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Valentin Loux

182
Documents
Identifiants chercheurs

Présentation

Valentin Loux is head of the INRAE Migale bioinformatics facility, part of the MaiAGE laboratory. [The Migale bioinformatics facility](https://migale.inrae.fr) 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](https://www.france-genomique.org) in charge of bionformatics development coordination **2002-2015 :** Bioinformatics Staff Engineer , INRAE Mig laboratory **CURSUS** **2002**: Master's degree in Bioinformatics (DESS), Versailles Saint-Quentin University

Publications

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Towards a more accurate metabarcoding approach for studying fungal communities of fermented foods

Olivier Rué , Monika Coton , Eric Dugat-Bony , Kate Howell , Françoise Irlinger
Peer Community Journal, 2023, ⟨10.24072/pci.microbiol.100007⟩
Article dans une revue hal-04234976v1
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Comparison of metabarcoding taxonomic markers to describe fungal communities in fermented foods

Olivier Rué , Monika Coton , Eric Dugat-Bony , Kate Howell , Françoise Irlinger
Peer Community Journal, 2023, 3 (e97), pp.1-25. ⟨10.24072/pcjournal.321⟩
Article dans une revue hal-04237955v2
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Comparative Genome Analysis of Enterococcus cecorum Reveals Intercontinental Spread of a Lineage of Clinical Poultry Isolates

Jeanne Laurentie , Valentin Loux , Christelle Hennequet-Antier , Emilie Chambellon , Julien Deschamps
MSphere, 2023, 8 (2), pp.e0049522. ⟨10.1128/msphere.00495-22⟩
Article dans une revue hal-04004063v1
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Omnicrobe, an open-access database of microbial habitats and phenotypes using a comprehensive text mining and data fusion approach

Sandra Dérozier , Robert Bossy , Louise Deléger , Mouhamadou Ba , Estelle Chaix
PLoS ONE, 2023, 18 (1), pp.e0272473. ⟨10.1371/journal.pone.0272473⟩
Article dans une revue hal-03984703v1
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Gene co-expression network analysis of the human gut commensal bacterium Faecalibacterium prausnitzii in R-Shiny

Sandrine Auger , Virginie Mournetas , Hélène Chiapello , Valentin Loux , Philippe Langella
PLoS ONE, 2022, 17 (11), pp. e0271847. ⟨10.1371/journal.pone.0271847⟩
Article dans une revue hal-04083924v1
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Integration of Multiomic Data to Characterize the Influence of Milk Fat Composition on Cantal-Type Cheese Microbiota

Marie Frétin , Amaury Gérard , Anne Ferlay , Bruno Martin , S Buchin
Microorganisms, 2022, 10 (2), ⟨10.3390/microorganisms10020334⟩
Article dans une revue hal-03579395v1

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

Caroline Isabel Kothe , Alexander Bolotin , Bochra-Farah Kraïem , Bedis Dridi , Sandra Dérozier
International Journal of Food Microbiology, 2021, 358, pp.109312. ⟨10.1016/j.ijfoodmicro.2021.109312⟩
Article dans une revue hal-04311697v1

Microbial and functional characterization of an allochthonous consortium applied to hydrogen production from Citrus Peel Waste in batch reactor in optimized conditions

Franciele Pereira Camargo , Isabel Kimiko Sakamoto , Tiago Palladino Delforno , Mahendra Mariadassou , Valentin Loux
Journal of Environmental Management, 2021, 291, pp.112631. ⟨10.1016/j.jenvman.2021.112631⟩
Article dans une revue hal-03211333v1

Insights into the cyanosphere: capturing the respective metabolisms of cyanobacteria and chemotrophic bacteria in natural conditions?

Noémie Pascault , Olivier Rué , Valentin Loux , Jacques Pédron , Véronique Martin
Environmental Microbiology Reports, 2021, 13 (3), pp.364-374. ⟨10.1111/1758-2229.12944⟩
Article dans une revue hal-03287195v1

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

Maxime Branger , Valentin Loux , Thierry Cochard , Maria Laura Boschiroli , Franck Biet
Infection, Genetics and Evolution, 2020, 82, 4 p. ⟨10.1016/j.meegid.2020.104309⟩
Article dans une revue hal-02905303v1
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Large-scale multivariate dataset on the characterization of microbiota diversity, microbial growth dynamics, metabolic spoilage volatilome and sensorial profiles of two industrially produced meat products subjected to changes in lactate concentration and packaging atmosphere

Simon Poirier , Ngoc-Du Martin Luong , Valérie Anthoine , Sandrine Guillou , Jeanne-Marie Membré
Data in Brief, 2020, 30, pp.1-8. ⟨10.1016/j.dib.2020.105453⟩
Article dans une revue hal-02914971v1
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Abundance, Diversity and Role of ICEs and IMEs in the Adaptation of Streptococcus salivarius to the Environment

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

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

Jeffrey Cornuault , Elisabeth Moncaut , Valentin Loux , Aurélie Mathieu , Harry Sokol
The International Society of Microbiologial Ecology Journal, 2020, 14 (3), pp.771-787. ⟨10.1038/s41396-019-0566-x⟩
Article dans une revue hal-02504597v1

Comparative metatranscriptomic analysis of anaerobic digesters treating anionic surfactant contaminated wastewater

Tiago P. Delforno , Thais Z. Macedo , Cedric Midoux , Gileno V. Lacerda , Olivier Rué
Science of the Total Environment, 2019, 2019 (649), pp.482-494. ⟨10.1016/j.scitotenv.2018.08.328⟩
Article dans une revue hal-01888286v1

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

Yves Vandenbrouck , David Christiany , Florence Combes , Valentin Loux , Virginie Brun
Proteomics, 2019, 19 (21-22), pp.e1800489. ⟨10.1002/pmic.201800489⟩
Article dans une revue hal-02296155v1
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Effect of sodium chloride reduction or partial substitution with potassium chloride on the microbiological, biochemical and sensory characteristics of semi-hard and soft cheeses

Eric Dugat-Bony , Pascal Bonnarme , Sébastien Fraud , Jessie Catellote , Anne-Sophie Sarthou
Food Research International, 2019, 125, pp.108643. ⟨10.1016/j.foodres.2019.108643⟩
Article dans une revue hal-02349939v1
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Detection of an amplification bias associated to Leuconostocaceae family with a universal primer routinely used for monitoring microbial community structures within food products

Simon Poirier , Olivier Rué , Gwendoline Coeuret , Marie-Christine Champomier-Verges , Valentin Loux
BMC Research Notes, 2018, 11 (1), pp.1-5. ⟨10.1186/s13104-018-3908-2⟩
Article dans une revue hal-02048857v1

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

Reine Malek , Pascal Bonnarme , Francoise Irlinger , Pascale Frey-Klett , Djamila Onesime
International Journal of Food Microbiology, 2018, 264, pp.53-62. ⟨10.1016/j.ijfoodmicro.2017.10.026⟩
Article dans une revue hal-01695894v1
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Complete 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-Verges , Stephane Chaillou
Genome Announcements, 2018, 6 (16), 3 p. ⟨10.1128/genomeA.00082-18⟩
Article dans une revue hal-02619093v1
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Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing

Simon Poirier , Olivier Rué , Raphaelle Peguilhan , Gwendoline Coeuret , Monique Zagorec
PLoS ONE, 2018, 13 (9), ⟨10.1371/journal.pone.0204629⟩
Article dans une revue hal-02621350v1
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Genomic diversity and evolution of the fish pathogen flavobacterium psychrophilum

Éric Duchaud , Tatiana Rochat , Christophe Habib , Paul Barbier , Valentin Loux
Frontiers in Microbiology, 2018, 9, pp.1-20. ⟨10.3389/fmicb.2018.00138⟩
Article dans une revue hal-02629284v1
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Complete genome sequence of the industrial fast-acidifying strain Streptococcus thermophilus N4L

Lucas Proust , Valentin Loux , Veronique Martin , Cristian Magnabosco , Martin Pedersen
Microbiology Resource Announcements, 2018, 7 (8), ⟨10.1128/MRA.01029-18⟩
Article dans une revue hal-02628963v1

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

Xavier Argemi , Veronique Martin , Valentin Loux , Sandrine Dahyot , Jérémie Lebeurre
Genome Biology and Evolution, 2017, 9 (5), pp.1183-1189. ⟨10.1093/gbe/evx077⟩
Article dans une revue hal-01604276v1

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

Eugene Christo-Foroux , Tatiana Vallaeys , Valentin Loux , Elie Dassa , Josef Deutscher
Systematic and Applied Microbiology, 2017, 40 (7), pp.401-410. ⟨10.1016/j.syapm.2017.07.002⟩
Article dans une revue hal-01604275v1
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Identification of proteins involved in the anti-inflammatory properties of Propionibacterium freudenreichii by means of a multi-strain study

Stéphanie-Marie Deutsch , Mahendra Mariadassou , Pierre Nicolas , Sandrine Parayre , Rozenn Le Guellec
Scientific Reports, 2017, 7, pp.46409. ⟨10.1038/srep46409⟩
Article dans une revue hal-01510019v1
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The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes

Vincent J. Henry , Anne Goelzer , Arnaud Ferré , Stéphan Fischer , Marc Dinh
Journal of Biomedical Semantics, 2017, 8 (53), 16 p. ⟨10.1186/s13326-017-0165-6⟩
Article dans une revue hal-01652923v1
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Complete Genome Sequence of Flavobacteriumpsychrophilum Strain OSU THCO2-90, Used for Functional Genetic Analysis.

Tatiana Rochat , Paul Barbier , Pierre Nicolas , Valentin Loux , David Perez Pascual
Genome Announcements, 2017, 5 (23), 2 p. ⟨10.1128/genomeA.01665-16⟩
Article dans une revue hal-01607798v1
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Draft Genome Sequences of 18 Psychrotolerant and 2 Thermotolerant Strains Representative of Particular Ecotypes in the Bacillus cereus Group

Marie Helene Guinebretière , Valentin Loux , Véronique Martin , Pierre Nicolas , Vincent Sanchis Borja
Genome Announcements, 2017, 5 (5), 3 p. ⟨10.1128/genomeA.01568-16⟩
Article dans une revue hal-01602632v1

La génomique comparative à l’ère des technologies NGS

Thomas Lacroix , Jean-Francois Gibrat , Valentin Loux
Biofutur, 2017, 36 (382), pp.42-45
Article dans une revue hal-01603170v1
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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
Scientific Reports, 2017, 7, pp.1-11. ⟨10.1038/srep44331⟩
Article dans une revue hal-01509688v1
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A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins

Charles Coluzzi , Gérard Guédon , Marie-Dominique Devignes , Chloé C. Ambroset , Valentin Loux
Frontiers in Microbiology, 2017, 8, pp.16. ⟨10.3389/fmicb.2017.00443⟩
Article dans une revue hal-01580789v1
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Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CFL1, a Lactic Acid Bacterium Isolated from French Handcrafted Fermented Milk

Julie Meneghel , Eric Dugat-Bony , Françoise Irlinger , Valentin Loux , Marie Vidal
Genome Announcements, 2016, 4 (2), pp.e00052-16. ⟨10.1128/genomeA.00052-16⟩
Article dans une revue hal-01511494v1
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New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration

Chloé C. Ambroset , Charles Coluzzi , Gérard Guédon , Marie-Dominique Devignes , Valentin Loux
Frontiers in Microbiology, 2016, 6 (6), pp.1483. ⟨10.3389/fmicb.2015.01483⟩
Article dans une revue hal-01262284v1
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Complete Genome Sequence of Lactococcus lactissubsp. lactis A12, a Strain Isolated from Wheat Sourdough

Maeva Guellerin , Delphine Passerini , Catherine Fontagné-Faucher , Hervé Robert , Valérie Gabriel
Genome Announcements, 2016, 4 (5), pp.2 P. ⟨10.1128/genomeA.00692-16⟩
Article dans une revue hal-01578250v1
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Permanent draft genome sequence of the probiotic strain Propionibacterium freudenreichii CIRM-BIA 129 (ITG P20).

Hélène Falentin , Stéphanie-Marie Deutsch , Valentin Loux , Amal Hammani , Julien Buratti
Standards in Genomic Sciences, 2016, 11, pp.6. ⟨10.1186/s40793-015-0120-z⟩
Article dans une revue hal-02640172v1
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Draft genome sequence of Corynebacterium variabile Mu292, isolated from Munster, a french smear-ripened cheese

Eric Dugat-Bony , Anne-Sophie Sarthou , Valentin Loux , Marie Vidal , Pascal Bonnarme
Genome Announcements, 2016, 4 (4), ⟨10.1128/genomeA.00669-16⟩
Article dans une revue hal-01480898v1

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

Thomas Lacroix , Sylvie Thérond , Marc Rugeri , Pierre P. Nicolas , Annie Gendrault
Bioinformatics, 2016, 32 (7), pp.1083-1084. ⟨10.1093/bioinformatics/btv689⟩
Article dans une revue hal-02630699v1
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Draft Anaplasma phagocytophilum Genome Sequences from Five Cows, Two Horses, and One Roe Deer Collected in Europe.

Thibaud Dugat , Marie-Noelle Rossignol , Olivier Rué , Valentin Loux , Sylvain Marthey
Genome Announcements, 2016, 4 (6), 2 p. ⟨10.1128/genomeA.00950-16⟩
Article dans une revue hal-01594527v1
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Genome Sequences of Two Bovine Mastitis-Causing [i]Escherichia coli[/i] Strains

Florent Kempf , Valentin Loux , Pierre Germon
Genome Announcements, 2015, 3 (2), pp.1. ⟨10.1128/genomeA.00259-15⟩
Article dans une revue hal-01171499v1
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Overview of a surface-ripened cheese community functioning by meta-omics analyses

Eric Dugat-Bony , Cecile Straub , Aurélie Teissandier , Djamila Onesime , Valentin Loux
PLoS ONE, 2015, 10 (4), pp.e0124360. ⟨10.1371/journal.pone.0124360⟩
Article dans une revue hal-01195505v1

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

Delphine Passerini , Marlène Vuillemin , Lisa Ufarté , Sandrine Morel , Valentin Loux
FEBS Journal, 2015, 282 (11), pp.2115-2130. ⟨10.1111/febs.13261⟩
Article dans une revue hal-02630462v1
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Surface proteins of Propionibacterium freudenreichii are involved in its anti-inflammatory properties.

Caroline Le Maréchal , Vincent Péton , Coline Plé , Christophe Vroland , Julien Jardin
Journal of Proteomics, 2015, 113, pp.447-461. ⟨10.1016/j.jprot.2014.07.018⟩
Article dans une revue hal-01209735v1
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Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii

Valentin Loux , Mahendra Mariadassou , Sintia Almeida , Hélène Chiapello , Amal Hammani
BMC Genomics, 2015, 16 (1), pp.35. ⟨10.1186/s12864-015-1467-7⟩
Article dans une revue hal-01142363v1

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

Noémie Pascault , Valentin Loux , Sandra Derozier , Véronique Martin , Didier Debroas
Genetica, 2014, 143 (2), pp.25216965. ⟨10.1007/s10709-014-9783-4⟩
Article dans une revue hal-01110172v1
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Complete Genome Sequence of Leuconostoc citreum Strain NRRL B-742

Delphine Passerini , Marlène Vuillemin , S. Laguerre , Myriam Amarir , Valentin Loux
Genome Announcements, 2014, 2 (6), ⟨10.1128/genomeA.01179-14⟩
Article dans une revue hal-02637077v1
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Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis subsp. lactis TOMSC161, Isolated from a Nonscalded Curd Pressed Cheese

Hélène Velly , Pierre Renault , Anne-Laure Abraham , Valentin Loux , Agnes Delacroix-Buchet
Genome Announcements, 2014, 2 (6), ⟨10.1128/genomeA.01121-14⟩
Article dans une revue hal-01193999v1
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Comparative genomics of first available bovine Anaplasma phagocytophilum genome obtained with targeted sequence capture.

Thibaud Dugat , Valentin Loux , Sylvain Marthey , Marco Moroldo , Anne-Claire Lagrée
BMC Genomics, 2014, 15 (1), pp.973. ⟨10.1186/1471-2164-15-973⟩
Article dans une revue hal-01193998v1
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Lactobacillus delbrueckii ssp. lactis and ssp. bulgaricus: a chronicle of evolution in action.

Hela El Kafsi , Johan Binesse , Valentin Loux , Julien Buratti , Samira Boudebbouze
BMC Genomics, 2014, 15 (1), pp.407. ⟨10.1186/1471-2164-15-407⟩
Article dans une revue pasteur-01017376v1
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Genome sequence of[i] Lactobacillus delbrueckii[/i] subsp. [i]lactis[/i] CNRZ327, a dairy bacterium with anti-inflammatory properties.

Hela El Kafsi , Johan Binesse , Valentin Loux , Julien Buratti , Samira Boudebbouze
Genome Announcements, 2014, 2 (4), pp.1-2. ⟨10.1128/genomeA.00328-14⟩
Article dans une revue hal-01204323v1
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Genome Sequence of "Candidatus Arthromitus" sp. Strain SFB-Mouse-NL, a Commensal Bacterium with a Key Role in Postnatal Maturation of Gut Immune Functions.

Alexandre Bolotine , Tomas de Wouters , Pamela Schnupf , Christiane Bouchier , Valentin Loux
Genome Announcements, 2014, 2 (4), ⟨10.1128/genomeA.00705-14⟩
Article dans une revue hal-01204391v1
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Bacterial protein signals are associated with Crohn's disease.

Catherine Juste , David P Kreil , Christian Beauvallet , Alain Guillot , Sebastian Vaca
Gut, 2014, 63 (10), pp.1566-1577. ⟨10.1136/gutjnl-2012-303786⟩
Article dans une revue hal-00933734v1
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Transcriptomic analysis of Staphylococcus xylosus in the presence of nitrate and nitrite in meat reveals its response to nitrosative stress

Aurore Vermassen , Anne de La Foye , Valentin Loux , Régine Talon , Sabine Leroy
Frontiers in Microbiology, 2014, 5, n.p. ⟨10.3389/fmicb.2014.00691⟩
Article dans une revue hal-02631923v1
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Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products

Mathieu Almeida , Agnes Hebert , Anne-Laure Abraham , Simon Rasmussen , Christophe Monnet
BMC Genomics, 2014, 15, article 1101 (16 p.). ⟨10.1186/1471-2164-15-1101⟩
Article dans une revue hal-01195502v1

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

Caroline Le Maréchal , Vincent Péton , Coline Le Plenier , Christophe Vroland , Julien Jardin
Data in Brief, 2014, 1, pp.46-50. ⟨10.1016/j.dib.2014.08.009⟩
Article dans une revue hal-01209746v1
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Genome Sequence of Lactococcus lactis subsp. lactis bv. diacetylactis LD61.

Hélène Falentin , Delphine Naquin , Valentin Loux , Frédérique Barloy-Hubler , Pascal Loubière
Genome Announcements, 2014, 2 (1), pp.1. ⟨10.1128/genomeA.01176-13⟩
Article dans une revue hal-01019560v1
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Insyght: navigating amongst abundant homologues, syntenies and gene functional annotations in bacteria, it's that symbol!

Thomas Lacroix , Valentin Loux , Annie Gendrault , Mark Hoebeke , Jean-François Gibrat
Nucleic Acids Research, 2014, 42 (21), pp.e162. ⟨10.1093/nar/gku867⟩
Article dans une revue hal-01332638v1
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Complete chromosome sequence of Carnobacterium maltaromaticum LMA 28.

Catherine C. Cailliez-Grimal , Stephane S. Chaillou , Jamila J. Anba-Mondoloni , Valentin Loux , Muhammad Inam M. I. Afzal
Genome Announcements, 2013, 1 (1), pp.1-2. ⟨10.1128/genomeA.00115-12⟩
Article dans une revue hal-00939584v1
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Draft Genome Sequence of [i][/i] Lactobacillus pasteurii[i][/i] CRBIP 24.76T.

Sylvie Cousin , Dominique Clermont , Sophie Creno , Laurence Ma , Valentin Loux
Genome Announcements, 2013, 1 (4), ⟨10.1128/genomeA.00660-13⟩
Article dans une revue hal-01190531v1
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Draft genome sequence of Lactobacillus hominis strain CRBIP 24.179τ, isolated from human intestine

Sylvie Cousin , Sophie Creno , Laurence Ma , Dominique Clermont , Valentin Loux
Genome Announcements, 2013, 1 (4), pp.1. ⟨10.1128/genomeA.00662-13⟩
Article dans une revue hal-00939673v1

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

Hélène Falentin , Sylvie Cousin , Dominique Clermont , Sophie Creno , Florence Ma
Genome Announcements, 2013, 1 (4), pp.e00658-13. ⟨10.1128/genomeA.00658-13⟩
Article dans une revue hal-01209470v1
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A unique in vivo experimental approach reveals metabolic adaptation of the probiotic Propionibacterium freudenreichii to the colon environment.

Taous Saraoui , Sandrine Parayre , Grégory Guernec , Valentin Loux , Jérôme Montfort
BMC Genomics, 2013, 14 (1), pp.911. ⟨10.1186/1471-2164-14-911⟩
Article dans une revue inserm-00923652v1
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Draft genome sequences of Lactobacillus equicursoris CIP 110162τ and Lactobacillus sp. strain CRBIP 24.137, isolated from thoroughbred racehorse feces and human urine, respectively

Sylvie Cousin , Valentin Loux , Laurence Ma , Sophie Creno , Dominique Clermont
Genome Announcements, 2013, 1 (4), pp.1-2. ⟨10.1128/genomeA.00663-13⟩
Article dans une revue hal-02645656v1

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

Sandrine Laguerre , Myriam Amari , Marlène Vuillemin , Hervé Robert , Valentin Loux
Journal of Bacteriology, 2012, 194 (6), pp.1610-1611. ⟨10.1128/JB.06789-11⟩
Article dans une revue hal-01267778v1

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

Olivier Grépinet , Zineb Boumart , Isabelle Virlogeux-Payant , Valentin Loux , Hélène Chiapello
Journal of Bacteriology, 2012, 194 (9), pp.2385-2386. ⟨10.1128/JB.00255-12⟩
Article dans une revue hal-02643377v1

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

Paul Barbier , Armel A. Houel , Valentin Loux , Julie Poulain , Jean-François Bernardet
Journal of Bacteriology, 2012, 194 (11), pp.3024-3025. ⟨10.1128/JB.00420-12⟩
Article dans une revue hal-02643519v1
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Genome sequence of Lactococcus raffinolactis strain 4877, isolated from natural dairy starter culture

Victoria Meslier Meslier , Valentin Loux , Pierre Renault
Journal of Bacteriology, 2012, 194 (22), pp.6364. ⟨10.1128/JB.01697-12⟩
Article dans une revue hal-01000376v1
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Genome sequence of corynebacterium casei UCMA 3821, isolated from a smear-ripened cheese

Christophe C. Monnet , Valentin Loux , Pascal P. Bento , Jean-Francois J.-F. Gibrat , Cecile C. Straub
Journal of Bacteriology, 2012, 194 (3), pp.738-739. ⟨10.1128/JB.06496-11⟩
Article dans une revue hal-01000221v1
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Genome sequence of weissella confusa LBAE C39-2, isolated from a wheat sourdough

Myriam Amari , Sandrine Laguerre , Marlène Vuillemin , Hervé Robert , Valentin Loux
Journal of Bacteriology, 2012, 194 (6), pp.1608-1609. ⟨10.1128/JB.06788-11⟩
Article dans une revue hal-01267779v1

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

Marion Dalmasso , Julie Aubert , Sergine Even , Hélène Falentin , Marie-Bernadette Maillard
Applied and Environmental Microbiology, 2012, 78 (17), pp.6357-6364. ⟨10.1128/AEM.00561-12⟩
Article dans une revue hal-02363390v1
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Genome sequence of Staphylococcus equorum subsp equorum Mu2, Isolated from a french smear-ripened cheese

Francoise Irlinger , Valentin Loux , Pascal Bento , Jean-Francois Gibrat , Cecile Straub
Journal of Bacteriology, 2012, 194 (18), pp.5141-5142. ⟨10.1128/JB.01038-12⟩
Article dans une revue hal-01019837v1

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

Olivier Grépinet , Aurore Rossignol , Valentin Loux , Helene Chiapello , Annie Gendrault
Journal of Bacteriology, 2012, 194 (9), pp.2387-2388. ⟨10.1128/JB.00256-12⟩
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Accumulation of intracellular glycogen and trehalose by [i]Propionibacterium Freudenreichii[/i] under conditions mimicking cheese ripening in the cold

Marion Dalmasso , Julie Aubert , Sergine Even , Hélène Falentin , Marie-Bernadette Maillard
Applied and Environmental Microbiology, 2012, 78 (17), pp.6357-6364. ⟨10.1128/AEM.00561-12⟩
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Genome sequence of Leuconostoc pseudomesenteroides strain 4882, isolated from a dairy starter culture

Victoria Meslier Meslier , Valentin Loux , Pierre Renault
Journal of Bacteriology, 2012, 194 (23), pp.6637. ⟨10.1128/JB.01696-12⟩
Article dans une revue hal-01000375v1
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Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis

Sophie S. Schbath , Veronique V. Martin , Matthias Zytnicki , Julien Fayolle , Valentin Loux
Journal of Computational Biology, 2012, 19 (6), pp.796-813. ⟨10.1089/cmb.2012.0022⟩
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CompaGB: An open framework for genome browsers comparison

Thomas Lacroix , Valentin Loux , Annie Gendrault-Jacquemard Gendrault , Jean-François Gibrat , Hélène Chiapello
BMC Research Notes, 2011, 4, pp.133. ⟨10.1186/1756-0500-4-133⟩
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Exploration of sulfur metabolism in the yeast Kluyveromyces lactis

Agnes A. Hebert , Marie-Pierre Forquin Forquin-Gomez , Aurélie A. Roux , Julie J. Aubert , Christophe C. Junot
Applied Microbiology and Biotechnology, 2011, 91 (5), pp.1409-1423. ⟨10.1007/s00253-011-3481-2⟩
Article dans une revue hal-01000029v1
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Complete genome sequence of the commensal Streptococcus salivarius strain JIM8777

Eric Guédon , Christine Delorme , Nicolas Pons , Corinne Cruaud , Valentin Loux
Journal of Bacteriology, 2011, 193 (18), pp.5024-5025. ⟨10.1128/JB.05390-11⟩
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Complete genome sequence of the pigmented Streptococcus thermophilus strain JIM8232

Christine C. Delorme , Claire C. Bartholini , Mélanie M. Luraschi , Nicolas N. Pons , Valentin Loux
Journal of Bacteriology, 2011, 193 (19), pp.5581-5582. ⟨10.1128/JB.05404-11⟩
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Complete genome sequence of the clinical Streptococcus salivarius strain CCHSS3

Christine C. Delorme , Eric Guédon , Nicolas N. Pons , Corinne Cruaud , Arnaud A. Couloux
Journal of Bacteriology, 2011, 193 (18), pp.5041-5042. ⟨10.1128/JB.05416-11⟩
Article dans une revue hal-01000176v1

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

Jasna Beganovic , Alain A. Guillot , Maarten van de Guchte , Anne Jouan , Christophe C. Gitton
Journal of Proteome Research, 2010, 9 (2), pp.677-688
Article dans une revue hal-02657656v1
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The complete genome of Propionibacterium freudenreichii CIRM-BIA1T, a Hardy actinobacterium with food and probiotic applications

Hélène Falentin , Stéphanie-Marie Deutsch , Gwénaël Jan , Valentin Loux , Anne Thierry
PLoS ONE, 2010, 5 (7), pp.1-12. ⟨10.1371/journal.pone.0011748⟩
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Complete genome sequence of the probiotic Lactobacillus casei strain BL23

Alain Mazé , Grégory Boël , Manuel Zùniga , Alexa Bourand , Valentin Loux
Journal of Bacteriology, 2010, 192 (10), pp.2647-2648. ⟨10.1128/JB.00076-10⟩
Article dans une revue hal-01204245v1
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The arthrobacter arilaitensis Re117 genome sequence reveals its genetic adaptation to the surface of cheese

Christophe Monnet , Valentin Loux , Jean-Francois Gibrat , Valérie Barbe , Benoit Vacherie
PLoS ONE, 2010, 5 (11), pp.e15489. ⟨10.1371/journal.pone.0015489⟩
Article dans une revue hal-01195440v1
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Identification of brevibacteriaceae by multilocus sequence typing and comparative genomic hybridization analyses.

Marie-Pierre Forquin , Hugo Duvergey , Caroline Proux , Valentin Loux , Jérôme Mounier
Applied and Environmental Microbiology, 2009, 75 (19), pp.6406-9. ⟨10.1128/AEM.00224-09⟩
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Prediction of surface exposed proteins in Streptococcus pyogenes, with a potential application to other Gram-positive bacteria

Aleksandr Barinov , Valentin Loux , Amal Hammani , Pierre P. Nicolas , Philippe P. Langella
Proteomics, 2009, 9 (1), pp.61-73. ⟨10.1002/pmic.200800195⟩
Article dans une revue hal-02663676v1

Complete genome sequence of the fish pathogen Flavobacterium psychrophilum

Éric Duchaud , Mekki Boussaha , Valentin Loux , Jean-François Bernardet , Christian Michel
Nature Biotechnology, 2007, 25 (7), pp.763 - 769. ⟨10.1038/nbt1313⟩
Article dans une revue hal-02666599v1
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The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution

Maarten van de Guchte , Stéphanie Penaud , Christine Grimaldi , Valérie Barbe , K. Bryson
Proceedings of the National Academy of Sciences of the United States of America, 2006, 103 (24), pp.9274-9279. ⟨10.1073/pnas.0603024103⟩
Article dans une revue hal-02668654v1
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AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system

K. Bryson , Valentin Loux , Robert R. Bossy , P. Nicolas , Stephane S. Chaillou
Nucleic Acids Research, 2006, 34 (12), pp.3533-3545. ⟨10.1093/nar/gkl471⟩
Article dans une revue hal-02665192v1

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

Stephane S. Chaillou , Marie-Christine Champomier Verges , Monique Cornet , Anne-Marie Crutz-Le Coq , Anne-Marie Dudez
Nature Biotechnology, 2005, 23 (12), pp.1527-1533. ⟨10.1038/nbt1160⟩
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Origins and rate of mutations in bacteriophage Lambda

Julien Lopez , Mahendra Mariadassou , Valentin Loux , Rafael Sanjuán , Marina Elez
Phages in Lyon 2023, phages.fr, Nov 2023, Lyon, France
Communication dans un congrès hal-04321371v1

MetaPDOcheese : investigation of the drivers of microbial communities from French PDO milks and cheeses

Francoise Irlinger , Mahendra Mariadassou , Eric Dugat-Bony , Cécile Neuvéglise , Olivier Rué
FORUM ON FERMENTED FOODS, COST PIMENTO, May 2023, Lyon, France
Communication dans un congrès hal-04221356v1

Variable and core functional rhizosphere microbiota associated with seven Medicago truncatula genotypes

Zhu, Liya , Olivier Rué , Florence Deau , Julie Cremaschi , Valentin Loux
Journée doctorants UMR Agroécologie, Nov 2023, Dijon, France
Communication dans un congrès hal-04317070v1

Variable and core functional microbiota associated with seven Medicago truncatula genotypes

Zhu, Liya , Olivier Rué , Florence Deau , Julie Cremaschi , Valentin Loux
12th International PGPR Workshop 2023, May 2023, Toulouse, France
Communication dans un congrès hal-04139303v1

Migale et son offre de service de text-mining

Valentin Loux , Mouhamadou Ba
Journées du PEPI IBIS, INRAE, Sep 2023, Paris, France
Communication dans un congrès hal-04294052v1

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

Julie Lao , Gérard Guédon , Thomas Lacroix , Florence Charron-Bourgoin , Virginie Libante
Réunion du GDR3546 Eléments transposables, Dec 2021, Paris, France
Communication dans un congrès hal-03495840v1

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

Cassandre Bedu-Ferrari , Paul Biscarrat , Sarah Vati , Cyril Chaudemanche , Valérie Benoit
International Scientific Association for Probiotics and Prebiotics Annual Meeting, Jun 2021, Online conference, France
Communication dans un congrès hal-04285897v1

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

Cassandre Bedu-Ferrari , Paul Biscarrat , Sarah Vati , Cyril Chaudemanche , Valerie Benoit
Society for Applied Microbiology Early Career Scientist Research Symposium, Mar 2021, Online Conference, France
Communication dans un congrès hal-04285885v1

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

Cassandre Bedu-Ferrari , Sarah Vati , Cyril Chaudemanche , Valérie Benoit , Thomas Lacroix
ABIES Days, Sep 2020, Paris, France
Communication dans un congrès hal-04285875v1

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

Sandra Derozier , Sam Ah-Lone , Valentin Loux , Hélène Chiapello
JOBIM : Journées Ouvertes Biologie Informatique Mathématiques, Jul 2019, Nantes, France
Communication dans un congrès hal-02733948v1

Shotgun metagenomics sequencing of the rhizosphere microbiota associated to seven ecotypes of Medicago truncatula

Julie Cremaschi , Olivier Rué , Florence Deau , Philippe Lemanceau , Valentin Loux
Rhizosphere 5, Jul 2019, Saskatoon, Saskatchewan, Canada
Communication dans un congrès hal-02735116v1

Evaluation of gyrB amplicon sequencing in comparison to 16S rDNA amplicon sequencing to evaluate intra-species bacterial diversity in food microbiota

Olivier Rué , Simon Poirier , Raphaelle Peguilhan , Valentin Loux , Marie-Christine Champomier-Vergès
JOBIM 20. Journées Ouvertes Biologie Informatique Mathématiques, Jul 2019, Nantes, France
Communication dans un congrès hal-02947091v1
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A metagenomic tool for cheese ecosystems

Anne-Laure Abraham , Quentin Cavaillé , Thibaut Guirimand , Pierre Renault , Sandra Derozier
17. European Conference on Computational Biology (ECCB 2018, Workshop "Recent Computational Advances in Metagenomics (RCAM)", Sep 2018, Athenes, Greece
Communication dans un congrès hal-02789036v1
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L'ontologie OntoBiotope pour l'étude de la biodiversité microbienne

Claire Nédellec , Estelle Chaix , Robert Bossy , Louise Deleger , Sandra Derozier
EGC'2018: 18èmes Conférence Internationale sur l'Extraction et la Gestion des Connaissances, Jan 2018, Paris, France
Communication dans un congrès hal-02737399v1

Functional signatures of soil fungal communities in response to forest tree phenology revealed by metatranscriptome analysis

Marc Buée , Lucas Auer , Patricia Luis , Olivier Rué , Valentin Loux
3rd MPItM-Labex ARBRE Workshop, Nov 2018, cologne, Germany
Communication dans un congrès hal-03339776v1

The journey of a team of engineers in learning packaging technology

Laure Quintric , Patrick Durand , Olivier Inizan , Valentin Marcon , Caroline Dussart
Galaxy Community Conference - GCC2018, Jun 2018, Portland, United States
Communication dans un congrès hal-02784992v1

Des microbes dans mon fromage ?

Sophie Schbath , Valentin Loux
Journées Nationales de la Science Ouverte, Dec 2018, Paris, France
Communication dans un congrès hal-01954713v1

Florilège: a database gathering microbial phenotypes of food interest

Hélène Falentin , Estelle Chaix , Bedis Dridi , Philippe Bessieres , S Buchin
2017 Scientific MEM days: Journées scientifiques MEM (Métaomiques et écosystèmes microbiens), Jan 2017, Paris, France
Communication dans un congrès hal-01607327v1
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Food-Microbiomes Transfert, a shotgun metagenomic tool and a database to analyze cheese ecosystems

Thibaut Guirimand , Anne-Laure Abraham , Sandra Derozier , Charlie Pauvert , Mahendra Mariadassou
JOBIM 2017 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2017, Lille, France
Communication dans un congrès hal-02788899v1
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Représentation systémique multi-échelle des processus biologiques de la bactérie

Vincent J. Henry , Arnaud Ferré , Christine Froidevaux , Anne Goelzer , Vincent V. Fromion
IC2016 - Ingénierie des Connaissances, Jun 2016, Montpellier, France
Communication dans un congrès hal-01442727v1
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Représentation systémique multi-échelle des processus biologiques de la bactérie

Vincent Henry , Arnaud Ferré , Christine Froidevaux , Anne Goelzer , Vincent Fromion
IC201: 27es Journées francophones d'Ingénierie des Connaissances, Jun 2016, Montpellier, France
Communication dans un congrès hal-02741418v1

Deciphering why Salmonella Gallinarum is less invasive in vitro than Salmonella Enteritidis

Aurore Rossignol , Sylvie Roche , Isabelle Virlogeux-Payant , Olivier Grépinet , Nadia Abed
I3S International Symposium Salmonella and Salmonellosis, Institut National de la Recherche Agronomique (INRA). FRA., May 2013, Saint Malo, France
Communication dans un congrès hal-02749048v1
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Mapping reads on a genomic sequence: a practical comparative analysis

Sophie S. Schbath , Veronique V. Martin , Matthias Zytnicki , Julien Fayolle , Valentin Loux
Kick-of meeting of PF7 RADIANT project, Jan 2013, Manchester, United Kingdom. 19 diapos
Communication dans un congrès hal-02804577v1
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Mapping reads on a genomic sequence: a practical comparative analysis

Sophie S. Schbath , Veronique V. Martin , Matthias Zytnicki , Julien Fayolle , Valentin Loux
Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), Jul 2012, Rennes, France. pp.496
Communication dans un congrès hal-02748738v1

Genomic diversity of Flavobacterium species.

Éric Duchaud , Paul Barbier , Jean-François Bernardet , Christian Michel , Céline Chantry-Darmon
Flavobacterium 2012, 2012, Turku, Finland
Communication dans un congrès hal-02746549v1

Genomic diversity of 24 Propionibacterium freudenreichii 1 strains

Hélène Falentin , Valentin Loux , Valérie Barbe , Amal Plaudet Hammani , Stéphanie-Marie Deutsch
6 Conference on Functional Genomics of Gram-positive Microorganisms 16 International Conference on Bacilli, Jun 2011, Montecatini, Italy
Communication dans un congrès hal-01454328v1

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

Benoît Foligné , Valentin Loux , Christophe Hervé , Jean-René Kerjean , Denis Matter
2nd International Symposium "Microbes For Health", Dec 2011, Paris, France
Communication dans un congrès hal-01190437v1

Web services for microbial genome annotation using data integration

Célia Michotey , Ludovic Legrand , Helene H. Chiapello , Valentin Loux , Annie A. Gendrault-Jacquemard
JOBIM 2010 : Journées Ouvertes en Biologie, Informatique et Mathématiques, Sep 2010, Montpellier, France
Communication dans un congrès hal-02752226v1
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Evaluating Genome Browsers Using a Software Qualification Method Evaluation

Thomas Lacroix , Valentin Loux , Annie Gendrault-Jacquemard Gendrault , Jean-François Gibrat , Helene H. Chiapello
JOBIM 2010, Sep 2010, Montpellier, France. pp.196
Communication dans un congrès hal-02751310v1

Bactéries pathogènes des poissons du genre Flavobacterium

Éric Duchaud , Jean-François Bernardet , Brigitte Kerouault , Christian Michel , Céline Chantry
2. Journées de la Recherche Filière Piscicole, Jul 2009, Paris, France. 1 p
Communication dans un congrès hal-02823179v1
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INSYGT : a multi-genes multi-genomes browser that highlights synteny conservation in prokaryotes.

Thomas Lacroix , Valentin Loux , Annie Gendrault-Jacquemard Gendrault , Mark M. Hoebeke , Jean-François Gibrat
JOBIM 2008, Jun 2008, Lille, France. 2 p
Communication dans un congrès hal-02824485v1
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Towards a semi-automatic functional annotation tool based on decision tree techniques

Jérôme Azé , L. Gentils , Claire Toffano-Nioche , Valentin Loux , Jean-François Gibrat
Machine Learning in Systems Biology: MLSB 2007, Sep 2007, Evry, France
Communication dans un congrès hal-02754400v1

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

Stephane S. Chaillou , Monique Cornet , Anne-Marie A.-M. Le Coq , Anne-Marie Loustau , Robert R. Bossy
Symposium SFM, Interactions Bactériennes dans les Environnements Agroalimentaires : Apport des Nouvelles Approches., Société Française de Microbiologie (SFM). FRA., Nov 2006, Paris, France
Communication dans un congrès hal-02816850v1

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

Stephane S. Chaillou , Monique Cornet , Anne-Marie A.-M. Le Coq , Anne-Marie Loustau , Robert R. Bossy
2. European Conference on Prokaryotic Genomes, Oct 2005, Göttingen, Germany
Communication dans un congrès hal-02828495v1

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

Stephane S. Chaillou , Monique Cornet , Anne-Marie Loustau , Robert R. Bossy , Valentin Loux
13. Colloque du Club des Bactéries Lactiques, Sep 2004, Nantes, France. 142 p
Communication dans un congrès hal-02759825v1
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Ferments du Futur : une plateforme unique en Europe pour accélérer la recherche et l’innovation sur les ferments, les aliments fermentés et la biopréservation dans les 10 prochaines années

Sophie Schbath , Maÿlis Urtebise , Valentin Loux , Madeleine Spatz , Damien Paineau
Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jun 2023, Tours (France), France.
Poster de conférence hal-04176537v1

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

Stéphanie Bougeard , Manon Dechêne-Tempier , Valentin Loux , Hélène Chiapello , Virginie Libante
5th International Workshop on Streptococcus suis, Jun 2023, Bangkok / Thailand, Thailand
Poster de conférence hal-04232466v1
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Implementing a Text Mining Service Offer on the Migale Bioinformatics Platform

Mouhamadou Ba , Véronique Martin , Olivier Rué , Sophie Schbath , Valérie Vidal
Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2022, Rennes, France. 2022
Poster de conférence hal-04176740v1
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Plateforme bioinformatique MIGALE

Mouhamadou Ba , Hélène Chiapello , Christelle Hennequet-Antier , Valentin Loux , Mahendra Mariadassou
Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2022, Rennes, France. 2022
Poster de conférence hal-04176761v1
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Omnicrobe : une base de données d’habitats et de phénotypes microbiens

Hélène Falentin , Olivier Harlé , Sandra Derozier , Louise Deléger , Estelle Chaix
23ème édition du colloque du Club des Bactéries Lactiques, Jun 2022, Rennes, France. , 2022
Poster de conférence hal-03694214v1

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

Zhu, Liya , Olivier Rué , Florence Deau , Julie Cremaschi , Valentin Loux
miCROPe 2022, international Symposium microbe-assisted crop production opportunities, challenges & needs, Jul 2022, Vienne, France
Poster de conférence hal-04199757v1

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

Sophie Payot , Julie Lao , Gérard Guédon , Thomas Lacroix , Florence Charron-Bourgoin
5th International Caparica Congress in Antibiotic Resistance (IC2AR 2022), Sep 2022, Caparica, Lisbon, Portugal
Poster de conférence hal-04232454v1
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Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics

Vuong Quoc Hoang Ngo , François Enault , Cédric Midoux , Mahendra Mariadassou , Olivier Chapleur
ISME18, 18th International Symposium on Microbial Ecology, Aug 2022, Lausanne, Switzerland.
Poster de conférence hal-04359643v1
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A bioinformatic pipeline to elucidate the links between viruses and their hosts in microbial communities, applied to viruses in anaerobic digestion processes

Vuong Quoc Hoang Ngo , Cédric Midoux , Mahendra Mariadassou , Valentin Loux , François Enault
JOBIM 2021 (JOBIM (Journées Ouvertes en Biologie, Informatique et Mathématiques), Jul 2021, Paris, France.
Poster de conférence hal-04359920v1
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Plateforme bioinformatique MIGALE

Mouhamadou Ba , Hélène Chiapello , Christelle Hennequet-Antier , Valentin Loux , Mahendra Mariadassou
Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2021, Paris, France. 2021
Poster de conférence hal-04176768v1

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

Cassandre Bedu-Ferrari , Paul Biscarrat , Sarah Vati , Cyril Chaudemanche , Valérie Benoit
12th International Symposium on Gut Microbiology, Oct 2021, Online conference, France
Poster de conférence hal-04285893v1
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A shotgun metagenomics analysis applied to the ecological engineering of anaerobic microbial communities for the production of hydrogen from Citrus Peel Waste

Cedric Midoux , Franciele Camargo , Olivier Rué , Mahendra Mariadassou , Valentin Loux
JOBIM, Jun 2020, Montpellier, France
Poster de conférence hal-02902758v1
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Shallow sequencing: a cost-effective and accurate alternative to WGS for taxonomic profiling ?

Benoit Goutorbe , Anne-Laure Abraham , Mahendra Mariadassou , Valentin Loux , Olivier Rué
JOBIM, Jun 2020, Montpellier, France.
Poster de conférence hal-03451271v1
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Testing markers to characterize microbial communities in food ecosystems using a metagenomics approach

Claire Vincent , Serge Casaregola , Monika Coton , Céline Delbes , Hugo Devillers
JOBIM, Jun 2020, Montpellier, France
Poster de conférence hal-02914960v1
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Florilege, a database gathering microbial habitats, phenotypes and uses

Sandra Derozier , Louise Deleger , Estelle Chaix , Reda Mekdad , Mouhamadou Ba
JOBIM 2020, Jun 2020, Montpellier, France
Poster de conférence hal-02904156v1
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Plateforme bioinformatique MIGALE

Mouhamadou Ba , Damien Berry , David Christiany , Hélène Chiapello , Olivier Inizan
Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jun 2020, Montpellier, France. 2020
Poster de conférence hal-04176782v1
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DeepOmics, a Digital Environmental Engineering Platform for meta-omics data

Ariane Bize , Guillaume Perréal , Aurélie Gramusset , Marion Predhumeau , Cédric Midoux
Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM2020), Jun 2020, Montpellier, France.
Poster de conférence hal-04493150v1
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Detection of an archaeal-specific viral family, previously thought to infect exclusively hyperthermophiles, in human gut metaviromes

Vuong Quoc Hoang Ngo , Cédric Midoux , Olivier Rué , Mahendra Mariadassou , Violette Da Cunha
Phages in Grenoble, Oct 2019, Grenoble, France.
Poster de conférence hal-04360160v1
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Feedback on a c omparative metatranscriptomic analysis

Cedric Midoux , Tiago P. Delforno , Thais Z. Macedo , Gileno V. Lacerda , Olivier Rué
JOBIM 2019 : Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. , 2019, JOBIM 2019
Poster de conférence hal-02735859v1
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Metagenomic analysis of an african beer ecosystem using Food Microbiome Transfert application

Anne-Laure Abraham , Sandra Derozier , Quentin Cavaillé , Thibaut Guirimand , Solange Aka
jobim 2019, Jul 2019, Nantes, France. 2019
Poster de conférence hal-02789073v1
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FoodMicrobiome transfert: Web based metagenomic analysis

Quentin Cavaillé , Thibaut Guirimand , Sandra Derozier , Anne-Laure Abraham , Bedis Dridi
JOBIM 2018 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. , 2018
Poster de conférence hal-02008726v1

The journey of a team of engineers in learning packaging technology

Valentin Marcon , Laure Quintric , Patrick Durand , Olivier Inizan , Caroline Dussart
Jobim (Journées Ouvertes Biologie Informatique Mathématiques), Jul 2018, Marseille, France. , 2018, JOBIM 2018
Poster de conférence hal-02733639v1
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Easy16S : a user-friendly Shiny interface for analysis and visualization of metagenomic data

Cedric Midoux , Olivier Rué , Olivier Chapleur , Mahendra Mariadassou , Théodore Bouchez
JOBIM 2018 : Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. , 2018, JOBIM 2018
Poster de conférence hal-02737257v1

Evaluation of gyrB amplicon sequencing in comparison to 16S rDNA amplicon sequencing to evaluate intra-species bacterial diversity in food microbiotaImproving

Simon Poirier , Raphaelle Peguilhan , Olivier Rué , Valentin Loux , Marie-Christine Champomier-Verges
Food Micro 2018, Sep 2018, Berlin, Germany. , 2018
Poster de conférence hal-02786728v1

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

Sandra Derozier , Veronique Martin , Jean-Marc Chatel , Nalini Rama Rao , Valentin Loux
JOBIM 2018, Jul 2018, Marseille, France. , 2018, ABSTRACTS JOBIM 2018
Poster de conférence hal-01827944v1
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Insyght : Analyse evolutionary conserved CDS, orthologs, syntenies, pan-genome, fusion, etc., for your bacteria of interest​

Thomas Lacroix , Valentin Loux , Jonathan Lorenzo , Bryan Brancotte , Christophe Blanchet
Annual Research in Computational Molecular Biology (RECOMB), Apr 2018, Paris, France. , 2018
Poster de conférence hal-02736501v1
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FLORILEGE: an integrative database using text mining and ontologies

Estelle Chaix , Sandra Derozier , Louise Deleger , Hélène Falentin , Jean-Baptiste Bohuon
JOBIM 2018, Jul 2018, Marseille, France. , 2018, ABSTRACTS JOBIM 2018
Poster de conférence hal-01827946v1

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

Catherine Madzak , Valentin Loux , Christophe Monnet
Journées MEM des métaprogrammes de l’INRA, 2017, paris, France. 2017
Poster de conférence hal-02786916v1
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New -omics data analysis activity on Migale platform for MEM community

Olivier Rué , Valentin Loux , Sophie Schbath
Journées d'Animation MEM 2017, Jan 2017, Paris la Vilklette, France. 2017
Poster de conférence hal-01730003v1
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Florilege : a database gathering microbial phenotypes of food interest

Hélène Falentin , Estelle Chaix , Bedis Dridi , Philippe Bessieres , S Buchin
4th International Conference on Microbial Diversity 2017, Oct 2017, Bari, Italy. , 2017
Poster de conférence hal-01651302v1
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Food Microbiome-Transfert a database to characterize cheese ecosystems.

Thibaut Guirimand , Sandra S. Derozier , Charlie Pauvert , Anne-Laure Abraham , Valentin Loux
Journées Bioinformatique Inra, Mar 2016, Toulouse, France. , 2016
Poster de conférence hal-02799027v1

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

Caroline Le Maréchal , Vincent Péton , Coline Plé , Julien Jardin , Valérie Briard-Bion
IDF Dairy Science & Technology Symposia 2016 Cheese Science & Technology, Apr 2016, Dublin, Ireland. , 2016
Poster de conférence hal-01512192v1
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Cheese ecosystems insights with shotgun metagenomics and a metadata extended genomics database.

Thibaut Guirimand , Charlie Pauvert , Sandra Derozier , Anne-Laure Abraham , Mahendra Mariadassou
JOBIM 2016 : Journées ouvertes de biologie informatique et mathématiques, Jun 2016, Lyon, France. , 2016
Poster de conférence hal-01512085v1
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The multiple-genomes browser of the IFB cloud

Marie-Laure Franchinard , Frederic Sapet , Sandra S. Derozier , Franck F. Samson , Valentin Loux
Journées SUCCES 2015, Nov 2015, Paris, France. , pp.1, 2015
Poster de conférence hal-02795851v1

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

Valentin Loux , Mahendra Mariadassou , Sintia Almeida da Silva , Hélène Chiapello , Amal Hammami
20. Colloque du Club des Bactéries Lactiques, Jun 2015, Lille, France. , 2015
Poster de conférence hal-01170054v1

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

Valentin Loux , Mahendra Mariadassou , Sintia Almeida da Silva , Helene Chiapello , Amal Hammami
JOBIM 16. Journées Ouvertes de Biologie, Informatique et Mathématiques, Jul 2015, Clermont-Ferrand, France. , 2015, ⟨10.1186/s12864-015-1467-7⟩
Poster de conférence hal-01209851v1

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

Caroline Le Maréchal , Vincent Péton , Julien Jardin , Valérie Briard-Bion , Stéphanie-Marie Deutsch
5th IDF Symposium on Science & Technology of Fermented Milk, Mar 2014, Melbourne, Australia. 2014
Poster de conférence hal-01209584v1

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

Taous Saraoui , Sandrine Parayre-Breton , Grégory Guernec , Valentin Loux , Jérôme Montfort
24. International ICFMH Conference, Food Micro 2014, Sep 2014, Nantes, France. , 2014, ICFMH Conference, Food Micro 2014
Poster de conférence hal-01209705v1

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

Gwénaël Jan , Taous Saraoui , Sandrine Parayre-Breton , Grégory Guernec , Valentin Loux
International Scientific Conference on Probiotics and Prebiotics – IPC2014, Jun 2014, Budapest, Hungary. PAMIDA International Ltd, 2014, IPC 2014
Poster de conférence hal-01209656v1

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

Coline Plé , Caroline Le Maréchal , Vincent Péton , Christophe Vroland , Valérie Briard-Bion
International Scientific Conference on Probiotics and Prebiotics – IPC2014, Jun 2014, Budapest, Hungary. PAMIDA International Ltd, 2014, IPC 2014
Poster de conférence hal-01209657v1
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Mapdecode : inventory and benchmark of read mapping tools

Jérome Compain , Jullien Renaud , Sivagangari Nandy , Olivier Collin , Jean-François Gibrat
ECCB'14 : European conference on Computational Biology, Sep 2014, Strasbourg, France. , pp.1, 2014
Poster de conférence hal-02792306v1
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Insyght: Using symbols to visualize homologies, conserved syntenies and genomic insertions across multiple genomes

Thomas Lacroix , Valentin Loux , Annie Gendrault-Jacquemard Gendrault , Mark M. Hoebeke , Jean-François Gibrat
JOBIM 2013 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2013, Toulouse, France. Société Française de Bio-Informatique -SFBI, pp.231, 2013, JOBIM TOULOUSE 2013 RÉSUMÉS COURS (affiches) - Volume 2/2
Poster de conférence hal-02748920v1
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IGO, Integration from Genomes to Organisms

Sandra S. Derozier , Helene H. Chiapello , Thomas Lacroix , Cyprien Guerin Guérin , Valentin Loux
JOBIM 2013, Jul 2013, Toulouse, France. , pp.246, 2013, JOBIM TOULOUSE 2013 - RÉSUMÉS COURTS (affiches)
Poster de conférence hal-02746442v1

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

Caroline Le Maréchal , Vincent Péton , Julien Jardin , Valérie Briard-Bion , Christophe Vroland
EUPA 2013, Oct 2013, Saint-Malo, France. , 2013
Poster de conférence hal-01209498v1

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

Sandrine Parayre-Breton , Taous Saraoui , Grégory Guernec , Valentin Loux , Jérôme Montfort
Colloque Génomique Environnementale, Nov 2013, Rennes, France. , 2013
Poster de conférence hal-01209535v1

Immunomodulatory properties of the probiotic Propionibacterium freudenreichii surface proteome

Gwénaël Jan , Benoit Foligne , Stéphanie-Marie Deutsch , Rozenn Le Guellec , Fabien Cousin
19 ième Colloque du Club des bactéries lactiques, Oct 2013, Bordeaux, France. , pp.72, 2013
Poster de conférence hal-01209501v1

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

Caroline Le Maréchal , Mahendra Mariadassou , Valentin Loux , Amal Plaudet Hammani , Julien Buratti
Journées ouvertes en biologie informatique mathématiques, Jul 2012, Rennes, France. , 2012
Poster de conférence hal-01209420v1

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

Caroline Le Maréchal , Mahendra Mariadassou , Valentin Loux , Amal Plaudet Hammani , Julien Buratti
Journées des Microbiologistes de l'INRA 2012, Nov 2012, L'Isle-sur-la-Sorgue, France. 2012
Poster de conférence hal-01209410v1
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Assemblage de génomes bactériens séquencés par NGS - Comparaison d’outils et choix de paramètres

Fabien Melchiore , Cyprien Guerin Guérin , Pierre P. Nicolas , Valentin Loux
JOBIM 2010, Sep 2010, Montpellier, France. MABLI : Methods Algorithmes Bio-Informatique LIRMM, pp.176, 2010, Proceeding of Journées Ouvertes de Biologie, Informatique et Mathématiques 2010 -Montpellier
Poster de conférence hal-02758166v1

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

Hélène Falentin , Stéphanie-Marie Deutsch , Sandrine Parayre-Breton , Julien Dherbecourt , Gwénaël Jan
3 International Symposium on Propionibacteria and Bifidobacteria: Dairy and Probiotic, Jun 2010, Oviédo, Spain. , International Journal of Food Microbiology, Volume 149, Issue 1, Pages 1-112 (1 September 2011), 2010, International Journal of Food Microbiology
Poster de conférence hal-01454344v1
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Comparison of mapping softwares for next generation sequencing data

Julien Fayolle , Jean-François Gibrat , Valentin Loux , Sophie S. Schbath
JOBIM 2010, Sep 2010, Montpellier, France. MABLI : Methods Algorithmes Bio-Informatique LIRMM, pp.176, 2010, proceeding of JOBIM 2010 - Journées Ouvertes en Biologie, Informatique et Mathématiques - Montpellier
Poster de conférence hal-02751434v1
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Bovine promoter annotation platform for the identification of transcription factor binding sites in genes involved in early pregnancy

Magalie Leveugle , Valentin Loux , Jean-François Gibrat
JOBIM 2010 : Journées Ouvertes en Biologie, Informatique et Mathématiques, Sep 2010, Montpellier, France. MABLI : Methods Algorithmes Bio-Informatique LIRMM, pp.176, 2010, proceeding of JOBIM 2010 Montpellier
Poster de conférence hal-02757163v1

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

Jean-François Bernardet , Éric Duchaud , Mekki Boussaha , Christian Michel , Valentin Loux
2. FEMS Congress of European Microbiologists, Jul 2006, Madrid, Spain. 1 p., 2006
Poster de conférence hal-02812810v1

GO enrichment analysis for differential proteomics using ProteoRE

Florence Combes , Valentin Loux , Yves Vandenbrouck
Proteomics Data Analysis, 2361, pp.179-196, 2021, Methods in Molecular Biology book series (MIMB), ⟨10.1007/978-1-0716-1641-3_11⟩
Chapitre d'ouvrage hal-03324650v1

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

Lien Nguyen , Virginie Brun , Florence Combes , Valentin Loux , Yves Vandenbrouck
Proteomics for biomarker discovery: Methods and protocols, 1959, pp.275-289, 2019, Methods in Molecular Biology book series (MIMB), ISBN: 978-1-4939-9164-8. ⟨10.1007/978-1-4939-9164-8_18⟩
Chapitre d'ouvrage hal-02284981v1

Introduction à l'annotation fonctionnelle in silico

Jean-François Gibrat , Valentin Loux
Bio-informatique - principes d'utilisation des outils, Editions Quae, 2010, 978-2-7592-0870-8
Chapitre d'ouvrage hal-02812661v1