
Simon Labarthe
Chargé de recherche INRAE
70
Documents
Affiliations actuelles
- Pleiade, from patterns to models in computational biodiversity and biotechnology (PLEIADE)
- Biodiversité, Gènes & Communautés (BioGeCo)
Identifiants chercheurs
Présentation
https://slabarthe.pages.mia.inra.fr/website/
- 2020 - ... : chargé de recherche dans l'équipe Pléiade. Inrae (Biogeco) - Inria (Bordeaux Sud-Ouest) team.
- 2019-2020 : visteur à UC Davis dans le laboratoire d'A.Bäumler.
- 2014-2019 : chargé de recherche à MaIAGE. Inrae (Jouy-en-Josas).
- 2010-2014 : Phd + ATER dans l'équipe Carmen (Inria Bordeaux sud-Ouest).
Publications
Publications
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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
Communication dans un congrès
hal-04996155
v1
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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
Communication dans un congrès
hal-04481765
v1
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Pesticide-Free viticulture: towards agroecological wine-producing socioecosystems45ème congrès mondial de la Vigne et du Vin, Oct 2024, Dijon, France
Communication dans un congrès
hal-04732866
v1
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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
Communication dans un congrès
hal-04229116
v1
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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⟩
Communication dans un congrès
hal-03635862
v2
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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
Communication dans un congrès
hal-03781287
v1
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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
Communication dans un congrès
hal-03694338
v1
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Characterizing microbial interactions in controlled and natural microbial communitiesWorkshop SymBioDiversity, May 2022, Santiago, Chile
Communication dans un congrès
hal-03857848
v2
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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⟩
Communication dans un congrès
hal-03753533
v1
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Metabolic modelling deciphers interactions in a cheese bacterial communityMetaboday 2021, Mar 2021, Bordeaux, France
Communication dans un congrès
hal-03531761
v1
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Modeling and inference of bacterial swimmers in biofilmsCEMRACS 2021, Jul 2021, Marseille, France
Communication dans un congrès
hal-03352441
v1
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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
Communication dans un congrès
hal-03352438
v1
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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
Communication dans un congrès
hal-04305004
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MISTIFY PROJECT. ECOLOGY OF SALMONELLA TYPHIMURIUM INFECTION: A MATHEMATICAL MODELING INSIGHTAnnual meeting of Agreenskills program, Apr 2019, Bruxelles, Belgium
Communication dans un congrès
hal-03352429
v1
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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
Communication dans un congrès
hal-00921262
v1
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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
Communication dans un congrès
hal-00802104
v2
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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⟩
Communication dans un congrès
hal-01606999
v1
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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⟩
Communication dans un congrès
hal-00837671
v1
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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
Communication dans un congrès
hal-00759191
v2
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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
Communication dans un congrès
hal-00760451
v1
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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
Communication dans un congrès
hal-00759210
v1
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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
Poster de conférence
hal-04996135
v1
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cMFA for multi-omics data integration in microbial community modelsJournées scientifiques 2025 Agroécologie et Numérique, Jan 2025, Dijon, France
Poster de conférence
hal-04939529
v1
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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
Poster de conférence
hal-04939527
v1
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Developing a culturomic approach to build a collection of grapevine foliar microorganisms with potential biocontrol activity against downy mildewJournées Jean Chevaugeon - 14e Rencontres de Phytopathologie - Mycologie, Jan 2024, Aussois, France.
Poster de conférence
hal-04842411
v1
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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.
Poster de conférence
hal-04874275
v1
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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.
Poster de conférence
hal-04183811
v1
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Towards microbiota-based disease management: analysis of grapevine microbiota in plots with contrasted levels of downy mildew infection22nd GiESCO CONGRESS (GiESCO 2023), Jul 2023, Ithaca, New York, United States. , IVES Conference Series Vine & Wine, 2023, IVES Conference Series Vine & Wine
Poster de conférence
hal-04180613
v1
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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.
Poster de conférence
hal-04229130
v1
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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
Poster de conférence
hal-03839374
v1
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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
Poster de conférence
hal-03777604
v1
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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.
Poster de conférence
hal-03834709
v1
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Dynamic Flux Balance Analysis with MetamodelsJOBIM 2022 - Les Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2022, Rennes, France.
Poster de conférence
hal-04236775
v1
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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
Poster de conférence
hal-03839405
v1
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Dynamic Flux Balance Analysis with MetamodelsMicrobial communities: current approaches and open challenges, Oct 2022, Cambridge, United Kingdom.
Poster de conférence
hal-04252041
v1
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Modelling metabolic network dynamics in a cheese bacterial communityJOBIM,Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2021, Paris, France
Poster de conférence
hal-03533781
v1
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Modelling metabolic network dynamics in a cheese bacterial communityCMSB, The 19th conference on Computational Methods in Systems Biology, Sep 2021, Bordeaux, France
Poster de conférence
hal-03533795
v1
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Modelling metabolic network dynamics in a cheese bacterial communityMPA, Metabolic Pathway Analysis, Aug 2021, Knoxville, United States
Poster de conférence
hal-03533786
v1
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Superposition de couches de fibres et propagations anormales : une étude numériquePrintemps de la Cardiologie, Apr 2013, Marseille, France
Poster de conférence
hal-00926480
v1
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Numerical modeling of the electrical activity of the atria and the pulmonary veinsWorkshop IHU Liryc, Oct 2013, Pessac, France
Poster de conférence
hal-00926441
v1
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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
Poster de conférence
hal-00785607
v1
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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
Poster de conférence
hal-00785621
v1
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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
Chapitre d'ouvrage
hal-02795569
v1
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Mathematical models in microbial ecology2019
Autre publication scientifique
hal-03352423
v1
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Biology-Informed inverse problems for insect pests detection using pheromone sensors2025
Pré-publication, Document de travail
hal-04572831
v3
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Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling2023
Pré-publication, Document de travail
hal-04088301
v2
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Deterministic limit of a stochastic individual-based model of biological tissue interacting with diffusing chemicals2025
Pré-publication, Document de travail
hal-04336174
v3
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A mixture model for the dynamic of the gut mucus layer2015
Pré-publication, Document de travail
hal-01270350
v1
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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 : ⟩
Thèse
tel-00925253
v1
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Contributions à la modélisation mathématiques en écologie microbienne, des données aux modèlesMathématiques [math]. Université de bordeaux, 2024
HDR
tel-04654712
v1
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