Valentin Loux
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
Publications
Publications
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Analyse croisée de données métabarcoding et métagénomiques sur des microbiotes d'hôtes animauxFROGSdays 2025, équipe FROGS INRAe, Dec 2025, Auzeville Tolosan, France |
Prevalence and diversity of Integrative and Conjugative or Mobilizable Elements carrying antimicrobial resistance genes in Streptococcus suisInternational Conference on type IV secretion system, UMR1128 DynAMic; PROPULS', Feb 2025, Nancy, France |
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Metagenomics reveal contrasted and dynamic responses of microbial soil communities to in situ wheat straw amendment in croplands or grasslandsSymposium on Environmental and Agronomical Genomics organisé par France Génomique and the Research Group “Environmental Genomics", Feb 2024, Toulouse, France |
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Drivers of microbial diversity in French Protected designation of Origin (PDO) cheesesIDF World Dairy Science, Oct 2024, Paris, France |
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Variable and core functional microbiota associated with seven Medicago truncatula genotypes12th International PGPR Workshop 2023, May 2023, Toulouse, France |
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Variable and core functional rhizosphere microbiota associated with seven Medicago truncatula genotypesJournée doctorants UMR Agroécologie, Nov 2023, Dijon, France |
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Migale et son offre de service de text-miningJournées 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 cheesesFORUM ON FERMENTED FOODS, COST PIMENTO, May 2023, Lyon, France |
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Origins and rate of mutations in bacteriophage LambdaPhages in Lyon 2023, phages.fr, Nov 2023, Lyon, France |
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Evidences for different abilities of human gut bacteria to metabolise prebiotics for the benefits of the digestive health and wellness.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.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?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.ABIES Days, Sep 2020, Paris, France |
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A workflow to build a relevant and reduced bacterial dataset from NCBIJOBIM : Journées Ouvertes Biologie Informatique Mathématiques, Jul 2019, Nantes, France |
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Evaluation of gyrB amplicon sequencing in comparison to 16S rDNA amplicon sequencing to evaluate intra-species bacterial diversity in food microbiotaJOBIM 20. Journées Ouvertes Biologie Informatique Mathématiques, Jul 2019, Nantes, France |
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Shotgun metagenomics sequencing of the rhizosphere microbiota associated to seven ecotypes of <em>Medicago truncatula</em>Rhizosphere 5, Jul 2019, Saskatoon, Saskatchewan, Canada |
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The journey of a team of engineers in learning packaging technologyGalaxy Community Conference - GCC2018, Jun 2018, Portland, United States |
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Des microbes dans mon fromage ?Journées Nationales de la Science Ouverte, Dec 2018, Paris, France |
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L'ontologie OntoBiotope pour l'étude de la biodiversité microbienneEGC'2018: 18èmes Conférence Internationale sur l'Extraction et la Gestion des Connaissances, Jan 2018, Paris, France |
Functional signatures of soil fungal communities in response to forest tree phenology revealed by metatranscriptome analysis3rd MPItM-Labex ARBRE Workshop, Nov 2018, cologne, Germany |
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A metagenomic tool for cheese ecosystems17. European Conference on Computational Biology (ECCB 2018, Workshop "Recent Computational Advances in Metagenomics (RCAM)", Sep 2018, Athenes, Greece |
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Food-Microbiomes Transfert, a shotgun metagenomic tool and a database to analyze cheese ecosystemsJOBIM 2017 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2017, Lille, France |
Florilège: a database gathering microbial phenotypes of food interest2017 Scientific MEM days: Journées scientifiques MEM (Métaomiques et écosystèmes microbiens), Jan 2017, Paris, France |
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Représentation systémique multi-échelle des processus biologiques de la bactérieIC2016 - Ingénierie des Connaissances, Jun 2016, Montpellier, France |
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Représentation systémique multi-échelle des processus biologiques de la bactérieIC201: 27es Journées francophones d'Ingénierie des Connaissances, Jun 2016, Montpellier, France |
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Mapping reads on a genomic sequence: a practical comparative analysisKick-of meeting of PF7 RADIANT project, Jan 2013, Manchester, United Kingdom. 19 diapos |
Deciphering why <em>Salmonella</em> Gallinarum is less invasive in vitro than <em>Salmonella</em> EnteritidisI3S International Symposium Salmonella and Salmonellosis, Institut National de la Recherche Agronomique (INRA). FRA., May 2013, Saint Malo, France |
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Genomic diversity of Flavobacterium species.Flavobacterium 2012, 2012, Turku, Finland |
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Mapping reads on a genomic sequence: a practical comparative analysisJournées Ouvertes Biologie Informatique Mathématiques (JOBIM), Jul 2012, Rennes, France. pp.496 |
SURFING: A national project to understand immunomodulatury effects of dairy starters2nd International Symposium "Microbes For Health", Dec 2011, Paris, France |
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Genomic diversity of 24 Propionibacterium freudenreichii 1 strains6 Conference on Functional Genomics of Gram-positive Microorganisms 16 International Conference on Bacilli, Jun 2011, Montecatini, Italy |
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Evaluating Genome Browsers Using a Software Qualification Method EvaluationJOBIM 2010, Sep 2010, Montpellier, France. pp.196 |
Web services for microbial genome annotation using data integrationJOBIM 2010 : Journées Ouvertes en Biologie, Informatique et Mathématiques, Sep 2010, Montpellier, France |
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Bactéries pathogènes des poissons du genre Flavobacterium2. Journées de la Recherche Filière Piscicole, Jul 2009, Paris, France. 1 p |
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INSYGT : a multi-genes multi-genomes browser that highlights synteny conservation in prokaryotes.JOBIM 2008, Jun 2008, Lille, France. 2 p |
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Towards a semi-automatic functional annotation tool based on decision tree techniquesMachine Learning in Systems Biology: MLSB 2007, Sep 2007, Evry, France |
La séquence complète du génome de la bactérie de la viande Lactobacillus sakeiSymposium SFM, Interactions Bactériennes dans les Environnements Agroalimentaires : Apport des Nouvelles Approches., Société Française de Microbiologie (SFM). FRA., Nov 2006, Paris, France |
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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 cultures2. European Conference on Prokaryotic Genomes, Oct 2005, Göttingen, Germany |
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Premiers regards sur le génome d’une bactérie lactique originale : structure, polymorphisme et analyse génétique ciblée du chromosome de Lactobacillus sakei 23K13. Colloque du Club des Bactéries Lactiques, Sep 2004, Nantes, France. 142 p |
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Holograph: a generic RDF schema to handle data from agroecological holobiontsSWAT4HCLS, Mar 2026, Amsterdam, France. 2026 |
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Data stewardship strategy of the Ferments du Futur grand challengeJournées Ouvertes Biologie, Informatique, Mathématiques 2025, Jul 2025, Bordeaux, France. 2025 |
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Cell-free genome-wide transcriptomics through machine learning optimizationSEED 2025, Jun 2025, Houston, United States |
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SIDURI: from an integrative information system to a user-friendly portal for data analysis and visualisation dedicated to fermentationJournées Ouvertes Biologie, Informatique, Mathématiques 2025, Jul 2025, Bordeaux, France. pp.1 |
When bacteriophages enter the cheese ripening process: An overview of the PHAGOFROM projectMicrobes 2025, Sep 2025, Bordeaux, France |
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Deciphering and cataloging the genomic and functional diversity of the French cheese microbiotaWDS 2024, Oct 2024, Paris, France |
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Siduri : an integrative information system for next generation fermented foodsJOBIM 2024 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2024, Toulouse, France. |
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HoloOLIGO corpus, a manually annotated text dataset supporting schema-based relational information extraction for mammalian milk oligosaccharide diversity pattern comprehensionJournées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jun 2024, Toulouse, France |
Factors contributing to the prevalence of Integrative and Conjugative or Mobilizable Elements carrying antimicrobial resistance genes in Streptococcus suis5th International Workshop on Streptococcus suis, Jun 2023, Bangkok / Thailand, Thailand |
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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 annéesJournées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jun 2023, Tours (France), France. |
Abundance and diversity of Mobile Genetic Elements carrying antibiotic resistance genes and transferring by conjugation in the human commensal bacterium Streptococcus salivarius.5th International Caparica Congress in Antibiotic Resistance (IC2AR 2022), Sep 2022, Caparica, Lisbon, Portugal |
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Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomicsISME18, 18th International Symposium on Microbial Ecology, Aug 2022, Lausanne, Switzerland. |
Different Medicago truncatula genotypes, expressing different phenotypes, modulate microbial functional genes in the rhizospheremiCROPe 2022, international Symposium microbe-assisted crop production opportunities, challenges & needs, Jul 2022, Vienne, France |
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Plateforme bioinformatique MIGALEJournées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2022, Rennes, France. 2022 |
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Omnicrobe : une base de données d’habitats et de phénotypes microbiens23ème édition du colloque du Club des Bactéries Lactiques, Jun 2022, Rennes, France. , 2022 |
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Implementing a Text Mining Service Offer on the Migale Bioinformatics PlatformJournées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2022, Rennes, France. 2022 |
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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 processesJOBIM 2021 (JOBIM (Journées Ouvertes en Biologie, Informatique et Mathématiques), Jul 2021, Paris, France. |
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Plateforme bioinformatique MIGALEJournées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2021, Paris, France. 2021 |
Functional characterisation of keystone intestinal bacteria to metabolize prebiotics for the benefits of the digestive health and wellness.12th International Symposium on Gut Microbiology, Oct 2021, Online conference, France |
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Plateforme bioinformatique MIGALEJournées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jun 2020, Montpellier, France. 2020 |
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Florilege, a database gathering microbial habitats, phenotypes and usesJOBIM 2020, Jun 2020, Montpellier, France |
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Testing markers to characterize microbial communities in food ecosystems using a metagenomics approachJOBIM, Jun 2020, Montpellier, France |
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DeepOmics, a Digital Environmental Engineering Platform for meta-omics dataJournées Ouvertes de Biologie, Informatique et Mathématique (JOBIM2020), Jun 2020, Montpellier, France. |
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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 WasteJOBIM, Jun 2020, Montpellier, France |
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Shallow sequencing: a cost-effective and accurate alternative to WGS for taxonomic profiling ?JOBIM, Jun 2020, Montpellier, France. |
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Metagenomic analysis of an african beer ecosystem using Food Microbiome Transfert applicationjobim 2019, Jul 2019, Nantes, France. 2019 |
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Feedback on a c omparative metatranscriptomic analysisJOBIM 2019 : Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. , 2019, JOBIM 2019 |
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Detection of an archaeal-specific viral family, previously thought to infect exclusively hyperthermophiles, in human gut metaviromesPhages in Grenoble, Oct 2019, Grenoble, France. |
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FLORILEGE: an integrative database using text mining and ontologiesJOBIM 2018, Jul 2018, Marseille, France. , 2018, ABSTRACTS JOBIM 2018 |
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Insyght : Analyse evolutionary conserved CDS, orthologs, syntenies, pan-genome, fusion, etc., for your bacteria of interestAnnual Research in Computational Molecular Biology (RECOMB), Apr 2018, Paris, France. , 2018 |
MetaFoldScan: a pipeline to scan metagenomes and identify structural homologs using HMMJOBIM 2018, Jul 2018, Marseille, France. , 2018, ABSTRACTS JOBIM 2018 |
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Evaluation of gyrB amplicon sequencing in comparison to 16S rDNA amplicon sequencing to evaluate intra-species bacterial diversity in food microbiotaImprovingFood Micro 2018, Sep 2018, Berlin, Germany. , 2018 |
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Easy16S : a user-friendly Shiny interface for analysis and visualization of metagenomic dataJOBIM 2018 : Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. , 2018, JOBIM 2018 |
The journey of a team of engineers in learning packaging technologyJobim (Journées Ouvertes Biologie Informatique Mathématiques), Jul 2018, Marseille, France. , 2018, JOBIM 2018 |
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FoodMicrobiome transfert: Web based metagenomic analysisJOBIM 2018 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. , 2018 |
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Florilege : a database gathering microbial phenotypes of food interest4. International Conference on Microbial Diversity 2017, Oct 2017, Bari, Italy. , 2017 |
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New -omics data analysis activity on Migale platform for MEM communityJournées d'Animation MEM 2017, Jan 2017, Paris la Vilklette, France. 2017 |
MicroFit project: developping a Tn-seq system in Yarrowia lipolytica to study the adaptation of this yeast to cheese ecosystemJournées MEM des métaprogrammes de l’INRA, 2017, paris, France. 2017 |
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Cheese ecosystems insights with shotgun metagenomics and a metadata extended genomics database.JOBIM 2016 : Journées ouvertes de biologie informatique et mathématiques, Jun 2016, Lyon, France. , 2016 |
Monoxenic experimental cheese reveals anti-inflammatory effect of Propionibacterium freudenreichii in vivo.IDF Dairy Science & Technology Symposia 2016 Cheese Science & Technology, Apr 2016, Dublin, Ireland. , 2016 |
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Food Microbiome-Transfert a database to characterize cheese ecosystems.Journées Bioinformatique Inra, Mar 2016, Toulouse, France. , 2016 |
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Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of <i>Propionibacterium freudenreichii</i>JOBIM 16. Journées Ouvertes de Biologie, Informatique et Mathématiques, Jul 2015, Clermont-Ferrand, France. , 2015, ⟨10.1186/s12864-015-1467-7⟩ |
Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii20. Colloque du Club des Bactéries Lactiques, Jun 2015, Lille, France. , 2015 |
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The multiple-genomes browser of the IFB cloudJournées SUCCES 2015, Nov 2015, Paris, France. , pp.1, 2015 |
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Mapdecode : inventory and benchmark of read mapping toolsECCB'14 : European conference on Computational Biology, Sep 2014, Strasbourg, France. , pp.1, 2014 |
Surface proteins of [i]Propionibacterium freudenreichii[/i] are involved in its anti-inflammatory properties.International Scientific Conference on Probiotics and Prebiotics – IPC2014, Jun 2014, Budapest, Hungary. PAMIDA International Ltd, 2014, IPC 2014 |
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A unique in vivo experimental approach reveals metabolic adaptation of the probiotic [i]Propionibacterium freudenreichii[/i] to the colon environment.International Scientific Conference on Probiotics and Prebiotics – IPC2014, Jun 2014, Budapest, Hungary. PAMIDA International Ltd, 2014, IPC 2014 |
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An integrative approach of [i]Propionibacterium freudenreichii[/i] immunomodulatory mechanisms5th IDF Symposium on Science & Technology of Fermented Milk, Mar 2014, Melbourne, Australia. 2014 |
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A unique in vivo experimental approach reveals metabolic adaptation of the probiotic [i]Propionibacterium freudenreichii[/i] to the colon environment24. International ICFMH Conference, Food Micro 2014, Sep 2014, Nantes, France. , 2014, ICFMH Conference, Food Micro 2014 |
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A unique in vivo approach reveals metabolic adaptation of the probiotic Propionibacterium freudenreichii to the colon environment.Colloque Génomique Environnementale, Nov 2013, Rennes, France. , 2013 |
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Immunomodulatory properties of the probiotic Propionibacterium freudenreichii surface proteome19 ième Colloque du Club des bactéries lactiques, Oct 2013, Bordeaux, France. , pp.72, 2013 |
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The probiotic[i] Propionibacterium freudenreichii[/i] surface proteomeEUPA 2013, Oct 2013, Saint-Malo, France. , 2013 |
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IGO, Integration from Genomes to OrganismsJOBIM 2013, Jul 2013, Toulouse, France. , pp.246, 2013, JOBIM TOULOUSE 2013 - RÉSUMÉS COURTS (affiches) |
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Insyght: Using symbols to visualize homologies, conserved syntenies and genomic insertions across multiple genomesJOBIM 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 |
Combination of in silico and proteomic approaches to identify candidate genes responsible for the immunomodulatory properties of Propionibacterium freudenreichiiJournées des Microbiologistes de l'INRA 2012, Nov 2012, L'Isle-sur-la-Sorgue, France. 2012 |
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Combination of in silico and proteomic approaches to identify candidate genes responsible for the immunomodulatory properties of[i] Propionibacterium freudenreichii[/i]Journées ouvertes en biologie informatique mathématiques, Jul 2012, Rennes, France. , 2012 |
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Comparison of mapping softwares for next generation sequencing dataJOBIM 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 |
The complete genome of Propionibacterium freudenreichii CIRM 1 a hardy actinobacteria with food and probiotic applications3 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 |
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Bovine promoter annotation platform for the identification of transcription factor binding sites in genes involved in early pregnancyJOBIM 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 |
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Assemblage de génomes bactériens séquencés par NGS - Comparaison d’outils et choix de paramètresJOBIM 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 |
Whole-genome sequence of the fish-pathogenic bacterium Flavobacterium psychrophilum2. FEMS Congress of European Microbiologists, Jul 2006, Madrid, Spain. 1 p., 2006 |
GO enrichment analysis for differential proteomics using ProteoREProteomics Data Analysis, 2361, pp.179-196, 2021, Methods in Molecular Biology book series (MIMB), ⟨10.1007/978-1-0716-1641-3_11⟩ |
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Designing an in silico strategy to select tissue-leakage biomarkers using the galaxy frameworkProteomics 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⟩ |
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Introduction à l'annotation fonctionnelle in silicoBio-informatique - principes d'utilisation des outils, Editions Quae, 2010, 978-2-7592-0870-8 |
F3M_database_V1.1.02025 |
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High quality food bacterial genomic ressources from fermented vegetables2024, ⟨10.57745/O4OJA2⟩ |
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MiCoReCa (Microbiome Community Resource Catalogue) - Towards Centralized Curation And Integration Of Microbiome Bioinformatics Resources2026 |
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Food Microbiome Metabolic Modules (F3M), a tool suite for functional profiling of food microbiomes2025 |
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Atypical Replication Error Pattern and Limited Repair Efficiency Contribute to Elevated Mutation Rate in Phage lambda2025 |
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Cell-free genome-wide transcriptomics through machine learning optimization2025 |
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Omnicrobe, an open-access database of microbial habitats and phenotypes using a comprehensive text mining and data fusion approach2022 |
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MilkOligoCorpus annotation guidelinesINRAE. 2024 |