Citations de la plateforme MIGALE
Les services de la plateforme MIGALE sont ouverts et accessibles, hors utilisation particulière, sans compensation financière. Dans le cas où certains travaux utilisant des ressources de la plateforme (calcul, stockage, ressources humaines...) mèneraient à une publication scientifique, nous vous demandons en contrepartie de citer ou de remercier la plateforme dans les remerciements.
Nous proposons trois modèles de citations en fonction du contexte :
Citation générique
"We are grateful to the INRA MIGALE bioinformatics facility (MIGALE, INRA, 2018. Migale bioinformatics Facility, doi: 10.15454/1.5572390655343293E12) for providing providing help and support"
Utilisation des ressources de calcul
"We are grateful to the INRA MIGALE bioinformatics facility (MIGALE, INRA, 2018. Migale bioinformatics Facility, doi: 10.15454/1.5572390655343293E12) for providing computational resources"
Exemple pour un projet associant plus directement un ou des membres de la plateforme (mini-projet...)
"We are grateful to Martin V., Xxxxx Y. from INRA MIGALE bioinformatics facility (MIGALE, INRA, 2018. Migale bioinformatics Facility, doi: 10.15454/1.5572390655343293E12) for providing help and support."
Si vous avez cité la plateforme dans l'une de vos publications, merci de nous le faire partager en remplissant le formulaire mis à disposition ici.
Vous trouvez ci-dessous un récapitulatif des citations, fournies par les utilisateurs, impliquant la plateforme Migale.
2019
Article
- Bioinformatics Tools and Workflow to Select Blood Biomarkers for Early Cancer Diagnosis: An Application to Pancreatic Cancer. - Vandenbrouck Y, Christiany D, Combes F, Loux V, Brun V - Proteomics
- Changes in rumen microbiota of cows in response to dietary supplementation with nitrate, linseed and saponin alone or in combination. - Milka Popova, Jessie Guyader, Mathieu Silberberg, Ahmad Reza Seradj, Cristina Saro, Aurélien Bernard, Christine Gérard, Cecile Martin, Diego P Morgavi - Applied and Environmental Microbiology
- Comparative metatranscriptomic analysis of anaerobic digesters treating anionic surfactant contaminated wastewater - Tiago P. Delforno, Thais Z. Macedo, Cédric Midoux, Gileno V. Lacerda Jr., Olivier Rué, Mahendra Mariadassou, Valentin Loux, Maria B.A. Varesche, Théodore Bouchez, Ariane Bize, Valéria M. Oliveira - Science of the Total Environment
- Designing an In Silico Strategy to Select Tissue-Leakage Biomarkers Using the Galaxy Framework. - Nguyen L, Brun V, Combes F, Loux V, Vandenbrouck Y - Methods Mol. Biol.
- Design of microbial consortia for the fermentation of pea-protein-enriched emulsions - Salma Ben-Harb, Anne Saint-Eve, Maud Panouillé, Isabelle Souchon, Pascal Bonnarme, Eric Dugat-Bony, Françoise Irlinger. - International Journal of Food Microbiology
- Influence of feed temperature to biofouling of ultrafiltration membrane during skim milk processing - Julien Chamberland, Thomas Messier, Eric Dugat-Bony, Marie-Hélène Lessard, Steve Labrie, Alain Doyen, Yves Pouliot - International Dairy Journal
- Transcription Profiling Reveals Cooperative Metabolic Interactions in a Microbial Cheese-Ripening Community Composed of Debaryomyces hansenii, Brevibacterium aurantiacum, and Hafnia alvei - Nguyen-Phuong Pham, Sophie Landaud, Pascale Lieben, Pascal Bonnarme and Christophe Monnet - Frontiers in microbiology
Poster
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A workflow to build a relevant and reduced bacterial dataset from NCBI -
Sam Ah-Lone, Sandra Dérozier, Valentin Loux, Hélène Chiapello -
JOBIM 2019, Nantes
Document:
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Metagenomic analysis of an african beer ecosystem using FoodMicrobiome Transfert application -
Anne-Laure Abraham, Sandra Dérozier, Quentin Cavaillé, Thibaut Guirimand, Solange Aka, Valentin Loux and Pierre Renault -
JOBIM 2019, Nantes
Document:
Présentation orale dans une conférence
- Bioinformatics tools and strategy to select microbial strains for fermented food products - Hélène Falentin, Stéphanie-Marie Deutsch, Valérie Gagnaire, Anne Thierry, Sandra Derozier, Claire Nédellec - Symposium on Bacterial Genetics and Ecology "Ecosystem drivers in a changing planet", Lisbonne
2018
Article
- Artificial barriers prevent genetic recovery of small isolated populations of a low mobility freshwater fish. - Coleman R., B. Gauffre, A. Pavlova, L. Beheregaray, J. Kearns, J. Lyon, M. Sasaki, R. Leblois, C. Sgro, P. Sunnucks - Heredity 120:515–532
- Assessment of Bona Fide sRNAs in Staphylococcus aureus. - Liu W, Rochat T, Toffano-Nioche C, Le Lam TN, Bouloc P, Morvan C. - Front Microbiol.
- Complete and Draft Genome Sequences of Nine Lactobacillus sakei Strains Selected from the Three Known Phylogenetic Lineages and Their Main Clonal Complexes - Valentin Loux, Gwendoline Coeuret, Monique Zagorec, Marie-Christine Champomier Vergès, Stéphane Chaillou - Genome Announcements
- Detection of an amplification bias associated to Leuconostocaceae family with a universal primer routinely used for monitoring microbial community structures within food products. - Poirier S, Rué O, Coeuret G, Champomier-Vergès M-C, Loux V, Chaillou S. - BMC Research Notes
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Estimation of the dispersal distances of an aphid-borne virus in a patchy landscape -
Pleydell DRJ, Soubeyran d S, Dallot S, Labonne G, Chad œ uf J, Jacquot E, et al. -
PLoS Comput Biol 14(4): e1006085
Document:
- Genomic Diversity and Evolution of the Fish Pathogen Flavobacterium psychrophilum - Eric Duchaud, Tatiana Rochat, Christophe Habib, Paul Barbier, Valentin Loux, Cyprien Guérin, Inger Dalsgaard, Lone Madsen, Hanne Nilsen, Krister Sundell, Tom Wiklund, Nicole Strepparava, Thomas Wahli, Greta Caburlotto, Amedeo Manfrin, Gregory D Wiens, Erina Fujiwara-Nagata, Ruben Avendaño-Herrera, Jean-François Bernardet, and Pierre Nicolas - Frontier Microbiology
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Inference of Adaptive Shifts for Multivariate Correlated Traits -
Paul Bastide, Cécile Ané, Stéphane Robin, and Mahendra Mariadassou -
Systematic Biology
Document:
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Integrative visual omics of the white‑rot fungus Polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw plant biomass -
Shingo Miyauchi, Anaïs Rancon, Elodie Drula, Hayat Hage, Delphine Chaduli, Anne Favel, Sacha Grisel, Bernard Henrissat, Isabelle Herpoël‑Gimbert, Francisco J. Ruiz‑Dueñas, Didier Chevret, Matthieu Hainaut, Junyan Lin, Mei Wang, Jasmyn Pangilinan, Anna Lipzen, Laurence Lesage‑Meessen, David Navarro, Robert Riley, Igor V. Grigoriev, Simeng Zhou, Sana Raouche and Marie‑Noëlle Rosso -
Biotechnology for Biofuels
Document:
- Lateral variations and vertical structure of the microbial methane cycle in the sediment of Lake Onego (Russia) - THOMAS C., FROSSARD V., PERGA M.E., TOFIELD-PASCHE N., HOFMANN H., DUBOIS N., BELKINA N., ZOBKOVA M., ROBERT S., LYAUTEY E. - Inland Waters, doi:10.1080/20442041.2018.1500227
- Likelihood computation and inference of demographic and mutational parameters from population genetic data under coalescent approximations. - Rousset F., C. R. Beeravolu, R. Leblois. - Journal de la Société Française de Statistique 159 : 142-166.
- Oak genome reveals facets of long lifespan - Christophe Plomion, Jean-Marc Aury, Joëlle Amselem, Thibault Leroy, Florent Murat, Sébastien Duplessis, Sébastien Faye, Nicolas Francillonne, Karine Labadie, Grégoire Le Provost, Isabelle Lesur,, Jérôme Bartholomé, Patricia Faivre-Rampant, Annegret Kohler, Jean-Charles Leplé, Nathalie Chantret, Jun Chen, Anne Diévart, Tina Alaeitabar, Valérie Barbe, Caroline Belser, Hélène Bergès, Catherine Bodénès, Marie-Béatrice Bogeat-Triboulot, Marie-Lara Bouffaud, Benjamin Brachi, Emilie Chancerel, David C - Nature Plants
- Postglacial range expansion shaped the spatial genetic structure in a marine habitat-forming species: implications for conservation plans in the Eastern Adriatic Sea. - Ledoux J.-B., M. Frleta-Valić, S. Kipson°, A. Antunes, E. Cebrian, C. Linares, P. Sánchez, R. Leblois, J. Garrabou - Journal of Biogeography 45: 2645-2657.
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Text mining tools for extracting information about microbial biodiversity in food -
Estelle Chaix, Louise Deléger, Robert Bossy, Claire Nédellec -
Food Microbiology
Document:
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The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus. -
Rochat T, Bohn C, Morvan C, Le Lam TN, Razvi F, Pain A, Toffano-Nioche C, Ponien P, Jacq A, Jacquet E, Fey PD, Gautheret D, Bouloc P. -
Nucleic Acids Res.
Document:
Poster
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A journey of a team of engineers in learning packaging technology -
Valentin Marcon, Laure Quintric, Durand Patrick, Olivier Inizan, Caroline Dussart, Valentin Loux, Maria Bernard, Géraldine Pascal -
JOBIM2018, Marseille
Document:
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Easy16S: a user-friendly Shiny interface for analysis and visualization of metagenomic data -
Cédric Midoux, Olivier Rué, Olivier Chapleur, Mahendra Mariadassou, Théodore Bouchez, Valentin Loux, Ariane Bize -
JOBIM 2018, Marseille
Document:
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FLORILEGE: an integrative database using text mining and ontologies -
Estelle Chaix, Sandra Dérozier, Louise Deléger, Hélène Falentin, Jean-Baptiste Bohuon, Mouhamadou Ba, Robert Bossy, Delphine Sicard, Valentin Loux, Claire Nédellec -
JOBIM 2018, Marseille
Document:
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FoodMicrobiome Transfert: web based Metagenomic Analysis -
Quentin Cavaillé, Thibaut Guirimand, Sandra Dérozier, Anne-Laure Abraham, Bedis Dridi, Valentin Loux, Pierre Renault -
JOBIM 2018, Marseille
Document:
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MetaFoldScan: a pipeline to scan metagenomes and identify structural homologs using HMM -
Sandra Dérozier*, Véronique Martin*, Jean-Marc Chatel, Nalini Rama Rao, Valentin Loux, Gwenaëlle André-Leroux -
JOBIM 2018, Marseille
Document:
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Plateforme bioinformatique MIGALE -
Plateforme Migale -
JOBIM 2018, Marseille
Document:
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Taking tools out of their laboratory: Methods and practices to make Bioinformatics tools accessible through Galaxy -
Valentin Marcon, Alexis Dereeper, Sarah Maman-Haddad, Melanie Petera, Luc Jouneau, Marie Tremblay-Franco, Olivier Inizan -
JOBIM2018, Marseille
Document:
Présentation orale dans une conférence
- Insight from epidemiological and animal movement data on bovine paratuberculosis infectious dynamics at a regional scale - G. Beaunée, P. Ezanno, A. Joly, P. Nicolas and E. Vergu - The 15th International Symposium of Veterinary Epidemiology and Economics, Chiang Mai, Thailand
- L'ontologie OntoBiotope pour l'étude de la biodiversité microbienne - Claire Nédellec, Estelle Chaix, Robert Bossy, Louise Deléger, Sandra Dérozier, Jean-Baptiste Bohuon, Valentin Loux - EGC'2018: 18èmes Conférence Internationale sur l'Extraction et la Gestion des Connaissances, Paris
2017
Article
- A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic. - Patrascu O, Béguet-Crespel F, Marinelli L, Le Chatelier E, Abraham AL, Leclerc M, Klopp C, Terrapon N, Henrissat B, Blottière HM, Doré J, Béra-Maillet C. - Sci Rep.
- A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins - Coluzzi C, Guédon G, Devignes M-D, Ambroset C, Loux V, Lacroix T, Payot S and Leblond-Bourget N - Frontiers in Microbiology
- A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes. - Bonnet T., R. Leblois, F. Rousset, P.-A. Crochet. - Evolution 71:2140-2158.
- Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria. - Ficko-Blean E, Préchoux A, Thomas F, Rochat T, Larocque R, Zhu Y, Stam M, Génicot S, Jam M, Calteau A, Viart B, Ropartz D, Pérez-Pascual D, Correc G, Matard-Mann M, Stubbs KA, Rogniaux H, Jeudy A, Barbeyron T, Médigue C, Czjzek M, Vallenet D, McBride MJ, Duchaud E, Michel G. - Nature Communications
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Characterization of the pollen beetle, Brassicogethes aeneus, dispersal from woodlands to winter oilseed rape fields -
Amandine Suzanne Juhel , Corentin Mario Barbu, Pierre Franck, Jean Roger-Estrade, Arnaud Butier, Mathieu Bazot, Muriel Valantin-Morison -
PlosOne
Document:
- Comparative genomic analysis of Brevibacterium strains: insights into key genetic determinants involved in adaptation to the cheese habitat - Nguyen-Phuong Pham, Séverine Layec, Eric Dugat-Bony, Marie Vidal, Françoise Irlinger and Christophe Monnet - BMC genomics
- Complete Genome Sequence of Flavobacterium psychrophilum Strain OSU THCO2-90, Used for Functional Genetic Analysis - atiana Rochat, Paul Barbier, Pierre Nicolas, Valentin Loux, David Pérez-Pascual, José A Guijarro, Jean-François Bernardet, and Eric Duchaud - Genome Announcements
- Complete Genome Sequences of Two Escherichia coli Phages, vB_EcoM_ ESCO5 and vB_EcoM_ESCO13, Which Are Related to phAPEC8. - Trotereau A, Gonnet M, Viardot A, Lalmanach AC, Guabiraba R, Chanteloup NK, Schouler C. - Genome Announc.
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Controlling bovine paratuberculosis at a regional scale: Towards a decision modelling tool -
Gaël Beaunée, Elisabeta Vergu, Alain Joly, Pauline Ezanno -
Journal of Theoretical Biology
Document:
- Deciphering the evolutionary history of allochronic differentiation in the pine processionary moth Thaumetopoea pityocampa. - Leblois R., M. Gautier, A. Rohfritsch, J. Foucaud, C. Burban, M. Galan, A. Loiseau, L. Saune, M. Branco, K. Gharbi, R. Vitalis, C. Kerdelhue - Molecular Ecology 2017: 1-15.
- Deciphering the genetic regulation of peripheral blood transcriptome in pigs through expression genome-wide association study and allele-specific expression analysis - Maroilley T, Lemonnier G, Lecardonnel J, Esquerré D, Ramayo-Caldas Y, Mercat MJ, Rogel-Gaillard C, Estellé J. - BMC Genomics
- Demographic inference through approximate-Bayesian-computation skyline plots. - Navascués M, Leblois R, Burgarella C. - PeerJ
- Draft Genome Sequence of Lactobacillus curvatus FLEC03, a Meat-Borne Isolate from Beef Carpaccio Packaged in a Modified Atmosphere. - Terán LC, Coeuret G, Raya R, Champomier-Vergès MC, Chaillou S. - Genome Announc.
- Draft Genome Sequence of Serratia proteamaculans MFPA44A14-05, a Model Organism for the Study of Meat and Seafood Spoilage. - Fougy L, Coeuret G, Champomier-Vergès MC, Chaillou S. - Genome Announc.
- Draft Genome Sequences of 18 Psychrotolerant and 2 Thermotolerant Strains Representative of Particular Ecotypes in the Bacillus cereus Group - Marie-Hélène Guinebretière, Valentin Loux, Véronique Martin, Pierre Nicolas, Vincent Sanchis, and Véronique Broussolle - Genome Announcement
- Estimating virus effective population size and selection without neutral markers. - Rousseau E, Moury B, Mailleret L, Senoussi R, Palloix A, Simon V, Valière S, Grognard F, Fabre F. - PLoS Pathog
- Fidelity of parent-offspring transmission and the evolution of social behavior in structured populations - Debarre, F - Journal of Theoretical Biology
- Gain of power of the general regression model compared to Cochran-Armitage Trend tests: simulation study and application to bipolar disorder. - Dizier MH, Demenais F, Mathieu F. - BMC Genet.
- Genetic diversity and structure related to expansion history and habitat isolation: stone marten populating rural-urban habitats. - Wereszczuk A., R. Leblois, A. Zalewski - BMC ecology 17:46.
- Genetic structure and invasion history of the house mouse (Mus musculus domesticus) in Senegal : a legacy of colonial times? - Lippens C., A. Estoup, K. Hima, A. Loiseau, C. Tatard, A. Dalecky, K. Bâ, M. Kane, M. Diallo, A. Sow, S. Piry, R. Leblois, J.-M. Duplantier, C. Brouat - Heridity 119 :64-75.
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Genome sequence of the type strain CLIB 1764 T (=CBS 14374 T ) of the yeast species Kazachstania saulgeensis isolated from French organic sourdough -
Véronique Sarilar, Lieven Sterck, Saki Matsumoto, Noémie Jacques, Cécile Neuvéglise, Colin R. Tinsley, Delphine Sicard , Serge Casaregola -
Genomics Data
Document:
- Genome sequence of the type strain CLIB 1764T (= CBS 14374T) of the yeast species Kazachstania saulgeensis isolated from French organic sourdough. - Sarilar V, Sterck L, Matsumoto S, Jacques N, Neuvéglise C, Tinsley CR, Sicard D, Casaregola S. - Genom Data.
- Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple - Urrestarazu J, Muranty H, Denancé C, Leforestier D, Ravon E, Guyader A, Guisnel R, Feugey L, Aubourg S, Celton JM, Daccord N, Dondini L, Gregori R, Lateur M, Houben P, Ordidge M, Paprstein F, Sedlak J, Nybom H, Garkava-Gustavsson L, Troggio M,Bianco L, Velasco R, Poncet C, Théron A, Moriya S, Bink MCAM, Laurens F, Tartarini S, Durel CE - Front Plant Sci
- Identification of proteins involved in the anti-inflammatory properties of Propionibacterium freudenreichii by means of a multi-strain study. - Deutsch SM, Mariadassou M, Nicolas P, Parayre S, Le Guellec R, Chuat V, Peton V, Le Maréchal C, Burati J, Loux V, Briard-Bion V, Jardin J, Plé C, Foligné B, Jan G, Falentin H. - Sci Rep
- Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression. - Arnaiz O, Van Dijk E, Bétermier M, Lhuillier-Akakpo M, de Vanssay A, Duharcourt S, Sallet E, Gouzy J, Sperling L. - BMC Genomics
- Influence of removal of lactate and acetate on the microbiota of French fresh pork meat sausages - agnès bouju, benoit remenant, marie-france pilet, sandrine guillou - food microbiology
- La génomique comparative à l’ère des technologies NGS - Thomas Lacroix, Jean-François Gibrat, Valentin Loux - Biofutur
- 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 - Christo-Foroux E, Vallaeys T, Loux V, Dassa E, Deutscher J, Wandersman C, Livernois A, Hot C, Criscuolo A, Dauga C, Clermont D, Chesneau O - Systematic and Applied Microbiology
- Metatranscriptomics Reveals the Active Bacterial and Eukaryotic Fibrolytic Communities in the Rumen of Dairy Cow Fed a Mixed Diet. - Comtet-Marre S, Parisot N, Lepercq P, Chaucheyras-Durand F, Mosoni P, Peyretaillade E, Bayat AR, Shingfield KJ, Peyret P, Forano E. - Front Microbiol.
- Optimization of multi-environment trials for genomic selection based on crop models. - Rincent R, Kuhn E, Monod H, Oury FX, Rousset M, Allard V, Le Gouis J. - Theor Appl Genet.
- PamR, a new MarR-like regulator affecting prophages and metabolic genes expression in Bacillus subtilis. - De San Eustaquio-Campillo A, Cornilleau C, Guérin C, Carballido-López R, Chastanet A. - PLoS One
- Resampling: an improvement of Importance Sampling in varying population size models. - Merle C., R. Leblois, F. Rousset, P. Pudlo - Theoretical Population Biology, 114, 70-87.
- The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes - Vincent J. Henry, Anne Goelzer, Arnaud Ferré, Stephan Fischer, Marc Dinh, Valentin Loux,Christine Froidevaux and Vincent Fromion - Journal of Biomedical Semantics (2017) 8:53 DOI 10.1186/s13326-017-0165-6
- The Complete Genome Sequence of the Fish Pathogen Tenacibaculum maritimum Provides Insights into Virulence Mechanisms - Pérez-Pascual D, Lunazzi A, Magdelenat G, Rouy Z, Roulet A, Lopez-Roques C, Larocque R, Barbeyron T, Gobet A, Michel G, Bernardet JF, Duchaud E. - Front Microbiol
- The Effects of Weaning Methods on Gut Microbiota Composition and Horse Physiology - Mach N, Foury A, Kittelmann S, Reigner F, Moroldo M, Ballester M, Esquerré D, Rivière J, Sallé G, Gérard P, Moisan MP, Lansade L. - Front Physiol
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The integrative omics of white-rot fungus Pycnoporus coccineus reveals co-regulated CAZymes for orchestrated lignocellulose breakdown -
Shingo Miyauchi, David Navarro, Sacha Grisel, Didier Chevret, Jean-Guy Berrin, Marie-Noelle Rosso -
PLoS One
Document:
- The integrative omics of white-rot fungus Pycnoporus coccineus reveals co-regulated CAZymes for orchestrated lignocellulose breakdown. - Miyauchi S, Navarro D, Grisel S, Chevret D, Berrin JG, Rosso MN. - PLoS One
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The Structural and Functional Capacity of Ruminal and Cecal Microbiota in Growing Cattle Was Unaffected by Dietary Supplementation of Linseed Oil and Nitrate -
Milka Popova, Emily McGovern, Matthew S. McCabe, Cécile Martin, Michel Doreau, Marie Arbre, Sarah J. Meale, Diego P. Morgavi and Sinéad M. Waters -
Frontiers in Microbiology
Document:
- Transcriptomic response of Debaryomyces hansenii during mixed culture in a liquid model cheese medium with Yarrowia lipolytica - Reine Maleka,⁎, Pascal Bonnarmeb, Françoise Irlingerb, Pascale Frey-Klettc, Djamila Onésimea, Julie Aubertd, Valentin Louxe, Jean-Marie Beckericha - International Journal of Food Microbiology
- Unprecedented large inverted repeats at the replication terminus of circular bacterial chromosomes suggest a novel mode of chromosome rescue - Hela El Kafsi,, Valentin Loux, Mahendra Mariadassou, Camille Blin, Hélène Chiapello, Anne-Laure Abraham, Emmanuelle Maguin & Maarten van de Guchte - Scientific Reports
- Whole-Genome Sequencing of Seven Strains of Staphylococcus lugdunensis Allows Identification of Mobile Genetic Elements - Argemi X, Martin V, Loux V, Dahyot S, Lebeurre J, Guffroy A, Martin M, Velay A, Keller D, Riegel P, Hansmann Y, Paul N, Prévost G. - Genome Biol Evol.
Présentation orale dans une conférence
- Temporal dynamics of benthic microbial communities over a 5-month period in the littoral area of Lake Bourget (France) - Emilie LYAUTEY, Damien BOUFFARD, Victor FROSSARD - SIL Austria Meeting, 26-27 october 2017, Innsbruck
2016
Article
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Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level -
Urrestarazu J., Denancé C. -
BMC Plant Biology
Document:
- Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level. - Jorge Urrestarazu, Caroline Denancé, Elisa Ravon, Arnaud Guyader, Rémi Guisnel, Laurence Feugey, Charles Poncet, Marc Lateur, Patrick Houben, Matthew Ordidge, Felicidad Fernandez-Fernandez, Kate M. Evans, Frantisek Paprstein, Jiri Sedlak, Hilde Nybom, Larisa Garkava-Gustavsson, Carlos Miranda, Jennifer Gassmann, Markus Kellerhals, Ivan Suprun, Anna V. Pikunova, Nina G. Krasova, Elnura Torutaeva, Luca Dondini, Stefano Tartarini, François Laurens, and Charles-Eric Durel - BMC Plant Biol
- Black rat invasion of inland Sahel: insights from interviews and population genetics in South Western Niger. - Berthier K., M. Garba, R. Leblois, M. Navascues, C. Tatard, P. Gauthier, S Gagaré, S. Piry, A. Dalecky, A. Loiseau , G. Dobigny. - Biological Journal of the Linean Society, 119, 748–765.
- Bovine Teat Microbiome Analysis Revealed Reduced Alpha Diversity and Significant Changes in Taxonomic Profiles in Quarters with a History of Mastitis. - Falentin H , Rault L , Nicolas A , Bouchard DS , Lassalas J , Lamberton P , Aubry JM , Marnet PG , Le Loir Y , Even S - Front Microbiol
- Complete Genome Sequence of Lactococcus lactis subsp. lactis A12, a Strain Isolated from Wheat Sourdough - Guellerin M, Passerini D, Fontagné-Faucher C, Robert H, Gabriel V, Loux V, Klopp C, Le Loir Y, Coddeville M, Daveran-Mingot M-L, Ritzenthaler P, Le Bourgeois P - Genome Announcements
- Detection of adaptive shifts on phylogenies by using shifted stochastic processes on a tree - P. Bastide, M. Mariadassou, S. Robin - Journal of the Royal Statistical Society: Series B (Statistical Methodology)
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Draft Anaplasma phagocytophilum Genome Sequences from Five Cows, Two Horses, and One Roe Deer Collected in Europe -
Thibaud Dugat, Marie-Noëlle Rossignol, Olivier Rué, Valentin Loux, Sylvain Marthey, Marco Moroldo, Cornelia Silaghi, Dirk Höper, Julia Fröhlich, Martin Pfeffer, Erich Zweygarth, Anne-Claire Lagrée, Henri-Jean Boulouis, Nadia Haddad -
Genome Announcements
Document:
- Draft Genome Sequence of Corynebacterium variabile Mu292, Isolated from Munster, a French Smear-Ripened Cheese - Dugat-Bony E, Sarthou A-S, Loux V, Vidal M, Bonnarme P, Irlinger F, Layec S - Genome Announcements
- Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CFL1, a Lactic Acid Bacterium Isolated from French Handcrafted Fermented Milk - Julie Meneghel, Eric Dugat-Bony, Françoise Irlinger, Valentin Loux, Marie Vidal, Stéphanie Passot, Catherine Béal, Severine Layec, and Fernanda Fonseca - Genome Announcements
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Functional Comparison of Bacteria from the Human Gut and Closely Related Non-Gut Bacteria Reveals the Importance of Conjugation and a Paucity of Motility and Chemotaxis Functions in the Gut Environment. -
Dobrijevic D , Abraham AL , Jamet A , Maguin E , van de Guchte M -
PLOS One
Document:
- High genetic structure and contrasting demographic history in the endangered Mediterranean tortoise Testudo hermanni hermanni. - Zenboudji S., M. Cheylan, V. Arnal, A. Bertolero, R. Leblois, G. Astruc, G. Bertorelle, J. L. Pretus, M. Lo Valvo, G. Sotgiu, C. Montgelard - Biological Conservation 195 : 279–291.
- Highlighting the microbial diversity of 12 French cheese varieties - Dugat-Bony, E., Garnier, L., Denonfoux, J., Ferreira, S., Sarthou, A.-S., Bonnarme, P., Irlinger, F. - International Journal of Food Microbiology
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Integrating phylogeographic patterns of mtDNA and nDNA divergence to infer the evolutionary history of Meriones shawii (Rodentia: Muridae): a comparison of genetic and fossil data. -
Lalis A., R. Leblois, E. Stoetzel, T. Benazzou, K. Souttou, C. Denys, V. Nicolas. -
Biological Journal of the Linean Society, 118 : 262–279.
Document:
- Market analyses of livestock trade networks to inform the prevention of joint economic and epidemiological risks - Mathieu Moslonka-Lefebvre, Christopher A. Gilligan, Hervé Monod, Catherine Belloc, Pauline Ezanno, João A. N. Filipe, Elisabeta Vergu - Journal of the Royal Society Interface (http://rsif.royalsocietypublishing.org/content/13/116/20151099)
- Market analyses of livestock trade networks to inform the prevention of joint economic and epidemiological risks. - Moslonka-Lefebvre M , Gilligan CA , Monod H , Belloc C , Ezanno P , Filipe JA , Vergu E - J R Soc Interface
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Mass spectrometry analysis of the extracellular peptidome of Lactococcus lactis: lines of evidence for the coexistence of extracellular protein hydrolysis and intracellular peptide excretion -
Alain Guillot, Mylène Boulay, Emilie Chambellon, Christophe Gitton, Véronique Monnet, Vincent Juillard -
Journal of Proteome Research
Document:
- New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration. - Chloé Ambroset, Charles Coluzzi, Gérard Guédon, Marie-Dominique Devignes, Valentin Loux, Thomas Lacroix, Sophie Payot, and Nathalie Leblond-Bourget - Frontiers in Microbiology
- New molecular data favor an anthropogenic introduction of the wood mouse (Apodemus sylvaticus) in North Africa - Lalis A., R. Leblois, S. Liefried, A. Ouarour, C. Reddy Beeravolu, J. Michaux, A. Hamani, C. Denys, V. Nicolas. - Journal of Zoological Systematics and Evolutionary Research 54 : 1-12. Doi : 10.1111/jzs.12111
- Permanent draft genome sequence of the probiotic strain Propionibacterium freudenreichii CIRM-BIA 129 (ITG P20) - Hélène Falentin, Stéphanie-Marie Deutsch, Valentin Loux, Amal Hammani, Julien Buratti, Sandrine Parayre, Victoria Chuat, Valérie Barbe, Jean-Marc Aury, Gwenaël Jan, and Yves Le Loir - Standards in Genomic Sciences
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Reducing Salt in Raw Pork Sausages Increases Spoilage and Correlates with Reduced Bacterial Diversity -
Lysiane Fougy, Marie-Hélène Desmonts, Gwendoline Coeuret, Christine Fassel, Erwann Hamon, Bernard Hézard, Marie-Christine Champomier-Vergès, Stéphane Chaillou -
Applied and Environmental Microbiology
Document:
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Visual Comparative Omics of Fungi for Plant Biomass Deconstruction -
Miyauchi S , Navarro D , Grigoriev IV , Lipzen A , Riley R , Chevret D , Grisel S , Berrin JG , Henrissat B , Rosso MN -
Frontiers in Microbiology
Document:
- Visual Comparative Omics of Fungi for Plant Biomass Deconstruction - Shingo Miyauchi, David Navarro, Igor V. Grigoriev, Anna Lipzen, Robert Riley, Didier Chevret, Sacha Grisel, Jean-Guy Berrin, Bernard Henrissat and Marie-Noëlle Rosso - frontiers in Microbiology
Poster
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Cheese ecosystems insights with shotgun metagenomics and a metadata extended genomics database. -
Thibaut Guirimand, Charlie Pauvert, Sandra Dérozier, Anne-Laure Abraham, Mahendra Mariadassou, Valentin Loux, Pierre Renault -
Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM) à Lyon
Document:
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Développement d’une interface web pour l’exploration interactive de profils transcriptomiques le long d’un génome -
Sandra Dérozier, Pierre Nicolas, Cyprien Guérin -
Journées nationales de bioinformatique à l'INRA - Toulouse
Document:
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Food Microbiome-Transfert, a database to characterize cheese ecosystems. -
Thibaut GUIRIMAND, Sandra DEROZIER, Charlie PAUVERT, Anne-Laure ABRAHAM, Valentin LOUX, Pierre RENAUD -
Journées Bioinformatiques de l'INRA
Document:
- Plateforme bioinformatique Migale - Valentin Loux - Journées nationales de bioinformatique à l'INRA - Toulouse
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Staphylococcus aureus transcriptome architecture: from laboratory to infection-mimicking conditions -
Ulrike Mäder•, Pierre Nicolas•, Maren Depke, Jan Pané-Farré, Michel Debarbouille, Magdalena M. van der Kooi-Pol, Cyprien Guérin, Sandra Dérozier, Aurelia Hiron, Hanne Jarmer, Aurélie Leduc, Stephan Michalik, Ewoud Reilman, Marc Schaffer, Frank Schmidt, Philippe Bessières, Philippe Noirot, Michael Hecker, Tarek Msadek, Uwe Volker and Jan Maarten van Dijl -
Journées nationales de bioinformatique à l'INRA - Toulouse
Document:
Présentation orale dans une conférence
- Estimation of key parameters of a metapopulation model of paratuberculosis regional spread in dairy cattle. - Beaunée, G., Ezanno, P., Joly, A., Vergu, E - 10th European Conference on Mathematical and Theoretical Biology (ECMTB), Nottingham, United Kingdom
2015
Article
- Aggressive Emerging Pathovars of Xanthomonas arboricola Represent Widespread Epidemic Clones Distinct from Poorly Pathogenic Strains, as Revealed by Multilocus Sequence Typing. - Fischer-Le Saux M , Bonneau S , Essakhi S , Manceau C , Jacques MA - Appl Environ Microbiol
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Congruent signals of population history but radically different patterns of genetic diversity between mitochondrial and nuclear markers in a mountain lizard -
Ferchaud A.-L., R. Eudeline, V. Arnal, M. Cheylan, G. Pottier, R. Leblois and P.-A. Crochet. -
Molecular Ecology 24 : 192–207 . doi : 10.1111/mec.13011
Document:
- Deciphering Genome Content and Evolutionary Relationships of Isolates from the Fungus Magnaporthe oryzae Attacking Different Host Plants. - Chiapello H , Mallet L , Guérin C , Aguileta G , Amselem J , Kroj T , Ortega-Abboud E , Lebrun MH , Henrissat B , Gendrault A , Rodolphe F , Tharreau D , Fournier E - Genome Biol Evol
- Enhanced degradation of softwood versus hardwood by the white - rot fungus Pycnoporus coccineus - Marie Couturier, David Navarro, Didier Chevret, Bernard Henrissat, François Piumi, Francisco J. Ruiz‑Dueñas, Angel T. Martinez, Igor V. Grigoriev, Robert Riley, Anna Lipzen, Jean‑Guy Berrin, Emma R. Master and Marie‑Noëlle Rosso - Biotechnology for Biofuels
- Enhanced degradation of softwood versus hardwood by the white-rot fungus Pycnoporus coccineus. - Couturier M , Navarro D , Chevret D , Henrissat B , Piumi F , Ruiz-Dueñas FJ , Martinez AT , Grigoriev IV , Riley R , Lipzen A , Berrin JG , Master ER , Rosso MN - Biotechnol Biofuels
- Genome Sequences of Two Bovine Mastitis-Causing Escherichia coli Strains - Florent Kempf, Valentin Loux, and Pierre Germon - Genome Announcements
- How Ecology and Landscape Dynamics Shape Phylogenetic Trees - Fanny Gascuel, Régis Ferrière, Robin Aguilée, Amaury Lambert - Systematic Biology
- Inventory of the GH70 enzymes encoded by Leuconostoc citreum NRRL B-1299 – identification of three novel a-transglucosylases - Delphine Passerini, Marlène Vuillemin, Lisa Ufarté, Sandrine Morel, Valentin Loux, Catherine Fontagné-Faucher, Pierre Monsan, Magali Remaud-Siméon, and Claire Moulis - FEBS Journal
- Microbial ecosystems are dominated by specialist taxa - Mahendra Mariadassou, Samuel Pichon, Dieter Ebert - Ecology Letters
- Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii - Valentin Loux, Mahendra Mariadassou, Sintia Almeida, Hélène Chiapello, Amal Hammani, Julien Buratti, Annie Gendrault, Valérie Barbe, Jean-Marc Aury, Stéphanie-Marie Deutsch, Sandrine Parayre, Marie-Noëlle Madec, Victoria Chuat, Gwenaël Jan, Pierre Peterlongo, Vasco Azevedo, Yves Le Loir, and Hélène Falentin - BMC Genomics
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Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage -
Ste ´phane Chaillou1,2, Aure ´lie Chaulot-Talmon1,2, He ´le `ne Caekebeke3, Mireille Cardinal4, Souad Christieans5, Catherine Denis6, Marie He ´le `ne Desmonts7, Xavier Dousset8,9, Carole Feurer10, Erwann Hamon7, Jean-Jacques Joffraud4, Ste ´phanie La Carbona6, Franc ¸oise Leroi4, Sabine Leroy11, Sylvie Lorre12, Sabrina Mace ´8,9, Marie-France Pilet8,9, Herve ´ Pre ´vost8,9, Marina Rivollier5, Dephine Roux3, Re ´gine Talon11, Monique Zagorec8,9 and Marie-Christine Champomier-Verges -
ISME journal
Document:
- Overview of a Surface-Ripened Cheese Community Functioning by Meta-Omics Analyses - Eric Dugat-Bony, Cécile Straub, Aurélie Teissandier, Djamila Onésime, Valentin Loux, Christophe Monnet, Françoise Irlinger, Sophie Landaud, Marie-Noëlle Leclercq-Perlat, Pascal Bento, Sébastien Fraud, Jean-François Gibrat, Julie Aubert, Frédéric Fer, Eric Guedon, Nicolas Pons, Sean Kennedy, Jean-Marie Beckerich, Dominique Swennen, and Pascal Bonnarme - PLOS One
- Synchronized navigation and comparative analyses across Ensembl complete bacterial genomes with INSYGHT - Thomas Lacroix; Sylvie Therond; Marc Rugeri; Pierre Nicolas; Annie Gendrault; Valentin Loux; Jean-Francois Gibrat - Bioinformatics
- The Decoy Substrate of a Pathogen Effector and a Pseudokinase Specify Pathogen-Induced Modified-Self Recognition and Immunity in Plants - Wang G, Roux B, Feng F, Guy E, Li L, Li N, Zhang X, Lautier M, Jardinaud MF, Chabannes M, Arlat M, Chen S, He C, Noël LD, Zhou JM - Cell Host Microbe
- YOC, A new strategy for pairwise alignment of collinear genomes. - Uricaru R , Michotey C , Chiapello H , Rivals E - BMC Bioinformatics
Démonstration
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View and synchronize several genotypes using IGV -
Marie-Laure Franchinard -
JOBIM
Document:
Poster
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Paratuberculosis spread at the regional scale in dairy cattle: insights from data -
Beaunée G., Ezanno P, Joly A, Vergu E. -
Epidemics 5, Clearwater beach, Florida, USA
Document:
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Shifted stochastic processes evolving on trees: application to models of adaptive evolution. -
Paul Bastide, Mahendra Mariadassou, Stéphane Robin -
Conférence "Mathematical and Computational Evolutionary Biology" (MCEB 2015), Porquerolles, France
Document:
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The multiple-genomes browser of the IFB cloud -
Marie-Laure Franchinard, Frédéric Sapet, Sandra Dérozier, Franck Samson, Valentin Loux, Jean-François Gibrat -
Journées SUCCES (rencontres Scientifiques des Utilisateurs du Calculs intensifs, de Cloud Et de Stockage), 5-6 Novembre 2015, à l'Institut de physique du globe, Paris
Document:
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View and synchronize several genotypes using IGV -
Marie-Laure Franchinard, Frédéric Sapet, Sandra Derozier, Franck Samson, Jean-François Gibrat -
JOBIM
Document:
Présentation orale dans une conférence
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Updating a production Galaxy platform : success and gotchas -
Sandra Derozier -
Galaxy Day, Paris (19 novembre 2015)
Document:
2014
Article
- Bacterial protein signals are associated with Crohn’s disease - Catherine Juste, David P Kreil, Christian Beauvallet, Alain Guillot, Sebastian Vaca, Christine Carapito, Stanislas Mondot, Peter Sykacek, Harry Sokol, Florence Blon, Pascale Lepercq, Florence Levenez, Benoît Valot, Wilfrid Carré, Valentin Loux, Nicolas Pons, Olivier David, Brigitte Schaëffer, Patricia Lepage, Patrice Martin, Véronique Monnet, Philippe Seksik, Laurent Beaugerie, S Dusko Ehrlich, Jean-François Gibrat, Alain Van Dorsselaer, and Joel Doré - Gut
- Blacktip reef sharks, Carcharhinus melanopterus, have high genetic structure and varying demographic histories in their Indo-Pacific range. - Vignaud T. M., J. Mourier, J. A. Maynard, R. Leblois, J. Spaet, E. Clua, V. Neglia, S. Planes. - Molecular Ecology, 23: 5193-5207. doi : 10.1111/mec.12936
- Comparative genomics of first available bovine Anaplasma phagocytophilum genome obtained with targeted sequence capture - Thibaud Dugat, Valentin Loux, Sylvain Marthey, Marco Moroldo, Anne-Claire Lagrée, Henri-Jean Boulouis, Nadia Haddad, and Renaud Maillard - BMC Genomics
- Complete Genome Sequence of Leuconostoc citreum Strain NRRL B-742 - Delphine Passerini, Marlène Vuillemin, Sandrine Laguerre, Myriam Amari, Valentin Loux, Valérie Gabriel, Hervé Robert, Sandrine Morel, Pierre Monsan, Bruno Gabriel, Catherine Fontagné-Faucher, Magali Remaud-Siméon, and Claire Moulis - Genome Announcements
- Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products. - Mathieu Almeida, Agnès Hébert, Anne-Laure Abraham, Simon Rasmussen, Christophe Monnet, Nicolas Pons, Céline Delbès, Valentin Loux, Jean-Michel Batto, Pierre Léonard, Sean Kennedy, Stanislas Dusko Ehrlich, Mihai Pop, Marie-Christine Montel, Françoise Irlinger, and Pierre Renault - BMC Genomics
- Data from an integrative approach decipher the surface proteome of Propionibacterium freudenreichii - Caroline Le Maréchal, Vincent Peton, Coline Plé, Christophe Vroland, Julien Jardin, Valérie Briard-Bion, Gaël Durant, Victoria Chuat, Valentin Loux, Benoit Foligné, Stéphanie-Marie Deutsch, Hélène Falentin, and Gwenaël Jan - Data in Brief
- Genetic structure of populations of whale sharks among ocean basins and evidence for their historic rise and recent decline. - Vignaud T.M., J.A. Maynard, R. Leblois, M.G. Meekan, R. Vazquez-Juarez, D. Ramirez-Macias, S.J. Pierce, D. Rowat, M.L. Berumen, C. Beeravolu, S. Baksay, S. Planes - Molecular Biology and Evolution 31: 2805-2823. doi: 10.1093/molbev/msu212
- Genome Sequence of “Candidatus Arthromitus” sp. Strain SFB- Mouse-NL, a Commensal Bacterium with a Key Role in Postnatal Maturation of Gut Immune Functions - Alexander Bolotin, Tomas de Wouters, Pamela Schnupf, Christiane Bouchier, Valentin Loux, Moez Rhimi, Alexandre Jamet, Rozenn Dervyn, Samira Boudebbouze, Hervé M Blottière, Alexei Sorokin, Johannes Snel, Nadine Cerf-Bensussan, Valérie Gaboriau-Routhiau, Maarten van de Guchte, and Emmanuelle Maguin - Genome Announcements
- Genome Sequence of Lactobacillus delbrueckii subsp. lactis CNRZ327, a Dairy Bacterium with Anti-Inflammatory Properties - Hela El Kafsi, Johan Binesse, Valentin Loux, Julien Buratti, Samira Boudebbouze, Rozenn Dervyn, Amal Hammani, Emmanuelle Maguin, and Maarten van de Guchte - Genome Announcements
- Genome Sequence of Lactobacillus delbrueckii subsp. lactis CNRZ327, a Dairy Bacterium with Anti-Inflammatory Properties - Hela El Kafsi, Johan Binesse, Valentin Loux, Julien Buratti, Samira Boudebbouze, Rozenn Dervyn, Amal Hammani, Emmanuelle Maguin, and Maarten van de Guchte - Genome Annoncements
- Genome Sequence of Lactococcus lactis subsp. lactis bv. diacetylactis LD61 - Hélène Falentin, Delphine Naquin, Valentin Loux, Frédérique Barloy-Hubler, Pascal Loubiere, Sébastien Nouaille, Dominique Lavenier, Pascal Le Bourgeois, Patrice François, Jacques Schrenzel, David Hernandez, Sergine Even, and Yves Le Loir - Genome Announcements
- Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis subsp. lactis TOMSC161, Isolated from a Nonscalded Curd Pressed Cheese - H Velly, P Renault, A L Abraham, Valentin Loux, A Delacroix-Buchet, F Fonseca, and M Bouix - Genome Announcements
- Insyght: navigating amongst abundant homologues, syntenies and gene functional annotations in bacteria, it’s that symbol! - Thomas Lacroix, Valentin Loux, Annie Gendrault, Mark Hoebeke, and Jean-François Gibrat - Nucleic Acids Research
- Lactobacillus delbrueckii ssp. lactis and ssp. bulgaricus: a chronicle of evolution in action - Hela El Kafsi, Johan Binesse, Valentin Loux, Julien Buratti, Samira Boudebbouze, Rozenn Dervyn, Sean Kennedy, Nathalie Galleron, Benoit Quinquis, Jean-Michel Batto, Bouziane Moumen, Emmanuelle Maguin, and Maarten van de Guchte - BMC Genomics
- Maximum likelihood inference of population size contractions from microsatellite data - Leblois R., P. Pudlo, J. Néron, F. Bertaux, C. Reddy Beeravolu, R. Vitalis, F. Rousset - Molecular Biology and Evolution 31: 2805-2823. doi: 10.1093/molbev/msu212
- Remodeling Cildb, a popular database for cilia and links for ciliopathies - Arnaiz O, Cohen J, Tassin AM, Koll F. - Cilia
- Surface proteins of Propionibacterium freudenreichii are involved in its anti-inflammatory properties - Caroline Le Maréchal, Vincent Peton, Coline Plé, Christophe Vroland, Julien Jardin, Valérie Briard-Bion, Gaël Durant, Victoria Chuat, Valentin Loux, Benoit Foligné, Stéphanie-Marie Deutsch, Hélène Falentin, and Gwenaël Jan - Journal of Proteomics
- Technical challenges in metatranscriptomic studies applied to the bacterial communities of freshwater ecosystems - N. Pascault, V. Loux, S. Derozier, V. Martin, S. Debroas, D.and Maloufi, J. F. Humbert, and J. Leloup - Genetica, 143(2): 157-167
- Transcriptomic analysis of Staphylococcus xylosus in the presence of nitrate and nitrite in meat reveals its response to nitrosative stress - Aurore Vermassen, Anne de la Foye, Valentin Loux, Régine Talon, and Sabine Leroy - Frontiers in Microbiology
2013
Article
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Population Genetics of L a c t o b a c i l l u s s a k e i Reveals Three Lineages with Distinct Evolutionary Histories -
Ste ´phane Chaillou1,2*, Isabelle Lucquin1,2, Afef Najjari3, Monique Zagorec1,2¤, MarieChristine Champomier-Verge `s -
PLOS One
Document: