Valentin Loux

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Présentation

Valentin Loux is head of the INRAE Migale bioinformatics facility, part of the MaiAGE laboratory. The Migale bioinformatics facility 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 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

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Publications

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MilkOligoCorpus: A semantically annotated resource for knowledge extraction on mammalian milk oligosaccharides

Mathilde Rumeau , Marine Courtin , Robert Bossy , Clara Sauvion , Valentin Loux et al.

PLoS ONE, 2025, 20 (8), pp.e0319729. ⟨10.1371/journal.pone.0319729⟩

Article dans une revue hal-05220365v1

Metagenomics reveals contrasted responses of microbial communities to wheat straw amendment in cropland and grassland soils

Domitille Jarrige , Vincent Tardy , Valentin Loux , Olivier Rué , Abad Chabbi et al.

Scientific Reports, 2025, 15 (1), pp.14723. ⟨10.1038/s41598-025-98903-2⟩

Article dans une revue hal-05070613v1
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Pan-immune system, mobilome and resistome in Streptococcus suis

Manon Dechêne-Tempier , Stéphanie Bougeard , Valentin Loux , Hélène Chiapello , Virginie Libante et al.

Microbial Genomics, 2025, 11 (9), pp.001521. ⟨10.1099/mgen.0.001521⟩

Article dans une revue hal-05289975v1
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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
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MilkOligoThesaurus, a dataset of mammalian milk oligosaccharide synonyms

Mathilde Rumeau , François Fenaille , Agnès Girard , Valentin Loux , Mouhamadou Ba et al.

Data in Brief, 2024, 54, pp.110404. ⟨10.1016/j.dib.2024.110404⟩

Article dans une revue (data paper) hal-04552648v1
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A comprehensive, large-scale analysis of “terroir” cheese and milk microbiota reveals profiles strongly shaped by both geographical and human factors

Francoise Irlinger , Mahendra Mariadassou , Eric Dugat-Bony , Olivier Rué , Cécile Neuvéglise et al.

ISME Communications, 2024, 4 (1), pp.ycae095. ⟨10.1093/ismeco/ycae095⟩

Article dans une revue hal-04668230v1
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Comparative Genome Analysis of Enterococcus cecorum Reveals Intercontinental Spread of a Lineage of Clinical Poultry Isolates

Jeanne Laurentie , Valentin Loux , Christelle Hennequet-Antier , Emilie Chambellon , Julien Deschamps et al.

MSphere, 2023, 8 (2), pp.e0049522. ⟨10.1128/msphere.00495-22⟩

Article dans une revue hal-04004063v1
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Comparison of metabarcoding taxonomic markers to describe fungal communities in fermented foods

Olivier Rué , Monika Coton , Eric Dugat-Bony , Kate Howell , Françoise Irlinger et al.

Peer Community Journal, 2023, 3, pp.e97. ⟨10.24072/pcjournal.321⟩

Article dans une revue hal-04234976v1
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Omnicrobe, an open-access database of microbial habitats and phenotypes using a comprehensive text mining and data fusion approach

Sandra Dérozier , Robert Bossy , Louise Deléger , Mouhamadou Ba , Estelle Chaix et al.

PLoS ONE, 2023, 18 (1), pp.e0272473. ⟨10.1371/journal.pone.0272473⟩

Article dans une revue hal-03984703v1
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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 et al.

Microorganisms, 2022, 10 (2), ⟨10.3390/microorganisms10020334⟩

Article dans une revue hal-03579395v1
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Gene co-expression network analysis of the human gut commensal bacterium Faecalibacterium prausnitzii in R-Shiny

Sandrine Auger , Virginie Mournetas , Hélène Chiapello , Valentin Loux , Philippe Langella et al.

PLoS ONE, 2022, 17 (11), pp. e0271847. ⟨10.1371/journal.pone.0271847⟩

Article dans une revue hal-04083924v1

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 et al.

Environmental Microbiology Reports, 2021, 13 (3), pp.364-374. ⟨10.1111/1758-2229.12944⟩

Article dans une revue hal-03287195v1

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

Unraveling the world of halophilic and halotolerant bacteria in cheese by combining cultural, genomic and metagenomic approaches

Caroline Isabel Kothe , Alexander Bolotin , Bochra-Farah Kraïem , Bedis Dridi , Sandra Dérozier et al.

International Journal of Food Microbiology, 2021, 358, pp.109312. ⟨10.1016/j.ijfoodmicro.2021.109312⟩

Article dans une revue hal-04311697v1
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Abundance, Diversity and Role of ICEs and IMEs in the Adaptation of Streptococcus salivarius to the Environment

Julie Lao , Gérard Guédon , Thomas Lacroix , Florence Charron-Bourgoin , Virginie Libante et al. Article dans une revue hal-02922962v1

The enemy from within: a prophage of Roseburia intestinalis systematically turns lytic in the mouse gut, driving bacterial adaptation by CRISPR spacer acquisition

Jeffrey Cornuault , Elisabeth Moncaut , Valentin Loux , Aurélie Mathieu , Harry Sokol et al.

The International Society of Microbiologial Ecology Journal, 2020, 14 (3), pp.771-787. ⟨10.1038/s41396-019-0566-x⟩

Article dans une revue hal-02504597v1
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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 et al.

Data in Brief, 2020, 30, pp.1-8. ⟨10.1016/j.dib.2020.105453⟩

Article dans une revue (data paper) hal-02914971v1

The complete genome sequence of Mycobacterium bovis Mb3601, a SB0120 spoligotype strain representative of a new clonal group

Maxime Branger , Valentin Loux , Thierry Cochard , Maria Laura Boschiroli , Franck Biet et al.

Infection, Genetics and Evolution, 2020, 82, 4 p. ⟨10.1016/j.meegid.2020.104309⟩

Article dans une revue hal-02905303v1

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
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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 et al.

Food Research International, 2019, 125, pp.108643. ⟨10.1016/j.foodres.2019.108643⟩

Article dans une revue hal-02349939v1

Bioinformatics tools and workflow to select blood biomarkers for early cancer diagnosis: an application to pancreatic cancer

Yves Vandenbrouck , David Christiany , Florence Combes , Valentin Loux , Virginie Brun

Proteomics, 2019, 19 (21-22), pp.e1800489. ⟨10.1002/pmic.201800489⟩

Article dans une revue hal-02296155v1
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Complete and Draft Genome Sequences of Nine<em> Lactobacillus</em> <em>sakei</em> Strains Selected from the Three Known Phylogenetic Lineages and Their Main Clonal Complexes

Valentin Loux , Gwendoline Coeuret , Monique Zagorec , Marie-Christine Champomier-Verges , Stephane Chaillou

Genome Announcements, 2018, 6 (16), 3 p. ⟨10.1128/genomeA.00082-18⟩

Article dans une revue hal-02619093v1
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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 et al.

PLoS ONE, 2018, 13 (9), ⟨10.1371/journal.pone.0204629⟩

Article dans une revue hal-02621350v1

Transcriptomic response of Debaryomyces hansenii during mixed culture in a liquid model cheese medium with Yarrowia lipolytica

Reine Malek , Pascal Bonnarme , Francoise Irlinger , Pascale Frey-Klett , Djamila Onesime et al.

International Journal of Food Microbiology, 2018, 264, pp.53-62. ⟨10.1016/j.ijfoodmicro.2017.10.026⟩

Article dans une revue hal-01695894v1
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Complete genome sequence of the industrial fast-acidifying strain <em>Streptococcus thermophilus</em> N4L

Lucas Proust , Valentin Loux , Veronique Martin , Cristian Magnabosco , Martin Pedersen et al.

Microbiology Resource Announcements, 2018, 7 (8), ⟨10.1128/MRA.01029-18⟩

Article dans une revue hal-02628963v1
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Genomic diversity and evolution of the fish pathogen flavobacterium psychrophilum

Éric Duchaud , Tatiana Rochat , Christophe Habib , Paul Barbier , Valentin Loux et al.

Frontiers in Microbiology, 2018, 9, pp.1-20. ⟨10.3389/fmicb.2018.00138⟩

Article dans une revue hal-02629284v1
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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 et al.

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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Whole genome sequencing of 7 strains of Staphylococcus lugdunensis allows identification of mobile genetic elements

Xavier Argemi , Veronique Martin , Valentin Loux , Sandrine Dahyot , Jérémie Lebeurre et al.

Genome Biology and Evolution, 2017, 9 (5), pp.1183-1189. ⟨10.1093/gbe/evx077⟩

Article dans une revue hal-01604276v1

La génomique comparative à l’ère des technologies NGS

Thomas Lacroix , Jean-Francois Gibrat , Valentin Loux

Biofutur, 2017, 36 (382), pp.42-45

Article dans une revue hal-01603170v1
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Complete Genome Sequence of Flavobacteriumpsychrophilum Strain OSU THCO2-90, Used for Functional Genetic Analysis.

Tatiana Rochat , Paul Barbier , Pierre Nicolas , Valentin Loux , David Perez Pascual et al.

Genome Announcements, 2017, 5 (23), 2 p. ⟨10.1128/genomeA.01665-16⟩

Article dans une revue hal-01607798v1
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A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins

Charles Coluzzi , Gérard Guédon , Marie-Dominique Devignes , Chloé C. Ambroset , Valentin Loux et al.

Frontiers in Microbiology, 2017, 8, pp.16. ⟨10.3389/fmicb.2017.00443⟩

Article dans une revue hal-01580789v1
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Unprecedented large inverted repeats at the replication terminus of circular bacterial chromosomes suggest a novel mode of chromosome rescue

Hela El Kafsi , Valentin Loux , Mahendra Mariadassou , Camille Blin , Hélène Chiapello et al.

Scientific Reports, 2017, 7, pp.1-11. ⟨10.1038/srep44331⟩

Article dans une revue hal-01509688v1
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Draft Genome Sequences of 18 Psychrotolerant and 2 Thermotolerant Strains Representative of Particular Ecotypes in the Bacillus cereus Group

Marie Helene Guinebretière , Valentin Loux , Véronique Martin , Pierre Nicolas , Vincent Sanchis Borja et al.

Genome Announcements, 2017, 5 (5), 3 p. ⟨10.1128/genomeA.01568-16⟩

Article dans une revue hal-01602632v1
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Identification of proteins involved in the anti-inflammatory properties of Propionibacterium freudenreichii by means of a multi-strain study

Stéphanie-Marie Deutsch , Mahendra Mariadassou , Pierre Nicolas , Sandrine Parayre , Rozenn Le Guellec et al.

Scientific Reports, 2017, 7, pp.46409. ⟨10.1038/srep46409⟩

Article dans une revue hal-01510019v1
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The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes

Vincent J. Henry , Anne Goelzer , Arnaud Ferré , Stéphan Fischer , Marc Dinh et al.

Journal of Biomedical Semantics, 2017, 8 (53), 16 p. ⟨10.1186/s13326-017-0165-6⟩

Article dans une revue hal-01652923v1

Manual and expert annotation of the nearly complete genome sequence of Staphylococcus sciuri strain ATCC 29059: a reference for the oxidase-positive staphylococci that supports the atypical phenotypic features of the species group

Eugene Christo-Foroux , Tatiana Vallaeys , Valentin Loux , Elie Dassa , Josef Deutscher et al.

Systematic and Applied Microbiology, 2017, 40 (7), pp.401-410. ⟨10.1016/j.syapm.2017.07.002⟩

Article dans une revue hal-01604275v1

Synchronized navigation and comparative analyses across Ensembl complete bacterial genomes with INSYGHT.

Thomas Lacroix , Sylvie Thérond , Marc Rugeri , Pierre P. Nicolas , Annie Gendrault et al.

Bioinformatics, 2016, 32 (7), pp.1083-1084. ⟨10.1093/bioinformatics/btv689⟩

Article dans une revue hal-02630699v1
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Permanent draft genome sequence of the probiotic strain Propionibacterium freudenreichii CIRM-BIA 129 (ITG P20).

Hélène Falentin , Stéphanie-Marie Deutsch , Valentin Loux , Amal Hammani , Julien Buratti et al.

Standards in Genomic Sciences, 2016, 11, pp.6. ⟨10.1186/s40793-015-0120-z⟩

Article dans une revue hal-02640172v1
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Complete Genome Sequence of Lactococcus lactis subsp. lactis A12, a Strain Isolated from Wheat Sourdough

Maeva Guellerin , Delphine Passerini , Catherine Fontagné-Faucher , Hervé Robert , Valérie Gabriel et al.

Genome Announcements, 2016, 4 (5), pp.2 P. ⟨10.1128/genomeA.00692-16⟩

Article dans une revue hal-01578250v1
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New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration

Chloé C. Ambroset , Charles Coluzzi , Gérard Guédon , Marie-Dominique Devignes , Valentin Loux et al.

Frontiers in Microbiology, 2016, 6 (6), pp.1483. ⟨10.3389/fmicb.2015.01483⟩

Article dans une revue hal-01262284v1
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Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CFL1, a Lactic Acid Bacterium Isolated from French Handcrafted Fermented Milk

Julie Meneghel , Eric Dugat-Bony , Françoise Irlinger , Valentin Loux , Marie Vidal et al.

Genome Announcements, 2016, 4 (2), pp.e00052-16. ⟨10.1128/genomeA.00052-16⟩

Article dans une revue hal-01511494v1
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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 et al.

Genome Announcements, 2016, 4 (6), 2 p. ⟨10.1128/genomeA.00950-16⟩

Article dans une revue hal-01594527v1
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Draft genome sequence of Corynebacterium variabile Mu292, isolated from Munster, a french smear-ripened cheese

Eric Dugat-Bony , Anne-Sophie Sarthou , Valentin Loux , Marie Vidal , Pascal Bonnarme et al.

Genome Announcements, 2016, 4 (4), ⟨10.1128/genomeA.00669-16⟩

Article dans une revue hal-01480898v1
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Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii

Valentin Loux , Mahendra Mariadassou , Sintia Almeida , Hélène Chiapello , Amal Hammani et al.

BMC Genomics, 2015, 16 (1), pp.35. ⟨10.1186/s12864-015-1467-7⟩

Article dans une revue hal-01142363v1
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Surface proteins of Propionibacterium freudenreichii are involved in its anti-inflammatory properties.

Caroline Le Maréchal , Vincent Péton , Coline Plé , Christophe Vroland , Julien Jardin et al.

Journal of Proteomics, 2015, 113, pp.447-461. ⟨10.1016/j.jprot.2014.07.018⟩

Article dans une revue hal-01209735v1

Inventory of the GH70 enzymes encoded by <em>Leuconostoc citreum</em> NRRL B-1299 - identification of three novel -transglucosylases

Delphine Passerini , Marlène Vuillemin , Lisa Ufarté , Sandrine Morel , Valentin Loux et al.

FEBS Journal, 2015, 282 (11), pp.2115-2130. ⟨10.1111/febs.13261⟩

Article dans une revue hal-02630462v1
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Overview of a surface-ripened cheese community functioning by meta-omics analyses

Eric Dugat-Bony , Cecile Straub , Aurélie Teissandier , Djamila Onesime , Valentin Loux et al.

PLoS ONE, 2015, 10 (4), pp.e0124360. ⟨10.1371/journal.pone.0124360⟩

Article dans une revue hal-01195505v1
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Genome Sequences of Two Bovine Mastitis-Causing Escherichia coli Strains

Florent Kempf , Valentin Loux , Pierre Germon

Genome Announcements, 2015, 3 (2), pp.1. ⟨10.1128/genomeA.00259-15⟩

Article dans une revue hal-01171499v1
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Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products

Mathieu Almeida , Agnes Hebert , Anne-Laure Abraham , Simon Rasmussen , Christophe Monnet et al.

BMC Genomics, 2014, 15, article 1101 (16 p.). ⟨10.1186/1471-2164-15-1101⟩

Article dans une revue hal-01195502v1

Data from an integrative approach decipher the surface proteome of [i]Propionibacterium freudenreichii[/i]

Caroline Le Maréchal , Vincent Péton , Coline Le Plenier , Christophe Vroland , Julien Jardin et al.

Data in Brief, 2014, 1, pp.46-50. ⟨10.1016/j.dib.2014.08.009⟩

Article dans une revue (data paper) hal-01209746v1
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Genome Sequence of "Candidatus Arthromitus" sp. Strain SFB-Mouse-NL, a Commensal Bacterium with a Key Role in Postnatal Maturation of Gut Immune Functions.

Alexandre Bolotine , Tomas de Wouters , Pamela Schnupf , Christiane Bouchier , Valentin Loux et al.

Genome Announcements, 2014, 2 (4), ⟨10.1128/genomeA.00705-14⟩

Article dans une revue hal-01204391v1
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Genome sequence of[i] Lactobacillus delbrueckii[/i] subsp. [i]lactis[/i] CNRZ327, a dairy bacterium with anti-inflammatory properties.

Hela El Kafsi , Johan Binesse , Valentin Loux , Julien Buratti , Samira Boudebbouze et al.

Genome Announcements, 2014, 2 (4), pp.1-2. ⟨10.1128/genomeA.00328-14⟩

Article dans une revue hal-01204323v1
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Genome Sequence of Lactococcus lactis subsp. lactis bv. diacetylactis LD61.

Hélène Falentin , Delphine Naquin , Valentin Loux , Frédérique Barloy-Hubler , Pascal Loubière et al.

Genome Announcements, 2014, 2 (1), pp.1. ⟨10.1128/genomeA.01176-13⟩

Article dans une revue hal-01019560v1
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Insyght: navigating amongst abundant homologues, syntenies and gene functional annotations in bacteria, it's that symbol!

Thomas Lacroix , Valentin Loux , Annie Gendrault , Mark Hoebeke , Jean-François Gibrat

Nucleic Acids Research, 2014, 42 (21), pp.e162. ⟨10.1093/nar/gku867⟩

Article dans une revue hal-01332638v1
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Bacterial protein signals are associated with Crohn's disease.

Catherine Juste , David P Kreil , Christian Beauvallet , Alain Guillot , Sebastian Vaca et al.

Gut, 2014, 63 (10), pp.1566-1577. ⟨10.1136/gutjnl-2012-303786⟩

Article dans une revue hal-00933734v1
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Transcriptomic analysis of Staphylococcus xylosus in the presence of nitrate and nitrite in meat reveals its response to nitrosative stress

Aurore Vermassen , Anne de La Foye , Valentin Loux , Régine Talon , Sabine Leroy

Frontiers in Microbiology, 2014, 5, n.p. ⟨10.3389/fmicb.2014.00691⟩

Article dans une revue hal-02631923v1
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Genome Sequence of the Lactic Acid Bacterium <i>Lactococcus lactis</i> subsp. <i>lactis</i> TOMSC161, Isolated from a Nonscalded Curd Pressed Cheese

Hélène Velly , Pierre Renault , Anne-Laure Abraham , Valentin Loux , Agnes Delacroix-Buchet et al.

Genome Announcements, 2014, 2 (6), ⟨10.1128/genomeA.01121-14⟩

Article dans une revue hal-01193999v1
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Complete Genome Sequence of Leuconostoc citreum Strain NRRL B-742

Delphine Passerini , Marlène Vuillemin , S. Laguerre , Myriam Amari , Valentin Loux et al.

Genome Announcements, 2014, 2 (6), ⟨10.1128/genomeA.01179-14⟩

Article dans une revue hal-02637077v1
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Comparative genomics of first available bovine Anaplasma phagocytophilum genome obtained with targeted sequence capture.

Thibaud Dugat , Valentin Loux , Sylvain Marthey , Marco Moroldo , Anne-Claire Lagrée et al.

BMC Genomics, 2014, 15 (1), pp.973. ⟨10.1186/1471-2164-15-973⟩

Article dans une revue hal-01193998v1
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Lactobacillus delbrueckii ssp. lactis and ssp. bulgaricus: a chronicle of evolution in action.

Hela El Kafsi , Johan Binesse , Valentin Loux , Julien Buratti , Samira Boudebbouze et al.

BMC Genomics, 2014, 15 (1), pp.407. ⟨10.1186/1471-2164-15-407⟩

Article dans une revue pasteur-01017376v1

Technical challenges in metatranscriptomic studies applied to the bacterial communities of freshwater ecosystems

Noémie Pascault , Valentin Loux , Sandra Derozier , Véronique Martin , Didier Debroas et al.

Genetica, 2014, 143 (2), pp.25216965. ⟨10.1007/s10709-014-9783-4⟩

Article dans une revue hal-01110172v1
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A unique in vivo experimental approach reveals metabolic adaptation of the probiotic Propionibacterium freudenreichii to the colon environment.

Taous Saraoui , Sandrine Parayre , Grégory Guernec , Valentin Loux , Jérôme Montfort et al.

BMC Genomics, 2013, 14 (1), pp.911. ⟨10.1186/1471-2164-14-911⟩

Article dans une revue inserm-00923652v1

Draft genome sequences of five strains of [i]Lactobacillus acidophilus[/i] , strain CIP 76.13 T , isolated from humans, strains CIRM-BIA 442 and CIRM-BIA 445, isolated from dairy products, and strains DSM 20242 and DSM 9126 of unknown origin

Hélène Falentin , Sylvie Cousin , Dominique Clermont , Sophie Creno , Florence Ma et al.

Genome Announcements, 2013, 1 (4), pp.e00658-13. ⟨10.1128/genomeA.00658-13⟩

Article dans une revue hal-01209470v1
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Draft genome sequence of Lactobacillus hominis strain CRBIP 24.179τ, isolated from human intestine

Sylvie Cousin , Sophie Creno , Laurence Ma , Dominique Clermont , Valentin Loux et al.

Genome Announcements, 2013, 1 (4), pp.1. ⟨10.1128/genomeA.00662-13⟩

Article dans une revue hal-00939673v1
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Draft genome sequences of Lactobacillus equicursoris CIP 110162τ and Lactobacillus sp. strain CRBIP 24.137, isolated from thoroughbred racehorse feces and human urine, respectively

Sylvie Cousin , Valentin Loux , Laurence Ma , Sophie Creno , Dominique Clermont et al.

Genome Announcements, 2013, 1 (4), pp.1-2. ⟨10.1128/genomeA.00663-13⟩

Article dans une revue hal-02645656v1
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Draft Genome Sequence of [i][/i] Lactobacillus pasteurii[i][/i] CRBIP 24.76T.

Sylvie Cousin , Dominique Clermont , Sophie Creno , Laurence Ma , Valentin Loux et al.

Genome Announcements, 2013, 1 (4), ⟨10.1128/genomeA.00660-13⟩

Article dans une revue hal-01190531v1
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Complete chromosome sequence of Carnobacterium maltaromaticum LMA 28.

Catherine C. Cailliez-Grimal , Stéphane Chaillou , Jamila J. Anba-Mondoloni , Valentin Loux , Muhammad Inam M. I. Afzal et al.

Genome Announcements, 2013, 1 (1), pp.1-2. ⟨10.1128/genomeA.00115-12⟩

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Accumulation of intracellular glycogen and trehalose by [i]Propionibacterium Freudenreichii[/i] under conditions mimicking cheese ripening in the cold

Marion Dalmasso , Julie Aubert , Sergine Even , Hélène Falentin , Marie-Bernadette Maillard et al.

Applied and Environmental Microbiology, 2012, 78 (17), pp.6357-6364. ⟨10.1128/AEM.00561-12⟩

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Genome Sequence of the Invasive Salmonella enterica subsp. enterica Serotype Enteritidis Strain LA5

Olivier Grépinet , Aurore Rossignol , Valentin Loux , Helene Chiapello , Annie Gendrault et al.

Journal of Bacteriology, 2012, 194 (9), pp.2387-2388. ⟨10.1128/JB.00256-12⟩

Article dans une revue hal-03044203v1
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Genome sequence of Staphylococcus equorum subsp equorum Mu2, Isolated from a french smear-ripened cheese

Francoise Irlinger , Valentin Loux , Pascal Bento , Jean-Francois Gibrat , Cecile Straub et al.

Journal of Bacteriology, 2012, 194 (18), pp.5141-5142. ⟨10.1128/JB.01038-12⟩

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Accumulation of Intracellular Glycogen and Trehalose by Propionibacterium freudenreichii under Conditions Mimicking Cheese Ripening in the Cold

Marion Dalmasso , Julie Aubert , Sergine Even , Hélène Falentin , Marie-Bernadette Maillard et al.

Applied and Environmental Microbiology, 2012, 78 (17), pp.6357-6364. ⟨10.1128/AEM.00561-12⟩

Article dans une revue hal-02363390v1
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Genome sequence of Lactococcus raffinolactis strain 4877, isolated from natural dairy starter culture

Victoria Meslier Meslier , Valentin Loux , Pierre Renault

Journal of Bacteriology, 2012, 194 (22), pp.6364. ⟨10.1128/JB.01697-12⟩

Article dans une revue hal-01000376v1
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Genome sequence of corynebacterium casei UCMA 3821, isolated from a smear-ripened cheese

Christophe C. Monnet , Valentin Loux , Pascal P. Bento , Jean-Francois J.-F. Gibrat , Cecile C. Straub et al.

Journal of Bacteriology, 2012, 194 (3), pp.738-739. ⟨10.1128/JB.06496-11⟩

Article dans une revue hal-01000221v1
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Genome sequence of weissella confusa LBAE C39-2, isolated from a wheat sourdough

Myriam Amari , Sandrine Laguerre , Marlène Vuillemin , Hervé Robert , Valentin Loux et al.

Journal of Bacteriology, 2012, 194 (6), pp.1608-1609. ⟨10.1128/JB.06788-11⟩

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Genome sequence of Leuconostoc pseudomesenteroides strain 4882, isolated from a dairy starter culture

Victoria Meslier Meslier , Valentin Loux , Pierre Renault

Journal of Bacteriology, 2012, 194 (23), pp.6637. ⟨10.1128/JB.01696-12⟩

Article dans une revue hal-01000375v1
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Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis

Sophie S. Schbath , Veronique V. Martin , Matthias Zytnicki , Julien Fayolle , Valentin Loux et al.

Journal of Computational Biology, 2012, 19 (6), pp.796-813. ⟨10.1089/cmb.2012.0022⟩

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Complete genome sequence of Flavobacterium indicum GPSTA100-9T, isolated from warm spring water

Paul Barbier , Armel A. Houel , Valentin Loux , Julie Poulain , Jean-François Bernardet et al.

Journal of Bacteriology, 2012, 194 (11), pp.3024-3025. ⟨10.1128/JB.00420-12⟩

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Genome sequences of three Leuconostoc Citreum Strains, LBAE C10, LBAE C11, and LBAE E16, isolated from wheat sourdoughs

Sandrine Laguerre , Myriam Amari , Marlène Vuillemin , Hervé Robert , Valentin Loux et al.

Journal of Bacteriology, 2012, 194 (6), pp.1610-1611. ⟨10.1128/JB.06789-11⟩

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Genome sequence of the persistent Salmonella enterica subsp enterica Serotype Senftenberg Strain SS209

Olivier Grépinet , Zineb Boumart , Isabelle Virlogeux-Payant , Valentin Loux , Hélène Chiapello et al.

Journal of Bacteriology, 2012, 194 (9), pp.2385-2386. ⟨10.1128/JB.00255-12⟩

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Complete genome sequence of the clinical Streptococcus salivarius strain CCHSS3

Christine C. Delorme , Eric Guédon , Nicolas N. Pons , Corinne Cruaud , Arnaud A. Couloux et al.

Journal of Bacteriology, 2011, 193 (18), pp.5041-5042. ⟨10.1128/JB.05416-11⟩

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Exploration of sulfur metabolism in the yeast Kluyveromyces lactis

Agnes A. Hebert , Marie-Pierre Forquin Forquin-Gomez , Aurélie A. Roux , Julie J. Aubert , Christophe C. Junot et al.

Applied Microbiology and Biotechnology, 2011, 91 (5), pp.1409-1423. ⟨10.1007/s00253-011-3481-2⟩

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Complete genome sequence of the pigmented Streptococcus thermophilus strain JIM8232

Christine C. Delorme , Claire C. Bartholini , Mélanie M. Luraschi , Nicolas N. Pons , Valentin Loux et al.

Journal of Bacteriology, 2011, 193 (19), pp.5581-5582. ⟨10.1128/JB.05404-11⟩

Article dans une revue hal-01000180v1
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CompaGB: An open framework for genome browsers comparison

Thomas Lacroix , Valentin Loux , Annie Gendrault-Jacquemard Gendrault , Jean-François Gibrat , Hélène Chiapello

BMC Research Notes, 2011, 4, pp.133. ⟨10.1186/1756-0500-4-133⟩

Article dans une revue hal-02644023v1
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The arthrobacter arilaitensis Re117 genome sequence reveals its genetic adaptation to the surface of cheese

Christophe Monnet , Valentin Loux , Jean-Francois Gibrat , Valérie Barbe , Benoit Vacherie et al.

PLoS ONE, 2010, 5 (11), pp.e15489. ⟨10.1371/journal.pone.0015489⟩

Article dans une revue hal-01195440v1
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The complete genome of Propionibacterium freudenreichii CIRM-BIA1T, a Hardy actinobacterium with food and probiotic applications

Hélène Falentin , Stéphanie-Marie Deutsch , Gwénaël Jan , Valentin Loux , Anne Thierry et al.

PLoS ONE, 2010, 5 (7), pp.1-12. ⟨10.1371/journal.pone.0011748⟩

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Complete genome sequence of the probiotic Lactobacillus casei strain BL23

Alain Mazé , Grégory Boël , Manuel Zùniga , Alexa Bourand , Valentin Loux et al.

Journal of Bacteriology, 2010, 192 (10), pp.2647-2648. ⟨10.1128/JB.00076-10⟩

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Characterization of the insoluble proteome of lactococcus lactis by SDS-PAGE LC-MS/MS leads to the identification of new markers of adaptation of the bacteria to the mouse digestive tract

Jasna Beganovic , Alain A. Guillot , Maarten van de Guchte , Anne Jouan , Christophe C. Gitton et al.

Journal of Proteome Research, 2010, 9 (2), pp.677-688

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Prediction of surface exposed proteins in Streptococcus pyogenes, with a potential application to other Gram-positive bacteria

Aleksandr Barinov , Valentin Loux , Amal Hammani , Pierre P. Nicolas , Philippe P. Langella et al.

Proteomics, 2009, 9 (1), pp.61-73. ⟨10.1002/pmic.200800195⟩

Article dans une revue hal-02663676v1
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Identification of brevibacteriaceae by multilocus sequence typing and comparative genomic hybridization analyses.

Marie-Pierre Forquin , Hugo Duvergey , Caroline Proux , Valentin Loux , Jérôme Mounier et al.

Applied and Environmental Microbiology, 2009, 75 (19), pp.6406-9. ⟨10.1128/AEM.00224-09⟩

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Complete genome sequence of the fish pathogen Flavobacterium psychrophilum

Éric Duchaud , Mekki Boussaha , Valentin Loux , Jean-François Bernardet , Christian Michel et al.

Nature Biotechnology, 2007, 25 (7), pp.763 - 769. ⟨10.1038/nbt1313⟩

Article dans une revue hal-02666599v1
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AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system

K. Bryson , Valentin Loux , Robert R. Bossy , P. Nicolas , Stéphane Chaillou et al.

Nucleic Acids Research, 2006, 34 (12), pp.3533-3545. ⟨10.1093/nar/gkl471⟩

Article dans une revue hal-02665192v1
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The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution

Maarten van de Guchte , Stéphanie Penaud , Christine Grimaldi , Valérie Barbe , K. Bryson et al.

Proceedings of the National Academy of Sciences of the United States of America, 2006, 103 (24), pp.9274-9279. ⟨10.1073/pnas.0603024103⟩

Article dans une revue hal-02668654v1

The complete genome sequence of the meat-borne lactic acid bacterium Lactobacillus sakei 23K

Stéphane Chaillou , Marie-Christine Champomier Verges , Monique Cornet , Anne-Marie Crutz-Le Coq , Anne-Marie Dudez et al.

Nature Biotechnology, 2005, 23 (12), pp.1527-1533. ⟨10.1038/nbt1160⟩

Article dans une revue hal-02683108v1
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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

Prevalence and diversity of Integrative and Conjugative or Mobilizable Elements carrying antimicrobial resistance genes in Streptococcus suis

Manon Dechêne-Tempier , Stéphanie Bougeard , Valentin Loux , Hélène Chiapello , Virginie Libante et al.

International Conference on type IV secretion system, UMR1128 DynAMic; PROPULS', Feb 2025, Nancy, France

Communication dans un congrès hal-05286237v1

Metagenomics reveal contrasted and dynamic responses of microbial soil communities to in situ wheat straw amendment in croplands or grasslands

Domitille Jarrige , Vincent Tardy , Valentin Loux , Olivier Rué , Abad Chabbi et al.

Symposium on Environmental and Agronomical Genomics organisé par France Génomique and the Research Group “Environmental Genomics", Feb 2024, Toulouse, France

Communication dans un congrès hal-04654371v1

Drivers of microbial diversity in French Protected designation of Origin (PDO) cheeses

Francoise Irlinger , Mahendra Mariadassou , Eric Dugat-Bony , Cécile Neuvéglise , Olivier Rué et al.

IDF World Dairy Science, Oct 2024, Paris, France

Communication dans un congrès hal-04820075v1

Variable and core functional microbiota associated with seven Medicago truncatula genotypes

Zhu, Liya , Olivier Rué , Florence Deau , Julie Cremaschi , Valentin Loux et al.

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 et al.

Journée doctorants UMR Agroécologie, Nov 2023, Dijon, France

Communication dans un congrès hal-04317070v1

Migale et son offre de service de text-mining

Valentin Loux , Mouhamadou Ba

Journées du PEPI IBIS, INRAE, Sep 2023, Paris, France

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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 et al.

FORUM ON FERMENTED FOODS, COST PIMENTO, May 2023, Lyon, France

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Origins and rate of mutations in bacteriophage Lambda

Julien Lopez , Mahendra Mariadassou , Valentin Loux , Rafael Sanjuán , Marina Elez et al.

Phages in Lyon 2023, phages.fr, Nov 2023, Lyon, France

Communication dans un congrès hal-04321371v1

Evidences for different abilities of human gut bacteria to metabolise prebiotics for the benefits of the digestive health and wellness.

Cassandre Bedu-Ferrari , Paul Biscarrat , Sarah Vati , Cyril Chaudemanche , Valérie Benoit et al.

International Scientific Association for Probiotics and Prebiotics Annual Meeting, Jun 2021, Online conference, France

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Mobile Genetic Elements transferring by conjugation in the human commensal bacterium Streptococcus salivarius: abundance, diversity and role in the adaptation to environment.

Julie Lao , Gérard Guédon , Thomas Lacroix , Florence Charron-Bourgoin , Virginie Libante et al.

Réunion du GDR3546 Eléments transposables, Dec 2021, Paris, France

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Prebiotics for digestive health and wellness: how to successfully promote the gut microbiome?

Cassandre Bedu-Ferrari , Paul Biscarrat , Sarah Vati , Cyril Chaudemanche , Valerie Benoit et al.

Society for Applied Microbiology Early Career Scientist Research Symposium, Mar 2021, Online Conference, France

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Impact of dietary fibers and prebiotics on the gut microbiota: consequences on the digestive health and wellness.

Cassandre Bedu-Ferrari , Sarah Vati , Cyril Chaudemanche , Valérie Benoit , Thomas Lacroix et al.

ABIES Days, Sep 2020, Paris, France

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A workflow to build a relevant and reduced bacterial dataset from NCBI

Sandra Derozier , Sam Ah-Lone , Valentin Loux , Hélène Chiapello

JOBIM : Journées Ouvertes Biologie Informatique Mathématiques, Jul 2019, Nantes, France

Communication dans un congrès hal-02733948v1

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 et al.

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 <em>Medicago truncatula</em>

Julie Cremaschi , Olivier Rué , Florence Deau , Philippe Lemanceau , Valentin Loux et al.

Rhizosphere 5, Jul 2019, Saskatoon, Saskatchewan, Canada

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The journey of a team of engineers in learning packaging technology

Laure Quintric , Patrick Durand , Olivier Inizan , Valentin Marcon , Caroline Dussart et al.

Galaxy Community Conference - GCC2018, Jun 2018, Portland, United States

Communication dans un congrès hal-02784992v1

Des microbes dans mon fromage ?

Sophie Schbath , Valentin Loux

Journées Nationales de la Science Ouverte, Dec 2018, Paris, France

Communication dans un congrès hal-01954713v1
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L'ontologie OntoBiotope pour l'étude de la biodiversité microbienne

Claire Nédellec , Estelle Chaix , Robert Bossy , Louise Deleger , Sandra Derozier et al.

EGC'2018: 18èmes Conférence Internationale sur l'Extraction et la Gestion des Connaissances, Jan 2018, Paris, France

Communication dans un congrès hal-02737399v1

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 et al.

3rd MPItM-Labex ARBRE Workshop, Nov 2018, cologne, Germany

Communication dans un congrès hal-03339776v1
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A metagenomic tool for cheese ecosystems

Anne-Laure Abraham , Quentin Cavaillé , Thibaut Guirimand , Pierre Renault , Sandra Derozier et al.

17. European Conference on Computational Biology (ECCB 2018, Workshop "Recent Computational Advances in Metagenomics (RCAM)", Sep 2018, Athenes, Greece

Communication dans un congrès hal-02789036v1
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Food-Microbiomes Transfert, a shotgun metagenomic tool and a database to analyze cheese ecosystems

Thibaut Guirimand , Anne-Laure Abraham , Sandra Derozier , Charlie Pauvert , Mahendra Mariadassou et al.

JOBIM 2017 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2017, Lille, France

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Florilège: a database gathering microbial phenotypes of food interest

Hélène Falentin , Estelle Chaix , Bedis Dridi , Philippe Bessieres , S Buchin et al.

2017 Scientific MEM days: Journées scientifiques MEM (Métaomiques et écosystèmes microbiens), Jan 2017, Paris, France

Communication dans un congrès hal-01607327v1
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Représentation systémique multi-échelle des processus biologiques de la bactérie

Vincent J. Henry , Arnaud Ferré , Christine Froidevaux , Anne Goelzer , Vincent V. Fromion et al.

IC2016 - Ingénierie des Connaissances, Jun 2016, Montpellier, France

Communication dans un congrès hal-01442727v1
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Représentation systémique multi-échelle des processus biologiques de la bactérie

Vincent Henry , Arnaud Ferré , Christine Froidevaux , Anne Goelzer , Vincent Fromion et al.

IC201: 27es Journées francophones d'Ingénierie des Connaissances, Jun 2016, Montpellier, France

Communication dans un congrès hal-02741418v1
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Mapping reads on a genomic sequence: a practical comparative analysis

Sophie S. Schbath , Veronique V. Martin , Matthias Zytnicki , Julien Fayolle , Valentin Loux et al.

Kick-of meeting of PF7 RADIANT project, Jan 2013, Manchester, United Kingdom. 19 diapos

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Deciphering why <em>Salmonella</em> Gallinarum is less invasive in vitro than <em>Salmonella</em> Enteritidis

Aurore Rossignol , Sylvie Roche , Isabelle Virlogeux-Payant , Olivier Grépinet , Nadia Abed et al.

I3S International Symposium Salmonella and Salmonellosis, Institut National de la Recherche Agronomique (INRA). FRA., May 2013, Saint Malo, France

Communication dans un congrès hal-02749048v1

Genomic diversity of Flavobacterium species.

Éric Duchaud , Paul Barbier , Jean-François Bernardet , Christian Michel , Céline Chantry-Darmon et al.

Flavobacterium 2012, 2012, Turku, Finland

Communication dans un congrès hal-02746549v1
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Mapping reads on a genomic sequence: a practical comparative analysis

Sophie S. Schbath , Veronique V. Martin , Matthias Zytnicki , Julien Fayolle , Valentin Loux et al.

Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), Jul 2012, Rennes, France. pp.496

Communication dans un congrès hal-02748738v1

SURFING: A national project to understand immunomodulatury effects of dairy starters

Benoît Foligné , Valentin Loux , Christophe Hervé , Jean-René Kerjean , Denis Matter et al.

2nd International Symposium "Microbes For Health", Dec 2011, Paris, France

Communication dans un congrès hal-01190437v1

Genomic diversity of 24 Propionibacterium freudenreichii 1 strains

Hélène Falentin , Valentin Loux , Valérie Barbe , Amal Plaudet Hammani , Stéphanie-Marie Deutsch et al.

6 Conference on Functional Genomics of Gram-positive Microorganisms 16 International Conference on Bacilli, Jun 2011, Montecatini, Italy

Communication dans un congrès hal-01454328v1
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Evaluating Genome Browsers Using a Software Qualification Method Evaluation

Thomas Lacroix , Valentin Loux , Annie Gendrault-Jacquemard Gendrault , Jean-François Gibrat , Helene H. Chiapello

JOBIM 2010, Sep 2010, Montpellier, France. pp.196

Communication dans un congrès hal-02751310v1

Web services for microbial genome annotation using data integration

Célia Michotey , Ludovic Legrand , Helene H. Chiapello , Valentin Loux , Annie A. Gendrault-Jacquemard et al.

JOBIM 2010 : Journées Ouvertes en Biologie, Informatique et Mathématiques, Sep 2010, Montpellier, France

Communication dans un congrès hal-02752226v1

Bactéries pathogènes des poissons du genre Flavobacterium

Éric Duchaud , Jean-François Bernardet , Brigitte Kerouault , Christian Michel , Céline Chantry et al.

2. Journées de la Recherche Filière Piscicole, Jul 2009, Paris, France. 1 p

Communication dans un congrès hal-02823179v1
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INSYGT : a multi-genes multi-genomes browser that highlights synteny conservation in prokaryotes.

Thomas Lacroix , Valentin Loux , Annie Gendrault-Jacquemard Gendrault , Mark M. Hoebeke , Jean-François Gibrat

JOBIM 2008, Jun 2008, Lille, France. 2 p

Communication dans un congrès hal-02824485v1
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Towards a semi-automatic functional annotation tool based on decision tree techniques

Jérôme Azé , L. Gentils , Claire Toffano-Nioche , Valentin Loux , Jean-François Gibrat et al.

Machine Learning in Systems Biology: MLSB 2007, Sep 2007, Evry, France

Communication dans un congrès hal-02754400v1

La séquence complète du génome de la bactérie de la viande Lactobacillus sakei

Stéphane Chaillou , Monique Cornet , Anne-Marie A.-M. Le Coq , Anne-Marie Loustau , Robert R. Bossy et al.

Symposium SFM, Interactions Bactériennes dans les Environnements Agroalimentaires : Apport des Nouvelles Approches., Société Française de Microbiologie (SFM). FRA., Nov 2006, Paris, France

Communication dans un congrès hal-02816850v1

Genome project of the meat born lactic acid bacterium Lactobacillus sakei 23K: understanding bacterial adaptation to meat and paving the way to the development of biopreservative cultures

Stéphane Chaillou , Monique Cornet , Anne-Marie A.-M. Le Coq , Anne-Marie Loustau , Robert R. Bossy et al.

2. European Conference on Prokaryotic Genomes, Oct 2005, Göttingen, Germany

Communication dans un congrès hal-02828495v1

Premiers regards sur le génome d’une bactérie lactique originale : structure, polymorphisme et analyse génétique ciblée du chromosome de Lactobacillus sakei 23K

Stéphane Chaillou , Monique Cornet , Anne-Marie Loustau , Robert R. Bossy , Valentin Loux et al.

13. Colloque du Club des Bactéries Lactiques, Sep 2004, Nantes, France. 142 p

Communication dans un congrès hal-02759825v1
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Holograph: a generic RDF schema to handle data from agroecological holobionts

Marie Lahaye , Alice Mataigne , Edmond Berne , Matéo Boudet , Olivier Dameron et al.

SWAT4HCLS, Mar 2026, Amsterdam, France. 2026

Poster de conférence hal-05486358v1
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Data stewardship strategy of the Ferments du Futur grand challenge

Erwan Le Floch , Agnès Barnabé , Jonathan Duperrier , Thomas Lacroix , Aaron Millan-oropeza et al.

Journées Ouvertes Biologie, Informatique, Mathématiques 2025, Jul 2025, Bordeaux, France. 2025

Poster de conférence hal-05149332v2
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Cell-free genome-wide transcriptomics through machine learning optimization

Léa Wagner , An Hoang , Olivier Rue , Olivier Delumeau , Valentin Loux et al.

SEED 2025, Jun 2025, Houston, United States

Poster de conférence hal-05155548v1
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SIDURI: from an integrative information system to a user-friendly portal for data analysis and visualisation dedicated to fermentation

Agnès Barnabé , Erwan Le Floch , Jonathan Duperrier , Mariène Wan , Aaron Millan-oropeza et al.

Journées Ouvertes Biologie, Informatique, Mathématiques 2025, Jul 2025, Bordeaux, France. pp.1

Poster de conférence hal-05142051v1

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

Deciphering and cataloging the genomic and functional diversity of the French cheese microbiota

Hélène Gardon , Françoise Irlinger , Céline Delbès , Éric Dugat-Bony , Julia Gendre et al.

WDS 2024, Oct 2024, Paris, France

Poster de conférence hal-05288574v1
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Siduri : an integrative information system for next generation fermented foods

Mariène Wan , Aaron Millan-oropeza , Thomas Lacroix , Jonathan Mineau-Cesari , Sophie Schbath et al.

JOBIM 2024 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2024, Toulouse, France.

Poster de conférence hal-04633572v1
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HoloOLIGO corpus, a manually annotated text dataset supporting schema-based relational information extraction for mammalian milk oligosaccharide diversity pattern comprehension

Mathilde Rumeau , Robert Bossy , Clara Sauvion , Valentin Loux , Mouhamadou Ba et al.

Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jun 2024, Toulouse, France

Poster de conférence hal-04666797v1

Factors contributing to the prevalence of Integrative and Conjugative or Mobilizable Elements carrying antimicrobial resistance genes in Streptococcus suis

Stéphanie Bougeard , Manon Dechêne-Tempier , Valentin Loux , Hélène Chiapello , Virginie Libante et al.

5th International Workshop on Streptococcus suis, Jun 2023, Bangkok / Thailand, Thailand

Poster de conférence hal-04232466v1
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Ferments du Futur : une plateforme unique en Europe pour accélérer la recherche et l’innovation sur les ferments, les aliments fermentés et la biopréservation dans les 10 prochaines années

Sophie Schbath , Maÿlis Urtebise , Valentin Loux , Madeleine Spatz , Damien Paineau

Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jun 2023, Tours (France), France.

Poster de conférence hal-04176537v1

Abundance and diversity of Mobile Genetic Elements carrying antibiotic resistance genes and transferring by conjugation in the human commensal bacterium Streptococcus salivarius.

Sophie Payot , Julie Lao , Gérard Guédon , Thomas Lacroix , Florence Charron-Bourgoin et al.

5th International Caparica Congress in Antibiotic Resistance (IC2AR 2022), Sep 2022, Caparica, Lisbon, Portugal

Poster de conférence hal-04232454v1
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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

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

Zhu, Liya , Olivier Rué , Florence Deau , Julie Cremaschi , Valentin Loux et al.

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 et al.

Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2022, Rennes, France. 2022

Poster de conférence hal-04176761v1
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Omnicrobe : une base de données d’habitats et de phénotypes microbiens

Hélène Falentin , Olivier Harlé , Sandra Derozier , Louise Deléger , Estelle Chaix et al.

23ème édition du colloque du Club des Bactéries Lactiques, Jun 2022, Rennes, France. , 2022

Poster de conférence hal-03694214v1
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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 et al.

Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2022, Rennes, France. 2022

Poster de conférence hal-04176740v1
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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
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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

Functional characterisation of keystone intestinal bacteria to metabolize prebiotics for the benefits of the digestive health and wellness.

Cassandre Bedu-Ferrari , Paul Biscarrat , Sarah Vati , Cyril Chaudemanche , Valérie Benoit et al.

12th International Symposium on Gut Microbiology, Oct 2021, Online conference, France

Poster de conférence hal-04285893v1
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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
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Florilege, a database gathering microbial habitats, phenotypes and uses

Sandra Derozier , Louise Deleger , Estelle Chaix , Reda Mekdad , Mouhamadou Ba et al.

JOBIM 2020, Jun 2020, Montpellier, France

Poster de conférence hal-02904156v1
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Testing markers to characterize microbial communities in food ecosystems using a metagenomics approach

Claire Vincent , Serge Casaregola , Monika Coton , Céline Delbès , Hugo Devillers et al.

JOBIM, Jun 2020, Montpellier, France

Poster de conférence hal-02914960v1
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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
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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 et al.

JOBIM, Jun 2020, Montpellier, France

Poster de conférence hal-02902758v1
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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 et al.

JOBIM, Jun 2020, Montpellier, France.

Poster de conférence hal-03451271v1
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Metagenomic analysis of an african beer ecosystem using Food Microbiome Transfert application

Anne-Laure Abraham , Sandra Derozier , Quentin Cavaillé , Thibaut Guirimand , Solange Aka et al.

jobim 2019, Jul 2019, Nantes, France. 2019

Poster de conférence hal-02789073v1
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Feedback on a c omparative 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
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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 et al.

Phages in Grenoble, Oct 2019, Grenoble, France.

Poster de conférence hal-04360160v1
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FLORILEGE: an integrative database using text mining and ontologies

Estelle Chaix , Sandra Derozier , Louise Deleger , Hélène Falentin , Jean-Baptiste Bohuon et al.

JOBIM 2018, Jul 2018, Marseille, France. , 2018, ABSTRACTS JOBIM 2018

Poster de conférence hal-01827946v1
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Insyght : Analyse evolutionary conserved CDS, orthologs, syntenies, pan-genome, fusion, etc., for your bacteria of interest

Thomas Lacroix , Valentin Loux , Jonathan Lorenzo , Bryan Brancotte , Christophe Blanchet et al.

Annual Research in Computational Molecular Biology (RECOMB), Apr 2018, Paris, France. , 2018

Poster de conférence hal-02736501v1

MetaFoldScan: a pipeline to scan metagenomes and identify structural homologs using HMM

Sandra Derozier , Veronique Martin , Jean-Marc Chatel , Nalini Rama Rao , Valentin Loux et al.

JOBIM 2018, Jul 2018, Marseille, France. , 2018, ABSTRACTS JOBIM 2018

Poster de conférence hal-01827944v1

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 et al.

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 et al.

JOBIM 2018 : Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. , 2018, JOBIM 2018

Poster de conférence hal-02737257v1

The journey of a team of engineers in learning packaging technology

Valentin Marcon , Laure Quintric , Patrick Durand , Olivier Inizan , Caroline Dussart et al.

Jobim (Journées Ouvertes Biologie Informatique Mathématiques), Jul 2018, Marseille, France. , 2018, JOBIM 2018

Poster de conférence hal-02733639v1
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FoodMicrobiome transfert: Web based metagenomic analysis

Quentin Cavaillé , Thibaut Guirimand , Sandra Derozier , Anne-Laure Abraham , Bedis Dridi et al.

JOBIM 2018 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. , 2018

Poster de conférence hal-02008726v1
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Florilege : a database gathering microbial phenotypes of food interest

Hélène Falentin , Estelle Chaix , Bedis Dridi , Philippe Bessieres , S Buchin et al.

4. International Conference on Microbial Diversity 2017, Oct 2017, Bari, Italy. , 2017

Poster de conférence hal-01651302v1
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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

MicroFit project: developping a Tn-seq system in Yarrowia lipolytica to study the adaptation of this yeast to cheese ecosystem

Catherine Madzak , Valentin Loux , Christophe Monnet

Journées MEM des métaprogrammes de l’INRA, 2017, paris, France. 2017

Poster de conférence hal-02786916v1
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Cheese ecosystems insights with shotgun metagenomics and a metadata extended genomics database.

Thibaut Guirimand , Charlie Pauvert , Sandra Derozier , Anne-Laure Abraham , Mahendra Mariadassou et al.

JOBIM 2016 : Journées ouvertes de biologie informatique et mathématiques, Jun 2016, Lyon, France. , 2016

Poster de conférence hal-01512085v1

Monoxenic experimental cheese reveals anti-inflammatory effect of Propionibacterium freudenreichii in vivo.

Caroline Le Maréchal , Vincent Péton , Coline Plé , Julien Jardin , Valérie Briard-Bion et al.

IDF Dairy Science & Technology Symposia 2016 Cheese Science & Technology, Apr 2016, Dublin, Ireland. , 2016

Poster de conférence hal-01512192v1
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Food Microbiome-Transfert a database to characterize cheese ecosystems.

Thibaut Guirimand , Sandra S. Derozier , Charlie Pauvert , Anne-Laure Abraham , Valentin Loux et al.

Journées Bioinformatique Inra, Mar 2016, Toulouse, France. , 2016

Poster de conférence hal-02799027v1

Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of <i>Propionibacterium freudenreichii</i>

Valentin Loux , Mahendra Mariadassou , Sintia Almeida da Silva , Helene Chiapello , Amal Hammami et al.

JOBIM 16. Journées Ouvertes de Biologie, Informatique et Mathématiques, Jul 2015, Clermont-Ferrand, France. , 2015, ⟨10.1186/s12864-015-1467-7⟩

Poster de conférence hal-01209851v1

Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii

Valentin Loux , Mahendra Mariadassou , Sintia Almeida da Silva , Hélène Chiapello , Amal Hammami et al.

20. Colloque du Club des Bactéries Lactiques, Jun 2015, Lille, France. , 2015

Poster de conférence hal-01170054v1
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The multiple-genomes browser of the IFB cloud

Marie-Laure Franchinard , Frederic Sapet , Sandra S. Derozier , Franck F. Samson , Valentin Loux et al.

Journées SUCCES 2015, Nov 2015, Paris, France. , pp.1, 2015

Poster de conférence hal-02795851v1
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Mapdecode : inventory and benchmark of read mapping tools

Jérome Compain , Jullien Renaud , Sivagangari Nandy , Olivier Collin , Jean-François Gibrat et al.

ECCB'14 : European conference on Computational Biology, Sep 2014, Strasbourg, France. , pp.1, 2014

Poster de conférence hal-02792306v1

Surface proteins of [i]Propionibacterium freudenreichii[/i] are involved in its anti-inflammatory properties.

Coline Plé , Caroline Le Maréchal , Vincent Péton , Christophe Vroland , Valérie Briard-Bion et al.

International Scientific Conference on Probiotics and Prebiotics – IPC2014, Jun 2014, Budapest, Hungary. PAMIDA International Ltd, 2014, IPC 2014

Poster de conférence hal-01209657v1

A unique in vivo experimental approach reveals metabolic adaptation of the probiotic [i]Propionibacterium freudenreichii[/i] to the colon environment.

Gwénaël Jan , Taous Saraoui , Sandrine Parayre-Breton , Grégory Guernec , Valentin Loux et al.

International Scientific Conference on Probiotics and Prebiotics – IPC2014, Jun 2014, Budapest, Hungary. PAMIDA International Ltd, 2014, IPC 2014

Poster de conférence hal-01209656v1

An integrative approach of [i]Propionibacterium freudenreichii[/i] immunomodulatory mechanisms

Caroline Le Maréchal , Vincent Péton , Julien Jardin , Valérie Briard-Bion , Stéphanie-Marie Deutsch et al.

5th IDF Symposium on Science & Technology of Fermented Milk, Mar 2014, Melbourne, Australia. 2014

Poster de conférence hal-01209584v1

A unique in vivo experimental approach reveals metabolic adaptation of the probiotic [i]Propionibacterium freudenreichii[/i] to the colon environment

Taous Saraoui , Sandrine Parayre-Breton , Grégory Guernec , Valentin Loux , Jérôme Montfort et al.

24. International ICFMH Conference, Food Micro 2014, Sep 2014, Nantes, France. , 2014, ICFMH Conference, Food Micro 2014

Poster de conférence hal-01209705v1

A unique in vivo approach reveals metabolic adaptation of the probiotic Propionibacterium freudenreichii to the colon environment.

Sandrine Parayre-Breton , Taous Saraoui , Grégory Guernec , Valentin Loux , Jérôme Montfort et al.

Colloque Génomique Environnementale, Nov 2013, Rennes, France. , 2013

Poster de conférence hal-01209535v1

Immunomodulatory properties of the probiotic Propionibacterium freudenreichii surface proteome

Gwénaël Jan , Benoit Foligne , Stéphanie-Marie Deutsch , Rozenn Le Guellec , Fabien Cousin et al.

19 ième Colloque du Club des bactéries lactiques, Oct 2013, Bordeaux, France. , pp.72, 2013

Poster de conférence hal-01209501v1

The probiotic[i] Propionibacterium freudenreichii[/i] surface proteome

Caroline Le Maréchal , Vincent Péton , Julien Jardin , Valérie Briard-Bion , Christophe Vroland et al.

EUPA 2013, Oct 2013, Saint-Malo, France. , 2013

Poster de conférence hal-01209498v1
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IGO, Integration from Genomes to Organisms

Sandra S. Derozier , Helene H. Chiapello , Thomas Lacroix , Cyprien Guerin Guérin , Valentin Loux et al.

JOBIM 2013, Jul 2013, Toulouse, France. , pp.246, 2013, JOBIM TOULOUSE 2013 - RÉSUMÉS COURTS (affiches)

Poster de conférence hal-02746442v1
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Insyght: Using symbols to visualize homologies, conserved syntenies and genomic insertions across multiple genomes

Thomas Lacroix , Valentin Loux , Annie Gendrault-Jacquemard Gendrault , Mark M. Hoebeke , Jean-François Gibrat

JOBIM 2013 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2013, Toulouse, France. Société Française de Bio-Informatique -SFBI, pp.231, 2013, JOBIM TOULOUSE 2013 RÉSUMÉS COURS (affiches) - Volume 2/2

Poster de conférence hal-02748920v1

Combination of in silico and proteomic approaches to identify candidate genes responsible for the immunomodulatory properties of Propionibacterium freudenreichii

Caroline Le Maréchal , Mahendra Mariadassou , Valentin Loux , Amal Plaudet Hammani , Julien Buratti et al.

Journées des Microbiologistes de l'INRA 2012, Nov 2012, L'Isle-sur-la-Sorgue, France. 2012

Poster de conférence hal-01209410v1

Combination of in silico and proteomic approaches to identify candidate genes responsible for the immunomodulatory properties of[i] Propionibacterium freudenreichii[/i]

Caroline Le Maréchal , Mahendra Mariadassou , Valentin Loux , Amal Plaudet Hammani , Julien Buratti et al.

Journées ouvertes en biologie informatique mathématiques, Jul 2012, Rennes, France. , 2012

Poster de conférence hal-01209420v1
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Comparison of mapping softwares for next generation sequencing data

Julien Fayolle , Jean-François Gibrat , Valentin Loux , Sophie S. Schbath

JOBIM 2010, Sep 2010, Montpellier, France. MABLI : Methods Algorithmes Bio-Informatique LIRMM, pp.176, 2010, proceeding of JOBIM 2010 - Journées Ouvertes en Biologie, Informatique et Mathématiques - Montpellier

Poster de conférence hal-02751434v1

The complete genome of Propionibacterium freudenreichii CIRM 1 a hardy actinobacteria with food and probiotic applications

Hélène Falentin , Stéphanie-Marie Deutsch , Sandrine Parayre-Breton , Julien Dherbecourt , Gwénaël Jan et al.

3 International Symposium on Propionibacteria and Bifidobacteria: Dairy and Probiotic, Jun 2010, Oviédo, Spain. , International Journal of Food Microbiology, Volume 149, Issue 1, Pages 1-112 (1 September 2011), 2010, International Journal of Food Microbiology

Poster de conférence hal-01454344v1
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Bovine promoter annotation platform for the identification of transcription factor binding sites in genes involved in early pregnancy

Magalie Leveugle , Valentin Loux , Jean-François Gibrat

JOBIM 2010 : Journées Ouvertes en Biologie, Informatique et Mathématiques, Sep 2010, Montpellier, France. MABLI : Methods Algorithmes Bio-Informatique LIRMM, pp.176, 2010, proceeding of JOBIM 2010 Montpellier

Poster de conférence hal-02757163v1
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Assemblage de génomes bactériens séquencés par NGS - Comparaison d’outils et choix de paramètres

Fabien Melchiore , Cyprien Guerin Guérin , Pierre P. Nicolas , Valentin Loux

JOBIM 2010, Sep 2010, Montpellier, France. MABLI : Methods Algorithmes Bio-Informatique LIRMM, pp.176, 2010, Proceeding of Journées Ouvertes de Biologie, Informatique et Mathématiques 2010 -Montpellier

Poster de conférence hal-02758166v1

Whole-genome sequence of the fish-pathogenic bacterium Flavobacterium psychrophilum

Jean-François Bernardet , Éric Duchaud , Mekki Boussaha , Christian Michel , Valentin Loux et al.

2. FEMS Congress of European Microbiologists, Jul 2006, Madrid, Spain. 1 p., 2006

Poster de conférence hal-02812810v1

GO enrichment analysis for differential proteomics using ProteoRE

Florence Combes , Valentin Loux , Yves Vandenbrouck

Proteomics Data Analysis, 2361, pp.179-196, 2021, Methods in Molecular Biology book series (MIMB), ⟨10.1007/978-1-0716-1641-3_11⟩

Chapitre d'ouvrage hal-03324650v1

Designing an in silico strategy to select tissue-leakage biomarkers using the galaxy framework

Lien Nguyen , Virginie Brun , Florence Combes , Valentin Loux , Yves Vandenbrouck

Proteomics for biomarker discovery: Methods and protocols, 1959, pp.275-289, 2019, Methods in Molecular Biology book series (MIMB), ISBN: 978-1-4939-9164-8. ⟨10.1007/978-1-4939-9164-8_18⟩

Chapitre d'ouvrage hal-02284981v1

Introduction à l'annotation fonctionnelle in silico

Jean-François Gibrat , Valentin Loux

Bio-informatique - principes d'utilisation des outils, Editions Quae, 2010, 978-2-7592-0870-8

Chapitre d'ouvrage hal-02812661v1