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  Jean Cury, Benjamin C Haller, Guillaume Achaz, Flora Jay. Simulation of bacterial populations with SLiM. Peer Community Journal, Peer Community In/Centre Mersenne, 2022, ⟨10.24072/pcjournal.72⟩. ⟨hal-03152153v3⟩
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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, MDPI, 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, Peer Community In/Centre Mersenne, 2021, 1, pp.e27. ⟨10.24072/pcjournal.16⟩. ⟨hal-03457264⟩
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  Théophile Sanchez, Erik Madison Bray, Pierre Jobic, Jérémy Guez, Anne-Catherine Letournel, et al.. dnadna: DEEP NEURAL ARCHITECTURES FOR DNA - A DEEP LEARNING FRAMEWORK FOR POPULATION GENETIC INFERENCE. 2021. ⟨hal-03352910v2⟩
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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, Elsevier, 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, Elsevier, 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, Public Library of Science, 2021, ⟨10.1371/journal.pgen.1009303⟩. ⟨hal-03149930⟩
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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, Nature Publishing Group, 2020, 11, ⟨10.1038/s41467-020-18112-5⟩. ⟨hal-02518582v2⟩
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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, Nature Publishing Group, 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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  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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  Olivier François, Flora Jay. Factor analysis of ancient population genomic samples. Nature Communications, Nature Publishing Group, 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, Wiley/Blackwell, 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, Elsevier, 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, BioMed Central, 2019, 18 (1), ⟨10.1186/s12934-019-1163-4⟩. ⟨hal-02531282⟩
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  Jorgelindo da Veiga Moreira, Minoo Hamraz, Mohammad Abolhassani, Laurent H Schwartz, Mario Jolicœur, et al.. Metabolic therapies inhibit tumor growth in vivo and in silico. Scientific Reports, Nature Publishing Group, 2019, 9 (1), ⟨10.1038/s41598-019-39109-1⟩. ⟨hal-02392935⟩
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  Pierre Andrieu, Bryan Brancotte, Laurent Bulteau, Sarah Cohen-Boulakia, Alain Denise, et al.. Reliability-Aware and Graph-Based Approach for Rank Aggregation of Biological Data. 2019 15th International Conference on eScience (eScience), Sep 2019, San Diego, France. pp.136-145, ⟨10.1109/eScience.2019.00022⟩. ⟨hal-02527738⟩
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  Christophe Pradal, Sarah Cohen-Boulakia, Patrick Valduriez, Dennis Shasha. VersionClimber: version upgrades without tears. Computing in Science and Engineering, Institute of Electrical and Electronics Engineers, 2019, 21 (5), pp.87-93. ⟨10.1109/MCSE.2019.2921898⟩. ⟨hal-02262591⟩
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  Frédéric Lemoine, Damien Correia, Vincent Lefort, Olivia Doppelt-Azeroual, Fabien Mareuil, et al.. NGPhylogeny.fr: new generation phylogenetic services for non-specialists. Nucleic Acids Research, Oxford University Press, 2019, 47 (W1), pp.W260-W265. ⟨10.1093/nar/gkz303⟩. ⟨hal-02341225⟩
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  Stefan Haar, Juraj Kolčák, Loïc Paulevé. Combining Refinement of Parametric Models with Goal-Oriented Reduction of Dynamics. VMCAI 2019 - 20th International Conference on Verification, Model Checking, and Abstract Interpretation, Jan 2019, Lisbon, Portugal. pp.555-576, ⟨10.1007/978-3-030-11245-5_26⟩. ⟨hal-01940174⟩