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. 2024. ⟨hal-04753079⟩

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⟩

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. 35èmes Journées d'Études sur la Parole (JEP 2024) 31ème Conférence sur le Traitement Automatique des Langues Naturelles (TALN 2024) 26ème Rencontre des Étudiants Chercheurs en Informatique pour le Traitement Automatique des Langues (RECITAL 2024), Jul 2024, Toulouse, France. pp.422-434. ⟨hal-04623033⟩

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⟩

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, 2024, Pisa, Italy. ⟨10.1007/978-3-031-71671-3_6⟩. ⟨hal-04629083⟩

Antoine Szatkownik, Cyril Furtlehner, Guillaume Charpiat, Burak Yelmen, Flora Jay. Towards creating longer genetic sequences with GANs: Generation in principal component space. MLCB 2023 - 18th Conference on Machine Learning in Computational Biology, Nov 2023, Seattle, United States. ⟨hal-04419057⟩

Maxime Mahout. Logic programming tools for metabolic fluxes analysis and biological applications. Quantitative Methods [q-bio.QM]. Université Paris-Saclay, 2023. English. ⟨NNT : 2023UPASG086⟩. ⟨tel-04345852⟩

Burak Yelmen, Aurélien Decelle, Leila Lea Boulos, Antoine Szatkownik, Cyril Furtlehner, et al.. Deep convolutional and conditional neural networks for large-scale genomic data generation. PLoS Computational Biology, 2023, 19 (10), pp.e1011584. ⟨10.1101/2023.03.07.530442⟩. ⟨hal-04244818⟩

Marine Djaffardjy. Pipelines d'Analyse Bioinformatiques : solutions offertes par les Systèmes de Workflows, Cadre de représentation et Étude de la Réutilisation. Bio-informatique [q-bio.QM]. Université Paris-Saclay, 2023. Français. ⟨NNT : 2023UPASG059⟩. ⟨tel-04496191⟩

Fernando Villanea, David Peede, Eli Kaufman, Valeria Añorve-Garibay, Kelsey Witt, et al.. The MUC19 gene in Denisovans, Neanderthals, and Modern Humans: An Evolutionary History of Recurrent Introgression and Natural Selection. 2023. ⟨hal-04244022⟩

Jazeps Medina Tretmanis, Flora Jay, María Ávila-Arcos, Emilia Huerta-Sanchez. Simulation-based Benchmarking of Ancient Haplotype Inference for Detecting Population Structure. 2023. ⟨hal-04244011⟩

Pierre Andrieu, Sarah Cohen-Boulakia, Miguel Couceiro, Alain Denise, Adeline Pierrot. A unifying rank aggregation framework to suitably and efficiently aggregate any kind of rankings. International Journal of Approximate Reasoning, 2023, 162, pp.109035. ⟨10.1016/j.ijar.2023.109035⟩. ⟨hal-04227695⟩

Burak Yelmen, Flora Jay. An Overview of Deep Generative Models in Functional and Evolutionary Genomics. Annual Review of Biomedical Data Science, 2023, 6 (1), pp.173-189. ⟨10.1146/annurev-biodatasci-020722-115651⟩. ⟨hal-04243980⟩

Apolline Petit, Jérémy Guez, Arnaud Le Rouzic. Correlated stabilizing selection shapes the topology of gene regulatory networks. Genetics, 2023, 224 (2), pp.iyad065. ⟨10.1101/2022.08.29.505706⟩. ⟨hal-03813178⟩

Thomas Cokelaer, Sarah Cohen-Boulakia, Frédéric Lemoine. Reprohackathons: promoting reproducibility in bioinformatics through training. Bioinformatics, 2023, 39 (Sup 1), pp.i11 - i20. ⟨10.1093/bioinformatics/btad227⟩. ⟨hal-04402365⟩

Viridiana Villa-Islas, Alan Izarraras-Gomez, Maximilian Larena, Elizabeth Mejía Perez Campos, Marcela Sandoval-Velasco, et al.. Demographic history and genetic structure in pre-Hispanic Central Mexico. Science, 2023, 380 (6645), pp.eadd6142. ⟨10.1126/science.add6142⟩. ⟨hal-04244008⟩

Jérémy Guez. Cultural transmission of reproductive success: Causal mechanisms, genetic consequences, and machine-learning-based inference. Populations and Evolution [q-bio.PE]. Muséum national d'histoire naturelle, 2023. English. ⟨NNT : ⟩. ⟨tel-04482448⟩

Jérémy Guez, Guillaume Achaz, François Bienvenu, Jean Cury, Bruno Toupance, et al.. Cultural transmission of reproductive success impacts genomic diversity, coalescent tree topologies and demographic inferences. Genetics, 2023, 223 (4), pp.iyad007. ⟨10.1093/genetics/iyad007⟩. ⟨hal-03875721⟩

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. Alphy/AIEM 2023 - Rencontres Alphy & AIEM, Jan 2023, Grenoble, France. ⟨hal-03960408⟩

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⟩

Isaac Overcast, Guillaume Achaz, R. Aguilée, Carmelo Andújar, Paula Arribas, et al.. Towards a genetic theory of island biogeography: Inferring processes from multidimensional community‐scale data. Global Ecology and Biogeography, 2023, 32, pp.4 - 23. ⟨10.1111/geb.13604⟩. ⟨inserm-04270149⟩

Théophile Sanchez, Erik Madison Bray, Pierre Jobic, Jérémy Guez, Anne-Catherine Letournel, et al.. dnadna: a deep learning framework for population genetics inference. Bioinformatics, 2023, 39 (1), pp.btac765. ⟨10.1093/bioinformatics/btac765⟩. ⟨hal-03352910v4⟩

Coline Gianfrotta, Vladimir Reinharz, Olivier Lespinet, Dominique Barth, Alain Denise. On the predictibility of A-minor motifs from their local contexts. RNA Biology, 2022, 19 (1), pp.1208-1227. ⟨10.1080/15476286.2022.2144611⟩. ⟨hal-03864666⟩

Coline Gianfrotta. Modélisation, analyse et classification de motifs structuraux d'ARN à partir de leur contexte, par des méthodes d'algorithmique de graphes. Bio-informatique [q-bio.QM]. Université Paris-Saclay, 2022. Français. ⟨NNT : 2022UPASG056⟩. ⟨tel-03867018⟩

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⟩

Arnaud Quelin, Jérémy Guez, Ferdinand Petit, Flora Jay, Frederic Austerlitz. Inference of the Cultural Transmission of Reproductive Success from human genomic data: ABC and machine learning methods. Junior Conference on DataScience and Engeneering 2022, Sep 2022, Palaiseau, France. ⟨hal-04011855⟩

Louis Ollivier, Flora Jay, Fanny Pouyet. Impact of yeast cell cycle specificity on demography inference. JOBIM (Journées Ouvertes en Biologie, Informatique et Mathématiques ) 2022, Jul 2022, Rennes, France. ⟨hal-04393823⟩

Quentin Lobbé, David Chavalarias, Alexandre Delanoë, Gabriel Ferrand, Sarah Cohen-Boulakia, et al.. Toward an observatory of the evolution of COVID-19 Vaccines Trials through phylomemy reconstruction. Journal of Clinical Epidemiology, 2022, 149, pp.34-44. ⟨10.1016/j.jclinepi.2022.05.004⟩. ⟨hal-03500847⟩

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⟩

Théophile Sanchez. Reconstructing our past ˸ deep learning for population genetics. Neural and Evolutionary Computing [cs.NE]. Université Paris-Saclay, 2022. English. ⟨NNT : 2022UPASG032⟩. ⟨tel-03701132⟩