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  Arnaud Quelin, Jérémy Guez, Ferdinand Petit, Flora Jay, Frédéric Austerlitz. Inference of the Cultural Transmission of Reproductive Success from human genomic data: ABC and machine learning methods. 2023 Alphy & AIEM Joint Meeting, Jan 2023, Grenoble, France. ⟨hal-03960408⟩
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  Clémence Sebe, Aurélie Névéol, Sarah Cohen-Boulakia, Alban Gaignard. Extraction d'informations sur les workflows scientifiques à partir de la littérature. 23ème conférence francophone sur l'Extraction et la Gestion des Connaissances (EGC), Jan 2023, Lyon, France. pp.313-320. ⟨hal-03991363⟩
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  Stéphanie Chevalier. Inférence logique de réseaux booléens à partir de connaissances et d'observations de processus de différenciation cellulaire. Bio-informatique [q-bio.QM]. Université Paris-Saclay, 2022. Français. ⟨NNT : 2022UPASG061⟩. ⟨tel-03917566⟩
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  Denis Maurel, Sandy Chéry, Nicole Bidoit, Philippe Chatalic, Aziza Filali, et al.. Transducer Cascades for Biological Literature-Based Discovery. Information, 2022, 13 (5), pp.262. ⟨10.3390/info13050262⟩. ⟨hal-03846458⟩
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  Jean Cury, Benjamin C Haller, Guillaume Achaz, Flora Jay. Simulation of bacterial populations with SLiM. Peer Community Journal, 2022, ⟨10.24072/pcjournal.72⟩. ⟨hal-03152153v3⟩
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  Florian Tesson, Alexandre Hervé, Ernest Mordret, Marie Touchon, Camille D’humières, et al.. Systematic and quantitative view of the antiviral arsenal of prokaryotes. Nature Communications, 2022, 13 (1), pp.2561. ⟨10.1038/s41467-022-30269-9⟩. ⟨hal-03823827v2⟩
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  Bertrand Néron, Eloi Littner, Matthieu Haudiquet, Amandine Perrin, Jean Cury, et al.. IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella. Microorganisms, 2022, 10 (4), pp.700. ⟨10.3390/microorganisms10040700⟩. ⟨hal-03655020⟩
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  Fanny Pouyet, Kimberbly J Gilbert. Towards an improved understanding of molecular evolution: the relative roles of selection, drift, and everything in between. Peer Community Journal, 2021, 1, pp.e27. ⟨10.24072/pcjournal.16⟩. ⟨hal-03457264⟩
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  Pierre Andrieu, Bryan Brancotte, Laurent Bulteau, Sarah Cohen-Boulakia, Alain Denise, et al.. Efficient, robust and effective rank aggregation for massive biological datasets. Future Generation Computer Systems, 2021, 124, pp.406-421. ⟨10.1016/j.future.2021.06.013⟩. ⟨hal-03388443⟩
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  Pierre Andrieu. Passage à l'échelle, propriétés et qualité des algorithmes de classements consensuels pour les données biologiques massives. Bio-informatique [q-bio.QM]. Université Paris-Saclay, 2021. Français. ⟨NNT : 2021UPASG041⟩. ⟨tel-03335281⟩
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  Coline Gianfrotta, Vladimir Reinharz, Dominique Barth, Alain Denise. A Graph-Based Similarity Approach to Classify Recurrent Complex Motifs from Their Context in RNA Structures. 19th Symposium on Experimental Algorithms, Jun 2021, Nice (virtuel), France. ⟨10.4230/LIPIcs.SEA.2021.19⟩. ⟨hal-03251765⟩
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  Pierre Andrieu, Sarah Cohen-Boulakia, Alain Denise. Classements consensuels de données biologiques massives. [Rapport de recherche] Université Paris-Saclay/Université Paris-Sud; Laboratoire Interdisciplinaire des Sciences du Numérique. 2021. ⟨hal-03230107⟩
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  Jean-Baptiste Lamy. A data science approach to drug safety: Semantic and visual mining of adverse drug events from clinical trials of pain treatments. Artificial Intelligence in Medicine, 2021, pp.102074. ⟨10.1016/j.artmed.2021.102074⟩. ⟨hal-03201049⟩
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  Burak Yelmen, Aurélien Decelle, Linda Ongaro, Davide Marnetto, Corentin Tallec, et al.. Creating artificial human genomes using generative neural networks. PLoS Genetics, 2021, ⟨10.1371/journal.pgen.1009303⟩. ⟨hal-03149930⟩
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  Van Thu Nguyen, Philippe Riviere, Pierre Ripoll, Julien Barnier, Romain Vuillemot, et al.. Research response to coronavirus disease 2019 needed better coordination and collaboration: a living mapping of registered trials. Journal of Clinical Epidemiology, 2021, 130, pp.107-116. ⟨10.1016/j.jclinepi.2020.10.010⟩. ⟨hal-02995875⟩
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  Jean-Baptiste Lamy. A data science approach to drug safety: Semantic and visual mining of adverse drug events from clinical trials of pain treatments. 2020. ⟨hal-02968302⟩
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  Jean-Baptiste Lamy. Comparison of four visual analytics techniques for the visualization of adverse drug event rates in clinical trials. International Conference Information Visualisation, Sep 2020, Vienna, Austria. ⟨hal-02968289⟩
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  Abdelmalek Mouazer, Karima Sedki, Rosy Tsopra, Jean-Baptiste Lamy. Visualization of drug interactions for supporting medication review. International Conference on Informatics, Management and Technology in Healthcare, Jul 2020, Athen, Greece. ⟨hal-02968284⟩
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  Jean-Baptiste Lamy. Visualization of potential drug synergies. International Conference on Informatics, Management and Technology in Healthcare, Jul 2020, Athen, Greece. ⟨hal-02968276⟩
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  Jean-Baptiste Lamy, Flora Jay. Combiner arbres phylogénétiques et visualisation d'ensembles. Atelier Visualisation d'informations, interaction et fouille de données, Jan 2020, Bruxelles, Belgique. ⟨hal-02968296⟩
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  Loïc Paulevé, Juraj Kolčák, Thomas Chatain, Stefan Haar. Reconciling Qualitative, Abstract, and Scalable Modeling of Biological Networks. Nature Communications, 2020, 11, ⟨10.1038/s41467-020-18112-5⟩. ⟨hal-02518582v2⟩
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  Stéphanie Chevalier, Vincent Noël, Laurence Calzone, Andrei Zinovyev, Loïc Paulevé. Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision. 18th International Conference on Computational Methods in Systems Biology (CMSB), 2020, Online, Germany. pp.193--209, ⟨10.1007/978-3-030-60327-4_11⟩. ⟨hal-02898849v2⟩
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  Vasili Pankratov, Francesco Montinaro, Alena Kushniarevich, Georgi Hudjashov, Flora Jay, et al.. Differences in local population history at the finest level: the case of the Estonian population. European Journal of Human Genetics, 2020, ⟨10.1038/s41431-020-0699-4⟩. ⟨hal-02942330⟩
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  Thomas Chatain, Stefan Haar, Juraj Kolčák, Loïc Paulevé. Most Permissive Semantics of Boolean Networks. [Research Report] Univ. Bordeaux, Bordeaux INP, CNRS, LaBRI, UMR5800, F-33400 Talence, France; LSV, ENS Cachan, CNRS, INRIA, Université Paris-Saclay, Cachan (France). 2020. ⟨hal-01864693v2⟩
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  Olivier François, Flora Jay. Factor analysis of ancient population genomic samples. Nature Communications, 2020, 11 (1), ⟨10.1038/s41467-020-18335-6⟩. ⟨hal-02942333⟩
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  Théophile Sanchez, Jean Cury, Guillaume Charpiat, Flora Jay. Deep learning for population size history inference: Design, comparison and combination with approximate Bayesian computation. Molecular Ecology Resources, 2020, ⟨10.1111/1755-0998.13224⟩. ⟨hal-02942328⟩
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  Burak Yelmen, Aurelien Decelle, Linda Ongaro, Davide Marnetto, Francesco Montinaro, et al.. Creating Artificial Human Genomes Using Generative Models. 2019. ⟨hal-02413942⟩
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  Olivier François, Séverine Liégeois, Benjamin Demaille, Flora Jay. Inference of population genetic structure from temporal samples of DNA. 2019. ⟨hal-02413974⟩
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  Juraj Kolčák, David Šafránek, Stefan Haar, Loïc Paulevé. Parameter Space Abstraction and Unfolding Semantics of Discrete Regulatory Networks. Theoretical Computer Science, 2019, 765, pp.120-144. ⟨10.1016/j.tcs.2018.03.009⟩. ⟨hal-01734805⟩
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  Xiaojie Ren, Jean-Sébastien Deschênes, Réjean Tremblay, Sabine Pérès, Mario Jolicœur. A kinetic metabolic study of lipid production in Chlorella protothecoides under heterotrophic condition. Microbial Cell Factories, 2019, 18 (1), ⟨10.1186/s12934-019-1163-4⟩. ⟨hal-02531282⟩