Clémence Frioux

Documents

Publications

	Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling Maxime Lecomte , Wenfan Cao , Julie Aubert , David James Sherman , Hélène Falentin Metabolic Engineering, 2024, 83, pp.24 - 38. ⟨10.1016/j.ymben.2024.02.014⟩ Article dans une revue hal-04509395v1
	Community-scale models of microbiomes: articulating metabolic modelling and metagenome sequencing Klara Cerk , Pablo Ugalde-Salas , Chabname Ghassemi Nedjad , Maxime Lecomte , Coralie Muller Microbial Biotechnology, 2024, ⟨10.1111/1751-7915.14396⟩ Article dans une revue hal-04409251v1
	Enterosignatures define common bacterial guilds in the human gut microbiome Clémence Frioux , Rebecca Ansorge , Ezgi Özkurt , Chabname Ghassemi Nedjad , Joachim Fritscher Cell Host & Microbe, 2023, 31 (7), pp.1111. ⟨10.1016/j.chom.2023.05.024⟩ Article dans une revue hal-04141300v1
	Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe Arnaud Belcour , Jeanne Got , Méziane Aite , Ludovic Delage , Jonas Collén Genome Research, 2023, 33, pp.972 - 987. ⟨10.1101/gr.277056.122⟩ Article dans une revue hal-04192851v3
	The functional microbiome of grapevine throughout plant evolutionary history and lifetime Paola Fournier , Lucile Pellan , Didac Barroso-Bergadà , David Bohan , Thierry Candresse Advances in Ecological Research, 2022, Advances in Ecological Research, 67, pp.27-99. ⟨10.1016/bs.aecr.2022.09.001⟩ Article dans une revue hal-03858395v1
	Insights into the potential for mutualistic and harmful host‐microbe interactions affecting brown alga freshwater acclimation Hetty Kleinjan , Clémence Frioux , Gianmaria Califano , Méziane Aite , Enora Fremy Molecular Ecology, inPress, 32 (3), pp.703-723. ⟨10.1111/mec.16766⟩ Article dans une revue hal-03868898v1
	Dispersal strategies shape persistence and evolution of human gut bacteria Falk Hildebrand , Toni I Gossmann , Clémence Frioux , Ezgi Özkurt , Pernille Neve Myers Cell Host & Microbe, 2021, 29 (7), pp.1167-1176.e9. ⟨10.1016/j.chom.2021.05.008⟩ Article dans une revue hal-03438942v1
	Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines Elham Karimi , Enora Geslain , Arnaud Belcour , Clémence Frioux , Méziane Aite PeerJ, 2021, 9, pp.1-24. ⟨10.7717/peerj.11344⟩ Article dans une revue hal-03223662v1
	Metagenomic assessment of the global distribution of bacteria and fungi Mohammad Bahram , Tarquin Netherway , Clémence Frioux , Pamela Ferretti , Luis Pedro Coelho Environmental Microbiology, 2020, ⟨10.1111/1462-2920.15314⟩ Article dans une revue hal-03033570v1
	Metabolic Complementarity Between a Brown Alga and Associated Cultivable Bacteria Provide Indications of Beneficial Interactions Bertille Burgunter-Delamare , Hetty Kleinjan , Clémence Frioux , Enora Fremy , Margot Wagner Frontiers in Marine Science, 2020, 7, pp.1-11. ⟨10.3389/fmars.2020.00085⟩ Article dans une revue hal-02866101v2
	Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species Arnaud Belcour , Clémence Frioux , Méziane Aite , Anthony Bretaudeau , Falk Hildebrand eLife, 2020, 9, ⟨10.7554/eLife.61968⟩ Article dans une revue hal-02395024v2
	From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes Clémence Frioux , Dipali Singh , Tamas Korcsmaros , Falk Hildebrand Computational and Structural Biotechnology Journal, 2020, ⟨10.1016/j.csbj.2020.06.028⟩ Article dans une revue hal-02883309v1
	Using automated reasoning to explore the metabolism of unconventional organisms: a first step to explore host–microbial interactions Clémence Frioux , Simon Dittami , Anne Siegel Biochemical Society Transactions, 2020, 48 (3), pp.901-913. ⟨10.1042/BST20190667⟩ Article dans une revue hal-02569935v1
	The genome of Ectocarpus subulatus – A highly stress-tolerant brown alga Simon M. Dittami , Erwan Corre , Loraine Brillet-Guéguen , Agnieszka Lipinska , Noé Pontoizeau Marine Genomics, 2020, 52, pp.100740. ⟨10.1016/j.margen.2020.100740⟩ Article dans une revue hal-02866117v1
	Genome–Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae Saccharina japonica and Cladosiphon okamuranus Delphine Nègre , Méziane Aite , Arnaud Belcour , Clémence Frioux , Loraine Brillet-Guéguen Antioxidants , 2019, 8 (11), pp.564. ⟨10.3390/antiox8110564⟩ Article dans une revue hal-02395080v1
	Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models Méziane Aite , Marie Chevallier , Clémence Frioux , Camille Trottier , Jeanne Got PLoS Computational Biology, 2018, 14 (5), pp.e1006146. ⟨10.1371/journal.pcbi.1006146⟩ Article dans une revue hal-01807842v1
	Hybrid Metabolic Network Completion Clémence Frioux , Torsten Schaub , Sebastian Schellhorn , Anne Siegel , Philipp Wanko Theory and Practice of Logic Programming, 2018, pp.1-23. ⟨10.1017/S1471068418000455⟩ Article dans une revue hal-01936778v1
	Scalable and exhaustive screening of metabolic functions carried out by microbial consortia Clémence Frioux , Enora Fremy , Camille Trottier , Anne Siegel Bioinformatics, 2018, 34 (17), pp.i934 - i943. ⟨10.1093/bioinformatics/bty588⟩ Article dans une revue hal-01871600v1
	Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks Sylvain Prigent , Clémence Frioux , Simon M Dittami , Sven Thiele , Abdelhalim Larhlimi PLoS Computational Biology, 2017, 13 (1), pp.32. ⟨10.1371/journal.pcbi.1005276⟩ Article dans une revue hal-01449100v1
	Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks Julie Laniau , Clémence Frioux , Jacques Nicolas , Caroline Baroukh , Maria-Paz Cortés PeerJ, 2017, 5, pp.e3860. ⟨10.7717/peerj.3860⟩ Article dans une revue hal-01635688v1

	Modelling the dynamics of Salmonella infection in the gut at the bacterial and host levels Coralie Muller , Pablo Ugalde Salas , Rafael Kaempfer , Arie Wortsman , Simon Labarthe SBMI 2023 - 7th International Symposium on Systems Biology of Microbial Infection, Sep 2023, Jena, Germany Communication dans un congrès hal-04229116v1
	Metatranscriptomics and metabolic modeling to identify bacterial metabolic interactions during the manufacture of a model pressed cheese. Wenfan Cao , Maxime Lecomte , Solène Le Fur , Julie J. Aubert , Marie-Bernadette Maillard FOODMICRO 2022, Aug 2022, Athènes, Greece Communication dans un congrès hal-03781287v1
	Reasoning approaches for the characterization of cooperation and competition in large-scale microbial communities Maxime Lecomte , David James Sherman , Hélène Falentin , Clémence Frioux Journée GT Bioss 2022, Nov 2022, Nantes, France Communication dans un congrès hal-03857781v1
	Characterizing microbial interactions in controlled and natural microbial communities Maxime Lecomte , Simon Labarthe , David James Sherman , Hélène Falentin , Clémence Frioux Workshop SymBioDiversity, May 2022, Santiago, Chile Communication dans un congrès hal-03857848v2
	Métatranscriptomique et modèle métabolique pour identifier la succession des métabolismes bactériens en interaction lors de la fabrication d’un fromage modèle à pâte pressée. Wenfan Cao , Maxime Lecomte , Solène Le Fur , Julie J. Aubert , Marie-Bernadette Maillard 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-03694338v1
	A logic programming exploration of metabolic networks to explain microbial community models Chabname Ghassemi Nedjad , Loïc Paulevé , Clémence Frioux GT Bioss 2022 - Journée annuelle du Groupe de Travail sur la Biologie Systémique Symbolique, Nov 2022, Nantes, France Communication dans un congrès hal-03910483v1
	Metabolic complementarity applied to the screening of microbiota and the identification of key species Clémence Frioux , Arnaud Belcour , Meziane Aite , Anthony Bretaudeau , Falk Hildebrand JOBIM 2021 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2021, Paris, France Communication dans un congrès hal-03440232v1
	Metabolic complementarity applied to the screening of microbiota and the identification of key species Clémence Frioux , Arnaud Belcour , Méziane Aite , Anthony Bretaudeau , Falk Hildebrand MPA 2021 - 8th Metabolic Pathway Analysis, Aug 2021, Knoxville, TN, United States. pp.1-27 Communication dans un congrès hal-03440221v1
	Metabolic modelling deciphers interactions in a cheese bacterial community Maxime Lecomte , David James Sherman , Hélène Falentin , Clémence Frioux , Simon Labarthe Metaboday 2021, Mar 2021, Bordeaux, France Communication dans un congrès hal-03531761v1
	Metabolic complementarity applied to the screening of microbiota and the identification of key species Clémence Frioux , Arnaud Belcour , Méziane Aite , Anthony Bretaudeau , Falk Hildebrand CMSB 2021 - 19th International Conference on Computational Methods in Systems Biology, Sep 2021, Bordeaux, France. pp.1-27 Communication dans un congrès hal-03440212v1
	Logic modelling of metabolism: from individual networks to communities Clémence Frioux Workshop Modélisation du Métabolisme, Nov 2021, Bordeaux, France Communication dans un congrès hal-03440196v1
	Scalable and exhaustive screening of metabolic functions carried out by microbial consortia Clémence Frioux , Enora Fremy , Camille Trottier , Anne Siegel ECCB - 2018 - 17th European Conference on Computational Biology, Sep 2018, Athènes, Greece. pp.i934-i943 Communication dans un congrès hal-01946860v1
	Toward the study of metabolic functions in algal holobionts Claire Lippold , Camille Trottier , Clémence Frioux , Marie Chevallier , Simon M Dittami 4ème Colloque de Génomique Environnementale, Sep 2017, Marseille, France Communication dans un congrès hal-01576484v1
	Hybrid Metabolic Network Completion Clémence Frioux , Torsten Schaub , Sebastian Schellhorn , Anne Siegel , Philipp Wanko 14th International Conference on Logic Programming and Nonmonotonic Reasoning - LPNMR 2017, Jul 2017, Espoo, Finland. pp.308-321 Communication dans un congrès hal-01557347v1
	Handling the heterogeneity of genomic and metabolic networks data within flexible workflows with the PADMet toolbox Marie Chevallier , Méziane Aite , Jeanne Got , Guillaume Collet , Nicolas Loira Jobim 2016 : 17ème Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2016, Lyon, France Communication dans un congrès hal-01377844v1

	Exploring and quantifying the soil genetic diversity captured by long and short-read shotgun metagenomic sequencing Carole Belliardo , Samuel Mondy , Arthur Pere , Claire Lemaitre , Riccardo Vicedomini Journées 2024 du programme Agroécologie et Numérique, Jan 2024, Rennes, France. , pp.1-1, 2024 Poster de conférence hal-04423917v1
	Unlocking the Soil Microbiome: Unraveling Soil Microbial Complexity Using Long-Read Metagenomics Carole Belliardo , Nicolas Maurice , Clémence Frioux , Claire Lemaitre , Riccardo Vicedomini EAGS 2024 - The International Environmental and Agronomical Genomics symposium, Feb 2024, Toulouse, France. , pp.1-1, 2024 Poster de conférence hal-04509213v1
	Metagenomic assembly of complex ecosystems with highly accurate long-reads Nicolas Maurice , Claire Lemaitre , Clémence Frioux , Riccardo Vicedomini Journées 2024 du PEPR Agroécologie et Numérique, Jan 2024, Rennes, France. pp.1-1, 2024 Poster de conférence hal-04425626v1
	Modelling the dynamics of Salmonella infection in the gut at the bacterial and host levels Coralie Muller , Pablo Ugalde Salas , Rafael Kaempfer , Arie Wortsman , Simon Labarthe ISMB/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-04183811v1
	Modelling the dynamics of Salmonella infection in the gut at the bacterial and host levels Coralie Muller , Pablo Ugalde Salas , Rafael Kaempfer , Arie Wortsman , Simon Labarthe SBMI 2023 - 7th International Symposium on Systems Biology of Microbial Infection, Sep 2023, Jena, Germany. Poster de conférence hal-04229130v1
	Logic and linear programming for seed identiﬁcation in metabolic networks Chabname Ghassemi Nedjad , Clémence Frioux , Loïc Paulevé Biorégul 2023 - Modélisation Formelle de Réseaux de Régulation Biologique, Jun 2023, Porquerolles (Hyères), France. pp.1-1, 2023 Poster de conférence hal-04328778v1
	Characterising competition and cooperation potentials in microbial communities using discrete models of metabolism. An exploratory analysis Maxime Lecomte , David James Sherman , Hélène Falentin , Clémence Frioux JOBIM 2022 - JOURNÉES OUVERTES EN BIOLOGIE, INFORMATIQUE ET MATHÉMATIQUES, Jul 2022, Rennes, France Poster de conférence hal-03839337v1
	Analyzing and modelling functions carried by key species in minimal microbial communities Chabname Ghassemi Nedjad , Clémence Frioux JOBIM 2022 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2022, Rennes, France Poster de conférence hal-03910438v1
	Modelling the dynamics of Salmonella infection in the gut at the bacterial and host levels Coralie Muller , Arie Wortsman , Pablo Ugalde-Salas , Clémence Frioux , Simon Labarthe JOBIM 2022 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2022, Rennes, France Poster de conférence hal-03839374v1
	Dynamic Flux Balance Analysis with Metamodels Clémence Frioux , Sylvie Huet , Simon Labarthe , Julien Martinelli , Thibault Malou Microbial communities: current approaches and open challenges, Oct 2022, Cambridge, United Kingdom. Poster de conférence hal-04252041v1
	Modelling the dynamics of Salmonella infection in the gut at the bacterial and the host level Coralie Muller , Arie Wortsman , Pablo Ugalde-Salas , Clémence Frioux , Simon Labarthe Microbial communities: current approaches and open challenges, Oct 2022, Cambridge, United Kingdom Poster de conférence hal-03839405v1
	Dynamic Flux Balance Analysis with Metamodels Clémence Frioux , Sylvie Huet , Simon Labarthe , Julien Martinelli , Thibault Malou JOBIM 2022 - Les Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2022, Rennes, France. Poster de conférence hal-04236775v1
	Modelling metabolic network dynamics in a cheese bacterial community Maxime Lecomte , David James Sherman , Hélène Falentin , Clémence Frioux , Simon Labarthe CMSB, The 19th conference on Computational Methods in Systems Biology, Sep 2021, Bordeaux, France Poster de conférence hal-03533795v1
	Modelling metabolic network dynamics in a cheese bacterial community Maxime Lecomte , David James Sherman , Hélène Falentin , Clémence Frioux , Simon Labarthe JOBIM,Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2021, Paris, France Poster de conférence hal-03533781v1
	Assessment of metabolic complementarity in large-scale microbiotas for the identification of key species Clémence Frioux , Arnaud Belcour , Méziane Aite , Anthony Bretaudeau , Falk Hildebrand IHMC 2021 - 8th International Human Microbiome Consortium Congress, Jun 2021, Barcelone, Spain. pp.1 Poster de conférence hal-03438983v1
	Modelling metabolic network dynamics in a cheese bacterial community Maxime Lecomte , David James Sherman , Hélène Falentin , Clémence Frioux , Simon Labarthe MPA, Metabolic Pathway Analysis, Aug 2021, Knoxville, United States Poster de conférence hal-03533786v1
	Metage2Metabo: metabolic complementarity applied to genomes of large-scale microbiotas for the identification of keystone species Arnaud Belcour , Clémence Frioux , Méziane Aite , Anthony Bretaudeau , Falk Hildebrand JOBIM 2020 - Journées Ouvertes de Biologie, Informatique et Mathématique, Jun 2020, Montpellier / Virtual, France. ⟨10.1101/803056⟩ Poster de conférence hal-03151934v1

	Problèmes d'optimisation combinatoire pour l'étude du métabolisme Clémence Frioux , Anne Siegel Approches symboliques de la modélisation et de l’analyse des systèmes biologiques, ISTE éditions, 2022, Encyclopédie Sciences, 9781789480290. ⟨10.51926/ISTE.9029.ch2⟩ Chapitre d'ouvrage hal-03885249v1

	Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling Maxime Lecomte , Wenfan Cao , Julie J. Aubert , David James Sherman , Hélène Falentin 2023 Pré-publication, Document de travail hal-04088301v2
	EsMeCaTa: Estimating metabolic capabilities from taxonomic affiliations Arnaud Belcour , Baptiste Ruiz , Clémence Frioux , Samuel Blanquart , Anne Siegel 2022 Pré-publication, Document de travail hal-03697249v1
	The genome of Ectocarpus subulatus -a highly stress-tolerant brown alga Simon M. Dittami , Erwan Corre , Loraine Brillet-Guéguen , Agnieszka Lipinska , Méziane Aite 2019 Pré-publication, Document de travail hal-02333021v1

Clémence Frioux

Publications

Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling

Community-scale models of microbiomes: articulating metabolic modelling and metagenome sequencing

Enterosignatures define common bacterial guilds in the human gut microbiome

Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe

The functional microbiome of grapevine throughout plant evolutionary history and lifetime

Insights into the potential for mutualistic and harmful host‐microbe interactions affecting brown alga freshwater acclimation

Dispersal strategies shape persistence and evolution of human gut bacteria

Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines

Metagenomic assessment of the global distribution of bacteria and fungi

Metabolic Complementarity Between a Brown Alga and Associated Cultivable Bacteria Provide Indications of Beneficial Interactions

Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species

From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes

Using automated reasoning to explore the metabolism of unconventional organisms: a first step to explore host–microbial interactions

The genome of Ectocarpus subulatus – A highly stress-tolerant brown alga

Genome–Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae Saccharina japonica and Cladosiphon okamuranus

Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models

Hybrid Metabolic Network Completion

Scalable and exhaustive screening of metabolic functions carried out by microbial consortia

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks

Modelling the dynamics of Salmonella infection in the gut at the bacterial and host levels

Metatranscriptomics and metabolic modeling to identify bacterial metabolic interactions during the manufacture of a model pressed cheese.

Reasoning approaches for the characterization of cooperation and competition in large-scale microbial communities

Characterizing microbial interactions in controlled and natural microbial communities

Métatranscriptomique et modèle métabolique pour identifier la succession des métabolismes bactériens en interaction lors de la fabrication d’un fromage modèle à pâte pressée.

A logic programming exploration of metabolic networks to explain microbial community models

Metabolic complementarity applied to the screening of microbiota and the identification of key species

Metabolic complementarity applied to the screening of microbiota and the identification of key species

Metabolic modelling deciphers interactions in a cheese bacterial community

Metabolic complementarity applied to the screening of microbiota and the identification of key species

Logic modelling of metabolism: from individual networks to communities

Scalable and exhaustive screening of metabolic functions carried out by microbial consortia

Toward the study of metabolic functions in algal holobionts

Hybrid Metabolic Network Completion

Handling the heterogeneity of genomic and metabolic networks data within flexible workflows with the PADMet toolbox

Exploring and quantifying the soil genetic diversity captured by long and short-read shotgun metagenomic sequencing

Unlocking the Soil Microbiome: Unraveling Soil Microbial Complexity Using Long-Read Metagenomics

Metagenomic assembly of complex ecosystems with highly accurate long-reads

Modelling the dynamics of Salmonella infection in the gut at the bacterial and host levels

Modelling the dynamics of Salmonella infection in the gut at the bacterial and host levels

Logic and linear programming for seed identiﬁcation in metabolic networks

Characterising competition and cooperation potentials in microbial communities using discrete models of metabolism. An exploratory analysis

Analyzing and modelling functions carried by key species in minimal microbial communities

Modelling the dynamics of Salmonella infection in the gut at the bacterial and host levels

Dynamic Flux Balance Analysis with Metamodels

Modelling the dynamics of Salmonella infection in the gut at the bacterial and the host level

Dynamic Flux Balance Analysis with Metamodels

Modelling metabolic network dynamics in a cheese bacterial community

Modelling metabolic network dynamics in a cheese bacterial community

Assessment of metabolic complementarity in large-scale microbiotas for the identification of key species

Modelling metabolic network dynamics in a cheese bacterial community

Metage2Metabo: metabolic complementarity applied to genomes of large-scale microbiotas for the identification of keystone species

Problèmes d'optimisation combinatoire pour l'étude du métabolisme

Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling

EsMeCaTa: Estimating metabolic capabilities from taxonomic affiliations

The genome of Ectocarpus subulatus -a highly stress-tolerant brown alga