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Clémence Frioux

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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⟩
Journal articles hal-04509395v1
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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⟩
Journal articles hal-04409251v1
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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⟩
Journal articles hal-04141300v1
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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⟩
Journal articles hal-04192851v3
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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⟩
Journal articles hal-03868898v1
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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⟩
Journal articles hal-03858395v1
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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⟩
Journal articles hal-03438942v1
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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⟩
Journal articles 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⟩
Journal articles hal-03033570v1
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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⟩
Journal articles hal-02866101v2
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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⟩
Journal articles hal-02866117v1
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Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species

Arnaud Belcour , Clémence Frioux , Méziane Aite , Anthony Bretaudeau , Falk Hildebrand
Journal articles hal-02395024v2
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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⟩
Journal articles hal-02883309v1
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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⟩
Journal articles hal-02569935v1
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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⟩
Journal articles hal-02395080v1
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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⟩
Journal articles 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⟩
Journal articles hal-01871600v1
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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⟩
Journal articles hal-01807842v1
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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⟩
Journal articles hal-01635688v1
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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⟩
Journal articles hal-01449100v1

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
Conference papers hal-04229116v1
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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
Conference papers hal-03781287v1
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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
Conference papers hal-03910483v1
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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
Conference papers hal-03857848v2
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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
Conference papers hal-03857781v1
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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.

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
Conference papers hal-03694338v1

Logic modelling of metabolism: from individual networks to communities

Clémence Frioux
Workshop Modélisation du Métabolisme, Nov 2021, Bordeaux, France
Conference papers hal-03440196v1

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
Conference papers hal-03440212v1

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
Conference papers 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
Conference papers 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
Conference papers hal-03531761v1
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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
Conference papers 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
Conference papers hal-01576484v1
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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
Conference papers hal-01557347v1
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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
Conference papers hal-01377844v1
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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
Conference poster hal-04423917v1
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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
Conference poster hal-04509213v1
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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
Conference poster hal-04425626v1
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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.
Conference poster hal-04183811v1
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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.
Conference poster hal-04229130v1
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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
Conference poster hal-04328778v1
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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
Conference poster hal-03839405v1
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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.
Conference poster hal-04236775v1
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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
Conference poster hal-03910438v1
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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
Conference poster hal-03839337v1
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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
Conference poster hal-03839374v1
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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.
Conference poster hal-04252041v1

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
Conference poster 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
Conference poster hal-03533781v1
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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
Conference poster 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
Conference poster hal-03533786v1
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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⟩
Conference poster hal-03151934v1
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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⟩
Book sections hal-03885249v1