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Keywords

Propionibacterium freudenreichii Comparative genomics Génomique BACTERIA Intestin Genome Fromage COMPLETE GENOME GENOMIQUE Database Probiotique Cheese Bioinformatics Santé humaine Génome Bacteria Immunomodulation Genomics Produit laitier NGS
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Number of documents

147

Valentin Loux - reponsable de la plateforme bioinformatique MIGALE

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 : Staff Engineer inf Bioinformatics, INRAE Mig laboratory

 

CURSUS

2002: Master's degree in Bioinformatics (DESS),  Versailles Saint-Quentin University

 

Journal articles81 documents

  • Simon Poirier, Ngoc-Du Martin Luong, Valérie Anthoine, Sandrine Guillou, Jeanne-Marie Membré, et al.. 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. Data in Brief, Elsevier, 2020, 30, pp.105453. ⟨10.1016/j.dib.2020.105453⟩. ⟨hal-02960277⟩
  • Maxime Branger, Valentin Loux, Thierry Cochard, Maria Laura Boschiroli, Franck Biet, et al.. The complete genome sequence of Mycobacterium bovis Mb3601, a SB0120 spoligotype strain representative of a new clonal group. Infection, Genetics and Evolution, Elsevier, 2020, 82, 4 p. ⟨10.1016/j.meegid.2020.104309⟩. ⟨hal-02905303⟩
  • Julie Lao, Gérard Guédon, Thomas Lacroix, Florence Charron-Bourgoin, Virginie Libante, et al.. Abundance, Diversity and Role of ICEs and IMEs in the Adaptation of Streptococcus salivarius to the Environment. Genes, MDPI, 2020, ⟨10.3390/genes11090999⟩. ⟨hal-02922962⟩
  • Simon Poirier, Ngoc-Du Martin Luong, Valérie Anthoine, Sandrine Guillou, Jeanne-Marie Membré, et al.. 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. Data in Brief, Elsevier, 2020, 30, pp.1-8. ⟨10.1016/j.dib.2020.105453⟩. ⟨hal-02914971⟩
  • Simon Poirier, Ngoc-Du Martin Luong, Valérie Anthoine, Sandrine Guillou, Jeanne-Marie Membré, et al.. 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. Data in Brief, Elsevier, 2020, 30, pp.105453. ⟨10.1016/j.dib.2020.105453⟩. ⟨hal-02961786⟩
  • Jeffrey Cornuault, Elisabeth Moncaut, Valentin Loux, Aurélie Mathieu, Harry Sokol, et al.. The enemy from within: a prophage of Roseburia intestinalis systematically turns lytic in the mouse gut, driving bacterial adaptation by CRISPR spacer acquisition. ISME Journal, Nature Publishing Group, 2020, 14 (3), pp.771-787. ⟨10.1038/s41396-019-0566-x⟩. ⟨hal-02504597⟩
  • Yves Vandenbrouck, David Christiany, Florence Combes, Valentin Loux, Virginie Brun. Bioinformatics tools and workflow to select blood biomarkers for early cancer diagnosis: an application to pancreatic cancer. Proteomics, Wiley-VCH Verlag, 2019, 19 (21-22), pp.e1800489. ⟨10.1002/pmic.201800489⟩. ⟨hal-02296155⟩
  • Tiago P. Delforno, Thais Z. Macedo, Cedric Midoux, Gileno V. Lacerda, Olivier Rué, et al.. Comparative metatranscriptomic analysis of anaerobic digesters treating anionic surfactant contaminated wastewater. Science of the Total Environment, Elsevier, 2019, 2019 (649), pp.482-494. ⟨10.1016/j.scitotenv.2018.08.328⟩. ⟨hal-01888286⟩
  • Eric Dugat-Bony, Pascal Bonnarme, Sébastien Fraud, Jessie Catellote, Anne-Sophie Sarthou, et al.. Effect of sodium chloride reduction or partial substitution with potassium chloride on the microbiological, biochemical and sensory characteristics of semi-hard and soft cheeses. Food Research International, 2019, 125, pp.108643. ⟨10.1016/j.foodres.2019.108643⟩. ⟨hal-02349939⟩
  • Reine Malek, Pascal Bonnarme, Francoise Irlinger, Pascale Frey-Klett, Djamila Onesime, et al.. Transcriptomic response of Debaryomyces hansenii during mixed culture in a liquid model cheese medium with Yarrowia lipolytica. International Journal of Food Microbiology, Elsevier, 2018, 264, pp.53-62. ⟨10.1016/j.ijfoodmicro.2017.10.026⟩. ⟨hal-01695894⟩
  • Valentin Loux, Gwendoline Coeuret, Monique Zagorec, Marie-Christine Champomier-Verges, Stephane Chaillou. Complete and Draft Genome Sequences of Nine Lactobacillus sakei Strains Selected from the Three Known Phylogenetic Lineages and Their Main Clonal Complexes. Genome Announcements, American Society for Microbiology, 2018, 6 (16), 3 p. ⟨10.1128/genomeA.00082-18⟩. ⟨hal-02619093⟩
  • Simon Poirier, Olivier Rué, Raphaelle Peguilhan, Gwendoline Coeuret, Monique Zagorec, et al.. 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. PLoS ONE, Public Library of Science, 2018, 13 (9), ⟨10.1371/journal.pone.0204629⟩. ⟨hal-02621350⟩
  • Eric Duchaud, Tatiana Rochat, Christophe Habib, Paul Barbier, Valentin Loux, et al.. Genomic diversity and evolution of the fish pathogen flavobacterium psychrophilum. Frontiers in Microbiology, Frontiers Media, 2018, 9, pp.1-20. ⟨10.3389/fmicb.2018.00138⟩. ⟨hal-02629284⟩
  • Simon Poirier, Olivier Rué, Gwendoline Coeuret, Marie-Christine Champomier-Verges, Valentin Loux, et al.. Detection of an amplification bias associated to Leuconostocaceae family with a universal primer routinely used for monitoring microbial community structures within food products. BMC Research Notes, BioMed Central, 2018, 11 (1), pp.1-5. ⟨10.1186/s13104-018-3908-2⟩. ⟨hal-02048857⟩
  • Lucas Proust, Valentin Loux, Veronique Martin, Cristian Magnabosco, Martin Pedersen, et al.. Complete genome sequence of the industrial fast-acidifying strain Streptococcus thermophilus N4L. Microbiology Resource Announcements, American Society for Microbiology, 2018, 7 (8), ⟨10.1128/MRA.01029-18⟩. ⟨hal-02628963⟩
  • Thomas Lacroix, Jean-Francois Gibrat, Valentin Loux. La génomique comparative à l’ère des technologies NGS. Biofutur, Elsevier - Cachan : Lavoisier, 2017, 36 (382), pp.42-45. ⟨hal-01603170⟩
  • Eugene Christo-Foroux, Tatiana Vallaeys, Valentin Loux, Elie Dassa, Josef Deutscher, et al.. 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. Systematic and Applied Microbiology, Elsevier, 2017, 40 (7), pp.401-410. ⟨10.1016/j.syapm.2017.07.002⟩. ⟨hal-01604275⟩
  • Xavier Argemi, Veronique Martin, Valentin Loux, Sandrine Dahyot, Jérémie Lebeurre, et al.. Whole genome sequencing of 7 strains of Staphylococcus lugdunensis allows identification of mobile genetic elements. Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2017, 9 (5), pp.1183-1189. ⟨10.1093/gbe/evx077⟩. ⟨hal-01604276⟩
  • Tatiana Rochat, Paul Barbier, Pierre Nicolas, Valentin Loux, David Perez Pascual, et al.. Complete Genome Sequence of Flavobacteriumpsychrophilum Strain OSU THCO2-90, Used for Functional Genetic Analysis.. Genome Announcements, American Society for Microbiology, 2017, 5 (23), 2 p. ⟨10.1128/genomeA.01665-16⟩. ⟨hal-01607798⟩
  • Vincent J. Henry, Anne Goelzer, Arnaud Ferré, Stéphan Fischer, Marc Dinh, et al.. The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes. Journal of Biomedical Semantics, BioMed Central, 2017, 8 (53), 16 p. ⟨10.1186/s13326-017-0165-6⟩. ⟨hal-01652923⟩
  • Marie Helene Guinebretière, Valentin Loux, Véronique Martin, Pierre Nicolas, Vincent Sanchis Borja, et al.. Draft Genome Sequences of 18 Psychrotolerant and 2 Thermotolerant Strains Representative of Particular Ecotypes in the Bacillus cereus Group. Genome Announcements, American Society for Microbiology, 2017, 5 (5), 3 p. ⟨10.1128/genomeA.01568-16⟩. ⟨hal-01602632⟩
  • Hela El Kafsi, Valentin Loux, Mahendra Mariadassou, Camille Blin, Hélène Chiapello, et al.. Unprecedented large inverted repeats at the replication terminus of circular bacterial chromosomes suggest a novel mode of chromosome rescue. Scientific Reports, Nature Publishing Group, 2017, 7, pp.44331. ⟨10.1038/srep44331⟩. ⟨hal-01509688⟩
  • Stéphanie-Marie Deutsch, Mahendra Mariadassou, Pierre Nicolas, Sandrine Parayre, Rozenn Le Guellec, et al.. Identification of proteins involved in the anti-inflammatory properties of Propionibacterium freudenreichii by means of a multi-strain study. Scientific Reports, Nature Publishing Group, 2017, 7, pp.46409. ⟨10.1038/srep46409⟩. ⟨hal-01510019⟩
  • Charles Coluzzi, Gérard Guédon, Marie-Dominique Devignes, Chloé Ambroset, Valentin Loux, et al.. A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins. Frontiers in Microbiology, Frontiers Media, 2017, 8, pp.16. ⟨10.3389/fmicb.2017.00443⟩. ⟨hal-01580789⟩
  • Julie Meneghel, Eric Dugat-Bony, Françoise Irlinger, Valentin Loux, Marie Vidal, et al.. Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CFL1, a Lactic Acid Bacterium Isolated from French Handcrafted Fermented Milk. Genome Announcements, American Society for Microbiology, 2016, 4 (2), pp.e00052-16. ⟨10.1128/genomeA.00052-16⟩. ⟨hal-01511494⟩
  • Thomas Lacroix, Sylvie Thérond, Marc Rugeri, Pierre Nicolas, Annie Gendrault, et al.. Synchronized navigation and comparative analyses across Ensembl complete bacterial genomes with INSYGHT.. Bioinformatics, Oxford University Press (OUP), 2016, 32 (7), pp.1083-1084. ⟨10.1093/bioinformatics/btv689⟩. ⟨hal-02630699⟩
  • Hélène Falentin, Stéphanie-Marie Deutsch, Valentin Loux, Amal Hammani, Julien Buratti, et al.. Permanent draft genome sequence of the probiotic strain Propionibacterium freudenreichii CIRM-BIA 129 (ITG P20).. Standards in Genomic Sciences, BioMedCentral, 2016, 11, pp.6. ⟨10.1186/s40793-015-0120-z⟩. ⟨hal-02640172⟩
  • Maeva Guellerin, Delphine Passerini, Catherine Fontagné-Faucher, Hervé Robert, Valérie Gabriel, et al.. Complete Genome Sequence of Lactococcus lactissubsp. lactis A12, a Strain Isolated from Wheat Sourdough. Genome Announcements, American Society for Microbiology, 2016, 4 (5), pp.2 P. ⟨10.1128/genomeA.00692-16⟩. ⟨hal-01578250⟩
  • Thibaud Dugat, Marie-Noelle Rossignol, Olivier Rué, Valentin Loux, Sylvain Marthey, et al.. Draft Anaplasma phagocytophilum Genome Sequences from Five Cows, Two Horses, and One Roe Deer Collected in Europe.. Genome Announcements, American Society for Microbiology, 2016, 4 (6), 2 p. ⟨10.1128/genomeA.00950-16⟩. ⟨hal-01594527⟩
  • Eric Dugat-Bony, Anne-Sophie Sarthou, Valentin Loux, Marie Vidal, Pascal Bonnarme, et al.. Draft genome sequence of Corynebacterium variabile Mu292, isolated from Munster, a french smear-ripened cheese. Genome Announcements, American Society for Microbiology, 2016, 4 (4), ⟨10.1128/genomeA.00669-16⟩. ⟨hal-01480898⟩
  • Chloé Ambroset, Charles Coluzzi, Gérard Guédon, Marie-Dominique Devignes, Valentin Loux, et al.. New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration. Frontiers in Microbiology, Frontiers Media, 2016, 6 (6), pp.1483. ⟨10.3389/fmicb.2015.01483⟩. ⟨hal-01262284⟩
  • Caroline Le Maréchal, Vincent Péton, Coline Plé, Christophe Vroland, Julien Jardin, et al.. Surface proteins of Propionibacterium freudenreichii are involved in its anti-inflammatory properties.. Journal of Proteomics, Elsevier, 2015, 113, pp.447-461. ⟨10.1016/j.jprot.2014.07.018⟩. ⟨hal-01209735⟩
  • Delphine Passerini, Marlène Vuillemin, Lisa Ufarté, Sandrine Morel, Valentin Loux, et al.. Inventory of the GH70 enzymes encoded by Leuconostoc citreum NRRL B-1299 - identification of three novel -transglucosylases. FEBS Journal, Wiley, 2015, 282 (11), pp.2115-2130. ⟨10.1111/febs.13261⟩. ⟨hal-02630462⟩
  • Eric Dugat-Bony, Cecile Straub, Aurélie Teissandier, Djamila Onesime, Valentin Loux, et al.. Overview of a surface-ripened cheese community functioning by meta-omics analyses. PLoS ONE, Public Library of Science, 2015, 10 (4), pp.e0124360. ⟨10.1371/journal.pone.0124360⟩. ⟨hal-01195505⟩
  • Valentin Loux, Mahendra Mariadassou, Sintia Almeida, Hélène Chiapello, Amal Hammani, et al.. Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii. BMC Genomics, BioMed Central, 2015, 16 (1), pp.35. ⟨10.1186/s12864-015-1467-7⟩. ⟨hal-01142363⟩
  • Florent Kempf, Valentin Loux, Pierre Germon. Genome Sequences of Two Bovine Mastitis-Causing [i]Escherichia coli[/i] Strains. Genome Announcements, American Society for Microbiology, 2015, 3 (2), pp.1. ⟨10.1128/genomeA.00259-15⟩. ⟨hal-01171499⟩
  • Caroline Le Maréchal, Vincent Péton, Coline Le Plenier, Christophe Vroland, Julien Jardin, et al.. Data from an integrative approach decipher the surface proteome of [i]Propionibacterium freudenreichii[/i]. Data in Brief, Elsevier, 2014, 1, pp.46-50. ⟨10.1016/j.dib.2014.08.009⟩. ⟨hal-01209746⟩
  • Thomas Lacroix, Valentin Loux, Annie Gendrault, Mark Hoebeke, Jean-François Gibrat. Insyght: navigating amongst abundant homologues, syntenies and gene functional annotations in bacteria, it's that symbol!. Nucleic Acids Research, Oxford University Press, 2014, 42 (21), pp.e162. ⟨10.1093/nar/gku867⟩. ⟨hal-01332638⟩
  • Delphine Passerini, Marlène Vuillemin, S. Laguerre, Myriam Amarir, Valentin Loux, et al.. Complete Genome Sequence of Leuconostoc citreum Strain NRRL B-742.. Genome Announcements, American Society for Microbiology, 2014, 2 (6), ⟨10.1128/genomeA.01179-14⟩. ⟨hal-02637077⟩
  • Aurore Vermassen, Anne de la Foye, Valentin Loux, Régine Talon, Sabine Leroy. Transcriptomic analysis of Staphylococcus xylosus in the presence of nitrate and nitrite in meat reveals its response to nitrosative stress. Frontiers in Microbiology, Frontiers Media, 2014, 5, n.p. ⟨10.3389/fmicb.2014.00691⟩. ⟨hal-02631923⟩
  • Hela El Kafsi, Johan Binesse, Valentin Loux, Julien Buratti, Samira Boudebbouze, et al.. Genome sequence of[i] Lactobacillus delbrueckii[/i] subsp. [i]lactis[/i] CNRZ327, a dairy bacterium with anti-inflammatory properties.. Genome Announcements, American Society for Microbiology, 2014, 2 (4), pp.1-2. ⟨10.1128/genomeA.00328-14⟩. ⟨hal-01204323⟩
  • Alexandre Bolotine, Tomas de Wouters, Pamela Schnupf, Christiane Bouchier, Valentin Loux, et al.. Genome Sequence of "Candidatus Arthromitus" sp. Strain SFB-Mouse-NL, a Commensal Bacterium with a Key Role in Postnatal Maturation of Gut Immune Functions.. Genome Announcements, American Society for Microbiology, 2014, 2 (4), ⟨10.1128/genomeA.00705-14⟩. ⟨hal-01204391⟩
  • Hélène Falentin, Delphine Naquin, Valentin Loux, Frédérique Barloy-Hubler, Pascal Loubière, et al.. Genome Sequence of Lactococcus lactis subsp. lactis bv. diacetylactis LD61.. Genome Announcements, American Society for Microbiology, 2014, 2 (1), pp.1. ⟨10.1128/genomeA.01176-13⟩. ⟨hal-01019560⟩
  • Catherine Juste, David P Kreil, Christian Beauvallet, Alain Guillot, Sebastian Vaca, et al.. Bacterial protein signals are associated with Crohn's disease.. Gut, BMJ Publishing Group, 2014, 63 (10), pp.1566-1577. ⟨10.1136/gutjnl-2012-303786⟩. ⟨hal-00933734⟩
  • Hela El Kafsi, Johan Binesse, Valentin Loux, Julien Buratti, Samira Boudebbouze, et al.. Lactobacillus delbrueckii ssp. lactis and ssp. bulgaricus: a chronicle of evolution in action.. BMC Genomics, BioMed Central, 2014, 15 (1), pp.407. ⟨10.1186/1471-2164-15-407⟩. ⟨pasteur-01017376⟩
  • Thibaud Dugat, Valentin Loux, Sylvain Marthey, Marco Moroldo, Anne-Claire Lagree, et al.. Comparative genomics of first available bovine Anaplasma phagocytophilum genome obtained with targeted sequence capture.. BMC Genomics, BioMed Central, 2014, 15 (1), pp.973. ⟨10.1186/1471-2164-15-973⟩. ⟨hal-01193998⟩
  • Hélène Velly, Pierre Renault, Anne-Laure Abraham, Valentin Loux, Agnes Delacroix-Buchet, et al.. Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis subsp. lactis TOMSC161, Isolated from a Nonscalded Curd Pressed Cheese. Genome Announcements, American Society for Microbiology, 2014, 2 (6), ⟨10.1128/genomeA.01121-14⟩. ⟨hal-01193999⟩
  • Mathieu Almeida, Agnes Hebert, Anne-Laure Abraham, Simon Rasmussen, Christophe Monnet, et al.. Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products. BMC Genomics, BioMed Central, 2014, 15, article 1101 (16 p.). ⟨10.1186/1471-2164-15-1101⟩. ⟨hal-01195502⟩
  • Noémie Pascault, Valentin Loux, Sandra Derozier, Véronique Martin, Didier Debroas, et al.. Technical challenges in metatranscriptomic studies applied to the bacterial communities of freshwater ecosystems. Genetica, Springer Verlag, 2014, 143 (2), pp.25216965. ⟨10.1007/s10709-014-9783-4⟩. ⟨hal-01110172⟩
  • Taous Saraoui, Sandrine Parayre, Grégory Guernec, Valentin Loux, Jérôme Montfort, et al.. A unique in vivo experimental approach reveals metabolic adaptation of the probiotic Propionibacterium freudenreichii to the colon environment.. BMC Genomics, BioMed Central, 2013, 14 (1), pp.911. ⟨10.1186/1471-2164-14-911⟩. ⟨inserm-00923652⟩
  • Hélène Falentin, Sylvie Cousin, Dominique Clermont, Sophie Creno, Florence Ma, et al.. 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. Genome Announcements, American Society for Microbiology, 2013, 1 (4), pp.e00658-13. ⟨10.1128/genomeA.00658-13⟩. ⟨hal-01209470⟩
  • Sylvie Cousin, Valentin Loux, Laurence Ma, Sophie Creno, Dominique Clermont, et al.. Draft genome sequences of Lactobacillus equicursoris CIP 110162τ and Lactobacillus sp. strain CRBIP 24.137, isolated from thoroughbred racehorse feces and human urine, respectively. Genome Announcements, American Society for Microbiology, 2013, 1 (4), pp.1-2. ⟨10.1128/genomeA.00663-13⟩. ⟨hal-02645656⟩
  • Sylvie Cousin, Sophie Creno, Laurence Ma, Dominique Clermont, Valentin Loux, et al.. Draft genome sequence of Lactobacillus hominis strain CRBIP 24.179τ, isolated from human intestine. Genome Announcements, American Society for Microbiology, 2013, 1 (4), pp.1. ⟨10.1128/genomeA.00662-13⟩. ⟨hal-00939673⟩
  • Catherine Cailliez-Grimal, Stephane Chaillou, Jamila Anba-Mondoloni, Valentin Loux, Muhammad Inam Afzal, et al.. Complete chromosome sequence of Carnobacterium maltaromaticum LMA 28.. Genome Announcements, American Society for Microbiology, 2013, 1 (1), pp.1-2. ⟨10.1128/genomeA.00115-12⟩. ⟨hal-00939584⟩
  • Sylvie Cousin, Dominique Clermont, Sophie Creno, Laurence Ma, Valentin Loux, et al.. Draft Genome Sequence of [i][/i] Lactobacillus pasteurii[i][/i] CRBIP 24.76T.. Genome Announcements, American Society for Microbiology, 2013, 1 (4), ⟨10.1128/genomeA.00660-13⟩. ⟨hal-01190531⟩
  • Christophe Monnet, Valentin Loux, Pascal Bento, Jean-Francois Gibrat, Cecile Straub, et al.. Genome sequence of corynebacterium casei UCMA 3821, isolated from a smear-ripened cheese. Journal of Bacteriology, American Society for Microbiology, 2012, 194 (3), pp.738-739. ⟨10.1128/JB.06496-11⟩. ⟨hal-01000221⟩
  • Sandrine Laguerre, Myriam Amari, Marlène Vuillemin, Hervé Robert, Valentin Loux, et al.. Genome sequences of three Leuconostoc Citreum Strains, LBAE C10, LBAE C11, and LBAE E16, isolated from wheat sourdoughs. Journal of Bacteriology, American Society for Microbiology, 2012, 194 (6), pp.1610-1611. ⟨hal-01267778⟩
  • Myriam Amari, Sandrine Laguerre, Marlène Vuillemin, Hervé Robert, Valentin Loux, et al.. Genome sequence of weissella confusa LBAE C39-2, isolated from a wheat sourdough. Journal of Bacteriology, American Society for Microbiology, 2012, 194 (6), pp.1608-1609. ⟨10.1128/JB.06788-11⟩. ⟨hal-01267779⟩
  • Olivier Grépinet, Zineb Boumart, Isabelle Virlogeux-Payant, Valentin Loux, Hélène Chiapello, et al.. Genome sequence of the persistent Salmonella enterica subsp enterica Serotype Senftenberg Strain SS209. Journal of Bacteriology, American Society for Microbiology, 2012, 194 (9), pp.2385-2386. ⟨hal-02643377⟩
  • Victoria Meslier, Valentin Loux, Pierre Renault. Genome sequence of Leuconostoc pseudomesenteroides strain 4882, isolated from a dairy starter culture. Journal of Bacteriology, American Society for Microbiology, 2012, 194 (23), pp.6637. ⟨10.1128/JB.01696-12⟩. ⟨hal-01000375⟩
  • Paul Barbier, Armel Houel, Valentin Loux, Julie Poulain, Jean Francois Bernardet, et al.. Complete genome sequence of Flavobacterium indicum GPSTA100-9T, isolated from warm spring water. African Journal of Biotechnology, Academic Journals, 2012, 194 (11), pp.3024-3025. ⟨10.1128/JB.00420-12⟩. ⟨hal-02643519⟩
  • Victoria Meslier, Valentin Loux, Pierre Renault. Genome sequence of Lactococcus raffinolactis strain 4877, isolated from natural dairy starter culture. Journal of Bacteriology, American Society for Microbiology, 2012, 194 (22), pp.6364. ⟨hal-01000376⟩
  • Marion Dalmasso, Julie Aubert, Sergine Even, Hélène Falentin, Marie-Bernadette Maillard, et al.. Accumulation of intracellular glycogen and trehalose by [i]Propionibacterium Freudenreichii[/i] under conditions mimicking cheese ripening in the cold. Applied and Environmental Microbiology, American Society for Microbiology, 2012, 78 (17), pp.6357-6364. ⟨10.1128/AEM.00561-12⟩. ⟨hal-01191223⟩
  • Marion Dalmasso, Julie Aubert, Sergine Even, Hélène Falentin, Marie-Bernadette Maillard, et al.. Accumulation of Intracellular Glycogen and Trehalose by Propionibacterium freudenreichii under Conditions Mimicking Cheese Ripening in the Cold. Applied and Environmental Microbiology, American Society for Microbiology, 2012, 78 (17), pp.6357-6364. ⟨10.1128/AEM.00561-12⟩. ⟨hal-02363390⟩
  • Sophie Schbath, Veronique Martin, Matthias Zytnicki, Julien Fayolle, Valentin Loux, et al.. Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis. Journal of Computational Biology, Mary Ann Liebert, 2012, 19 (6), pp.796-813. ⟨10.1089/cmb.2012.0022⟩. ⟨hal-02645697⟩
  • Francoise Irlinger, Valentin Loux, Pascal Bento, Jean-Francois Gibrat, Cecile Straub, et al.. Genome sequence of Staphylococcus equorum subsp equorum Mu2, Isolated from a french smear-ripened cheese. Journal of Bacteriology, American Society for Microbiology, 2012, 194 (18), pp.5141-5142. ⟨10.1128/JB.01038-12⟩. ⟨hal-01019837⟩
  • Thomas Lacroix, Valentin Loux, Annie Gendrault, Jean-François Gibrat, Hélène Chiapello. CompaGB: An open framework for genome browsers comparison. BMC Research Notes, BioMed Central, 2011, 4, pp.133. ⟨10.1186/1756-0500-4-133⟩. ⟨hal-02644023⟩
  • Christine Delorme, Eric Guédon, Nicolas Pons, Corinne Cruaud, Arnaud Couloux, et al.. Complete genome sequence of the clinical Streptococcus salivarius strain CCHSS3. Journal of Bacteriology, American Society for Microbiology, 2011, 193 (18), pp.5041-5042. ⟨10.1128/JB.05416-11⟩. ⟨hal-01000176⟩
  • Christine Delorme, Claire Bartholini, Mélanie Luraschi, Nicolas Pons, Valentin Loux, et al.. Complete genome sequence of the pigmented Streptococcus thermophilus strain JIM8232. Journal of Bacteriology, American Society for Microbiology, 2011, 193 (19), pp.5581-5582. ⟨10.1128/JB.05404-11⟩. ⟨hal-01000180⟩
  • Eric Guedon, Christine Delorme, Nicolas Pons, Corinne Cruaud, Valentin Loux, et al.. Complete genome sequence of the commensal Streptococcus salivarius strain JIM8777. Journal of Bacteriology, American Society for Microbiology, 2011, 193 (18), pp.5024-5025. ⟨10.1128/JB.05390-11⟩. ⟨hal-01019305⟩
  • Agnes Hebert, Marie-Pierre Forquin-Gomez, Aurélie Roux, Julie Aubert, Christophe Junot, et al.. Exploration of sulfur metabolism in the yeast Kluyveromyces lactis. Applied Microbiology and Biotechnology, Springer Verlag, 2011, 91 (5), pp.1409-1423. ⟨10.1007/s00253-011-3481-2⟩. ⟨hal-01000029⟩
  • Christophe Monnet, Valentin Loux, Jean-Francois Gibrat, Valérie Barbe, Benoit Vacherie, et al.. The arthrobacter arilaitensis Re117 genome sequence reveals its genetic adaptation to the surface of cheese. PLoS ONE, Public Library of Science, 2010, 5 (11), pp.e15489. ⟨10.1371/journal.pone.0015489⟩. ⟨hal-01195440⟩
  • Hélène Falentin, Stéphanie-Marie Deutsch, Gwénaël Jan¨, Valentin Loux, Anne Thierry, et al.. The complete genome of Propionibacterium freudenreichii CIRM-BIA1T, a Hardy actinobacterium with food and probiotic applications. PLoS ONE, Public Library of Science, 2010, 5 (7), pp.1-12. ⟨10.1371/journal.pone.0011748⟩. ⟨hal-01204238⟩
  • Jasna Beganovic, Alain Guillot, Maarten van de Guchte, Anne Jouan, Christophe Gitton, et al.. 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. Journal of Proteome Research, American Chemical Society, 2010, 9 (2), pp.677-688. ⟨hal-02657656⟩
  • Alain Mazé, Grégory Boël, Manuel Zùniga, Alexa Bourand, Valentin Loux, et al.. Complete genome sequence of the probiotic Lactobacillus casei strain BL23. Journal of Bacteriology, American Society for Microbiology, 2010, 192 (10), pp.2647-2648. ⟨10.1128/JB.00076-10⟩. ⟨hal-01204245⟩
  • Marie-Pierre Forquin, Hugo Duvergey, Caroline Proux, Valentin Loux, Jérôme Mounier, et al.. Identification of brevibacteriaceae by multilocus sequence typing and comparative genomic hybridization analyses.. Applied and Environmental Microbiology, American Society for Microbiology, 2009, 75 (19), pp.6406-9. ⟨10.1128/AEM.00224-09⟩. ⟨hal-00557018⟩
  • Aleksandr Barinov, Valentin Loux, Amal Hammani, Pierre Nicolas, Philippe Langella, et al.. Prediction of surface exposed proteins in Streptococcus pyogenes, with a potential application to other Gram-positive bacteria. Proteomics, Wiley-VCH Verlag, 2009, 9 (1), pp.61-73. ⟨10.1002/pmic.200800195⟩. ⟨hal-02663676⟩
  • Eric Duchaud, Mekki Boussaha, Valentin Loux, Jean Francois Bernardet, Christian Michel, et al.. Complete genome sequence of the fish pathogen Flavobacterium psychrophilum. Nature Biotechnology, Nature Publishing Group, 2007, 25 (7), pp.763 - 769. ⟨10.1038/nbt1313⟩. ⟨hal-02666599⟩
  • K. Bryson, Valentin Loux, Robert Bossy, P. Nicolas, Stephane Chaillou, et al.. AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. Nucleic Acids Research, Oxford University Press, 2006, 34 (12), pp.3533-3545. ⟨10.1093/nar/gkl471⟩. ⟨hal-02665192⟩
  • Maarten van de Guchte, Stéphanie Penaud, Christine Grimaldi, Valérie Barbe, K. Bryson, et al.. The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution. Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 2006, 103 (24), pp.9274-9279. ⟨10.1073/pnas.0603024103⟩. ⟨hal-02668654⟩
  • Stephane Chaillou, Marie-Christine Champomier Verges, Monique Cornet, Anne-Marie Crutz-Le Coq, Anne-Marie Dudez, et al.. The complete genome sequence of the meat-borne lactic acid bacterium Lactobacillus sakei 23K. Nature Biotechnology, Nature Publishing Group, 2005, 23 (12), pp.1527-1533. ⟨10.1038/nbt1160⟩. ⟨hal-02683108⟩

Conference papers26 documents

  • Sandra Derozier, Sam Ah-Lone, Valentin Loux, Hélène Chiapello. A workflow to build a relevant and reduced bacterial dataset from NCBI. JOBIM : Journées Ouvertes Biologie Informatique Mathématiques, Jul 2019, Nantes, France. ⟨hal-02733948⟩
  • Olivier Rué, Simon Poirier, Raphaelle Peguilhan, Valentin Loux, Marie-Christine Champomier-Vergès, et al.. Evaluation of gyrB amplicon sequencing in comparison to 16S rDNA amplicon sequencing to evaluate intra-species bacterial diversity in food microbiota. JOBIM 20. Journées Ouvertes Biologie Informatique Mathématiques, Jul 2019, Nantes, France. ⟨hal-02947091⟩
  • Julie Cremaschi, Olivier Rué, Florence Deau, Philippe Lemanceau, Valentin Loux, et al.. Shotgun metagenomics sequencing of the rhizosphere microbiota associated to seven ecotypes of Medicago truncatula. Rhizosphere 5, Jul 2019, Saskatoon, Saskatchewan, Canada. ⟨hal-02735116⟩
  • Sophie Schbath, Valentin Loux. Des microbes dans mon fromage ?. Journées Nationales de la Science Ouverte, Dec 2018, Paris, France. ⟨hal-01954713⟩
  • Claire Nédellec, Estelle Chaix, Robert Bossy, Louise Deleger, Sandra Derozier, et al.. L'ontologie OntoBiotope pour l'étude de la biodiversité microbienne. EGC'2018: 18èmes Conférence Internationale sur l'Extraction et la Gestion des Connaissances, Jan 2018, Paris, France. ⟨hal-02737399⟩
  • Anne-Laure Abraham, Quentin Cavaillé, Thibaut Guirimand, Pierre Renault, Sandra Derozier, et al.. A metagenomic tool for cheese ecosystems. 17. European Conference on Computational Biology (ECCB 2018, Workshop "Recent Computational Advances in Metagenomics (RCAM)", Sep 2018, Athenes, Greece. ⟨hal-02789036⟩
  • Anne-Laure Abraham, Quentin Cavaillé, Thibaut Guirimand, Sandra Derozier, Valentin Loux, et al.. FoodMicrobiome transfert: Web based metagenomic analysis. JOBIM 2018 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. ⟨hal-02008726⟩
  • Laure Quintric, Patrick Durand, Olivier Inizan, Valentin Marcon, Caroline Dussart, et al.. The journey of a team of engineers in learning packaging technology. Galaxy Community Conference - GCC2018, Jun 2018, Portland, United States. ⟨hal-02784992⟩
  • Anne-Laure Abraham, Thibaut Guirimand, Charlie Pauvert, Sandra Derozier, Mahendra Mariadassou, et al.. Food-Microbiomes Transfert, a shotgun metagenomic tool and a database to analyze cheese ecosystems. JOBIM 2017 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2017, Lille, France. ⟨hal-02788899⟩
  • Hélène Falentin, Estelle Chaix, Bedis Dridi, Philippe Bessieres, S Buchin, et al.. Florilège: a database gathering microbial phenotypes of food interest. 2017 Scientific MEM days: Journées scientifiques MEM (Métaomiques et écosystèmes microbiens), Jan 2017, Paris, France. ⟨hal-01607327⟩
  • Vincent Henry, Arnaud Ferré, Christine Froidevaux, Anne Goelzer, Vincent Fromion, et al.. Représentation systémique multi-échelle des processus biologiques de la bactérie. IC2016 - Ingénierie des Connaissances, Jun 2016, Montpellier, France. ⟨hal-01442727⟩
  • Vincent Henry, Arnaud Ferré, Christine Froidevaux, Anne Goelzer, Vincent Fromion, et al.. Représentation systémique multi-échelle des processus biologiques de la bactérie. IC201: 27es Journées francophones d'Ingénierie des Connaissances, Jun 2016, Montpellier, France. ⟨hal-02741418⟩
  • Sophie Schbath, Veronique Martin, Matthias Zytnicki, Julien Fayolle, Valentin Loux, et al.. Mapping reads on a genomic sequence: a practical comparative analysis. Kick-of meeting of PF7 RADIANT project, Jan 2013, Manchester, United Kingdom. 19 diapos. ⟨hal-02804577⟩
  • Aurore Rossignol, Sylvie Roche, Isabelle Virlogeux-Payant, Olivier Grépinet, Nadia Abed, et al.. Deciphering why Salmonella Gallinarum is less invasive in vitro than Salmonella Enteritidis. I3S International Symposium Salmonella and Salmonellosis, Institut National de la Recherche Agronomique (INRA). FRA., May 2013, Saint Malo, France. ⟨hal-02749048⟩
  • Eric Duchaud, Paul Barbier, Jean Francois Bernardet, Christian Michel, Céline Chantry-Darmon, et al.. Genomic diversity of Flavobacterium species.. Flavobacterium 2012, 2012, Turku, Finland. ⟨hal-02746549⟩
  • Sophie Schbath, Veronique Martin, Matthias Zytnicki, Julien Fayolle, Valentin Loux, et al.. Mapping reads on a genomic sequence: a practical comparative analysis. Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), Jul 2012, Rennes, France. pp.496. ⟨hal-02748738⟩
  • Hélène Falentin, Valentin Loux, Valérie Barbe, Amal Plaudet Hammani, Stéphanie-Marie Deutsch, et al.. Genomic diversity of 24 Propionibacterium freudenreichii 1 strains. 6 Conference on Functional Genomics of Gram-positive Microorganisms 16 International Conference on Bacilli, Jun 2011, Montecatini, Italy. ⟨hal-01454328⟩
  • Benoît Foligné, Valentin Loux, Christophe Hervé, Jean-René Kerjean, Denis Matter, et al.. SURFING: A national project to understand immunomodulatury effects of dairy starters. 2nd International Symposium "Microbes For Health", Dec 2011, Paris, France. ⟨hal-01190437⟩
  • Thomas Lacroix, Valentin Loux, Annie Gendrault, Jean-François Gibrat, Helene Chiapello. Evaluating Genome Browsers Using a Software Qualification Method Evaluation. JOBIM 2010, Sep 2010, Montpellier, France. pp.196. ⟨hal-02751310⟩
  • Célia Michotey, Ludovic Legrand, Helene Chiapello, Valentin Loux, Annie Gendrault-Jacquemard, et al.. Web services for microbial genome annotation using data integration. JOBIM 2010 : Journées Ouvertes en Biologie, Informatique et Mathématiques, Sep 2010, Montpellier, France. ⟨hal-02752226⟩
  • Eric Duchaud, Jean Francois Bernardet, Brigitte Kerouault, Christian Michel, Céline Chantry, et al.. Bactéries pathogènes des poissons du genre Flavobacterium. 2. Journées de la Recherche Filière Piscicole, Jul 2009, Paris, France. 1 p. ⟨hal-02823179⟩
  • Thomas Lacroix, Valentin Loux, Annie Gendrault, Mark Hoebeke, Jean-François Gibrat. INSYGT : a multi-genes multi-genomes browser that highlights synteny conservation in prokaryotes.. JOBIM 2008, Jun 2008, Lille, France. 2 p. ⟨hal-02824485⟩
  • Jérôme Azé, L. Gentils, Claire Toffano-Nioche, Valentin Loux, Jean-François Gibrat, et al.. Towards a semi-automatic functional annotation tool based on decision tree techniques. Machine Learning in Systems Biology: MLSB 2007, Sep 2007, Evry, France. ⟨hal-02754400⟩
  • Stephane Chaillou, Monique Cornet, Anne-Marie Le Coq, Anne-Marie Loustau, Robert Bossy, et al.. La séquence complète du génome de la bactérie de la viande Lactobacillus sakei. Symposium SFM, Interactions Bactériennes dans les Environnements Agroalimentaires : Apport des Nouvelles Approches., Société Française de Microbiologie (SFM). FRA., Nov 2006, Paris, France. ⟨hal-02816850⟩
  • Stephane Chaillou, Monique Cornet, Anne-Marie Le Coq, Anne-Marie Loustau, Robert Bossy, et al.. 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. 2. European Conference on Prokaryotic Genomes, Oct 2005, Göttingen, Germany. ⟨hal-02828495⟩
  • Stephane Chaillou, Monique Cornet, Anne-Marie Loustau, Robert Bossy, Valentin Loux, et al.. Premiers regards sur le génome d’une bactérie lactique originale : structure, polymorphisme et analyse génétique ciblée du chromosome de Lactobacillus sakei 23K. 13. Colloque du Club des Bactéries Lactiques, Sep 2004, Nantes, France. 142 p. ⟨hal-02759825⟩

Poster communications36 documents

  • Sandra Derozier, Louise Deleger, Estelle Chaix, Reda Mekdad, Mouhamadou Ba, et al.. Florilege, a database gathering microbial habitats, phenotypes and uses. JOBIM 2020, Jun 2020, Montpellier, France. ⟨hal-02904156⟩
  • Cedric Midoux, Franciele Camargo, Olivier Rué, Mahendra Mariadassou, Valentin Loux, et al.. A shotgun metagenomics analysis applied to the ecological engineering of anaerobic microbial communities for the production of hydrogen from Citrus Peel Waste. JOBIM, Jun 2020, Montpellier, France. ⟨hal-02902758⟩
  • Claire Vincent, Serge Casaregola, Monika Coton, Céline Delbes, Hugo Devillers, et al.. Testing markers to characterize microbial communities in food ecosystems using a metagenomics approach. JOBIM, Jun 2020, Montpellier, France. ⟨hal-02914960⟩
  • Cedric Midoux, Tiago P. Delforno, Thais Z. Macedo, Gileno V. Lacerda, Olivier Rué, et al.. Feedback on a c omparative metatranscriptomic analysis. JOBIM 2019 : Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. 2019, JOBIM 2019. ⟨hal-02735859⟩
  • Estelle Chaix, Sandra Derozier, Louise Deleger, Hélène Falentin, Jean-Baptiste Bohuon, et al.. FLORILEGE: an integrative database using text mining and ontologies. JOBIM 2018, Jul 2018, Marseille, France. 2018, ABSTRACTS JOBIM 2018. ⟨hal-01827946⟩
  • Thomas Lacroix, Valentin Loux, Jonathan Lorenzo, Bryan Brancotte, Christophe Blanchet, et al.. Insyght : Analyse evolutionary conserved CDS, orthologs, syntenies, pan-genome, fusion, etc., for your bacteria of interest​. Annual Research in Computational Molecular Biology (RECOMB), Apr 2018, Paris, France. 2018. ⟨hal-02736501⟩
  • Sandra Derozier, Veronique Martin, Jean-Marc Chatel, Nalini Rama Rao, Valentin Loux, et al.. MetaFoldScan: a pipeline to scan metagenomes and identify structural homologs using HMM. JOBIM 2018, Jul 2018, Marseille, France. 2018, ABSTRACTS JOBIM 2018. ⟨hal-01827944⟩
  • Simon Poirier, Raphaelle Peguilhan, Olivier Rué, Valentin Loux, Marie-Christine Champomier-Verges, et al.. Evaluation of gyrB amplicon sequencing in comparison to 16S rDNA amplicon sequencing to evaluate intra-species bacterial diversity in food microbiotaImproving. Food Micro 2018, Sep 2018, Berlin, Germany. 2018. ⟨hal-02786728⟩
  • Cedric Midoux, Olivier Rué, Olivier Chapleur, Mahendra Mariadassou, Théodore Bouchez, et al.. Easy16S : a user-friendly Shiny interface for analysis and visualization of metagenomic data. JOBIM 2018 : Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. 2018, JOBIM 2018. ⟨hal-02737257⟩
  • Valentin Marcon, Laure Quintric, Patrick Durand, Olivier Inizan, Caroline Dussart, et al.. The journey of a team of engineers in learning packaging technology. Jobim (Journées Ouvertes Biologie Informatique Mathématiques), Jul 2018, Marseille, France. 2018, JOBIM 2018. ⟨hal-02733639⟩
  • Olivier Rué, Valentin Loux, Sophie Schbath. New -omics data analysis activity on Migale platform for MEM community. Journées d'Animation MEM 2017, Jan 2017, Paris la Vilklette, France. 2017. ⟨hal-01730003⟩
  • Catherine Madzak, Valentin Loux, Christophe Monnet. MicroFit project: developping a Tn-seq system in Yarrowia lipolytica to study the adaptation of this yeast to cheese ecosystem. Journées MEM des métaprogrammes de l’INRA, 2017, paris, France. 2017. ⟨hal-02786916⟩
  • Hélène Falentin, Estelle Chaix, Bedis Dridi, Philippe Bessieres, S Buchin, et al.. Florilege : a database gathering microbial phenotypes of food interest. 4th International Conference on Microbial Diversity 2017, Oct 2017, Bari, Italy. 2017. ⟨hal-01651302⟩
  • Caroline Le Maréchal, Vincent Péton, Coline Plé, Julien Jardin, Valérie Briard-Bion, et al.. 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. ⟨hal-01512192⟩
  • Thibaut Guirimand, Charlie Pauvert, Sandra Derozier, Anne-Laure Abraham, Mahendra Mariadassou, et al.. 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. ⟨hal-01512085⟩
  • Thibaut Guirimand, Sandra Derozier, Charlie Pauvert, Anne-Laure Abraham, Valentin Loux, et al.. Food Microbiome-Transfert a database to characterize cheese ecosystems.. Journées Bioinformatique Inra, Mar 2016, Toulouse, France. 2016. ⟨hal-02799027⟩
  • Marie-Laure Franchinard, Frederic Sapet, Sandra Derozier, Franck Samson, Valentin Loux, et al.. The multiple-genomes browser of the IFB cloud. Journées SUCCES 2015, Nov 2015, Paris, France. pp.1, 2015. ⟨hal-02795851⟩
  • Valentin Loux, Mahendra Mariadassou, Sintia Almeida da Silva, Hélène Chiapello, Amal Hammami, et al.. Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii. 20. Colloque du Club des Bactéries Lactiques, Jun 2015, Lille, France. 2015. ⟨hal-01170054⟩
  • Valentin Loux, Mahendra Mariadassou, Sintia Almeida da Silva, Helene Chiapello, Amal Hammami, et al.. 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. ⟨hal-01209851⟩
  • Jérome Compain, Jullien Renaud, Sivagangari Nandy, Olivier Collin, Jean-François Gibrat, et al.. Mapdecode : inventory and benchmark of read mapping tools. ECCB'14 : European conference on Computational Biology, Sep 2014, Strasbourg, France. pp.1, 2014. ⟨hal-02792306⟩
  • Gwénaël Jan¨, Taous Saraoui, Sandrine Parayre-Breton, Grégory Guernec, Valentin Loux, et al.. 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. ⟨hal-01209656⟩
  • Taous Saraoui, Sandrine Parayre-Breton, Grégory Guernec, Valentin Loux, Jérôme Montfort, et al.. A unique in vivo experimental approach reveals metabolic adaptation of the probiotic [i]Propionibacterium freudenreichii[/i] to the colon environment. 24. International ICFMH Conference, Food Micro 2014, Sep 2014, Nantes, France. 2014, ICFMH Conference, Food Micro 2014. ⟨hal-01209705⟩
  • Caroline Le Maréchal, Vincent Péton, Julien Jardin, Valérie Briard-Bion, Stéphanie-Marie Deutsch, et al.. An integrative approach of [i]Propionibacterium freudenreichii[/i] immunomodulatory mechanisms. 5th IDF Symposium on Science & Technology of Fermented Milk, Mar 2014, Melbourne, Australia. 2014. ⟨hal-01209584⟩
  • Coline Plé, Caroline Le Maréchal, Vincent Péton, Christophe Vroland, Valérie Briard-Bion, et al.. 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. ⟨hal-01209657⟩
  • Sandra Derozier, Helene Chiapello, Thomas Lacroix, Cyprien Guérin, Valentin Loux, et al.. IGO, Integration from Genomes to Organisms. JOBIM 2013, Jul 2013, Toulouse, France. pp.246, 2013, JOBIM TOULOUSE 2013 - RÉSUMÉS COURTS (affiches). ⟨hal-02746442⟩
  • Thomas Lacroix, Valentin Loux, Annie Gendrault, Mark Hoebeke, Jean-François Gibrat. Insyght: Using symbols to visualize homologies, conserved syntenies and genomic insertions across multiple genomes. 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. ⟨hal-02748920⟩
  • Sandrine Parayre-Breton, Taous Saraoui, Grégory Guernec, Valentin Loux, Jérôme Montfort, et al.. 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. ⟨hal-01209535⟩
  • Gwénaël Jan¨, Benoit Foligne, Stéphanie-Marie Deutsch, Rozenn Le Guellec, Fabien Cousin, et al.. Immunomodulatory properties of the probiotic Propionibacterium freudenreichii surface proteome. 19 ième Colloque du Club des bactéries lactiques, Oct 2013, Bordeaux, France. pp.72, 2013. ⟨hal-01209501⟩
  • Caroline Le Maréchal, Vincent Péton, Julien Jardin, Valérie Briard-Bion, Christophe Vroland, et al.. The probiotic[i] Propionibacterium freudenreichii[/i] surface proteome. EUPA 2013, Oct 2013, Saint-Malo, France. 2013. ⟨hal-01209498⟩
  • Caroline Le Maréchal, Mahendra Mariadassou, Valentin Loux, Amal Plaudet Hammani, Julien Buratti, et al.. Combination of in silico and proteomic approaches to identify candidate genes responsible for the immunomodulatory properties of Propionibacterium freudenreichii. Journées des Microbiologistes de l'INRA 2012, Nov 2012, L'Isle-sur-la-Sorgue, France. 2012. ⟨hal-01209410⟩
  • Caroline Le Maréchal, Mahendra Mariadassou, Valentin Loux, Amal Plaudet Hammani, Julien Buratti, et al.. 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. ⟨hal-01209420⟩
  • Julien Fayolle, Jean-François Gibrat, Valentin Loux, Sophie Schbath. Comparison of mapping softwares for next generation sequencing data. 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. ⟨hal-02751434⟩
  • Magalie Leveugle, Valentin Loux, Jean-François Gibrat. Bovine promoter annotation platform for the identification of transcription factor binding sites in genes involved in early pregnancy. 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. ⟨hal-02757163⟩
  • Hélène Falentin, Stéphanie-Marie Deutsch, Sandrine Parayre-Breton, Julien Dherbecourt, Gwénaël Jan¨, et al.. The complete genome of Propionibacterium freudenreichii CIRM 1 a hardy actinobacteria with food and probiotic applications. 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. ⟨hal-01454344⟩
  • Fabien Melchiore, Cyprien Guérin, Pierre Nicolas, Valentin Loux. Assemblage de génomes bactériens séquencés par NGS - Comparaison d’outils et choix de paramètres. 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. ⟨hal-02758166⟩
  • Jean Francois Bernardet, Eric Duchaud, Mekki Boussaha, Christian Michel, Valentin Loux, et al.. Whole-genome sequence of the fish-pathogenic bacterium Flavobacterium psychrophilum. 2. FEMS Congress of European Microbiologists, Jul 2006, Madrid, Spain. 1 p., 2006. ⟨hal-02812810⟩

Book sections2 documents

  • Lien Nguyen, Virginie Brun, Florence Combes, Valentin Loux, Yves Vandenbrouck. Designing an In Silico Strategy to Select Tissue-Leakage Biomarkers Using the Galaxy Framework. Designing an in silico strategy to select tissue-leakage biomarkers using the galaxy framework, pp.275-289, 2019. ⟨hal-02284981⟩
  • Jean-François Gibrat, Valentin Loux. Introduction à l'annotation fonctionnelle in silico. Bio-informatique - principes d'utilisation des outils, Editions Quae, 2010, 978-2-7592-0870-8. ⟨hal-02812661⟩

Directions of work or proceedings1 document

  • Anne-Laure Abraham, Sandra Derozier, Quentin Cavaillé, Thibaut Guirimand, Solange Aka, et al.. Metagenomic analysis of an african beer ecosystem using Food Microbiome Transfert application. jobim 2019, Jul 2019, Nantes, France. 2019. ⟨hal-02789073⟩

Software1 document

  • Thomas Lacroix, Valentin Loux, Annie Gendrault-Jacquemard, Jean-François Gibrat. Insyght. 2014. ⟨hal-02795962⟩