. ⟨hal-05301347⟩
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Article dans une revue
Yi Qiu, Yoon Mo Kang, Christopher Korfmann, Fanny Pouyet, Andrew Eckford, et al.. The GC-content at the 5′ ends of human protein-coding genes is undergoing mutational decay. Genome Biology, 2024, 25 (1), pp.219. ⟨10.1186/s13059-024-03364-x⟩. ⟨hal-05238528⟩