Logiciel
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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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⟩
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Poster de conférence
Maël Lefeuvre, Michael D. Martin, Flora Jay, Marie-Claude Marsolier, Alexis Corrochano, et al.. GRUPS-rs: a high-performance ancient DNA genetic relatedness estimation software based on pedigree simulations. Bulletins et mémoires de la Société d’Anthropologie de Paris 35(S), Jan 2023, Paris, France. 35 (S), pp.30, 2023, ⟨10.4000/bmsap.11299⟩. ⟨hal-05242408⟩
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Poster de conférence
Maël Lefeuvre, Michael D. Martin, Flora Jay, Marie-Claude Marsolier, Alexis Corrochano, et al.. GRUPS-rs, a high-performance ancient DNA genetic relatedness estimation software relying on pedigree simulations. JOBIM 2023 – Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2023, Multisite, France. ⟨hal-05242467⟩
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Communication dans un congrès
Clémence Sebe, Sarah Cohen-Boulakia, Olivier Ferret, Aurélie Névéol. Extracting Information in a Low-resource Setting: Case Study on Bioinformatics Workflows. Symposium on Intelligent Data Analysis (IDA 2025), May 2025, Konstanz, Germany. pp.274-287, ⟨10.1007/978-3-031-91398-3_21⟩. ⟨hal-05244222⟩
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Ouvrages
Christine Froidevaux, Martin-Magniette Marie-Laure, Guillem Rigaill (Dir.). Intégration de données biologiques. Approches informatiques et statistiques. ISTE, 2022, 978-1789480306. ⟨hal-05175499⟩
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Communication dans un congrès
Ulysse Le Clanche, Sarah Cohen-Boulakia, Yann Le Cunff, Olivier Dameron, Alban Gaignard. Assessing bioinformatics software annotations: bio.tools case-study. JOBIM 2025 – Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2025, Bordeaux & Online, France. pp.1-7. ⟨hal-05096849⟩