Dernières publications

Patrice Loisel, Marielle Brunette, Stéphane Couture (2025). Ambiguity, value of information and forest rotation decision under storm risk. Resource and Energy Economics.

HAL Citation DOI

Hanna Bacave, Paul Huguet, Edgar Belin, Elodie Gilbault, Olivier O. Zurfluh, O Loudet, Véronique Letort, Anne Goelzer (2025). From Phenoscope to GreenLab model of Arabidopsis to decipher genotype and treatment effects. 2025 Joint International Conference on Crop/Plant Modeling, Big Data and Applications (2025PMBDA）.

HAL PDF Citation

David Benaben, Jerôme Mariette, Jobim Twenty-Five Organizing Committee (2025). Carbon footprint estimation of JOBIM 2025 congress.

HAL PDF Citation

Achim Zeileis, Roger Bivand, Dirk Eddelbuettel, Kurt Hornik, Julia Piaskowski, Nathalie Vialaneix (2025). The CRAN Task View Initiative. The R Journal.

HAL Citation DOI

Lysiane Dunière, Philippe Ruiz, Frédérique Chaucheyras-Durand, Mathieu Silberberg, Anne Boudon, Pierre Nozière, Evelyne Forano (2025). Evaluation of esophageal tubing and buccal swabbing versus rumen cannula to characterize ruminal microbiota in cows fed contrasting diets. Scientific Reports.

HAL PDF Citation DOI

Orlane Rossini, Meritxell Vinyals, Alice Cleynen, Benoîte de Saporta, Régis Sabbadin (2025). Bayes-Adaptive Impulse Control of Piecewise-Deterministic Markov Processes.

HAL PDF Citation

Valentin Sorin, Maulana Mughitz Naji, Clément Birbes, Cécile Grohs, Clémentine Escouflaire, Sébastien Fritz, Camille Eché, Camille Marcuzzo, Amandine Suin, Cécile Donnadieu, Christine Gaspin, Carole Iampietro, Denis Milan, Laurence Drouilhet, Gwenola Tosser-Klopp, Didier Boichard, Christophe Klopp, Marie-Pierre Sanchez, Mekki Boussaha (2025). Application of a French cattle pangenome, from structural variant discovery to association studies on key phenotypes. Genetics Selection Evolution.

HAL PDF Citation DOI

Mekki Boussaha, Camille Eché, Christophe Klopp, Cécile Grohs, Marine Milhes, Amandine Suin, Tabatha Bulach, Rachel Fourdin, Thomas Faraut, Claire Kuchly, Sébastien Fritz, Caroline Vernette, Maulana Naji, Valentin Sorin, Aurélien Capitan, Christine Gaspin, Denis Milan, Didier Boichard, Carole Iampietro, Cécile Donnadieu (2025). Whole genome short read data from 567 bulls of 14 breeds provides insight into genetic diversity of French cattle. Data in Brief.

HAL PDF Citation DOI

Leon Dirick, Y. Liu, S. Dong, J. Yu, Laurent Ouerdane, M. Storti, A. Alboresi, Catherine Curie, B. Goffinet (2025). Multiple independent acquisitions of a metallophore-synthesis gene by plants through horizontal microbial gene transfer. Nature Communications.

HAL PDF Citation DOI

Marcelo Hurtado, Abdelmounim Essabbar, Leila Khajavi, Vera Pancaldi (2025). multideconv - an integrative pipeline for efficiently combining first and second generation cell type deconvolution results.

HAL Citation DOI

Ronan Trépos, Régis Sabbadin, Sam Nicol, Nathalie Peyrard (2025). Inference in a Factorial Hidden Semi-Markov Model with Variational EM.

HAL PDF Citation

Marie Pegard, Adela Poublan-Couzardot, Philippe Barre, Simon de Givry, Christine Gaspin, Fabrice Legeai, Frédéric Choulet, Christophe Klopp, Bernadette Julier (2025). Enhanced Genome Assemblies of French-Bred Dactylis glomerata and Medicago sativa: Achieving High-Quality Tetraploid Genomes. Breeding and Genetic Improvement for a Net-Zero Future.

HAL PDF Citation

Olivier Inizan, Fatiha Saïs, Anne Goelzer, Joe Raad, Danai Symeonidou (2025). Abstracting Entity Matching for Analysing and Explaining Identity and Difference Decision and Indecision. 29th International Conference on Knowledge-Based and Intelligent Information & Engineering Systems (KES 2025).

HAL PDF Citation DOI

Pauline Desvignes, Philippe Ruiz, Laurie Guillot, Jeanne Danon, Alexandra Durand, Martin Beaumont, Frédérique Chaucheyras-Durand, Evelyne Forano (2025). Transcriptomic analysis of the interactions between Fibrobacter succinogenes S85, Selenomonas ruminantium PC18 and a live yeast strain used as a ruminant feed additive. BMC Genomics.

HAL PDF Citation DOI

Natasha Horta Araújo, David Landry, Johan Quilbé, Marjorie Pervent, Nico Nouwen, Christophe Klopp, Julie Cullimore, Djamel Gully, Céline Vicedo, Virginie Gasciolli, Laurent Brottier, Carole Pichereaux, Martin Racoupeau, Maëlle Rios, Frédéric Gressent, Clémence Chaintreuil, Clare Gough, Eric Giraud, Benoit Lefebvre, Jean-François Arrighi (2025). The receptor-like cytoplasmic kinase AeRLCK2 mediates Nod-independent rhizobial symbiosis in Aeschynomene legumes. The Plant cell.

HAL PDF Citation DOI

Marielle Brunette, Stéphane Couture, Kene Boun My (2025). Probabilistic ambiguity, outcome ambiguity or both: Does it matter for the decision-maker?. Journal of Behavioral and Experimental Economics.

HAL Citation DOI

Laëtitia Leclerc, Gabryelle Agoutin, Thierry Brévault, Antony Champion, Jean Mainguy, Nicolas Nègre, Sudeeptha Yainna, Géraldine Pascal, Sophie Gaudriault, Jean-Claude Ogier (2025). Nested PCR to optimize rpoB metabarcoding for lowconcentration and host-associated bacterial DNA. Microbiology Spectrum.

HAL PDF Citation DOI

Olivier Rué, Nurul Novelia Fuandila, Saliha Hammoumi, Christine Gaspin, Jean-Christophe Avarre (2025). Micro-RNA expression data from common carp brain cells infected by Cyvirus cyprinidallo3 at permissive and non-permissive temperatures. Data in Brief.

HAL Citation DOI

Louis Paré, Philippe Bordron, Laurent David, Maxime Mahé, Audrey Bihouée, Damien Eveillard (2025). HUMESS: integrating quantitative transcriptomic analysis and metabolic modeling to unveil condition-specific gene signatures. Bioinformatics.

HAL PDF Citation DOI

Florent Blaise, Philippe Bordron, Patrice Dehais, Vincent Dominguez, Christine Gaspin, Fabien Graziani, Claire Hoede, Christophe Klopp, Didier Laborie, Céline Noirot, Philippe Ruiz, Adela Poublan-Couzardot, Martin Racoupeau, Marie-Stéphane Trotard, Nathalie Vialaneix, Matthias Zytnicki (2025). The Genotoul-Bioinfo platform. JOBIM2025.

HAL PDF Citation

Philippe Bordron, Julien Touchais, Christine Gaspin (2025). SnoBoard: surfing on ncRNA modifications and snoRNA guides. JOBIM2025.

HAL PDF Citation

Soraya Arias, Michel Bergmann, Fabien Campillo, Marie-Agnès Enard, Christian Fabre, Frédérick Garcia, Benjamin Guedj, Emmanuel Jeannot, Giovanni Neglia, Diane Peurichard, Daniel Racoceanu, Benoît Sagot, Gaëlle Tworkowski (2025). Reflections on the Use of Generative AI for Research Professions.

HAL PDF Citation

Lucien Piat, Sukanya Denni, Siegfried Dubois, Florent Couturier, Nicolas Lapalu, Benjamin Linard, Claire Lemaitre, Ludovic Duvaux (2025). MSpangepop: Simulating complex structural variants under advanced demographic scenarios using the coalescent. JOBIM 2025 - Journées Ouvertes en Biologie, Informatique et Mathématiques.

HAL PDF Citation

Guilmois„ Céline, Tom Rohmer, Maria Poparoch (2025). Learning basic mathematic skills in primary school: Testing the effectiveness of socio-constructivist and explicit instruction. School Effectiveness and School Improvement.

HAL Citation DOI

Celestine Belloeil, Vanesa Sanchez Garcia de la Torre, Ruben Contreras Aguilera, Hendrik Kupper, Celine Lopez-Roques, Carole Iampetro, Celine Vandecasteele, Christophe Klopp, Alexandra Launay-Avon, Wiebke Leemhuis, Jitpanu Yamjabok, Joost van den Heuvel, Mark G.M. Aarts, Celestino Quintela Sabaris, Sebastien Thomine, Sylvain Merlot (2025). Gain and loss of gene function shaped the nickel hyperaccumulation trait in Noccaea caerulescens. BioRxiv.

HAL Citation DOI

Noémien Maillard, Christophe Klopp, Donnadieu Cécile, Julie Demars, Raphaël Mourad (2025). Cross-Species Predictions of Chromatin Annotations using Neural Networks. European Conference on Computational Biology 2025 (ECCB 2025).

HAL PDF Citation

Adela Poublan-Couzardot, Bernadette Julier, Marie Pégard, Simon De Givry, Christine Gaspin, Fabrice Legeai, Frédéric Choulet, Christophe Klopp (2025). A Strategy for Balanced Haplotype-Resolved De Novo Assembly of the Autotetraploid Genome of Medicago sativa. JOBIM 2025 (Journées ouvertes de Bio-Informatique 2025).

HAL PDF Citation

Élise Jorge, Sylvain Foissac, Pierre Neuvial, Matthias Zytnicki, Nathalie Vialaneix (2025). A comprehensive review and benchmark of differential analysis tools for Hi-C data. ISMB/ECCB.

HAL Citation

Camille Guilmineau, Rémi Servien, Marie Tremblay-Franco, Nathalie Vialaneix (2025). phoenics : une nouvelle approche statistique pour l'analyse différentielle longitudinale de voies métaboliques. 56. Journées de Statistique de la SFdS (JdS 2025).

HAL PDF Citation

Élise Jorge, Pierre Neuvial, Nathalie Vialaneix, Sylvain Foissac (2025). Inférence post hoc pour l'analyse différentielle de données Hi-C. 56e Journées de Statistique de la SFdS (JdS 2025).

HAL PDF Citation

Aurélie Manicki, Gaëlle Brahy, Christophe Klopp, Aurélie Berard, Damien Hinsinger, Maika Minjou, Christine Ducos, Franois Gueraud, Sylvie Muratorio, Jacques Labonne (2025). Diversité et structure génomique d'une population de truite en expansion aux Iles Kerguelen : mise au point d'une approche de Poolseq. INRAE Genomics.

HAL Citation

Jean Mainguy, Claire Hoede (2025). Binette. version.

HAL Citation DOI

Bessam Azizi, Thomas Schiex, Sophie Barbe (2025). AI Diffusion Models for Computational Protein Design. GGMM.

HAL Citation

Lucie Barthe, Damien Balestrino, Bessam Azizi, Delphine Dessaux, Vanessa Soldan, Jérémy Esque, Thomas Schiex, Sophie Barbe, Luis F Garcia-Alles (2025). Promiscuous structural cross-compatibilities between major shell components of Klebsiella pneumoniae bacterial microcompartments. PLoS ONE.

HAL PDF Citation DOI

Sarah Maman, Philippe Bardou, Emilien Lasguignes, Faustine Oudin, Floréal Cabanettes, Christophe Klopp (2025). IntronSeeker. version.

HAL Citation DOI

Aurelie Mercadie (2025). Intégration de données omiques de la peau issues d'expériences multi-groupes.

HAL PDF Citation

Sonia E Eynard, Kossi-Julien Kowou, Cécile Donnadieu, Loïc Flatres-Grall, Carole Iampietro, Sandrine Lagarrigue, Sophie Leroux, Joanna Lledo, Marie-José Mercat, Juliette Riquet, Céline Vandecasteele, Frédérique Pitel, Bertrand Servin (2025). Genetic and epigenetic selection signatures from pool sequencing experiment. Biology of genomes.

HAL Citation

Mohamed Anwar Abouabdallah, Olivier Coulaud, Nathalie Peyrard, Alain Franc (2025). Computing WSBM conditional marginals with Tensor-Train decomposition.

HAL PDF Citation

A. Régimbeau, F. Tian, G. Smith, V Riddell, C. Andreani, P. Bordron, M. Budinich, C. Howard-Varona, A. Larhlimi, E. Ser-Giacomi, C. Trottier, L. Guidi, S.J. Hallam, D. Iudicone, E. Karsenti, A. Maass, M.B. Sullivan, Damien Eveillard (2025). Planetary-scale heterotrophic microbial community modeling assesses metabolic synergy and viral impacts.

HAL Citation DOI

Paul Terzian, Céline Vandecasteele, Joanna Lledo, Rémy-Félix Serre, Jules Sabban, Claire Kuchly, Frédérique Pitel, Sophie Leroux, Julie Demars, Nathalie Iannuccelli, Katia Fève, Michèle Bonnet, Christine Gaspin, Denis Milan, Carole Iampietro, Christophe Klopp, Cécile Donnadieu (2025). Pig and quail CpG methylation datasets from short and long read sequencing technologies. *Scientific Data *.

HAL PDF Citation DOI

Camille Guilmineau, Marie Tremblay-Franco, Nathalie Vialaneix, Rémi Servien (2025). Phoenics: a novel statistical approach for longitudinal metabolomic pathway analysis. BMC Bioinformatics.

HAL PDF Citation DOI

Louis Paré, Philippe Bordron, Laurent David, Maxime Mahé, Audrey Bihouée, Damien Eveillard (2025). HUMESS: Integrating Quantitative Transcriptomic Analysis and Metabolic Modeling to Unveil Condition-Specific Gene Signatures.

HAL Citation DOI

Nathalie Rousse, Patrick Chabrier, Rachid Yahiaoui, Manuel P Martin, Eric Casellas, Estelle Ancelet (2025). Communiquer avec SIWAA via une API web: Un exemple de pilotage à distance de simulations mis en oeuvre sur le projet CarboSeq. Séminaire MIAT.

HAL PDF Citation

Léo Biré, Quynh Nga Phung, Patrick Taillandier, Diep Anh Phung, Ngoc Doanh Nguyen, Alexis Drogoul (2025). RÁC, a Serious Agent-Based Simulation Game to Drive Discussion on Waste Management in Vietnamese Irrigation Systems. Journal of Artificial Societies and Social Simulation.

HAL PDF Citation DOI

Lucie Barthe, Damien Balestrino, Bessam Azizi, Delphine Dessaux, Vanessa Soldan, Jérémy Esque, Thomas Schiex, Sophie Barbe, Luis Fernando Garcia-Alles (2025). Promiscuous structural cross-compatibilities between major shell components of Klebsiella pneumoniae bacterial microcompartments.

HAL Citation DOI

Laure Gress, Sarah Maman-Haddad, Nathalie Marty-Gasset, Nathalie Vialaneix, Agnès Bonnet (2025). Plan de gestion des données CO-LOcATION Version Finale.

HAL PDF Citation

Frédérick Garcia, Sophie Schbath (2025). Les impacts de l'IA sur l'environnement. Conseil général de l’Économie, ministère de l’Économie et des Finances.

HAL PDF Citation

Jean-Marc Azaïs, Céline Delmas (2025). Landscape k-complexity of isotropic centered Gaussian fields.

HAL PDF Citation

Nina Marthe, Matthias Zytnicki, Francois Sabot (2025). GrAnnoT, a tool for efficient and reliable annotation transfer through pangenome graph.

HAL PDF Citation DOI

Lucile Martin, Philippe Ruiz, Sabine Leroy, Sapountzis Panagiotis (2025). Escobase and AcR: Escherichia coli databases of genomes and acid resistance genes from isolates from cattle farms.

HAL Citation DOI

Elise Jorge, Sylvain Foissac, Pierre Neuvial, Matthias Zytnicki, Nathalie Vialaneix (2025). A comprehensive review and benchmark of differential analysis tools for Hi-C data. Briefings in Bioinformatics.

HAL PDF Citation DOI

Florent Couturier, Lucien Piat, Sukanya Denni, Alexis Mergez, Gabriele Magris, Aglaia Szukala, Maria Valbuena, Christophe Plomion, Sara Pinosio, Enrique Saez-Laguna, Christophe Klopp, Ludovic Duvaux (2025). The pangenome of European white oaks : A new approach to assess genetic diversity. Doctorales de la forêt.

HAL PDF Citation

Aurélie Mercadié, Éléonore Gravier, Gwendal Josse, Isabelle Fournier, Cécile Viodé, Nathalie Vialaneix, Céline Brouard (2025). NMFProfiler: a multi-omics integration method for samples stratified in groups. Bioinformatics.

HAL Citation DOI

Chloé Bessière, Fabienne Meggetto, Christine Gaspin, Steffen Fuchs (2025). Identification of Circular RNA Variants by Oxford Nanopore Long-Read Sequencing. Gene Expression Analysis.

HAL Citation DOI

N I Prasianakis, E. Laloy, D. Jacques, J C L Meeussen, G D Miron, D A Kulik, A. Idiart, E. Demirer, E. Coene, B. Cochepin, M. Leconte, M E Savino, J. Samper-Pilar, M. de Lucia, S V Churakov, O. Kolditz, C. Yang, J. Samper, Francis Claret (2025). Geochemistry and machine learning: methods and benchmarking. Environmental Earth Sciences.

HAL PDF Citation DOI

Katherine Albanese, Sophie Barbe, Shunsuke Tagami, Derek Woolfson, Thomas Schiex (2025). Computational Protein Design. Nature Reviews Methods Primers.

HAL Citation DOI

Natasha Horta Araújo, David Landry, Johan Quilbé, Marjorie Pervent, Nico Nouwen, Christophe Klopp, Julie V Cullimore, Djamel Gully, Laurent Brottier, Carole Pichereaux, Carole Pichereaux, Martin Racoupeau, Maëlle Rios, Frédéric Gressent, Clémence Chaintreuil, Clare Gough, Eric Giraud, Benoit Lefebvre, Jean-François Arrighi (2025). A Receptor Like Cytoplasmic Kinase evolved in Aeschynomene legumes to mediate Nod-independent rhizobial symbiosis.

HAL PDF Citation DOI

Franck Taillandier, Patrick Taillandier, Pénélope Brueder, Noé Brosse (2025). The dynamic sketch map to support reflection on urban flooding. International Journal of Disaster Risk Reduction.

HAL Citation DOI

Charles-Elie Rabier, Céline Delmas (2025). The AdaptSgenoLasso, an extended version of the SgenoLasso, for gene mapping and for genomic prediction using the extremes. Statistics.

HAL PDF Citation DOI

Nathalie Vialaneix, Elise Maigne, Jerome Mariette, Madalina Olteanu, Fabrice Rossi (2025). SOMbrero: SOM Bound to Realize Euclidean and Relational Outputs. version 1.4.2.

HAL Citation Code

Soraya Arias, Michel Bergmann, Fabien Campillo, Marie-Agnès Enard, Christian Fabre, Frédérick Garcia, Benjamin Guedj, Emmanuel Jeannot, Giovanni Neglia, Diane Peurichard, Daniel Racoceanu, Benoît Sagot, Gaëlle Tworkowski (2025). Réflexions sur l'usage de l'IA générative pour les métiers de la recherche.

HAL PDF Citation

Hanna Bacave, Pierre-Olivier Cheptou, Nikolaos Limnios, Nathalie Peyrard (2025). Non parametric observation-driven hidden Markov model. Communications in Statistics - Theory and Methods.

HAL Citation DOI

Caroline Vilarem, Vincent Piou, Lucie Bouly, Frédéric Julien, Rachel Fourdin, Nathalie Vialaneix, Matthias Zytnicki, Angélique Vétillard (2025). Mutation Rate in Phage lambdaMutation Rate in Phage lambda. Ecotoxicology and Environmental Safety.

HAL Citation DOI

Carmen Bessa-Gomes, Anaïs Cazals, Blanche Collard, François Chiron, Matthieu Jules, Améline Vallet, Emmanuelle Baudry, Nathalie Laforge, Anne-Gaëlle Planson, Quentin Berger, Sabine G. Gebhardt-Henrich, Michael Toscano, Tatiana Zerjal, Vayssière Alice, Frédérique Tellier, Anaïs da Costa, Bellec Yannick, Anouchka Guyon-Debast, Tracy Francois, Gissot Lionel, Eric Biot, Fabien Nogué, Tepfer Mark, J.-D. Faure, V. Sauveplane, Christina Vernant, Teddy Charbonnier, Delphine Sourdeval, Céline Brosse, Stéphanie Boutet, Loïc Rajjou, Léa Wagner, An Hoang, Olivier Borkowski, Anita Boisramé, Kristell Couturier-Becavin, Jean-Luc Cacas, Cécile Neuvéglise, Nicolas Darcel, Anaëlle Bolo, Sarah Chabert, Juhui Wang, François Mariotti, Hélène Fouillet, Jean-François Huneau, Patrick Taillandier, Thierry Spataro, Shuang Peng, Chandrodhay Saccaram, Massimiliano Corso, Quentin Dutertre, Igor Pokotylo, Edith Honvo-Houeto, Pierre Larraufie, Christine Delorme, Séverine Layec, Sarah Ben-Sadoun, Cyril Bauland, Laurence Moreau, Alain Charcosset, Julia Zinsmeister, Paul Schouveiler, Boris Collet, Hubert Schaller, Sabine D'andrea, Antonin Royer, Helen M North, Abdelilah Benamar, Olga Davidenko, David Blumenthal, Olivier Allais, Isabelle Denis, Valérie Guénard-Lampron, Anne Saint-Eve, Marine Masson, Jalil Chadli, Valérie Berthelot, Gomes Pierre, Pascale Mosoni, Laurent Broudiscou, Aurélie Maurice (2025). Journées Scientifiques du Département Sciences de la Vie et Santé - AgroParisTech. Journées Scientifiques du Département Sciences de la Vie et Santé - AgroParisTech.

HAL PDF Citation

Liming Peng, Maksym Odnoroh, Mathias Destarac, Yannick Coppel, Céline Delmas, Florence Benoit-Marquié, Christophe Mingotaud, Jean-Daniel Marty (2025). How tailor-made copolymers can control the structure and properties of hybrid nanomaterials: the case of polyionic complexes. Nanoscale.

HAL Citation DOI

Elyas Mouhou, Fabien Genty, Walid El M'Selmi, Hanae Chouali, Jean-François Zagury, Sigrid Le Clerc, Charlotte Proudhon, Josselin Noirel (2025). High tissue specificity of lncRNAs maximises the prediction of tissue of origin of circulating DNA. Scientific Reports.

HAL PDF Citation DOI

Prasanna Maddila, Sabbadin Régis, Vinyals Meritxell (2025). Efficiently computing Nash Equilibria in Multi-Adversarial Team Games.

HAL PDF Citation

Anaïs Marquisseau, Kamila Canale-Tabet, Emmanuelle Labarthe, Géraldine Pascal, Christophe Klopp, André Pornon, Nathalie Escaravage, Rémi Rudelle, Alain Vignal, Annie Ouin, Mélodie Ollivier, Magalie Pichon (2025). Building a reliable 16S mini-barcode library of wild bees from Occitania, south-west of France. Biodiversity Data Journal.

HAL PDF Citation DOI

Matthias Zytnicki (2025). Assessing genome conservation on pangenome graphs with PanSel. Bioinformatics Advances.

HAL Citation DOI

Stéphanie Bocs, Camille Carrette, Johann Confais, Siegfried Dubois, Ludovic Duvaux, Christophe Klopp, Nicolas Lapalu, Pauline Lasserre-Zuber, Fabrice Legeai, Claire Lemaitre, Benjamin Linard, Nina Marthe, Baptiste Pierre, Gautier Sarah, François Sabot, Christine Tranchant-Dubreuil, Matthias Zytnicki (2025). A roadmap for the adoption of pangenomics in agronomy.

HAL PDF Citation DOI

Sonia E. Eynard, Christophe Klopp, Kamila Canale-Tabet, William Marande, Céline Vandecasteele, Céline Roques, Cécile Donnadieu, Quentin Boone, Bertrand Servin, Alain Vignal (2024). The black honey bee genome: insights on specific structural elements and a first step towards pangenomes. Genetics Selection Evolution.

HAL PDF Citation DOI

Sarah Maman-Haddad, Laure Gress, Amandine Suin, Nathalie Vialaneix, Agnès Bonnet (2024). RNA-seq data of pig placenta and endometrium during late gestation. Data in Brief.

HAL PDF Citation DOI

Siegfried Dubois, Matthias Zytnicki, Claire Lemaitre, Thomas Faraut (2024). Pairwise graph edit distance characterizes the impact of the construction method on pangenome graphs. Bioinformatics.

HAL PDF Citation DOI

Jean Mainguy, Maïna Vienne, Joanna Fourquet, Vincent Darbot, Céline Noirot, Adrien Castinel, Sylvie Combes, Christine Gaspin, Denis Milan, Cécile Donnadieu, Carole Iampietro, Olivier Bouchez, Géraldine Pascal, Claire Hoede (2024). metagWGS, a comprehensive workflow to analyze metagenomic data using Illumina or PacBio HiFi reads.

HAL PDF Citation DOI

Frédérick Garcia, Bruno Moulia, Aroune Duclos, Eric Ballestero, Adelin Barbacci (2024). Ce que le son fait aux plantes. Pour la science.

HAL Citation

Prasanna Maddila, Régis Sabbadin, Meritxell Vinyals (2024). Un modèle de jeu stochastique pour la lutte anti-braconnage et un benchmark pour l'Apprentissage par Renforcement Multi-agents. JFSMA 2024: 32èmes Journées Francophones sur les Systèmes Multi-Agents.

HAL Citation

Aldair Martin Martinez Pineda, Bertille Pouget, Claire Hoede, Christine Gaspin, Romain Volmer (2024). The first risk assessment tool to predict the emergence of high pathogenicity H5/H7 Avian Influenza variants. Virus Genomics, Evolution and Bioinformatics 2024..

HAL PDF Citation

Patrick Taillandier, Arthur Brugière, Alexis Drogoul (2024). SIMPLE Toolchain: Coupling GAMA simulation with VR universe. GAMA Days 2024.

HAL PDF Citation

Matthias Zytnicki (2024). pansel. version.

HAL Citation Code

Nghia Truong Tuan, Patrick Taillandier, Ines Langlet, Maxine Bisbau, Arnaud Grignard, Alexis Drogoul (2024). Moov'Hanoi : A Data-Driven Agent-Based Model for Simulating Multimodal Urban Mobility in Hanoi. GAMA Days 2024.

HAL PDF Citation

Sarah Maman, Philippe Bardou, Emilien Lasguignes, Faustine Oudin, Floréal Cabanettes, Christoph Klopp (2024). Finding and removing introns from RNA-Seq de novo assemblies with IntronSeeker. Journal of Open Source Software.

HAL PDF Citation DOI

Hanna Bacave (2024). Extension des modèles de (semi-)Markov cachés et algorithmes pour estimer la dynamique de (méta)populations partiellement observables.

HAL PDF Citation

Hanna Bacave (2024). Extension des modèles de (semi-)Markov cachés et algorithmes pour estimer la dynamique de (méta)populations partiellement observables.

HAL PDF Citation

Abdourahmane Diallo, Annabelle Larmure, Ronan Trépos, Eric Casellas, Marion Prudent (2024). Comment adapter la culture de pois au changement climatique ? Approche par simulation de combinaisons ``génotype x environnement x pratiques culturales'' dans des climats français contrastés - 2024-2027.

HAL Citation

Maillard Noémien, Klopp Christophe, Donnadieu Cécile, Riquet Juliette, Fève Katia, Julie Demars, Mourad Raphaël (2024). Can Neural Networks be used to Predict Cross-Species Annotations of Chromatin Regulation ?. Journée Bioinfo/Biostat GenoToul.

HAL PDF Citation

Baptiste Lesquoy, Patrick Taillandier, Benoit Gaudou, Kevin Chapuis, Arnaud Grignard, Nghi Quang Huynh, Arthur Brugiere, Lucas Grosjean, Alexis Drogoul (2024). Behind the scenes: an overview of the GAMA platform's environment and development practices. GAMA Days 2024.

HAL PDF Citation

Maxence Lanoizelet, Léo Michel, Ronan Lagadec, Hélène Mayeur, Lucile Guichard, Valentin Logeux, Dany Séverac, Kyle Martin, Christophe Klopp, Sylvain Marcellini, Héctor Castillo, Nicolas Pollet, Eva Candal, Mélanie Debiais-Thibaud, Catherine Boisvert, Bernard Billoud, Michael Schubert, Patrick Blader, Sylvie Mazan (2024). Analysis of a shark reveals ancient, Wnt-dependent, habenular asymmetries in vertebrates. Nature Communications.

HAL PDF Citation DOI

Pierre Montalbano, Simon de Givry, George Katsirelos (2024). A Conflict-Free Learning Approach for MILP and WCSP Optimisation. 1st International Workshop on Solving Linear Optimization Problems for Pseudo-Booleans and Yonder (SLOPPY ‘24).

HAL Citation

Stacy Rousse, Chloé Cerutti, Sophie Leroux, Paul Terzian, Joanna Lledo, David Gourichon, Rémy-Félix Serre, Céline Vandecasteele, Christophe Klopp, Carole Iampietro, Christine Gaspin, Denis Milan, Cécile Donnadieu, Frédérique Pitel, Guillaume Devailly, Sonia E Eynard (2024). Transgenerational epigenetics in quail: targeting DNA methylation patterns to address the interplay between genetic and epigenetic mechanisms. Ecology and Evolution.

HAL PDF Citation

Hanna Bacave, Pierre-Olivier Cheptou, Nikolaos Limnios, Nathalie Peyrard (2024). Non-parametric Observation Driven HMM.

HAL PDF Citation

Jean Mainguy, Claire Hoede (2024). Binette: a fast and accurate bin refinement tool to construct high quality Metagenome Assembled Genomes.. Journal of Open Source Software.

HAL PDF Citation DOI

Prasanna Maddila, Eric Casellas, Patrick Chabrier, Régis Sabbadin, Meritxell Vinyals (2024). APE: An Anti-poaching Multi-Agent Reinforcement Learning Benchmark. 17th European Workshop on Reinforcement Learning (EWRL 2024).

HAL Citation

Julien Guidihounme, Simon De Givry, Benjamin Linard (2024). Simplified pangenome graph traversals with PSSM scoring : search for motifs differentials. Methods for Interfacing with Graphs of Genomic Sequences.

HAL PDF Citation

Han Phan, Céline Brouard, Raphaël Mourad (2024). Semi-supervised learning with pseudo-labeling compares favorably with large language models for regulatory sequence prediction. Briefings in Bioinformatics.

HAL PDF Citation DOI

Matthias Zytnicki (2024). PanSel: a tool finding conserved/divergent regions. Methods for Interfacing with Graphs of Genomic Sequences.

HAL PDF Citation

Siegfried Dubois, Matthias Zytnicki, Thomas Faraut, Claire Lemaitre (2024). Pangenome graph manipulation for local visualisation with pancat. MIGGS1 2024 - 1st symposium on Methods for Interfacing with Graphs of Genomic Sequences.

HAL PDF Citation

Jean Mainguy, Maïna Vienne, Joanna Fourquet, Pierre Martin, Vincent Darbot, Céline Noirot, Philippe Ruiz, Géraldine Pascal, Claire Hoede (2024). metagWGS. version v2.4.2.

HAL Citation Code DOI

Marianne Defresne, Sophie Barbe, Thomas Schiex (2024). Learning how to design biomolecules using a neuro-symbolic architecture. AISSAI - Heterogeneous Data and Large Representation Models in Science.

HAL Citation

Hanna Bacave, Pierre-Olivier Cheptou, Nathalie Peyrard (2024). Interacting Partially Observable DBN to model the dynamics of partially observable metapopulations : opportunities and open challenges.

HAL PDF Citation

Khaoula Hadj-Amor, Ophélie Léger, Sylvain Raffaele, Magdalena Kovacic, Aroune Duclos, Pedro Carvalho-Silva, Frédérick Garcia, Adelin Barbacci (2024). ``Out of sight, out of mind''. The antagonistic role of the transcriptional memory associated with repeated acoustic stimuli on the priming of plant defense.

HAL Citation DOI