Cédric Midoux

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Affiliations actuelles

Procédés biotechnologiques au service de l'environnement (UR PROSE)
Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE)
IR BioInfOmics

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Publications

	Electromethanogenesis from H2S containing biogas: H2S and cathode potential drive microbial selection and methane yields Ankit Rao , Manuel Guillermo Rodriguez Ancieta , Chrystelle Bureau , Cedric Midoux , Jean-Marie Fontmorin et al. Bioresource Technology Reports, 2026, pp.102910. ⟨10.1016/j.biteb.2026.102910⟩ Article dans une revue hal-05674009v1
	Propionic acid-related inhibition during anaerobic digestion: insights into methane production and microbial community responses Xiaojun Liu , Chloé Soulard , Véronique Jamilloux , André Pauss , Laura André et al. Journal of Environmental Chemical Engineering, 2026, 14 (5), pp.123824. ⟨10.1016/j.jece.2026.123824⟩ Article dans une revue hal-05674029v1
	Host-virus dynamics in anaerobic digesters facing abiotic inhibition Marion Coves , Cédric Midoux , Julien Lossouarn , Mahendra Mariadassou , Vuong Quoc Hoang Ngo et al. Water Research, In press, pp.126521. ⟨10.1016/j.watres.2026.126521⟩ Article dans une revue hal-05695906v1
	Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data. Cédric Midoux , Olivier Rué , Olivier Chapleur , Ariane Bize , Valentin Loux et al. Journal of Open Source Software, 2024, 9 (103), pp.6704. ⟨10.21105/joss.06704⟩ Article dans une revue hal-04785149v1
	The electrochemical microbial tree: A new concept for wastewater treatment Morgane Hoareau , Luc Etcheverry , Olivier Chapleur , Chrystelle Bureau , Cédric Midoux et al. Chemical Engineering Journal, 2023, 454 (3), pp.140295. ⟨10.1016/j.cej.2022.140295⟩ Article dans une revue hal-03851691v1
	Study of a Pilot Scale Microbial Electrosynthesis Reactor for Organic Waste Biorefinery Jiang-Hao Tian , Rémy Lacroix , Asim Ali Yaqoob , Chrystelle Bureau , Cédric Midoux et al. Energies, 2023, 16 (2), pp.591. ⟨10.3390/en16020591⟩ Article dans une revue hal-03922462v1
	Investigation of the Phageome and Prophages in French Cider, a Fermented Beverage Pierre Ledormand , Nathalie Desmasures , Cédric Midoux , Olivier Rué , Marion Dalmasso Microorganisms, 2022, 10 (6), pp.1203. ⟨10.3390/microorganisms10061203⟩ Article dans une revue hal-03693766v1
	Molecular approaches to uncover phage-lactic acid bacteria interactions in a model community simulating fermented beverages Pierre Ledormand , Nathalie Desmasures , Benoit Bernay , Didier Goux , Oliver Rué et al. Food Microbiology, 2022, 107, pp.104069. ⟨10.1016/j.fm.2022.104069⟩ Article dans une revue hal-03696589v1
	Methane production and microbial community acclimation of five manure inocula during psychrophilic anaerobic digestion of swine manure Thomas Lendormi , Kaïs Jaziri , Fabrice Béline , Sophie Leroux , Chrystelle Bureau et al. Journal of Cleaner Production, 2022, 340, 11 p. ⟨10.1016/j.jclepro.2022.130772⟩ Article dans une revue hal-03574579v1
	Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics Vuong Quoc Hoang Ngo , François Enault , Cédric Midoux , Mahendra Mariadassou , Olivier Chapleur et al. Environmental Microbiology, 2022, ⟨10.1111/1462-2920.16120⟩ Article dans une revue hal-03727436v1
	Impacts of disinfected wastewater irrigation on soil characteristics, microbial community composition, and crop yield Lays Paulino Leonel , Ariane Bize , Mahendra Mariadassou , Cédric Midoux , Jerusa Schneider et al. Blue-Green Systems, 2022, 4 (2), pp.247-271. ⟨10.2166/bgs.2022.126⟩ Article dans une revue hal-03894086v1
	A longitudinal study of the effect of temperature modification in full-scale anaerobic digesters – dataset combining 16S rDNA gene sequencing, metagenomics, and metabolomics data Francesc Puig-Castellví , Cédric Midoux , Angéline Guenne , Delphine Conteau , Oscar Franchi et al. Data in Brief, 2022, 41, pp.107960. ⟨10.1016/j.dib.2022.107960⟩ Article dans une revue (data paper) hal-03585428v1
	Virulent Phages Isolated from a Smear-Ripened Cheese Are Also Detected in Reservoirs of the Cheese Factory Thomas Paillet , Julien Lossouarn , Clarisse Figueroa , Cédric Midoux , Olivier Rué et al. Viruses, 2022, 14 (8), pp.1620. ⟨10.3390/v14081620⟩ Article dans une revue hal-03738602v1
	Mining the equine gut metagenome: poorly-characterized taxa associated with cardiovascular fitness in endurance athletes Núria Mach , Cédric Midoux , Sébastien Leclercq , Samuel Pennarun , Laurence Le Moyec et al. Communications Biology, 2022, 5, pp.1032. ⟨10.1038/s42003-022-03977-7⟩ Article dans une revue hal-03794437v2
	Microbial and functional characterization of granulated sludge from full-scale UASB thermophilic reactor applied to sugarcane vinasse treatment Franciele Pereira Camargo , Isabel Kimiko Sakamoto , Tiago Palladino Delforno , Cédric Midoux , Iolanda Cristina Silveira Duarte et al. Environmental Technology, 2022, pp.1-42. ⟨10.1080/09593330.2022.2052361⟩ Article dans une revue hal-03634517v1
	Metataxonomics, metagenomics, metabolomics analysis of the influence of temperature modification in full-scale anaerobic digesters Francesc Puig-Castellví , Cédric Midoux , Angéline Guenne , Delphine Conteau , Oscar Franchi et al. Bioresource Technology, 2022, 346, pp.126612. ⟨10.1016/j.biortech.2021.126612⟩ Article dans une revue hal-03507080v1
	Oxygen-reducing bidirectional microbial electrodes designed in real domestic wastewater Morgane Hoareau , Benjamin Erable , Olivier Chapleur , Cédric Midoux , Chrystelle Bureau et al. Bioresource Technology, 2021, 326, pp.0. ⟨10.1016/j.biortech.2021.124663⟩ Article dans une revue hal-03129147v1
	Microbial and functional characterization of an allochthonous consortium applied to hydrogen production from Citrus Peel Waste in batch reactor in optimized conditions Franciele Pereira Camargo , Isabel Kimiko Sakamoto , Tiago Palladino Delforno , Mahendra Mariadassou , Valentin Loux et al. Journal of Environmental Management, 2021, 291, pp.112631. ⟨10.1016/j.jenvman.2021.112631⟩ Article dans une revue hal-03211333v1
	Denitrifying bio-cathodes developed from constructed wetland sediments exhibit electroactive nitrate reducing biofilms dominated by the genera Azoarcus and Pontibacter Timothé Philippon , Jiang-Hao Tian , Chrystelle Bureau , Cédric Chaumont , Cédric Midoux et al. Bioelectrochemistry, 2021, 140, pp.107819. ⟨10.1016/j.bioelechem.2021.107819⟩ Article dans une revue hal-03196902v1
	Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions E. Lejal , J. Chiquet , J. Aubert , S. Robin , A. Estrada-Peña et al. Microbiome, 2021, 9 (1), pp.153. ⟨10.1186/s40168-021-01051-8⟩ Article dans une revue hal-03287263v1
	Exploring short k-mer profiles in cells and mobile elements from Archaea highlights the major influence of both the ecological niche and evolutionary history Ariane Bize , Cédric Midoux , Mahendra Mariadassou , Sophie Schbath , Patrick Forterre et al. BMC Genomics, 2021, 22, ⟨10.1186/s12864-021-07471-y⟩ Article dans une revue hal-03176011v1
	Electrochemical analysis of a microbial electrochemical snorkel in laboratory and constructed wetlands Joanna Rogińska , Michel Perdicakis , Cédric Midoux , Théodore Bouchez , Christelle Despas et al. Bioelectrochemistry, 2021, 142, pp.107895. ⟨10.1016/j.bioelechem.2021.107895⟩ Article dans une revue hal-03318075v1
	Integrating independent microbial studies to build predictive models of anaerobic digestion inhibition by ammonia and phenol Simon Poirier , Sébastien Dejean , Cédric Midoux , Kim-Anh Lê Cao , Olivier Chapleur Bioresource Technology, 2020, 316, pp.123952. ⟨10.1016/j.biortech.2020.123952⟩ Article dans une revue hal-02907466v1
	Taxon appearance from extraction and amplification steps demonstrates the value of multiple controls in tick microbiota analysis Emilie Lejal , Agustin Estrada-Peña , Maud Marsot , Jean-Francois J.-F. Cosson , Olivier Rué et al. Frontiers in Microbiology, 2020, 11, ⟨10.3389/fmicb.2020.01093⟩ Article dans une revue hal-02790980v1
	The Basis for Natural Multiresistance to Phage in Pseudomonas aeruginosa Christine Pourcel , Cédric Midoux , Gilles Vergnaud , Libera Latino Antibiotics, 2020, 9 (6), pp.339. ⟨10.3390/antibiotics9060339⟩ Article dans une revue hal-02890481v1
	The Basis for Natural Multiresistance to Phage in Pseudomonas aeruginosa Christine Pourcel , Cédric Midoux , Gilles Vergnaud , Libera Latino Antibiotics, 2020, 9 (6), pp.339. ⟨10.3390/antibiotics9060339⟩ Article dans une revue hal-05271041v1
	Assessing the quality of fresh Whitemouth croaker (Micropogonias furnieri) meat based on micro‐organism and histamine analysis using NGS, qPCR and HPLC‐DAD Alessandra Danile de Lira , Caroline Isabel Kothe , Olivier Rué , Cédric Midoux , Michele Bertoni Mann et al. Journal of Applied Microbiology, 2020, 128 (5), pp.1448-1459. ⟨10.1111/jam.14566⟩ Article dans une revue hal-02903118v1
	Investigation of $Pseudomonas\ aeruginosa$ strain PcyII-10 variants resisting infection by N4-like phage Ab09 in search for genes involved in phage adsorption Libera Latino , Cédric Midoux , Gilles Vergnaud , Christine Pourcel PLoS ONE, 2019, 14 (4), pp.e0215456. ⟨10.1371/journal.pone.0215456⟩ Article dans une revue hal-02173138v1
	Comparative metatranscriptomic analysis of anaerobic digesters treating anionic surfactant contaminated wastewater Tiago P. Delforno , Thais Z. Macedo , Cedric Midoux , Gileno V. Lacerda , Olivier Rué et al. Science of the Total Environment, 2019, 2019 (649), pp.482-494. ⟨10.1016/j.scitotenv.2018.08.328⟩ Article dans une revue hal-01888286v1
	Transposition behavior revealed by high-resolution description of $Pseudomonas\ Aeruginosa$ saltovirus integration sites Gilles Vergnaud , Cédric Midoux , Yann Blouin , Maria Bourkaltseva , Victor Krylov et al. Viruses, 2018, 10 (5), pp.245. ⟨10.3390/v10050245⟩ Article dans une revue hal-02184815v1
	Large Preferred Region for Packaging of Bacterial DNA by phiC725A, a Novel Pseudomonas aeruginosa F116-Like Bacteriophage Christine Pourcel , Cédric Midoux , Yolande Hauck , Gilles Vergnaud , Libera Latino PLoS ONE, 2017, 12 (1), pp.e0169684. ⟨10.1371/journal.pone.0169684⟩ Article dans une revue hal-01879155v1
	A carrier state is established in Pseudomonas aeruginosa by phage LeviOr01, a newly isolated ssRNA levivirus Christine Pourcel , Cédric Midoux , Gilles Vergnaud , Libera Latino Journal of General Virology, 2017, 98 (8), pp.2181 - 2189. ⟨10.1099/jgv.0.000883⟩ Article dans une revue hal-01879191v1
	Complete Genome Sequence of PM105, a New Pseudomonas aeruginosa B3-Like Transposable Phage. Christine Pourcel , Cédric Midoux , Maria Bourkaltseva , Elena Pleteneva , Victor Krylov Genome Announcements, 2016, 4 (2), pp.e01543-15. ⟨10.1128/genomeA.01543-15⟩ Article dans une revue hal-01443828v1
	Pseudolysogeny and sequential mutations build multiresistance to virulent bacteriophages in Pseudomonas aeruginosa Libera Latino , Cédric Midoux , Yolande Hauck , Gilles Vergnaud , Christine Pourcel Microbiology, 2016, ⟨10.1099/mic.0.000263⟩ Article dans une revue hal-01280758v1
	Complete Genome Sequences of Pseudomonas aeruginosa Phages vB_PaeP_PcyII-10_P3P1 and vB_PaeM_PcyII-10_PII10A. Christine Pourcel , Cédric Midoux , Libera Latino , Marie-Agnès Petit , Gilles Vergnaud Genome Announcements, 2016, 4 (6), pp.e00916-16. ⟨10.1128/genomeA.00916-16⟩ Article dans une revue hal-01439325v1
	Investigation of a Large Collection of Pseudomonas aeruginosa Bacteriophages Collected from a Single Environmental Source in Abidjan, Côte d'Ivoire. Christiane Essoh , Libera Latino , Cédric Midoux , Yann Blouin , Guillaume Loukou et al. PLoS ONE, 2015, 10 (6), pp.e0130548. ⟨10.1371/journal.pone.0130548⟩ Article dans une revue hal-01188392v1
	Interpretation and approximation tools for big, dense Markov chain transition matrices in population genetics. Katja Reichel , Valentin Bahier , Cédric Midoux , Nicolas Parisey , Jean-Pierre Masson et al. Algorithms for Molecular Biology, 2015, 10 (1), pp.31. ⟨10.1186/s13015-015-0061-5⟩ Article dans une revue hal-01286505v1

	Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data Cédric Midoux , Olivier Rué , Olivier Chapleur , Ariane Bize , Valentin Loux et al. 2024, ⟨swh:1:rel:35d2caacc87474efa1f1e277f5eb13352962793d⟩ Logiciel hal-04304559v2

	Analyse croisée de données métabarcoding et métagénomiques sur des microbiotes d'hôtes animaux Núria Mach , Maverick Monié--Ibanes , Cédric Midoux , Olivier Rué , Eric Barrey et al. FROGSdays 2025, équipe FROGS INRAe, Dec 2025, Auzeville Tolosan, France Communication dans un congrès hal-05397464v1
	Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data. Cédric Midoux Symposium FROGSdays, INRAE, Dec 2025, Toulouse, France Communication dans un congrès hal-05393313v1
	Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data Cédric Midoux , Mahendra Mariadassou Rencontres R, Société Française de Statistique, Jun 2024, Vannes, France Communication dans un congrès hal-04611225v1
	Inhibition de la digestion anaérobie des boues d'épuration urbaines par le propionate de sodium : production de biogaz et évolution de la communauté microbienne dans des réacteurs semi-continus Joel Awinzure Agumah , Xiaojun Liu , Chloé Soulard , Laura André , André Pauss et al. 19e Congrès de la Société Française du Génie des Procédés (SFGP 2024), Société Française du Génie des Procédés, Oct 2024, Deauville, France Communication dans un congrès hal-05306554v1
	Easy16S : a user-friendly Shiny web-service for exploration and visualization of microbiome data. Cédric Midoux Journées NEM, INRAE, Apr 2024, Paris, France Communication dans un congrès hal-04549290v1
	Role of the glycome-microbiome axis on susceptibility to bovine viral infections and on animal welfare Núria Mach , Alice de Boyer Des Roches , Dorothee Ledoux , Maverick Monie-Ibanes , Nao Yamakawa et al. Séminaire du métaprogramme SANBA, Oct 2024, Paris, France Communication dans un congrès hal-04888568v1
	Packages R pour contrôler son travail et ainsi mieux optimiser, réutiliser et communiquer autour de ses analyses Cédric Midoux , Philippe Ruiz Journées du PEPI IBIS, PEPI IBIS, Sep 2023, Paris, France Communication dans un congrès hal-04229825v1
	Co-digestion anaérobie de boues urbaines : effets du fumier et de la fraction organique des déchets ménagers employés comme cosubstrats, sur la composition des communautés microbienne Ariane Bize , Sabrina Guérin-Rechdaoui , Franciele Pereira Camargo , Vincent Rocher , Elise Alibert et al. 25ème édition des Journées Information Eaux (JIE), Oct 2022, Poitiera, France Communication dans un congrès hal-04493115v1
	Développer ses applications et partager ses résultats avec R et GitLab Cédric Midoux Café des sciences, BioSP - INRAE, Feb 2022, Avignon (FR), France Communication dans un congrès hal-04249221v1
	Diversity of novel viruses infecting methanogenic archaea, discovered through coupling of stable isotope probing and metagenomics Hoang Ngo , François Enault , Cédric Midoux , Mahendra Mariadassou , Olivier Chapleur et al. Phages in Paris, Phages.fr, Oct 2022, Paris, France Communication dans un congrès hal-04357012v1
	Characterization of virus-host dynamics in anaerobic digesters under abiotic stress Marion Coves , Laurent Mazéas , Olivier Chapleur , Cédric Midoux , Ludwig E Jardillier et al. 17e Congrès National de la Société Française de Microbiologie, Société Française de Microbiologie, Oct 2022, Montpellier, France Communication dans un congrès hal-04356630v1
	Implementation of a Nanopore metagenomic workflow for time-series of complex microbial communities: MAG catalog and functional annotation Cédric Midoux , Chrystelle Bureau , Baptiste Quentin , Olivier Chapleur Journée thématique du PEPI IBIS - Métagénomique, PEPI IBIS, Nov 2022, Dijon, France Communication dans un congrès hal-04229643v1
	Transcriptomic and proteomic response of a Liquorilactobacillus mali strain from cider to a lytic phage infection Pierre Ledormand , Nathalie Desmasures , Benoit Bernay , Olivier Rué , Cédric Midoux et al. Société Francaise Microbiologie, 2021, Nantes, France Communication dans un congrès hal-03896401v1
	K-mer approaches provide valuable insight into mobilome evolution in the domain Archaea Ariane Bize , Violette Da Cunha , Cédric Midoux , Sophie Schbath , Patrick Forterre Phages in Bordeaux, Phages.fr, Sep 2018, Bordeaux, France Communication dans un congrès hal-04360213v1
	K-mer approaches provide valuable insight into mobilome evolution in the domain Archaea Ariane Bize , Violette Da Cunha , Cédric Midoux , Sophie Schbath , Patrick Forterre Viruses of Microbes 2018, Jul 2018, Wroclaw, Poland Communication dans un congrès hal-04360247v1

	{affiliationExplorer} a Shiny webapp to resolve taxonomy conflicts Cédric Midoux , Sandra Dérozier , Olivier Rué , Mahendra Mariadassou JOBIM, Jun 2026, Strasbourg, France Poster de conférence hal-05644280v1
	Création d’un réseau SHINY::ESR Élise Maigné , Jean-François Rey , Olivier Delaigue , Jean-Christophe Helbling , François Tilmant et al. Rencontres R 2026, Jun 2026, Nantes, France Poster de conférence hal-05698089v1
	When bacteriophages enter the cheese ripening process: An overview of the PHAGOFROM project Marion Dalmasso , Eric Dugat-Bony , Alicia Bertry , Camille Leneveu , Margareth Renault et al. Microbes 2025, Sep 2025, Bordeaux, France Poster de conférence hal-05162180v1
	DeepOmics, a Digital Environnemental Engineering Platform for Omics data Véronique Jamilloux , Ariane Bize , Cédric Midoux , Aurélie Gramusset , Cédric Gil et al. JOBIM 2024 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2024, Toulouse, France. Poster de conférence hal-04619395v1
	Deciphering the effect of propionic acid on anaerobic digestion of sludge: gas production and microbial community structure Chloé Soulard , Xiaojun Liu , André Pauss , Laura André , Thierry Ribeiro et al. 18th IWA World Conference On Anaerobic Digestion, Jun 2024, Istanbul, Turkey. , 18th IWA World Conference on Anaerobic Digestion CONFERENCE PROCEEDINGS, 2024 Poster de conférence hal-04647849v1
	Plateforme bioinformatique MIGALE Mouhamadou Ba , Hélène Chiapello , Christelle Hennequet-Antier , Valentin Loux , Mahendra Mariadassou et al. Journées Ouvertes Biologie Informatique Mathématique (JOBIM), Jun 2024, Toulouse, France Poster de conférence hal-04843798v1
	SK8 : Un service institutionnel de gestion et d'hébergement d'applications Shiny Élise Maigné , Isabelle Sanchez , David Carayon , Joseph Tran , Jean-François Rey et al. Rencontres R 2023 et 2024, Jun 2023, Avignon (FR), France. Poster de conférence hal-04141247v2
	Characterization of virus-host dynamics in anaerobic digesters under abiotic stress Marion Coves , Laurent Mazéas , Olivier Chapleur , Cédric Midoux , Ludwig E Jardillier et al. Viruses of Microbes, Jul 2022, Braga, Portugal. Poster de conférence hal-04356367v1
	Implementation of a Nanopore metagenomic workflow for time-series of complex microbial communities: MAG catalog and functional annotation. Cédric Midoux , Chrystelle Bureau , Baptiste Quentin , Olivier Chapleur MICROBES symposium, Sep 2022, Orsay, France. Poster de conférence hal-03765009v1
	Plateforme bioinformatique MIGALE Mouhamadou Ba , Hélène Chiapello , Christelle Hennequet-Antier , Valentin Loux , Mahendra Mariadassou et al. Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2022, Rennes, France. 2022 Poster de conférence hal-04176761v1
	Bacteriophages infecting surface bacteria from a smear-ripened cheese are persistent and contaminate the dairy plant Thomas Paillet , Julien Lossouarn , Clarisse Figueroa , Inès Pedros , Cédric Midoux et al. Viruses of Microbes (VoM) 2022, Jul 2022, Guimarães, Portugal Poster de conférence hal-04416527v1
	Le cidre est une matrice délicate pour l’étude des bactériophages et des phageomes. Pierre Ledormand , Nathalie Desmasures , Céline Caillard , Erwan Renard , Didier Goux et al. Société Française de Microbiologie 2022, 2022, Nantes, France Poster de conférence hal-03896438v1
	Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics Vuong Quoc Hoang Ngo , François Enault , Cédric Midoux , Mahendra Mariadassou , Olivier Chapleur et al. ISME18, 18th International Symposium on Microbial Ecology, Aug 2022, Lausanne, Switzerland. Poster de conférence hal-04359643v1
	A bioinformatic pipeline to elucidate the links between viruses and their hosts in microbial communities, applied to viruses in anaerobic digestion processes Vuong Quoc Hoang Ngo , Cédric Midoux , Mahendra Mariadassou , Valentin Loux , François Enault et al. JOBIM 2021 (JOBIM (Journées Ouvertes en Biologie, Informatique et Mathématiques), Jul 2021, Paris, France. Poster de conférence hal-04359920v1
	Plateforme bioinformatique MIGALE Mouhamadou Ba , Hélène Chiapello , Christelle Hennequet-Antier , Valentin Loux , Mahendra Mariadassou et al. Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2021, Paris, France. 2021 Poster de conférence hal-04176768v1
	Bacteriophage ecology of cider, an alcoholic fermented beverage: phages, are you there? Pierre Ledormand , Nathalie Desmasures , Didier Goux , Cédric Midoux , Olivier Rué et al. LAB symposium, 2021, Egmond aan Zee, Netherlands Poster de conférence hal-03896414v1
	New virulent bacteriophages isolated from the surface of Epoisses cheese infect ripening bacteria Thomas Paillet , Julien Lossouarn , Inès Pedros , Cédric Midoux , Olivier Rué et al. Sixth symposium of the French PHAGE Network, Oct 2021, Roscoff, France Poster de conférence hal-03441698v1
	Plateforme bioinformatique MIGALE Mouhamadou Ba , Damien Berry , David Christiany , Hélène Chiapello , Olivier Inizan et al. Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jun 2020, Montpellier, France. 2020 Poster de conférence hal-04176782v1
	DeepOmics, a Digital Environmental Engineering Platform for meta-omics data Ariane Bize , Guillaume Perréal , Aurélie Gramusset , Marion Predhumeau , Cédric Midoux et al. Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM2020), Jun 2020, Montpellier, France. Poster de conférence hal-04493150v1
	Chemometric analysis of a metagenomic dataset to decipher the functional role of the micrpbiota from anaerobic digesters Francesc Puig-Castellví , Cédric Midoux , Laëtitia Cardona , Olivier Chapleur , Delphine Conteau et al. Chimiométrie 2020, Jan 2020, Liège, Belgium Poster de conférence hal-04231788v1
	A shotgun metagenomics analysis applied to the ecological engineering of anaerobic microbial communities for the production of hydrogen from Citrus Peel Waste Cedric Midoux , Franciele Camargo , Olivier Rué , Mahendra Mariadassou , Valentin Loux et al. JOBIM, Jun 2020, Montpellier, France Poster de conférence hal-02902758v1
	Feedback on a comparative metatranscriptomic analysis Cedric Midoux , Tiago P. Delforno , Thais Z. Macedo , Gileno V. Lacerda , Olivier Rué et al. JOBIM 2019 : Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. , 2019, JOBIM 2019 Poster de conférence hal-02735859v1
	Mining anaerobic digestion data with Deep-omics, a new digital environmental engineering platform for omics data Cédric Midoux , Guillaume Perréal , Manon Prédhumeau , Olivier Rué , Yannick Fayolle et al. AD16 (16th IWA World Conference on Anaerobic Digestion), Jun 2019, Delft, Netherlands Poster de conférence hal-04361137v1
	Detection of an archaeal-specific viral family, previously thought to infect exclusively hyperthermophiles, in human gut metaviromes Vuong Quoc Hoang Ngo , Cédric Midoux , Olivier Rué , Mahendra Mariadassou , Violette Da Cunha et al. Phages in Grenoble, Oct 2019, Grenoble, France. Poster de conférence hal-04360160v1
	Plateforme bioinformatique MIGALE Hélène Chiapello , Sandra Dérozier , Olivier Inizan , Mahendra Mariadassou , Véronique Martin et al. Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2019, Nantes, France. 2019 Poster de conférence hal-04176805v1
	Easy16S : a user-friendly Shiny interface for analysis and visualization of metagenomic data Cedric Midoux , Olivier Rué , Olivier Chapleur , Mahendra Mariadassou , Théodore Bouchez et al. JOBIM 2018 : Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. , 2018, JOBIM 2018 Poster de conférence hal-02737257v1

	Plan de gestion des données de l’unité de recherche PROSE (UR1461 INRAE) Cédric Midoux INRAE - UR PROSE. 2026, 34 p Rapport (plan de gestion de données/data management plan) hal-05442197v1

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Cédric Midoux

Publications

Publications

Electromethanogenesis from H2S containing biogas: H2S and cathode potential drive microbial selection and methane yields

Propionic acid-related inhibition during anaerobic digestion: insights into methane production and microbial community responses

Host-virus dynamics in anaerobic digesters facing abiotic inhibition

Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data.

The electrochemical microbial tree: A new concept for wastewater treatment

Study of a Pilot Scale Microbial Electrosynthesis Reactor for Organic Waste Biorefinery

Investigation of the Phageome and Prophages in French Cider, a Fermented Beverage

Molecular approaches to uncover phage-lactic acid bacteria interactions in a model community simulating fermented beverages

Methane production and microbial community acclimation of five manure inocula during psychrophilic anaerobic digestion of swine manure

Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics

Impacts of disinfected wastewater irrigation on soil characteristics, microbial community composition, and crop yield

A longitudinal study of the effect of temperature modification in full-scale anaerobic digesters – dataset combining 16S rDNA gene sequencing, metagenomics, and metabolomics data

Virulent Phages Isolated from a Smear-Ripened Cheese Are Also Detected in Reservoirs of the Cheese Factory

Mining the equine gut metagenome: poorly-characterized taxa associated with cardiovascular fitness in endurance athletes

Microbial and functional characterization of granulated sludge from full-scale UASB thermophilic reactor applied to sugarcane vinasse treatment

Metataxonomics, metagenomics, metabolomics analysis of the influence of temperature modification in full-scale anaerobic digesters

Oxygen-reducing bidirectional microbial electrodes designed in real domestic wastewater

Microbial and functional characterization of an allochthonous consortium applied to hydrogen production from Citrus Peel Waste in batch reactor in optimized conditions

Denitrifying bio-cathodes developed from constructed wetland sediments exhibit electroactive nitrate reducing biofilms dominated by the genera Azoarcus and Pontibacter

Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions

Exploring short k-mer profiles in cells and mobile elements from Archaea highlights the major influence of both the ecological niche and evolutionary history

Electrochemical analysis of a microbial electrochemical snorkel in laboratory and constructed wetlands

Integrating independent microbial studies to build predictive models of anaerobic digestion inhibition by ammonia and phenol

Taxon appearance from extraction and amplification steps demonstrates the value of multiple controls in tick microbiota analysis

The Basis for Natural Multiresistance to Phage in Pseudomonas aeruginosa

The Basis for Natural Multiresistance to Phage in Pseudomonas aeruginosa

Assessing the quality of fresh Whitemouth croaker (Micropogonias furnieri) meat based on micro‐organism and histamine analysis using NGS, qPCR and HPLC‐DAD

Investigation of $Pseudomonas\ aeruginosa$ strain PcyII-10 variants resisting infection by N4-like phage Ab09 in search for genes involved in phage adsorption

Comparative metatranscriptomic analysis of anaerobic digesters treating anionic surfactant contaminated wastewater

Transposition behavior revealed by high-resolution description of $Pseudomonas\ Aeruginosa$ saltovirus integration sites

Large Preferred Region for Packaging of Bacterial DNA by phiC725A, a Novel Pseudomonas aeruginosa F116-Like Bacteriophage

A carrier state is established in Pseudomonas aeruginosa by phage LeviOr01, a newly isolated ssRNA levivirus

Complete Genome Sequence of PM105, a New Pseudomonas aeruginosa B3-Like Transposable Phage.

Pseudolysogeny and sequential mutations build multiresistance to virulent bacteriophages in Pseudomonas aeruginosa

Complete Genome Sequences of Pseudomonas aeruginosa Phages vB_PaeP_PcyII-10_P3P1 and vB_PaeM_PcyII-10_PII10A.

Investigation of a Large Collection of Pseudomonas aeruginosa Bacteriophages Collected from a Single Environmental Source in Abidjan, Côte d'Ivoire.

Interpretation and approximation tools for big, dense Markov chain transition matrices in population genetics.

Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data

Analyse croisée de données métabarcoding et métagénomiques sur des microbiotes d'hôtes animaux

Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data.

Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data

Inhibition de la digestion anaérobie des boues d'épuration urbaines par le propionate de sodium : production de biogaz et évolution de la communauté microbienne dans des réacteurs semi-continus

Easy16S : a user-friendly Shiny web-service for exploration and visualization of microbiome data.

Role of the glycome-microbiome axis on susceptibility to bovine viral infections and on animal welfare

Packages R pour contrôler son travail et ainsi mieux optimiser, réutiliser et communiquer autour de ses analyses

Co-digestion anaérobie de boues urbaines : effets du fumier et de la fraction organique des déchets ménagers employés comme cosubstrats, sur la composition des communautés microbienne

Développer ses applications et partager ses résultats avec R et GitLab

Diversity of novel viruses infecting methanogenic archaea, discovered through coupling of stable isotope probing and metagenomics

Characterization of virus-host dynamics in anaerobic digesters under abiotic stress

Implementation of a Nanopore metagenomic workflow for time-series of complex microbial communities: MAG catalog and functional annotation

Transcriptomic and proteomic response of a Liquorilactobacillus mali strain from cider to a lytic phage infection

K-mer approaches provide valuable insight into mobilome evolution in the domain Archaea

K-mer approaches provide valuable insight into mobilome evolution in the domain Archaea

{affiliationExplorer} a Shiny webapp to resolve taxonomy conflicts

Création d’un réseau SHINY::ESR

When bacteriophages enter the cheese ripening process: An overview of the PHAGOFROM project

DeepOmics, a Digital Environnemental Engineering Platform for Omics data

Deciphering the effect of propionic acid on anaerobic digestion of sludge: gas production and microbial community structure

Plateforme bioinformatique MIGALE

SK8 : Un service institutionnel de gestion et d'hébergement d'applications Shiny

Characterization of virus-host dynamics in anaerobic digesters under abiotic stress

Implementation of a Nanopore metagenomic workflow for time-series of complex microbial communities: MAG catalog and functional annotation.

Plateforme bioinformatique MIGALE

Bacteriophages infecting surface bacteria from a smear-ripened cheese are persistent and contaminate the dairy plant

Le cidre est une matrice délicate pour l’étude des bactériophages et des phageomes.

Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics

A bioinformatic pipeline to elucidate the links between viruses and their hosts in microbial communities, applied to viruses in anaerobic digestion processes

Plateforme bioinformatique MIGALE

Bacteriophage ecology of cider, an alcoholic fermented beverage: phages, are you there?

New virulent bacteriophages isolated from the surface of Epoisses cheese infect ripening bacteria

Plateforme bioinformatique MIGALE

DeepOmics, a Digital Environmental Engineering Platform for meta-omics data

Chemometric analysis of a metagenomic dataset to decipher the functional role of the micrpbiota from anaerobic digesters

A shotgun metagenomics analysis applied to the ecological engineering of anaerobic microbial communities for the production of hydrogen from Citrus Peel Waste

Feedback on a comparative metatranscriptomic analysis

Mining anaerobic digestion data with Deep-omics, a new digital environmental engineering platform for omics data

Detection of an archaeal-specific viral family, previously thought to infect exclusively hyperthermophiles, in human gut metaviromes