Pré-publication, Document de travail
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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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, 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⟩
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Communication dans un congrès
Xiao Xiao, Sarah Fdili Alaoui. Tuning In to Intangibility : Reflections from My First 3 Years of Theremin Learning. DIS 2024 – Designing Interactive Systems Conference, Jul 2024, Copenhagen, Denmark. pp.2649-2659, ⟨10.1145/3643834.3661584⟩. ⟨hal-04930549⟩
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Article dans une revue
Maxime Mahout, Laurent Schwartz, Romain Attal, Ashraf Bakkar, Sabine Peres. Metabolic modelling links Warburg effect to collagen formation, angiogenesis and inflammation in the tumoral stroma. PLoS ONE, 2024, 19 (12), pp.e0313962. ⟨10.1371/journal.pone.0313962⟩. ⟨hal-04873696⟩
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Pré-publication, Document de travail
Dilek Koptekin, Ayça Aydoğan, Cansu Karamurat, N. Ezgi Altınışık, Kıvılcım Başak Vural, et al.. Out-of-Anatolia: cultural and genetic interactions during the Neolithic expansion in the Aegean. 2024. ⟨hal-04801125⟩
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Pré-publication, Document de travail
Antoine Szatkownik, Léo Planche, Maïwen Demeulle, Titouan Chambe, María Ávila-Arcos, et al.. Diffusion-based artificial genomes and their usefulness for local ancestry inference. 2024. ⟨hal-04801121⟩
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Pré-publication, Document de travail
Antoine Szatkownik, Cyril Furtlehner, Guillaume Charpiat, Burak Yelmen, Flora Jay. Latent generative modeling of long genetic sequences with GANs. 2024. ⟨hal-04801130⟩
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Pré-publication, Document de travail
Burak Yelmen, Maris Alver, Estonian Biobank Research Team, Flora Jay, Lili Milani. Interpreting artificial neural networks to detect genome-wide association signals for complex traits. 2024. ⟨hal-04801114⟩
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Article dans une revue, Article dans une revue
Stéphanie Chevalier, Julia Becker, Yujuan Gui, Vincent Noël, Cui Su, et al.. Data-driven inference of Boolean networks from transcriptomes to predict cellular differentiation and reprogramming. npj Systems Biology and Applications, 2025, 11, pp.105. ⟨10.1038/s41540-025-00569-z⟩. ⟨hal-04753079v2⟩
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Article dans une revue
Maël Lefeuvre, Michael David Martin, Flora Jay, Marie-Claude Marsolier, Céline Bon. GRUPS-rs, a high-performance ancient DNA genetic relatedness estimation software relying on pedigree simulations. Human Population Genetics and Genomics, 2024, 4 (1), pp.0001. ⟨10.47248/hpgg2404010001⟩. ⟨hal-04709778⟩
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Communication dans un congrès, Communication dans un congrès
Carlos Cuevas Villarmin, Sarah Cohen-Boulakia, Nona Naderi. Reproducibility in Named Entity Recognition: A Case Study Analysis. 2024 IEEE 20th International Conference on e-Science (e-Science), Sep 2024, Osaka, Japan. ⟨10.1109/e-Science62913.2024.10678721⟩. ⟨hal-04706673⟩
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Communication dans un congrès
Léa Guyon, Jérémy Guez, Evelyne Heyer, Raphaëlle Chaix. Is the post-Neolithic Y chromosome bottleneck necessarily explained by violent competition between lineages?. Journées de la Société d’Anthropologie de Paris, Jan 2023, Paris, France. ⟨10.4000/bmsap.11136⟩. ⟨hal-04671432⟩
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Article dans une revue
George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen-Boulakia. BioFlow-Insight: facilitating reuse of Nextflow workflows with structure reconstruction and visualization. NAR Genomics and Bioinformatics, 2024, 6 (3), pp.lqae092. ⟨10.1093/nargab/lqae092⟩. ⟨pasteur-04670359⟩
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Communication dans un congrès
Stéphanie Chevalier, Déborah Boyenval, Gustavo Magaña-López, Théo Roncalli, Athénaïs Vaginay, et al.. BoNesis: a Python-based declarative environment for the verification, reprogramming, and synthesis of Most Permissive Boolean networks. CMSB 2024: 22nd International Conference on Computational Methods in Systems Biology, Sep 2024, Pisa, Italy. ⟨10.1007/978-3-031-71671-3_6⟩. ⟨hal-04629083⟩
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Communication dans un congrès
Clémence Sebe, Sarah Cohen-Boulakia, Olivier Ferret, Aurélie Névéol. Extraction d’entités nommées décrivant des chaînes de traitement bioinformatiques dans des articles scientifiques en anglais. 31ème Conférence sur le Traitement Automatique des Langues Naturelles (TALN 2024), Jul 2024, Toulouse, France. pp.422-434. ⟨hal-04623033⟩
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Article dans une revue
Julien Demiselle, Guillaume Duval, Jean-François Hamel, Anne Renault, Laëtitia Bodet-Contentin, et al.. Determinants of hospital and one-year mortality among older patients admitted to intensive care units: results from the multicentric SENIOREA cohort. Annals of Intensive Care, 2021, 11 (1), pp.35. ⟨10.1186/s13613-021-00804-w⟩. ⟨hal-04592566⟩