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Valentin Loux

28
Documents
Identifiants chercheurs

Présentation

Valentin Loux is head of the INRAE Migale bioinformatics facility, part of the MaiAGE laboratory. [The Migale bioinformatics facility](https://migale.inrae.fr) provides storage, computational resources and standard bioinformatics analyses pipelines and software for sequence analyses. Valentin Loux has an established expertise in the analysis of large scale metagenomics projects, annotation and comparison of bacterial genomes. **POSTIONS** **2015-Present :** Research Engineer in Bioinformatics, head of Migale Bioinformatics Facilty, INRAE, MaIAGE laboratory **2013-2019 :** Member of steering comitee of [France-Genomique project](https://www.france-genomique.org) in charge of bionformatics development coordination **2002-2015 :** Bioinformatics Staff Engineer , INRAE Mig laboratory **CURSUS** **2002**: Master's degree in Bioinformatics (DESS), Versailles Saint-Quentin University

Publications

olivier-rue
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Towards a more accurate metabarcoding approach for studying fungal communities of fermented foods

Olivier Rué , Monika Coton , Eric Dugat-Bony , Kate Howell , Françoise Irlinger
Peer Community Journal, 2023, ⟨10.24072/pci.microbiol.100007⟩
Article dans une revue hal-04234976v1
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Integration of Multiomic Data to Characterize the Influence of Milk Fat Composition on Cantal-Type Cheese Microbiota

Marie Frétin , Amaury Gérard , Anne Ferlay , Bruno Martin , S Buchin
Microorganisms, 2022, 10 (2), ⟨10.3390/microorganisms10020334⟩
Article dans une revue hal-03579395v1

Insights into the cyanosphere: capturing the respective metabolisms of cyanobacteria and chemotrophic bacteria in natural conditions?

Noémie Pascault , Olivier Rué , Valentin Loux , Jacques Pédron , Véronique Martin
Environmental Microbiology Reports, 2021, 13 (3), pp.364-374. ⟨10.1111/1758-2229.12944⟩
Article dans une revue hal-03287195v1
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Large-scale multivariate dataset on the characterization of microbiota diversity, microbial growth dynamics, metabolic spoilage volatilome and sensorial profiles of two industrially produced meat products subjected to changes in lactate concentration and packaging atmosphere

Simon Poirier , Ngoc-Du Martin Luong , Valérie Anthoine , Sandrine Guillou , Jeanne-Marie Membré
Data in Brief, 2020, 30, pp.1-8. ⟨10.1016/j.dib.2020.105453⟩
Article dans une revue hal-02914971v1

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⟩
Article dans une revue hal-01888286v1
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Effect of sodium chloride reduction or partial substitution with potassium chloride on the microbiological, biochemical and sensory characteristics of semi-hard and soft cheeses

Eric Dugat-Bony , Pascal Bonnarme , Sébastien Fraud , Jessie Catellote , Anne-Sophie Sarthou
Food Research International, 2019, 125, pp.108643. ⟨10.1016/j.foodres.2019.108643⟩
Article dans une revue hal-02349939v1
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Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing

Simon Poirier , Olivier Rué , Raphaelle Peguilhan , Gwendoline Coeuret , Monique Zagorec
PLoS ONE, 2018, 13 (9), ⟨10.1371/journal.pone.0204629⟩
Article dans une revue hal-02621350v1
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Detection of an amplification bias associated to Leuconostocaceae family with a universal primer routinely used for monitoring microbial community structures within food products

Simon Poirier , Olivier Rué , Gwendoline Coeuret , Marie-Christine Champomier-Verges , Valentin Loux
BMC Research Notes, 2018, 11 (1), pp.1-5. ⟨10.1186/s13104-018-3908-2⟩
Article dans une revue hal-02048857v1
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Draft Anaplasma phagocytophilum Genome Sequences from Five Cows, Two Horses, and One Roe Deer Collected in Europe.

Thibaud Dugat , Marie-Noelle Rossignol , Olivier Rué , Valentin Loux , Sylvain Marthey
Genome Announcements, 2016, 4 (6), 2 p. ⟨10.1128/genomeA.00950-16⟩
Article dans une revue hal-01594527v1

Variable and core functional microbiota associated with seven Medicago truncatula genotypes

Zhu, Liya , Olivier Rué , Florence Deau , Julie Cremaschi , Valentin Loux
12th International PGPR Workshop 2023, May 2023, Toulouse, France
Communication dans un congrès hal-04139303v1

Variable and core functional rhizosphere microbiota associated with seven Medicago truncatula genotypes

Zhu, Liya , Olivier Rué , Florence Deau , Julie Cremaschi , Valentin Loux
Journée doctorants UMR Agroécologie, Nov 2023, Dijon, France
Communication dans un congrès hal-04317070v1

MetaPDOcheese : investigation of the drivers of microbial communities from French PDO milks and cheeses

Francoise Irlinger , Mahendra Mariadassou , Eric Dugat-Bony , Cécile Neuvéglise , Olivier Rué
FORUM ON FERMENTED FOODS, COST PIMENTO, May 2023, Lyon, France
Communication dans un congrès hal-04221356v1

Evaluation of gyrB amplicon sequencing in comparison to 16S rDNA amplicon sequencing to evaluate intra-species bacterial diversity in food microbiota

Olivier Rué , Simon Poirier , Raphaelle Peguilhan , Valentin Loux , Marie-Christine Champomier-Vergès
JOBIM 20. Journées Ouvertes Biologie Informatique Mathématiques, Jul 2019, Nantes, France
Communication dans un congrès hal-02947091v1

Shotgun metagenomics sequencing of the rhizosphere microbiota associated to seven ecotypes of Medicago truncatula

Julie Cremaschi , Olivier Rué , Florence Deau , Philippe Lemanceau , Valentin Loux
Rhizosphere 5, Jul 2019, Saskatoon, Saskatchewan, Canada
Communication dans un congrès hal-02735116v1

Functional signatures of soil fungal communities in response to forest tree phenology revealed by metatranscriptome analysis

Marc Buée , Lucas Auer , Patricia Luis , Olivier Rué , Valentin Loux
3rd MPItM-Labex ARBRE Workshop, Nov 2018, cologne, Germany
Communication dans un congrès hal-03339776v1

Different Medicago truncatula genotypes, expressing different phenotypes, modulate microbial functional genes in the rhizosphere

Zhu, Liya , Olivier Rué , Florence Deau , Julie Cremaschi , Valentin Loux
miCROPe 2022, international Symposium microbe-assisted crop production opportunities, challenges & needs, Jul 2022, Vienne, France
Poster de conférence hal-04199757v1
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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
Poster de conférence hal-04176761v1
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Implementing a Text Mining Service Offer on the Migale Bioinformatics Platform

Mouhamadou Ba , Véronique Martin , Olivier Rué , Sophie Schbath , Valérie Vidal
Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2022, Rennes, France. 2022
Poster de conférence hal-04176740v1
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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
Poster de conférence hal-04176768v1
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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
Poster de conférence hal-04176782v1
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Testing markers to characterize microbial communities in food ecosystems using a metagenomics approach

Claire Vincent , Serge Casaregola , Monika Coton , Céline Delbes , Hugo Devillers
JOBIM, Jun 2020, Montpellier, France
Poster de conférence hal-02914960v1
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Shallow sequencing: a cost-effective and accurate alternative to WGS for taxonomic profiling ?

Benoit Goutorbe , Anne-Laure Abraham , Mahendra Mariadassou , Valentin Loux , Olivier Rué
JOBIM, Jun 2020, Montpellier, France.
Poster de conférence hal-03451271v1
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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
Poster de conférence hal-02902758v1
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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
Poster de conférence hal-02735859v1
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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.
Poster de conférence hal-04360160v1

Evaluation of gyrB amplicon sequencing in comparison to 16S rDNA amplicon sequencing to evaluate intra-species bacterial diversity in food microbiotaImproving

Simon Poirier , Raphaelle Peguilhan , Olivier Rué , Valentin Loux , Marie-Christine Champomier-Verges
Food Micro 2018, Sep 2018, Berlin, Germany. , 2018
Poster de conférence hal-02786728v1
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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
Poster de conférence hal-02737257v1
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New -omics data analysis activity on Migale platform for MEM community

Olivier Rué , Valentin Loux , Sophie Schbath
Journées d'Animation MEM 2017, Jan 2017, Paris la Vilklette, France. 2017
Poster de conférence hal-01730003v1