
Valentin Loux
190
Documents
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Publications
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
Communication dans un congrès
hal-04654371
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Drivers of microbial diversity in French Protected designation of Origin (PDO) cheesesIDF World Dairy Science, Oct 2024, Paris, France
Communication dans un congrès
hal-04820075
v1
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Variable and core functional microbiota associated with seven Medicago truncatula genotypes12th International PGPR Workshop 2023, May 2023, Toulouse, France
Communication dans un congrès
hal-04139303
v1
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Variable and core functional rhizosphere microbiota associated with seven Medicago truncatula genotypesJournée doctorants UMR Agroécologie, Nov 2023, Dijon, France
Communication dans un congrès
hal-04317070
v1
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Migale et son offre de service de text-miningJournées du PEPI IBIS, INRAE, Sep 2023, Paris, France
Communication dans un congrès
hal-04294052
v1
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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
Communication dans un congrès
hal-04221356
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Origins and rate of mutations in bacteriophage LambdaPhages in Lyon 2023, phages.fr, Nov 2023, Lyon, France
Communication dans un congrès
hal-04321371
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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
Communication dans un congrès
hal-03495840
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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
Communication dans un congrès
hal-04285897
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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
Communication dans un congrès
hal-04285885
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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
Communication dans un congrès
hal-04285875
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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
Communication dans un congrès
hal-02733948
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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
Communication dans un congrès
hal-02947091
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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
Communication dans un congrès
hal-02735116
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The journey of a team of engineers in learning packaging technologyGalaxy Community Conference - GCC2018, Jun 2018, Portland, United States
Communication dans un congrès
hal-02784992
v1
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Des microbes dans mon fromage ?Journées Nationales de la Science Ouverte, Dec 2018, Paris, France
Communication dans un congrès
hal-01954713
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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
Communication dans un congrès
hal-02789036
v1
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Functional signatures of soil fungal communities in response to forest tree phenology revealed by metatranscriptome analysis3rd MPItM-Labex ARBRE Workshop, Nov 2018, cologne, Germany
Communication dans un congrès
hal-03339776
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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
Communication dans un congrès
hal-02737399
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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
Communication dans un congrès
hal-02788899
v1
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Florilège: a database gathering microbial phenotypes of food interest2017 Scientific MEM days: Journées scientifiques MEM (Métaomiques et écosystèmes microbiens), Jan 2017, Paris, France
Communication dans un congrès
hal-01607327
v1
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Représentation systémique multi-échelle des processus biologiques de la bactérieIC2016 - Ingénierie des Connaissances, Jun 2016, Montpellier, France
Communication dans un congrès
hal-01442727
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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
Communication dans un congrès
hal-02741418
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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
Communication dans un congrès
hal-02804577
v1
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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
Communication dans un congrès
hal-02749048
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Genomic diversity of Flavobacterium species.Flavobacterium 2012, 2012, Turku, Finland
Communication dans un congrès
hal-02746549
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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
Communication dans un congrès
hal-02748738
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SURFING: A national project to understand immunomodulatury effects of dairy starters2nd International Symposium "Microbes For Health", Dec 2011, Paris, France
Communication dans un congrès
hal-01190437
v1
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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
Communication dans un congrès
hal-01454328
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Evaluating Genome Browsers Using a Software Qualification Method EvaluationJOBIM 2010, Sep 2010, Montpellier, France. pp.196
Communication dans un congrès
hal-02751310
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Web services for microbial genome annotation using data integrationJOBIM 2010 : Journées Ouvertes en Biologie, Informatique et Mathématiques, Sep 2010, Montpellier, France
Communication dans un congrès
hal-02752226
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Bactéries pathogènes des poissons du genre Flavobacterium2. Journées de la Recherche Filière Piscicole, Jul 2009, Paris, France. 1 p
Communication dans un congrès
hal-02823179
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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
Communication dans un congrès
hal-02824485
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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
Communication dans un congrès
hal-02754400
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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
Communication dans un congrès
hal-02816850
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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
Communication dans un congrès
hal-02828495
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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
Communication dans un congrès
hal-02759825
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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
Poster de conférence
hal-04666797
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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.
Poster de conférence
hal-04633572
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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
Poster de conférence
hal-04232466
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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.
Poster de conférence
hal-04176537
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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
Poster de conférence
hal-04232454
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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.
Poster de conférence
hal-04359643
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Plateforme bioinformatique MIGALEJournées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2022, Rennes, France. 2022
Poster de conférence
hal-04176761
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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
Poster de conférence
hal-03694214
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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
Poster de conférence
hal-04199757
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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
Poster de conférence
hal-04176740
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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.
Poster de conférence
hal-04359920
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Plateforme bioinformatique MIGALEJournées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2021, Paris, France. 2021
Poster de conférence
hal-04176768
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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
Poster de conférence
hal-04285893
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Plateforme bioinformatique MIGALEJournées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jun 2020, Montpellier, France. 2020
Poster de conférence
hal-04176782
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Florilege, a database gathering microbial habitats, phenotypes and usesJOBIM 2020, Jun 2020, Montpellier, France
Poster de conférence
hal-02904156
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Testing markers to characterize microbial communities in food ecosystems using a metagenomics approachJOBIM, Jun 2020, Montpellier, France
Poster de conférence
hal-02914960
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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.
Poster de conférence
hal-04493150
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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
Poster de conférence
hal-02902758
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Shallow sequencing: a cost-effective and accurate alternative to WGS for taxonomic profiling ?JOBIM, Jun 2020, Montpellier, France.
Poster de conférence
hal-03451271
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Metagenomic analysis of an african beer ecosystem using Food Microbiome Transfert applicationjobim 2019, Jul 2019, Nantes, France. 2019
Poster de conférence
hal-02789073
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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
Poster de conférence
hal-02735859
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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.
Poster de conférence
hal-04360160
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FLORILEGE: an integrative database using text mining and ontologiesJOBIM 2018, Jul 2018, Marseille, France. , 2018, ABSTRACTS JOBIM 2018
Poster de conférence
hal-01827946
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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
Poster de conférence
hal-02736501
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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
Poster de conférence
hal-02786728
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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
Poster de conférence
hal-02737257
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MetaFoldScan: a pipeline to scan metagenomes and identify structural homologs using HMMJOBIM 2018, Jul 2018, Marseille, France. , 2018, ABSTRACTS JOBIM 2018
Poster de conférence
hal-01827944
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The journey of a team of engineers in learning packaging technologyJobim (Journées Ouvertes Biologie Informatique Mathématiques), Jul 2018, Marseille, France. , 2018, JOBIM 2018
Poster de conférence
hal-02733639
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FoodMicrobiome transfert: Web based metagenomic analysisJOBIM 2018 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. , 2018
Poster de conférence
hal-02008726
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Florilege : a database gathering microbial phenotypes of food interest4th International Conference on Microbial Diversity 2017, Oct 2017, Bari, Italy. , 2017
Poster de conférence
hal-01651302
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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
Poster de conférence
hal-02786916
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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
Poster de conférence
hal-01730003
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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
Poster de conférence
hal-01512085
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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
Poster de conférence
hal-01512192
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Food Microbiome-Transfert a database to characterize cheese ecosystems.Journées Bioinformatique Inra, Mar 2016, Toulouse, France. , 2016
Poster de conférence
hal-02799027
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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⟩
Poster de conférence
hal-01209851
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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
Poster de conférence
hal-01170054
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The multiple-genomes browser of the IFB cloudJournées SUCCES 2015, Nov 2015, Paris, France. , pp.1, 2015
Poster de conférence
hal-02795851
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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
Poster de conférence
hal-02792306
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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
Poster de conférence
hal-01209657
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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
Poster de conférence
hal-01209656
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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
Poster de conférence
hal-01209584
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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
Poster de conférence
hal-01209705
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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
Poster de conférence
hal-01209535
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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
Poster de conférence
hal-01209501
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The probiotic[i] Propionibacterium freudenreichii[/i] surface proteomeEUPA 2013, Oct 2013, Saint-Malo, France. , 2013
Poster de conférence
hal-01209498
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IGO, Integration from Genomes to OrganismsJOBIM 2013, Jul 2013, Toulouse, France. , pp.246, 2013, JOBIM TOULOUSE 2013 - RÉSUMÉS COURTS (affiches)
Poster de conférence
hal-02746442
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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
Poster de conférence
hal-02748920
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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
Poster de conférence
hal-01209410
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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
Poster de conférence
hal-01209420
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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
Poster de conférence
hal-02751434
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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
Poster de conférence
hal-01454344
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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
Poster de conférence
hal-02757163
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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
Poster de conférence
hal-02758166
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Whole-genome sequence of the fish-pathogenic bacterium Flavobacterium psychrophilum2. FEMS Congress of European Microbiologists, Jul 2006, Madrid, Spain. 1 p., 2006
Poster de conférence
hal-02812810
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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⟩
Chapitre d'ouvrage
hal-03324650
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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⟩
Chapitre d'ouvrage
hal-02284981
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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
Chapitre d'ouvrage
hal-02812661
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Omnicrobe, an open-access database of microbial habitats and phenotypes using a comprehensive text mining and data fusion approach2022
Pré-publication, Document de travail
(preprint/prepublication)
hal-03828105
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MilkOligoCorpus annotation guidelinesINRAE. 2024
Rapport
hal-04830410
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