Communication dans un congrès
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
Thémis Lemarchand, Fanny Pouyet, Maud Fagny. Detecting polygenic selection signatures using tree sequences statistics. Journée des doctorants du département BAP, May 2026, Versailles, France. ⟨hal-05757195⟩
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Article dans une revue
Clémence Sebe, Olivier Ferret, Aurélie Névéol, Mahdi Esmailoghli, Ulf Leser, et al.. Supporting workflow reproducibility by linking bioinformatics tools across papers and executable code. Bioinformatics, 2026, 42 (8), pp.btag565. ⟨10.1093/bioinformatics/btag565⟩. ⟨hal-05755094⟩
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Communication dans un congrès
Jaffar Gura, Khalid Belhajjame, Frédéric Lemoine, Sarah Cohen-Boulakia. From Execution Traces to Queryable Provenance in Nextflow Workflows. 22nd IEEE International Conference on e-Science (eScience 2026), IEEE, Sep 2026, Naples (Napoli), Italy. ⟨hal-05757229⟩
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Poster de conférence
Thémis Lemarchand, Maud Tenaillon, Fanny Pouyet, Maud Fagny. Detecting polygenic selection signatures using tree sequences statistics. SMBE, Jun 2026, Copenhague, Denmark. ⟨hal-05752890⟩
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Article dans une revue
Léo Planche, Anna Ilina, María C Ávila-Arcos, Flora Jay, Emilia Huerta-Sanchez, et al.. An archaic reference-free method to jointly infer Neanderthal and Denisovan introgressed segments in modern human genomes. Molecular Biology and Evolution, 2025, ⟨10.1101/2025.03.17.643330⟩. ⟨hal-05747173⟩
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Article dans une revue
Marco Rosario Capodiferro, Léo Planche, Emily M Breslin, Linda Ongaro, María C Ávila-Arcos, et al.. Archaic ancestry inference in imputed ancient human genomes. Nature Communications, 2026, 17 (1), pp.9480. ⟨10.1038/s41467-026-76204-0⟩. ⟨hal-05747161⟩
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Article dans une revue
George Marchment, Sarah Cohen-Boulakia, Alain Denise, Frédéric Lemoine. Workflow abstractions for automatic modularity: improving workflow code reusability. Future Generation Computer Systems, 2027, 187, pp.108776. ⟨10.1016/j.future.2026.108776⟩. ⟨hal-05737452⟩
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Communication dans un congrès
Beranger Ovono-Ekore, J. Deparis, Moncef Hidane, Julien Mille, Farid Smaï, et al.. Physics-Consistent Neural Inversion of 2-D DC Resistivity Data. NSG 2026: 32nd Meeting of Environmental and Engineering Geophysics, European Association of Geoscientists and Engineers (EAGE), Sep 2026, Thessaloniki, Greece. pp.1-5, ⟨10.3997/2214-4609.202620086⟩. ⟨hal-05706633⟩
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Logiciel
Bruno Aristimunha, Igor Carrara, Pierre Guetschel, Sara Sedlar, Pedro Rodrigues, et al.. Mother of all BCI Benchmarks. 2026, ⟨swh:1:dir:6d89a182d4e69572a73784c6616ef1cee5493d77⟩. ⟨hal-05675918⟩
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Communication dans un congrès
Marie Schmit, Melvin Selim Atay, Khalid Belhajjame, Ulysse Le Clanche, Emmanuel Coquery, et al.. ShareFAIR-KG, a centralised knowledge base of scientific workflows. JOBIM 2026 – Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2026, Strasbourg, France. ⟨hal-05666980⟩
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Logiciel
George Marchment, Sarah Cohen-Boulakia, Frédéric Lemoine, Bryan Brancotte. BioFlow-Insight. 2026, ⟨swh:1:dir:9cbc8a04afc7b791fb5796f9b286ddb1f0f7af01;origin=https://gitlab.liris.cnrs.fr/sharefair/bioflow-insight;visit=swh:1:snp:0073ce5b2737e3fa95b37406b1436f2fd7e9f369;anchor=swh:1:rev:e6005d56f5bb93c7cf63248d43451fd07abb71aa⟩. ⟨pasteur-05650681⟩
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Chapitre d'ouvrage
Sarah Cohen-Boulakia, Frédéric Lemoine, George Marchment, Marine Djaffardjy, Alban Gaignard, et al.. Reuse and reproduce bioinformatic pipelines using scientific workflow systems. Berlin Universities Publishing. Workflow systems for large-scale scientific data analysis, Berlin Universities Publishing, 2026, 978-3-98781-067-1. ⟨10.14279/depositonce-25828⟩. ⟨pasteur-05640482⟩
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Poster de conférence
Arnaud Quelin, Flora Jay, Frederic Austerlitz. Inferring demographic history of diverging populations from human genomic data. SMBE, Jul 2023, Ferrara, Italy. ⟨hal-05570993⟩
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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. 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 – Journées Ouvertes en Biologie, Informatique et Mathématiques, 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 test 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⟩