Access content directly

Cédric Midoux

Bioinfo
84%
Open access
63
Documents
Current affiliations
  • 1002496
  • 1002434
  • 1169987
Researcher identifiers
  • IdHAL cedric-midoux
  • ORCID 0000-0002-7964-0929
  • Google Scholar : https://scholar.google.fr/citations?user=lAzGLCIAAAAJ&hl=fr
Contact

Publications

Image document

The electrochemical microbial tree: A new concept for wastewater treatment

Morgane Hoareau , Luc Etcheverry , Olivier Chapleur , Chrystelle Bureau , Cédric Midoux
Chemical Engineering Journal, 2023, 454 (3), pp.140295. ⟨10.1016/j.cej.2022.140295⟩
Journal articles hal-03851691v1
Image document

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

Jiang-Hao Tian , Rémy Lacroix , Asim Ali Yaqoob , Chrystelle Bureau , Cédric Midoux
Energies, 2023, 16 (2), pp.591. ⟨10.3390/en16020591⟩
Journal articles hal-03922462v1
Image document

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
Communications Biology, 2022, 5, pp.1032. ⟨10.1038/s42003-022-03977-7⟩
Journal articles hal-03794437v2
Image document

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⟩
Journal articles hal-03693766v1
Image document

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
Data in Brief, 2022, 41, pp.107960. ⟨10.1016/j.dib.2022.107960⟩
Journal articles hal-03585428v1

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
Food Microbiology, 2022, 107, pp.104069. ⟨10.1016/j.fm.2022.104069⟩
Journal articles hal-03696589v1
Image document

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
Bioresource Technology, 2022, 346, pp.126612. ⟨10.1016/j.biortech.2021.126612⟩
Journal articles hal-03507080v1
Image document

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
Journal of Cleaner Production, 2022, 340, 11 p. ⟨10.1016/j.jclepro.2022.130772⟩
Journal articles hal-03574579v1
Image document

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
Environmental Technology, 2022, pp.1-42. ⟨10.1080/09593330.2022.2052361⟩
Journal articles hal-03634517v1
Image document

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
Viruses, 2022, 14 (8), pp.1620. ⟨10.3390/v14081620⟩
Journal articles hal-03738602v1

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
Blue-Green Systems, 2022, 4 (2), pp.247-271. ⟨10.2166/bgs.2022.126⟩
Journal articles hal-03894086v1
Image document

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
Environmental Microbiology, 2022, ⟨10.1111/1462-2920.16120⟩
Journal articles hal-03727436v1
Image document

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
BMC Genomics, 2021, 22, ⟨10.1186/s12864-021-07471-y⟩
Journal articles hal-03176011v1
Image document

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
Bioelectrochemistry, 2021, 140, pp.107819. ⟨10.1016/j.bioelechem.2021.107819⟩
Journal articles hal-03196902v1
Image document

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

Joanna Rogińska , Michel Perdicakis , Cédric Midoux , Théodore Bouchez , Christelle Despas
Bioelectrochemistry, 2021, 142, pp.107895. ⟨10.1016/j.bioelechem.2021.107895⟩
Journal articles hal-03318075v1
Image document

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
Microbiome, 2021, 9 (1), pp.153. ⟨10.1186/s40168-021-01051-8⟩
Journal articles hal-03287263v1

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
Journal of Environmental Management, 2021, 291, pp.112631. ⟨10.1016/j.jenvman.2021.112631⟩
Journal articles hal-03211333v1
Image document

Oxygen-reducing bidirectional microbial electrodes designed in real domestic wastewater

Morgane Hoareau , Benjamin Erable , Olivier Chapleur , Cédric Midoux , Chrystelle Bureau
Bioresource Technology, 2021, 326, pp.0. ⟨10.1016/j.biortech.2021.124663⟩
Journal articles hal-03129147v1
Image document

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⟩
Journal articles hal-02890481v1
Image document

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
Journal of Applied Microbiology, 2020, 128 (5), pp.1448-1459. ⟨10.1111/jam.14566⟩
Journal articles hal-02903118v1
Image document

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

Emilie Lejal , Agustin Estrada-Peña , Maud Marsot , Jean-Francois J.-F. Cosson , Olivier Rué
Frontiers in Microbiology, 2020, 11, ⟨10.3389/fmicb.2020.01093⟩
Journal articles hal-02790980v1
Image document

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⟩
Journal articles hal-02907466v1

Comparative metatranscriptomic analysis of anaerobic digesters treating anionic surfactant contaminated wastewater

Tiago P. Delforno , Thais Z. Macedo , Cedric Midoux , Gileno V. Lacerda , Olivier Rué
Science of the Total Environment, 2019, 2019 (649), pp.482-494. ⟨10.1016/j.scitotenv.2018.08.328⟩
Journal articles hal-01888286v1
Image document

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⟩
Journal articles hal-02173138v1
Image document

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

Gilles Vergnaud , Cédric Midoux , Yann Blouin , Maria Bourkaltseva , Victor Krylov
Viruses, 2018, 10 (5), pp.245. ⟨10.3390/v10050245⟩
Journal articles hal-02184815v1
Image document

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⟩
Journal articles 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⟩
Journal articles hal-01879191v1
Image document

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⟩
Journal articles hal-01280758v1
Image document

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⟩
Journal articles hal-01439325v1
Image document

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⟩
Journal articles hal-01443828v1
Image document

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
Algorithms for Molecular Biology, 2015, 10 (1), pp.31. ⟨10.1186/s13015-015-0061-5⟩
Journal articles hal-01286505v1
Image document

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
PLoS ONE, 2015, 10 (6), pp.e0130548. ⟨10.1371/journal.pone.0130548⟩
Journal articles hal-01188392v1
Image document

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

Cédric Midoux
Journées NEM, INRAE, Apr 2024, Paris, France
Conference papers hal-04549290v1

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
Conference papers hal-04229825v1
Image document

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
Phages in Paris, Phages.fr, Oct 2022, Paris, France
Conference papers hal-04357012v1
Image document

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
Conference papers hal-04229643v1
Image document

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

Marion Coves , Laurent Mazéas , Olivier Chapleur , Cédric Midoux , Ludwig E Jardillier
17e Congrès National de la Société Française de Microbiologie, Société Française de Microbiologie, Oct 2022, Montpellier, France
Conference papers hal-04356630v1
Image document

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
25ème édition des Journées Information Eaux (JIE), Oct 2022, Poitiera, France
Conference papers 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
Conference papers hal-04249221v1

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
Société Francaise Microbiologie, 2021, Nantes, France
Conference papers hal-03896401v1
Image document

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
Conference papers hal-04360247v1
Image document

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
Conference papers hal-04360213v1
Image document

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

Élise Maigné , Isabelle Sanchez , David Carayon , Joseph Tran , Jean-François Rey
Rencontres R 2023 et 2024, Jun 2023, Avignon (FR), France.
Conference poster hal-04141247v2

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

Pierre Ledormand , Nathalie Desmasures , Céline Caillard , Erwan Renard , Didier Goux
Société Française de Microbiologie 2022, 2022, Nantes, France
Conference poster hal-03896438v1
Image document

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
ISME18, 18th International Symposium on Microbial Ecology, Aug 2022, Lausanne, Switzerland.
Conference poster hal-04359643v1
Image document

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

Marion Coves , Laurent Mazéas , Olivier Chapleur , Cédric Midoux , Ludwig E Jardillier
Viruses of Microbes, Jul 2022, Braga, Portugal.
Conference poster hal-04356367v1
Image document

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.
Conference poster hal-03765009v1
Image document

Plateforme bioinformatique MIGALE

Mouhamadou Ba , Hélène Chiapello , Christelle Hennequet-Antier , Valentin Loux , Mahendra Mariadassou
Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2022, Rennes, France. 2022
Conference poster hal-04176761v1
Image document

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
Viruses of Microbes (VoM) 2022, Jul 2022, Guimarães, Portugal
Conference poster hal-04416527v1
Image document

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
JOBIM 2021 (JOBIM (Journées Ouvertes en Biologie, Informatique et Mathématiques), Jul 2021, Paris, France.
Conference poster hal-04359920v1
Image document

Plateforme bioinformatique MIGALE

Mouhamadou Ba , Hélène Chiapello , Christelle Hennequet-Antier , Valentin Loux , Mahendra Mariadassou
Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2021, Paris, France. 2021
Conference poster hal-04176768v1
Image document

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

Thomas Paillet , Julien Lossouarn , Inès Pedros , Cédric Midoux , Olivier Rué
Sixth symposium of the French PHAGE Network, Oct 2021, Roscoff, France
Conference poster hal-03441698v1

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

Pierre Ledormand , Nathalie Desmasures , Didier Goux , Cédric Midoux , Olivier Rué
LAB symposium, 2021, Egmond aan Zee, Netherlands
Conference poster hal-03896414v1
Image document

Plateforme bioinformatique MIGALE

Mouhamadou Ba , Damien Berry , David Christiany , Hélène Chiapello , Olivier Inizan
Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jun 2020, Montpellier, France. 2020
Conference poster hal-04176782v1
Image document

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

Ariane Bize , Guillaume Perréal , Aurélie Gramusset , Marion Predhumeau , Cédric Midoux
Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM2020), Jun 2020, Montpellier, France.
Conference poster hal-04493150v1
Image document

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
JOBIM, Jun 2020, Montpellier, France
Conference poster hal-02902758v1

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

F. Puig-Castellví , C. Midoux , Laëtitia Cardona , O. Chapleur , D. Conteau
Chimiométrie 2020, Jan 2020, Liège, Belgium
Conference poster hal-04231788v1
Image document

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

Cédric Midoux , Guillaume Perréal , Marion Predhumeau , Olivier Rué , Yannick Fayolle
AD16 (16th IWA World Conference on Anaerobic Digestion), Jun 2019, Delft, Netherlands
Conference poster hal-04361137v1
Image document

Feedback on a c omparative metatranscriptomic analysis

Cedric Midoux , Tiago P. Delforno , Thais Z. Macedo , Gileno V. Lacerda , Olivier Rué
JOBIM 2019 : Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. , 2019, JOBIM 2019
Conference poster hal-02735859v1
Image document

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
Phages in Grenoble, Oct 2019, Grenoble, France.
Conference poster hal-04360160v1
Image document

Plateforme bioinformatique MIGALE

Hélène Chiapello , Sandra Dérozier , Olivier Inizan , Mahendra Mariadassou , Véronique Martin
Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2019, Nantes, France. 2019
Conference poster hal-04176805v1
Image document

Easy16S : a user-friendly Shiny interface for analysis and visualization of metagenomic data

Cedric Midoux , Olivier Rué , Olivier Chapleur , Mahendra Mariadassou , Théodore Bouchez
JOBIM 2018 : Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. , 2018, JOBIM 2018
Conference poster hal-02737257v1