Rechercher

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.

Article de revue

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

Preprint

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

Preprint

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.

Article de conférence

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.

Article de revue

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.

Article de revue

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.

Article de revue

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.

Article de revue

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.

Article de revue

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

Poster

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.

Rapport

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.

Poster

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).

Poster

Adela Poublan-Couzardot, Bernadette Julier, Marie Pegard, 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).

Poster

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.

Poster

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).

Article de conférence

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).

Article de conférence

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.

Article de conférence

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

Logiciel

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

Poster

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.

Article de revue

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

Logiciel

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

Thèse

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

Poster

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

Preprint

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

Preprint

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

Article de revue

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.

Preprint

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.

Article de revue

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.

Preprint

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

Rapport

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.

Non catégorisé

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

Preprint

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

Preprint

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.

Preprint

Élise 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.

Article de revue

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.

Poster

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

Article de revue

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

Chapitre de livre

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.

Article de revue

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

Article de revue

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.

Article de revue

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.

Article de revue

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

Logiciel

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.

Rapport

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

Article de revue

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.

Article de revue

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.

Article de revue

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

Preprint

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.

Article de revue

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

Article de revue

Sonia E. Eynard, Christophe Klopp, Kamila Canale-Tabet, William Marande, Celine 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.

Article de revue

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.

Article de revue

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

Article de revue

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.

Preprint

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

Article de revue

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.

Article de conférence

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..

Poster

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

Article de conférence

Matthias ZYTNICKI (2024). pansel. version.

Logiciel

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.

Article de conférence

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.

Article de revue

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

Thèse

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

Thèse

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.

Non catégorisé

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.

Article de conférence

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.

Article de conférence

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).

Article de conférence

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

Preprint

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.

Article de revue

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).

Article de conférence

Valentin Sorin, Marie-Pierre Sanchez, Carole Iampietro, Camille Eché, Amandine Suin, Camille Marcuzzo, Laurence Drouilhet, Denis Milan, Gwenola Tosser-Klopp, Cécile Donnadieu, Christine Gaspin, Clément Birbes, Christophe Klopp, Didier Boichard, Mekki Boussaha (2024). The construction of a cattle pangenome for 14 French dairy and beef breeds provides new insights into their genetic diversity.. Annual Meeting of the European Association for Animal Production.

Article de conférence

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.

Article de conférence

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.

Article de revue

Marianne Defresne, Sophie Barbe, Thomas Schiex (2024). Scalable Coupling of Deep Learning with Logical Reasoning. First International Workshop on Discrete Optimization with Soft Constraint..

Article de conférence

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

Article de conférence

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.

Article de conférence

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

Logiciel

HAL Citation Code DOI

Sara Alina Neumann, Jacinthe Azevedo-Favory, Rémy Merret, Marie-Christine Carpentier, Julien Henry, V. Marchand, Anne Debures, Magali Rompais, Christine Carapito, Yuri Motorin, Julio Sáez-Vásquez (2024). Mechanisms and impact of ribosomal RNA methylation in plants. The 2024 Post-transcriptional Gene Regulation in Plants meeting.

Poster

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.

Article de conférence

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

Preprint

Maya Hiltpold, Ronan Trépos, Frédéric Douhard (2024). Exploring potential GxE interactions in the lifetime performance of suckling ewes. Wageningen Academic Publishers.

Non catégorisé

Valentin Sorin, Julien Sarry, Clément Birbes, Carole Iampietro, Camille Eché, Amandine Suin, Camille Marcuzzo, Laurence Drouilhet, Denis Milan, M Boussaha, M P Sanchez, Cécile Donnadieu, Christine Gaspin, Christophe Klopp, Gwenola Tosser-Klopp (2024). Construction and characterization of a comprehensive ovine pangenome from 11 breeds provides new insights into their genetic diversity. 75. Annual Meeting of the European Federation of Animal Science (EAAP 2024).

Article de conférence

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.

Preprint

Alexandre Lhuisset (2024). Assurances forestières et politiques publiques : Une approche basée sur la théorie des jeux.

Aurélie Mercadié, Eric Casellas, Eléonore Gravier, Gwendal Josse, Nathalie Vialaneix, Brouard Céline (2024). NMFProfiler. version 0.2.1.

Logiciel

HAL Citation Code

Rapport

Kene Boun My, Marielle Brunette, Stéphane Couture, Sarah van Driessche (2024). Are ambiguity preferences aligned with risk preferences?. Journal of Behavioral and Experimental Economics.

Article de revue

Hanna Bacave, Pierre-Olivier Cheptou, Nathalie Peyrard (2024). Partially observable DBN to model the dynamics of partially observable metapopulations : advantages and open challenges. International Statistical Ecology Conference.

Article de conférence