Simon Labarthe
- Pleiade, from patterns to models in computational biodiversity and biotechnology (PLEIADE)
- Biodiversité, Gènes & Communautés (BioGeCo)
Présentation
https://slabarthe.pages-forge.inrae.fr/website/
Publications
Publications
Mining microbiota data to identify antagonists of grapevine downy mildew.E3GP3 2025 - Webinaire “Microbiome & Santé des Plantes”, Jun 2025, Online, France |
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cMFA for multi-omics data integration in microbial community modelsPopulation Dynamics : From Data to Models 2025, Mar 2025, Sophia antipolis, France |
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Modeling Microbial Communities: Toward Digital TwinsMicrobes 2025 - 20e congrès national de la SFM « Microbes dans un monde de transition », SFM, Sep 2025, Bordeaux, France |
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Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling 6 may 2025 / Modélisation du microbiomeNEM 2025 - Journées Nutrition & Ecologie Microbienne, workshop modélisation du microbiome, May 2025, Rennes (Distanciel), France |
Thermodynamic-based modeling of syntrophic organic acid oxidation in anaerobic digestionMicrobes 2025 - 20e congrès national de la SFM « Microbes dans un monde de transition », Société Française de Microbiologuie (SFM), Sep 2025, Bordeaux, France |
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Developing a microfluidic qPCR chip to quantify microbial taxa with a potential biocontrol activity against grapevine downy mildewGiESCO 2025 - 23rd international GiESCO conference, Jul 2025, Geisenheim, Germany |
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Révéler les consortiums microbiens qui interfèrent avec le mildiou de la vigne grâce à l'épidémiologie du microbiome.17e rencontres Plantes-Bactéries 2025, Jan 2025, Aussois, France |
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Mining belowground and aboveground microbiome data to identify microbial biomarkers of grapevine health and yield20. Congrès national de la SFM : Microbes dans un monde de transition (MICROBES 2025), Société Française de Microbiologie (SFM), Sep 2025, Bordeaux, France |
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Development of a microfluidic quantitative PCR chip to monitor the dynamics of a synthetic microbial community on grapevine with potential biocontrol effects against downy mildewApéro VITAE - webinaire interne, VITAE (Léa Cabrol-Froget), Feb 2025, Villenave-d'Ornon, France |
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Four functional profiles for fibre and mucin metabolism in the human gut microbiome65th ISI World Statistics Congress 2025, Oct 2025, The Hague, Netherlands |
cMFA Inference method for multi-omics data integration in microbial community modelsSMAI 2025 - 12ème Biennale Française des Mathématiques Appliquées et Industrielles, SMAI, Jun 2025, Carcans-Maubuisson (Gironde), France |
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Apport des recherches sur le microbiote aux futures stratégies de biocontrôle - Résultats du projet VITAESéminaire Chaire ASVV & INNO’VIN – « Vins & Environnement » #8 | Le biocontrôle est-il opérant ?, Apr 2025, Villenave d'Ornon, France |
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Exploration des données du microbiote pour identifier les antagonistes du mildiou de la vigneJournée Scientifique Vigne & Vin 2025 – Les communautés microbiennes en œnologie, May 2025, Montpellier, France |
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cMFA for multi-omics data integration in microbial community models25e Forum des jeunes mathématiciennes et mathématiciens 2025, Nov 2025, Bordeaux, France |
Towards pesticide-free viticulture: analysing the microbiota of grapevines and vineyard soils to develop microbial biocontrol of downy mildewIW 2025 - International scientific workshop French Priority Research Programme 'Growing and Protecting crops Differently', Sep 2025, Online, France |
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Mining belowground and aboveground microbiome data to identify microbial biomarkers of grapevine health and yield23. GiESCO 2025 - 23. Group of International Experts of vitivinicultural Systems for CoOperation, Jul 2025, Geisenheim, Germany |
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Monitor and steer the microbiota to protect grapevines against downy mildew2025 Annual Meeting of the VITAE project, PPR 'Growing and Protecting Differently', Mar 2025, Angers, France |
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Pest detection from a biology-informed inverse problem and pheromone sensorsEGU General Assembly 2025, Apr 2025, Vienna, Austria. ⟨10.5194/egusphere-egu25-5850⟩ |
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Pesticide-Free viticulture: towards agroecological wine-producing socioecosystems45. World Congress of Vine and Wine, Oct 2024, Dijon, France |
Pest detection from a biology-informed inverse problem and pheromone sensorsDSABNS 2024 - 15th Conference on Dynamical Systems Applied to Biology and Natural Sciences, Feb 2024, Lisbonne, Portugal |
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Mining microbiome data to identify antagonists of grapevine downy mildew (Plasmopara viticola)Open GPB 2024 - Open Conference on Grapevine Physiology and Biotechnology, Jul 2024, Logrono La Riora, Spain |
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Gérer le microbiote de la vigne pour réduire l’utilisation des pesticides - Synthèse des résultats du WP1 du projet VITAE et perspectivesAssemblée générale du projet VITAE, PPR "Cultiver et Protéger Autrement", Mar 2024, Cognac, France |
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Modelling the dynamics of Salmonella infection in the gut at the bacterial and host levelsSBMI 2023 - 7th International Symposium on Systems Biology of Microbial Infection, Sep 2023, Jena, Germany |
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Vers un jumeau numérique du métabolisme bactérien pendant la production de fromageFerment'IA, Sep 2023, Saclay, France |
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Towards microbiota-based disease management: analysis of grapevine microbiota in plots with contrasted levels of downy mildew infection22nd GiESCO (Group of international Experts for Cooperation on Vitivinicultural Systems) 2023, Jul 2023, Ithaca, New York, United States |
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Accelerating metabolic models evaluation with statistical metamodels: application to Salmonella infection modelsCEMRACS 2021 - Data Assimilation and Reduced Modeling for High Dimensional Problems, Jul 2021, Luminy (CIRM, Centre International de Rencontres Mathématiques), France. pp.187-217, ⟨10.1051/proc/202373187⟩ |
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Metatranscriptomics and metabolic modeling to identify bacterial metabolic interactions during the manufacture of a model pressed cheese.FOODMICRO 2022, Aug 2022, Athènes, Greece |
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Métatranscriptomique et modèle métabolique pour identifier la succession des métabolismes bactériens en interaction lors de la fabrication d’un fromage modèle à pâte pressée.23ème édition du colloque du Club des Bactéries Lactiques, UMR INRAE - Institut Agro STLO (Science et Technologie du Lait et de l’Œuf), Jun 2022, Rennes, France |
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Characterizing microbial interactions in controlled and natural microbial communitiesWorkshop SymBioDiversity, May 2022, Santiago, Chile |
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Inferring characteristics of bacterial swimming in biofilm matrix from time-lapse confocal laser scanning microscopyIbSB 2022 - 6th International Symposium "Image-based Systems Biology", Sep 2022, Jena, Germany. ⟨10.7554/eLife.76513⟩ |
Metabolic modelling deciphers interactions in a cheese bacterial communityMetaboday 2021, Mar 2021, Bordeaux, France |
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Modeling and inference of bacterial swimmers in biofilmsCEMRACS 2021, Jul 2021, Marseille, France |
Identification de la fraction active des bactéries du microbiote améliorant la résistance à la colonisation intestinale contre les entérocoques résistants à la vancomycineWebinaire MICA-INRAE : Comprendre et valoriser les communautés microbiennes, Sep 2020, Distanciel, France |
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Omic-based model of the gut microbiotaWorkshop 'Transport in the digestive tract : experiments, modeling, applications to microbiology', Oct 2020, Paris, France |
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MISTIFY PROJECT. ECOLOGY OF SALMONELLA TYPHIMURIUM INFECTION: A MATHEMATICAL MODELING INSIGHTAnnual meeting of Agreenskills program, Apr 2019, Bruxelles, Belgium |
Parameter estimation for dynamical systems using an FDA approach11th International Conference of the ERCIM WG on Computational and Methodological Statistics (CMStatistics 2018), Dec 2018, Pise, Italy |
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A computational bilayer surface model of human atriaFIMH 2013 - 7th International Conference on Functional Imaging and Modeling of the Heart, Jun 2013, London, United Kingdom. pp.27-34, ⟨10.1007/978-3-642-38899-6_4⟩ |
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A Computational Bilayer Surface Model of Human AtriaFIMH 2013 - 7th International Conference on Fonctional Imaging and Modeling of the Heart, S.Ourselin, D.Ruecker, N.Smith, Jun 2013, London, United Kingdom |
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Influence of Transmural Slow-Conduction Zones on the Long- Time Behaviour Of Atrial Arrhythmia. A Numerical Study with a Human Bilayer Atrial ModelCINC - Computing in Cardiology 2013, Sep 2013, Zaragoza, Spain. pp.1187-1190 |
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A Bilayer Representation of the Human AtriaEMBC - 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 2013, EMBS, Jul 2013, Osaka, Japan. pp.1530-1533, ⟨10.1109/EMBC.2013.6609804⟩ |
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A Semi-Automatic Method To Construct Atrial Fibre Structures : a Tool for Atrial SimulationsCinC 2012 - Computing in Cardiology, Sep 2012, Krakow, Poland. pp.881-884 |
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Global and Directional Activation Maps for Cardiac Mapping in ElectrophysiologyCINC 2012 - Computing In Cardiology - 2012, Sep 2012, Krakow, Poland. pp.349-352 |
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From Body Surface Potential to Activation Maps on the Atria: a Machine Learning TechniqueCINC - Computing in Cardiology 2012, Sep 2012, Krakow, Poland. pp.125-128 |
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cMFA for multi-omics data integration in microbial community modelsCompSysBio 2025 - Advanced lecture course on computational systems biology, Oct 2025, Aussois, France |
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cMFA for multi-omics data integration in microbial community modelsCMSB 2025 - 23rd International Conference on Computational Methods in Systems Biology, Sep 2025, Lyon, France |
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cMFA for multi-omics data integration in microbial community modelsDSABNS 2025 - 16th Dynamical Systems applied on Biology and Natural Sciences, Jan 2025, Naples, Italy |
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Statistical method inference cMFA for multi-omics data integration in microbial community modelsJOBIM 2025 - Journées Ouvertes en Biologie Informatique et mathématiques, Jul 2025, Bordeaux, France |
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cMFA for multi-omics data integration in microbial community modelsJournées scientifiques 2025 Agroécologie et Numérique, Jan 2025, Dijon, France |
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cMFA for multi-omics data integration in microbial community modelsPopulation Dynamics : From Data to Models 2025, Mar 2025, Sophia Antipolis, France |
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Developing a culturomic approach to build a collection of grapevine foliar microorganisms with potential biocontrol activity against downy mildew14. Journées Jean Chevaugeon - Rencontres de Phytopathologie - Mycologie, Jan 2024, Aussois, France. |
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cMFA for multi-omics data integration in microbial community modelsCJC MA2024 - Congrès des Jeunes Chercheur.e.s en Mathématiques Appliquées, Oct 2024, Lyon, France. |
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Modelling the dynamics of Salmonella infection in the gut at the bacterial and host levelsISMB/ECCB 2023 - 31st Annual Intelligent Systems For Molecular Biology and the 22nd Annual European Conference on Computational Biology, Jul 2023, Lyon, France. |
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Towards microbiota-based disease management: analysis of grapevine microbiota in plots with contrasted levels of downy mildew infection22. GiESCO International Meeting, Jul 2023, Ithaca, United States. , 2023, IVES Conference Series Vine & Wine |
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Modelling the dynamics of Salmonella infection in the gut at the bacterial and host levelsSBMI 2023 - 7th International Symposium on Systems Biology of Microbial Infection, Sep 2023, Jena, Germany. |
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Pest detection by inversion of a pheromone dispersion modelECMTB 2022 - 12th European Conference on Mathematical and Theoretical Biology, Sep 2022, Heidelberg, Germany |
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A multi-scale epidemic model of enteric infection with heterogeneous shedding resulting from host-microbiota-pathogen interactionsECMTB 2022 - 12th European Conference on Mathematical and Theoretical Biology, Sep 2022, Heidelberg, Germany. |
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Modelling the dynamics of Salmonella infection in the gut at the bacterial and the host levelMicrobial communities: current approaches and open challenges, Oct 2022, Cambridge, United Kingdom |
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Dynamic Flux Balance Analysis with MetamodelsJOBIM 2022 - Les Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2022, Rennes, France. |
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Modelling the dynamics of Salmonella infection in the gut at the bacterial and host levelsJOBIM 2022 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2022, Rennes, France |
Modelling metabolic network dynamics in a cheese bacterial communityCMSB, The 19th conference on Computational Methods in Systems Biology, Sep 2021, Bordeaux, France |
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Modelling metabolic network dynamics in a cheese bacterial communityMPA, Metabolic Pathway Analysis, Aug 2021, Knoxville, United States |
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Modelling metabolic network dynamics in a cheese bacterial communityJOBIM,Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2021, Paris, France |
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A spatially structured model to investigate key drivers of the gut microbiota biogeography in humans11th European Conference on Mathematical and Theoretical Biology (ECMTB 2018) https://www.ecmtb2018.org/, Jul 2018, Lisbon, Portugal. |
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Numerical modeling of the electrical activity of the atria and the pulmonary veinsWorkshop IHU Liryc, Oct 2013, Pessac, France |
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Superposition de couches de fibres et propagations anormales : une étude numériquePrintemps de la Cardiologie, Apr 2013, Marseille, France |
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Simulation numérique de l'activité électrique dans l'oreillette gauche et les veines pulmonairesPrintemps de la Cardiologie, Apr 2012, Bordeaux, France |
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Modélisation bidimensionnelle d'un problème de réaction-diffusion anisotrope hétérogène en couche mince appliquée à la cardiologieCANUM - 2012, May 2012, Super-Besse, France |
Mathématiques et cardiologie : modéliser pour mieux comprendre les arythmies auriculaires5 jeunes chercheurs d'avenir 2015, 1, Editions le Pommier, pp.192, 2015, Promesses de la Science, 978-2-7465-0937-5 |
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Coupling microbial communities models with data2025 |
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Revealing microbial consortia that interfere with grapevine downy mildew through microbiome epidemiology2025 |
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Mathematical models in microbial ecology2019 |
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Inference Method cMFA for multi-omics data integration in microbial community models2025 |
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Pest localization through sequential data assimilation with pheromone sensors2025 |
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Biology-Informed inverse problems for insect pests detection using pheromone sensors2025 |
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Deterministic limit of a stochastic individual-based model of biological tissue interacting with diffusing chemicals2025 |
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Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling2023 |
A mixture model for the dynamic of the gut mucus layer2015 |
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Modélisation de l'activité électrique des oreillettes et des veines pulmonairesModélisation et simulation. Université Victor Segalen - Bordeaux II, 2013. Français. ⟨NNT : ⟩ |
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Contributions à la modélisation mathématiques en écologie microbienne, des données aux modèlesMathématiques [math]. Université de bordeaux, 2024 |