20 documents
Journal articles
- Maxime Lecomte, Wenfan Cao, Julie Aubert, David James Sherman, Hélène Falentin, et al.. Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling. Metabolic Engineering, 2024, 83, pp.24 - 38. ⟨10.1016/j.ymben.2024.02.014⟩. ⟨hal-04509395⟩
- Klara Cerk, Pablo Ugalde-Salas, Chabname Ghassemi Nedjad, Maxime Lecomte, Coralie Muller, et al.. Community-scale models of microbiomes: articulating metabolic modelling and metagenome sequencing. Microbial Biotechnology, 2024, ⟨10.1111/1751-7915.14396⟩. ⟨hal-04409251⟩
Conference papers
- Sthyve Junior Tatho Djeanou, Simon Labarthe, Valentina Baldazzi. cMFA for multi-omics data integration in microbial community models. Population Dynamics : From Data to Models 2025, Mar 2025, Sophia antipolis, France. ⟨hal-04996155⟩
- Nicolas Maurice, Clémence Frioux, Claire Lemaitre, Riccardo Vicedomini. Assessing assembly quality in metagenomes of increasing complexity sequenced with HiFi long reads. 2024 - 24th Genome Informatics meeting, Nov 2024, Hinxton, United Kingdom. pp.1-21. ⟨hal-04822870⟩
Poster communications
- Sthyve Junior Tatho Djeanou, Simon Labarthe, Valentina Baldazzi. cMFA for multi-omics data integration in microbial community models. Population Dynamics : From Data to Models 2025, Mar 2025, Sophia Antipolis, France. ⟨hal-04996135⟩
- Carole Belliardo, Arthur Péré, Alain Franc, Jean-Marc Frigerio, Nicolas Maurice, et al.. Enhancing Microbial Genome Reconstruction in Complex Environments by combining Short-and Long-read Sequencing. 2025 - Journées scientifiques Agroécologie et Numérique, Jan 2025, Dijon, France. , pp.1-1, 2025. ⟨hal-04920790⟩
- Sthyve Junior Tatho Djeanou, Simon Labarthe, Valentina Baldazzi. cMFA for multi-omics data integration in microbial community models. Journées scientifiques 2025 Agroécologie et Numérique, Jan 2025, Dijon, France. ⟨hal-04939529⟩
- Nicolas Maurice, Clémence Frioux, Claire Lemaitre, Riccardo Vicedomini. Mapler: Assessing assembly quality in taxonomically-rich metagenomes sequenced with HiFi reads. 2025 - Journées scientifiques Agroécologie et Numérique, Jan 2025, Dijon, France. , pp.1-1, 2025. ⟨hal-04941137⟩
- Coralie Muller, Sylvain Prigent, Clémence Frioux. Generation of metabolomic-informed models of metabolism in complex microbial communities. Journées scientifiques Agroécologie et Numérique 2025, Jan 2025, Dijon, France. . ⟨hal-04919231⟩
- Sthyve Junior Tatho Djeanou, Simon Labarthe, Valentina Baldazzi. cMFA for multi-omics data integration in microbial community models. DSABNS 2025 - 16th Dynamical Systems applied on Biology and Natural Sciences, Jan 2025, Naples, Italy. ⟨hal-04939527⟩
- Sthyve Junior Tatho Djeanou, Simon Labarthe, Valentina Baldazzi. cMFA for multi-omics data integration in microbial community models. CJC MA2024 - Congrès des Jeunes Chercheur.e.s en Mathématiques Appliquées, Oct 2024, Lyon, France. . ⟨hal-04874275⟩
- Carole Belliardo, Nicolas Maurice, Clémence Frioux, Claire Lemaitre, Riccardo Vicedomini, et al.. Unlocking the Soil Microbiome: Unraveling Soil Microbial Complexity Using Long-Read Metagenomics. EAGS 2024 - The International Environmental and Agronomical Genomics symposium, Feb 2024, Toulouse, France. , pp.1-1, 2024. ⟨hal-04509213⟩
- Nicolas Maurice, Claire Lemaitre, Clémence Frioux, Riccardo Vicedomini. Metagenomic assembly of complex ecosystems with highly accurate long-reads. Journées 2024 du PEPR Agroécologie et Numérique, Jan 2024, Rennes, France. pp.1-1, 2024. ⟨hal-04425626⟩
- Carole Belliardo, Samuel Mondy, Arthur Pere, Claire Lemaitre, Riccardo Vicedomini, et al.. Exploring and quantifying the soil genetic diversity captured by long and short-read shotgun metagenomic sequencing. Journées 2024 du programme Agroécologie et Numérique, Jan 2024, Rennes, France. , pp.1-1, 2024. ⟨hal-04423917⟩
Scientific blog post
- Clémence Frioux, Simon Labarthe. Modéliser les communautés bactériennes pour mieux comprendre leur fonctionnement.. 2023. ⟨hal-04120888⟩
Preprints, Working Papers
- Nicolas Maurice, Claire Lemaitre, Clémence Frioux, Riccardo Vicedomini. Mapler: Assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads. 2025. ⟨hal-04993862⟩
- Chabname Ghassemi Nedjad, Mathieu Bolteau, Lucas Bourneuf, Loic Pauleve, Clémence Frioux. Seed2LP: seed inference in metabolic networks for reverse ecology applications. 2024. ⟨hal-04713829⟩
- Constanza M Andreani-Gerard, Natalia E Jiménez, Ricardo Palma, Coralie Muller, Pauline Hamon-Giraud, et al.. Modeling the emergent metabolic potential of soil microbiomes in Atacama landscapes. 2024. ⟨hal-04854948⟩
- Maxime Lecomte, Wenfan Cao, Julie J. Aubert, David James Sherman, Hélène Falentin, et al.. Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling. 2023. ⟨hal-04088301v2⟩
Logiciel
- Julie Aubert, Hélène Falentin, Clémence Frioux, Simon Labarthe, Maxime Lecomte, et al.. TANGO models: numerical multi-omics reconciliation of bacterial fermentation in cheese production. 2024, ⟨swh:1:dir:0a1da28c523c2f32e1214b5d1c1a60ac17ec29df;origin=https://forgemia.inra.fr/tango/tango_models.git;visit=swh:1:snp:722365d9bf1004d05edfe63717763283d4adf26f;anchor=swh:1:rev:bc0bd9895942ed6d82faa9553c1f0a32f60cbbef⟩. ⟨hal-04562266⟩
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