Clémence Frioux

68
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Publications

Publications

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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 et al.
Metabolic Engineering, 2024, 83, pp.24 - 38. ⟨10.1016/j.ymben.2024.02.014⟩
Article dans une revue hal-04509395 v1
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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 et al.
Microbial Biotechnology, 2024, ⟨10.1111/1751-7915.14396⟩
Article dans une revue hal-04409251 v1
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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 et al.
Molecular Ecology, In press, 32 (3), pp.703-723. ⟨10.1111/mec.16766⟩
Article dans une revue hal-03868898 v1
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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 et al.
Genome Research, 2023, 33, pp.972 - 987. ⟨10.1101/gr.277056.122⟩
Article dans une revue hal-04192851 v3
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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 et al.
Cell Host & Microbe, 2023, 31 (7), pp.1111. ⟨10.1016/j.chom.2023.05.024⟩
Article dans une revue hal-04141300 v1
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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 et al.
Advances in Ecological Research, 2022, Advances in Ecological Research, 67, pp.27-99. ⟨10.1016/bs.aecr.2022.09.001⟩
Article dans une revue (article de synthèse) hal-03858395 v1
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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 et al.
Cell Host & Microbe, 2021, 29 (7), pp.1167-1176.e9. ⟨10.1016/j.chom.2021.05.008⟩
Article dans une revue hal-03438942 v1
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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 et al.
PeerJ, 2021, 9, pp.1-24. ⟨10.7717/peerj.11344⟩
Article dans une revue hal-03223662 v1
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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 et al.
Frontiers in Marine Science, 2020, 7, pp.1-11. ⟨10.3389/fmars.2020.00085⟩
Article dans une revue hal-02866101 v2

Metagenomic assessment of the global distribution of bacteria and fungi

Mohammad Bahram , Tarquin Netherway , Clémence Frioux , Pamela Ferretti , Luis Pedro Coelho et al.
Environmental Microbiology, 2020, ⟨10.1111/1462-2920.15314⟩
Article dans une revue hal-03033570 v1
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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⟩
Article dans une revue hal-02569935 v1
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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 et al.
Marine Genomics, 2020, 52, pp.100740. ⟨10.1016/j.margen.2020.100740⟩
Article dans une revue hal-02866117 v1
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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⟩
Article dans une revue hal-02883309 v1
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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 et al.
Article dans une revue hal-02395024 v2
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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 et al.
Antioxidants , 2019, 8 (11), pp.564. ⟨10.3390/antiox8110564⟩
Article dans une revue hal-02395080 v1
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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⟩
Article dans une revue hal-01936778 v1
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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 et al.
PLoS Computational Biology, 2018, 14 (5), pp.e1006146. ⟨10.1371/journal.pcbi.1006146⟩
Article dans une revue hal-01807842 v1
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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-01871600 v1
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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 et al.
PeerJ, 2017, 5, pp.e3860. ⟨10.7717/peerj.3860⟩
Article dans une revue hal-01635688 v1
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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 et al.
PLoS Computational Biology, 2017, 13 (1), pp.32. ⟨10.1371/journal.pcbi.1005276⟩
Article dans une revue hal-01449100 v1

Crystal structure and biochemical characterization of a manganese superoxide dismutase from Chaetomium thermophilum

Teemu Haikarainen , Clémence Frioux , Li-Qing Zhnag , Duo-Chuan Li , Anastassios Papageorgiou
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2014, 1844 (2), pp.422-429. ⟨10.1016/j.bbapap.2013.11.014⟩
Article dans une revue hal-04678021 v1
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Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling 6 may 2025 / Modélisation du microbiome

David James Sherman , Hélène Falentin , Clémence Frioux , Simon Labarthe , Maxime Lecomte
NEM 2025 - Journées Nutrition & Ecologie Microbienne, workshop modélisation du microbiome, May 2025, Rennes (Distanciel), France
Communication dans un congrès hal-05059688 v1

Assessing assembly quality in metagenomes of increasing complexity sequenced with HiFi long reads

Nicolas Maurice , Clémence Frioux , Claire Lemaitre , Riccardo Vicedomini
2024 - 24th Genome Informatics meeting, Nov 2024, Hinxton, United Kingdom. pp.1-21
Communication dans un congrès hal-04822870 v1

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 et al.
SBMI 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 models

Clémence Frioux , Sylvie Huet , Simon Labarthe , Julien Martinelli , Thibault Malou et al.
CEMRACS 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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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-03910483 v1
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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 et al.
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.

Wenfan Cao , Maxime Lecomte , Solène Le Fur , Julie J. Aubert , Marie-Bernadette Maillard et al.
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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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-03857781 v1
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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
Communication dans un congrès hal-03857848 v2

Logic modelling of metabolism: from individual networks to communities

Clémence Frioux
Workshop Modélisation du Métabolisme, Nov 2021, Bordeaux, France
Communication dans un congrès hal-03440196 v1

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

Clémence Frioux , Arnaud Belcour , Méziane Aite , Anthony Bretaudeau , Falk Hildebrand et al.
CMSB 2021 - 19th International Conference on Computational Methods in Systems Biology, Sep 2021, Bordeaux, France. pp.1-27
Communication dans un congrès hal-03440212 v1

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-03531761 v1

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

Clémence Frioux , Arnaud Belcour , Meziane Aite , Anthony Bretaudeau , Falk Hildebrand et al.
JOBIM 2021 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2021, Paris, France
Communication dans un congrès hal-03440232 v1

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

Clémence Frioux , Arnaud Belcour , Méziane Aite , Anthony Bretaudeau , Falk Hildebrand et al.
MPA 2021 - 8th Metabolic Pathway Analysis, Aug 2021, Knoxville, TN, United States. pp.1-27
Communication dans un congrès hal-03440221 v1
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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, ⟨10.1093/bioinformatics/bty588⟩
Communication dans un congrès hal-01946860 v1
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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
Communication dans un congrès hal-01557347 v1

Toward the study of metabolic functions in algal holobionts

Claire Lippold , Camille Trottier , Clémence Frioux , Marie Chevallier , Simon M Dittami et al.
4ème Colloque de Génomique Environnementale, Sep 2017, Marseille, France
Communication dans un congrès hal-01576484 v1
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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 et al.
Jobim 2016 : 17ème Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2016, Lyon, France
Communication dans un congrès hal-01377844 v1
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Generation of metabolomic-informed models of metabolism in complex microbial communities

Coralie Muller , Sylvain Prigent , Clémence Frioux
Journées scientifiques Agroécologie et Numérique 2025, Jan 2025, Dijon, France.
Poster de conférence hal-04919231 v1
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Mapler: Assessing assembly quality in taxonomically-rich metagenomes sequenced with HiFi reads

Nicolas Maurice , Clémence Frioux , Claire Lemaitre , Riccardo Vicedomini
2025 - Journées scientifiques Agroécologie et Numérique, Jan 2025, Dijon, France. , pp.1-1, 2025
Poster de conférence hal-04941137 v1
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Enhancing Microbial Genome Reconstruction in Complex Environments by combining Short-and Long-read Sequencing

Carole Belliardo , Arthur Péré , Alain Franc , Jean-Marc Frigerio , Nicolas Maurice et al.
2025 - Journées scientifiques Agroécologie et Numérique, Jan 2025, Dijon, France. , pp.1-1, 2025
Poster de conférence hal-04920790 v1
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Generation of metabolomic-informed models of metabolism in complex microbial communities

Coralie Muller , Sylvain Prigent , Clémence Frioux
Journées Jeunes Chercheurs Chercheuses du département BAP de INRAE, May 2025, Villenave d'Ornon, France
Poster de conférence hal-05073304 v1
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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 et al.
Journées 2024 du programme Agroécologie et Numérique, Jan 2024, Rennes, France. , pp.1-1, 2024
Poster de conférence hal-04423917 v1
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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
Poster de conférence hal-04425626 v1
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Metagenome-scale metabolic modelling for the characterization of cross-feeding interactions in Microcystis-associated microbial communities, in the context of freshwater cyanobacterial blooms

Juliette Audemard , Sébastien Halary , Gabriel Markov , Jeanne Got , Anne Siegel et al.
JOBIM 2024 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2024, Toulouse, France. pp.1-1, 2024
Poster de conférence hal-04654522 v1
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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 et al.
EAGS 2024 - The International Environmental and Agronomical Genomics symposium, Feb 2024, Toulouse, France. , pp.1-1, 2024
Poster de conférence hal-04509213 v1
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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 et al.
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-04183811 v1
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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
Poster de conférence hal-04328778 v1
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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 et al.
SBMI 2023 - 7th International Symposium on Systems Biology of Microbial Infection, Sep 2023, Jena, Germany.
Poster de conférence hal-04229130 v1
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Dynamic Flux Balance Analysis with Metamodels

Clémence Frioux , Sylvie Huet , Simon Labarthe , Julien Martinelli , Thibault Malou et al.
JOBIM 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 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-03839405 v1
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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
Poster de conférence hal-03910438 v1
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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
Poster de conférence hal-03839337 v1
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Dynamic Flux Balance Analysis with Metamodels

Clémence Frioux , Sylvie Huet , Simon Labarthe , Julien Martinelli , Thibault Malou et al.
Microbial communities: current approaches and open challenges, Oct 2022, Cambridge, United Kingdom.
Poster de conférence hal-04252041 v1
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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
Poster de conférence hal-03839374 v1

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-03533795 v1

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-03533786 v1
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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 et al.
IHMC 2021 - 8th International Human Microbiome Consortium Congress, Jun 2021, Barcelone, Spain. pp.1
Poster de conférence hal-03438983 v1

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-03533781 v1
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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 et al.
JOBIM 2020 - Journées Ouvertes de Biologie, Informatique et Mathématique, Jun 2020, Montpellier / Virtual, France. ⟨10.1101/803056⟩
Poster de conférence hal-03151934 v1
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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⟩
Chapitre d'ouvrage hal-03885249 v1