Valentin Loux

Identifiants chercheurs

IdHAL :

valentin-loux

ORCID :

0000-0002-8268-915X

IdRef :

253136016

Présentation

Valentin Loux is head of the INRAE Migale bioinformatics facility, part of the MaiAGE laboratory. The Migale bioinformatics facility provides storage, computational resources and standard bioinformatics analyses pipelines and software for sequence analyses.

Valentin Loux has an established expertise in the analysis of large scale metagenomics projects, annotation and comparison of bacterial genomes.

POSTIONS

2015-Present : Research Engineer in Bioinformatics, head of Migale Bioinformatics Facilty, INRAE, MaIAGE laboratory

2013-2019 : Member of steering comitee of France-Genomique project in charge of bionformatics development coordination

2002-2015 : Bioinformatics Staff Engineer , INRAE Mig laboratory

CURSUS

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

Publications

Article dans une revue (93)

MilkOligoCorpus: A semantically annotated resource for knowledge extraction on mammalian milk oligosaccharides Mathilde Rumeau,Marine Courtin,Robert Bossy,Clara Sauvion,Valentin Louxet al. PLoS ONE, 2025, 20 (8), pp.e0319729. ⟨10.1371/journal.pone.0319729⟩ Article dans une revue hal-05220365v1
Metagenomics reveals contrasted responses of microbial communities to wheat straw amendment in cropland and grassland soils Domitille Jarrige,Vincent Tardy,Valentin Loux,Olivier Rué,Abad Chabbiet al. Scientific Reports, 2025, 15 (1), pp.14723. ⟨10.1038/s41598-025-98903-2⟩ Article dans une revue hal-05070613v1
Pan-immune system, mobilome and resistome in Streptococcus suis Manon Dechêne-Tempier,Stéphanie Bougeard,Valentin Loux,Hélène Chiapello,Virginie Libanteet al. Microbial Genomics, 2025, 11 (9), pp.001521. ⟨10.1099/mgen.0.001521⟩ Article dans une revue hal-05289975v1
A comprehensive, large-scale analysis of “terroir” cheese and milk microbiota reveals profiles strongly shaped by both geographical and human factors Francoise Irlinger,Mahendra Mariadassou,Eric Dugat-Bony,Olivier Rué,Cécile Neuvégliseet al. ISME Communications, 2024, 4 (1), pp.ycae095. ⟨10.1093/ismeco/ycae095⟩ Article dans une revue hal-04668230v1
Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data. Cédric Midoux,Olivier Rué,Olivier Chapleur,Ariane Bize,Valentin Louxet al. Journal of Open Source Software, 2024, 9 (103), pp.6704. ⟨10.21105/joss.06704⟩ Article dans une revue hal-04785149v1
MilkOligoThesaurus, a dataset of mammalian milk oligosaccharide synonyms Mathilde Rumeau,François Fenaille,Agnès Girard,Valentin Loux,Mouhamadou Baet al. Data in Brief, 2024, 54, pp.110404. ⟨10.1016/j.dib.2024.110404⟩ Article dans une revue (data paper) hal-04552648v1
Comparison of metabarcoding taxonomic markers to describe fungal communities in fermented foods Olivier Rué,Monika Coton,Eric Dugat-Bony,Kate Howell,Françoise Irlingeret al. Peer Community Journal, 2023, 3, pp.e97. ⟨10.24072/pcjournal.321⟩ Article dans une revue hal-04234976v1
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 Chaixet al. PLoS ONE, 2023, 18 (1), pp.e0272473. ⟨10.1371/journal.pone.0272473⟩ Article dans une revue hal-03984703v1
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 Deschampset al. MSphere, 2023, 8 (2), pp.e0049522. ⟨10.1128/msphere.00495-22⟩ Article dans une revue hal-04004063v1
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 Langellaet al. PLoS ONE, 2022, 17 (11), pp. e0271847. ⟨10.1371/journal.pone.0271847⟩ Article dans une revue hal-04083924v1
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 Buchinet al. Microorganisms, 2022, 10 (2), ⟨10.3390/microorganisms10020334⟩ Article dans une revue hal-03579395v1
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 Martinet al. Environmental Microbiology Reports, 2021, 13 (3), pp.364-374. ⟨10.1111/1758-2229.12944⟩ Article dans une revue hal-03287195v1
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 Louxet al. Journal of Environmental Management, 2021, 291, pp.112631. ⟨10.1016/j.jenvman.2021.112631⟩ Article dans une revue hal-03211333v1
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 Dérozieret al. International Journal of Food Microbiology, 2021, 358, pp.109312. ⟨10.1016/j.ijfoodmicro.2021.109312⟩ Article dans une revue hal-04311697v1
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 Membréet al. Data in Brief, 2020, 30, pp.1-8. ⟨10.1016/j.dib.2020.105453⟩ Article dans une revue (data paper) hal-02914971v1
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 Libanteet al. Genes, 2020, ⟨10.3390/genes11090999⟩ 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 Sokolet al. 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
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 Bietet al. Infection, Genetics and Evolution, 2020, 82, 4 p. ⟨10.1016/j.meegid.2020.104309⟩ Article dans une revue hal-02905303v1
Comparative metatranscriptomic analysis of anaerobic digesters treating anionic surfactant contaminated wastewater Tiago P. Delforno,Thais Z. Macedo,Cedric Midoux,Gileno V. Lacerda,Olivier Ruéet al. Science of the Total Environment, 2019, 2019 (649), pp.482-494. ⟨10.1016/j.scitotenv.2018.08.328⟩ Article dans une revue hal-01888286v1
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 Sarthouet al. Food Research International, 2019, 125, pp.108643. ⟨10.1016/j.foodres.2019.108643⟩ Article dans une revue hal-02349939v1
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
Complete and Draft Genome Sequences of Nine&lt;em&gt; Lactobacillus&lt;/em&gt; &lt;em&gt;sakei&lt;/em&gt; 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
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 Zagorecet al. PLoS ONE, 2018, 13 (9), ⟨10.1371/journal.pone.0204629⟩ Article dans une revue hal-02621350v1
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 Onesimeet al. International Journal of Food Microbiology, 2018, 264, pp.53-62. ⟨10.1016/j.ijfoodmicro.2017.10.026⟩ Article dans une revue hal-01695894v1
Complete genome sequence of the industrial fast-acidifying strain &lt;em&gt;Streptococcus thermophilus&lt;/em&gt; N4L Lucas Proust,Valentin Loux,Veronique Martin,Cristian Magnabosco,Martin Pedersenet al. Microbiology Resource Announcements, 2018, 7 (8), ⟨10.1128/MRA.01029-18⟩ Article dans une revue hal-02628963v1
Genomic diversity and evolution of the fish pathogen flavobacterium psychrophilum Éric Duchaud,Tatiana Rochat,Christophe Habib,Paul Barbier,Valentin Louxet al. Frontiers in Microbiology, 2018, 9, pp.1-20. ⟨10.3389/fmicb.2018.00138⟩ Article dans une revue hal-02629284v1
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 Louxet al. BMC Research Notes, 2018, 11 (1), pp.1-5. ⟨10.1186/s13104-018-3908-2⟩ Article dans une revue hal-02048857v1
Complete Genome Sequence of Flavobacteriumpsychrophilum Strain OSU THCO2-90, Used for Functional Genetic Analysis. Tatiana Rochat,Paul Barbier,Pierre Nicolas,Valentin Loux,David Perez Pascualet al. Genome Announcements, 2017, 5 (23), 2 p. ⟨10.1128/genomeA.01665-16⟩ Article dans une revue hal-01607798v1
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 Louxet al. Frontiers in Microbiology, 2017, 8, pp.16. ⟨10.3389/fmicb.2017.00443⟩ Article dans une revue hal-01580789v1
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 Chiapelloet al. Scientific Reports, 2017, 7, pp.1-11. ⟨10.1038/srep44331⟩ Article dans une revue hal-01509688v1
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
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 Borjaet al. Genome Announcements, 2017, 5 (5), 3 p. ⟨10.1128/genomeA.01568-16⟩ Article dans une revue hal-01602632v1
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 Guellecet al. Scientific Reports, 2017, 7, pp.46409. ⟨10.1038/srep46409⟩ Article dans une revue hal-01510019v1
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 Deutscheret al. Systematic and Applied Microbiology, 2017, 40 (7), pp.401-410. ⟨10.1016/j.syapm.2017.07.002⟩ Article dans une revue hal-01604275v1
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 Dinhet al. Journal of Biomedical Semantics, 2017, 8 (53), 16 p. ⟨10.1186/s13326-017-0165-6⟩ Article dans une revue hal-01652923v1
Whole genome sequencing of 7 strains of Staphylococcus lugdunensis allows identification of mobile genetic elements Xavier Argemi,Veronique Martin,Valentin Loux,Sandrine Dahyot,Jérémie Lebeurreet al. Genome Biology and Evolution, 2017, 9 (5), pp.1183-1189. ⟨10.1093/gbe/evx077⟩ Article dans une revue hal-01604276v1
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 Burattiet al. Standards in Genomic Sciences, 2016, 11, pp.6. ⟨10.1186/s40793-015-0120-z⟩ Article dans une revue hal-02640172v1
Complete Genome Sequence of Lactococcus lactis subsp. lactis A12, a Strain Isolated from Wheat Sourdough Maeva Guellerin,Delphine Passerini,Catherine Fontagné-Faucher,Hervé Robert,Valérie Gabrielet al. Genome Announcements, 2016, 4 (5), pp.2 P. ⟨10.1128/genomeA.00692-16⟩ Article dans une revue hal-01578250v1
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 Vidalet al. Genome Announcements, 2016, 4 (2), pp.e00052-16. ⟨10.1128/genomeA.00052-16⟩ Article dans une revue hal-01511494v1
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 Louxet al. Frontiers in Microbiology, 2016, 6 (6), pp.1483. ⟨10.3389/fmicb.2015.01483⟩ Article dans une revue hal-01262284v1
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 Martheyet al. Genome Announcements, 2016, 4 (6), 2 p. ⟨10.1128/genomeA.00950-16⟩ Article dans une revue hal-01594527v1
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 Bonnarmeet al. 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 Gendraultet al. Bioinformatics, 2016, 32 (7), pp.1083-1084. ⟨10.1093/bioinformatics/btv689⟩ Article dans une revue hal-02630699v1
Inventory of the GH70 enzymes encoded by &lt;em&gt;Leuconostoc citreum&lt;/em&gt; NRRL B-1299 - identification of three novel -transglucosylases Delphine Passerini,Marlène Vuillemin,Lisa Ufarté,Sandrine Morel,Valentin Louxet al. FEBS Journal, 2015, 282 (11), pp.2115-2130. ⟨10.1111/febs.13261⟩ Article dans une revue hal-02630462v1
Overview of a surface-ripened cheese community functioning by meta-omics analyses Eric Dugat-Bony,Cecile Straub,Aurélie Teissandier,Djamila Onesime,Valentin Louxet al. PLoS ONE, 2015, 10 (4), pp.e0124360. ⟨10.1371/journal.pone.0124360⟩ Article dans une revue hal-01195505v1
Genome Sequences of Two Bovine Mastitis-Causing Escherichia coli 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
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 Hammaniet al. BMC Genomics, 2015, 16 (1), pp.35. ⟨10.1186/s12864-015-1467-7⟩ Article dans une revue hal-01142363v1
Surface proteins of Propionibacterium freudenreichii are involved in its anti-inflammatory properties. Caroline Le Maréchal,Vincent Péton,Coline Plé,Christophe Vroland,Julien Jardinet al. Journal of Proteomics, 2015, 113, pp.447-461. ⟨10.1016/j.jprot.2014.07.018⟩ Article dans une revue hal-01209735v1
Genome Sequence of &quot;Candidatus Arthromitus&quot; 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 Louxet al. Genome Announcements, 2014, 2 (4), ⟨10.1128/genomeA.00705-14⟩ Article dans une revue hal-01204391v1
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 Boudebbouzeet al. Genome Announcements, 2014, 2 (4), pp.1-2. ⟨10.1128/genomeA.00328-14⟩ Article dans une revue hal-01204323v1
Genome Sequence of Lactococcus lactis subsp. lactis bv. diacetylactis LD61. Hélène Falentin,Delphine Naquin,Valentin Loux,Frédérique Barloy-Hubler,Pascal Loubièreet al. Genome Announcements, 2014, 2 (1), pp.1. ⟨10.1128/genomeA.01176-13⟩ Article dans une revue hal-01019560v1
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
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
Bacterial protein signals are associated with Crohn's disease. Catherine Juste,David P Kreil,Christian Beauvallet,Alain Guillot,Sebastian Vacaet al. Gut, 2014, 63 (10), pp.1566-1577. ⟨10.1136/gutjnl-2012-303786⟩ Article dans une revue hal-00933734v1
Complete Genome Sequence of Leuconostoc citreum Strain NRRL B-742 Delphine Passerini,Marlène Vuillemin,S. Laguerre,Myriam Amari,Valentin Louxet al. Genome Announcements, 2014, 2 (6), ⟨10.1128/genomeA.01179-14⟩ Article dans une revue hal-02637077v1
Lactobacillus delbrueckii ssp. lactis and ssp. bulgaricus: a chronicle of evolution in action. Hela El Kafsi,Johan Binesse,Valentin Loux,Julien Buratti,Samira Boudebbouzeet al. BMC Genomics, 2014, 15 (1), pp.407. ⟨10.1186/1471-2164-15-407⟩ Article dans une revue pasteur-01017376v1
Comparative genomics of first available bovine Anaplasma phagocytophilum genome obtained with targeted sequence capture. Thibaud Dugat,Valentin Loux,Sylvain Marthey,Marco Moroldo,Anne-Claire Lagréeet al. BMC Genomics, 2014, 15 (1), pp.973. ⟨10.1186/1471-2164-15-973⟩ Article dans une revue hal-01193998v1
Genome Sequence of the Lactic Acid Bacterium &lt;i&gt;Lactococcus lactis&lt;/i&gt; subsp. &lt;i&gt;lactis&lt;/i&gt; TOMSC161, Isolated from a Nonscalded Curd Pressed Cheese Hélène Velly,Pierre Renault,Anne-Laure Abraham,Valentin Loux,Agnes Delacroix-Buchetet al. Genome Announcements, 2014, 2 (6), ⟨10.1128/genomeA.01121-14⟩ Article dans une revue hal-01193999v1
Technical challenges in metatranscriptomic studies applied to the bacterial communities of freshwater ecosystems Noémie Pascault,Valentin Loux,Sandra Derozier,Véronique Martin,Didier Debroaset al. Genetica, 2014, 143 (2), pp.25216965. ⟨10.1007/s10709-014-9783-4⟩ Article dans une revue hal-01110172v1
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 Jardinet al. Data in Brief, 2014, 1, pp.46-50. ⟨10.1016/j.dib.2014.08.009⟩ Article dans une revue (data paper) hal-01209746v1
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 Monnetet al. BMC Genomics, 2014, 15, article 1101 (16 p.). ⟨10.1186/1471-2164-15-1101⟩ Article dans une revue hal-01195502v1
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 Maet al. Genome Announcements, 2013, 1 (4), pp.e00658-13. ⟨10.1128/genomeA.00658-13⟩ Article dans une revue hal-01209470v1
Draft genome sequence of Lactobacillus hominis strain CRBIP 24.179τ, isolated from human intestine Sylvie Cousin,Sophie Creno,Laurence Ma,Dominique Clermont,Valentin Louxet al. Genome Announcements, 2013, 1 (4), pp.1. ⟨10.1128/genomeA.00662-13⟩ Article dans une revue hal-00939673v1
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 Clermontet al. Genome Announcements, 2013, 1 (4), pp.1-2. ⟨10.1128/genomeA.00663-13⟩ Article dans une revue hal-02645656v1
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 Montfortet al. BMC Genomics, 2013, 14 (1), pp.911. ⟨10.1186/1471-2164-14-911⟩ Article dans une revue inserm-00923652v1
Draft Genome Sequence of [i][/i] Lactobacillus pasteurii[i][/i] CRBIP 24.76T. Sylvie Cousin,Dominique Clermont,Sophie Creno,Laurence Ma,Valentin Louxet al. Genome Announcements, 2013, 1 (4), ⟨10.1128/genomeA.00660-13⟩ Article dans une revue hal-01190531v1
Complete chromosome sequence of Carnobacterium maltaromaticum LMA 28. Catherine C. Cailliez-Grimal,Stéphane Chaillou,Jamila J. Anba-Mondoloni,Valentin Loux,Muhammad Inam M. I. Afzalet al. Genome Announcements, 2013, 1 (1), pp.1-2. ⟨10.1128/genomeA.00115-12⟩ Article dans une revue hal-00939584v1
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 Straubet al. Journal of Bacteriology, 2012, 194 (18), pp.5141-5142. ⟨10.1128/JB.01038-12⟩ Article dans une revue hal-01019837v1
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 Maillardet al. Applied and Environmental Microbiology, 2012, 78 (17), pp.6357-6364. ⟨10.1128/AEM.00561-12⟩ Article dans une revue hal-02363390v1
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. Straubet al. Journal of Bacteriology, 2012, 194 (3), pp.738-739. ⟨10.1128/JB.06496-11⟩ Article dans une revue hal-01000221v1
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
Genome sequence of weissella confusa LBAE C39-2, isolated from a wheat sourdough Myriam Amari,Sandrine Laguerre,Marlène Vuillemin,Hervé Robert,Valentin Louxet al. Journal of Bacteriology, 2012, 194 (6), pp.1608-1609. ⟨10.1128/JB.06788-11⟩ Article dans une revue hal-01267779v1
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
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 Louxet al. Journal of Computational Biology, 2012, 19 (6), pp.796-813. ⟨10.1089/cmb.2012.0022⟩ Article dans une revue hal-02645697v1
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 Maillardet al. Applied and Environmental Microbiology, 2012, 78 (17), pp.6357-6364. ⟨10.1128/AEM.00561-12⟩ Article dans une revue hal-01191223v1
Genome Sequence of the Invasive Salmonella enterica subsp. enterica Serotype Enteritidis Strain LA5 Olivier Grépinet,Aurore Rossignol,Valentin Loux,Helene Chiapello,Annie Gendraultet al. Journal of Bacteriology, 2012, 194 (9), pp.2387-2388. ⟨10.1128/JB.00256-12⟩ Article dans une revue hal-03044203v1
Complete genome sequence of Flavobacterium indicum GPSTA100-9T, isolated from warm spring water Paul Barbier,Armel A. Houel,Valentin Loux,Julie Poulain,Jean-François Bernardetet al. Journal of Bacteriology, 2012, 194 (11), pp.3024-3025. ⟨10.1128/JB.00420-12⟩ Article dans une revue hal-02643519v1
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 Louxet al. 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 Chiapelloet al. Journal of Bacteriology, 2012, 194 (9), pp.2385-2386. ⟨10.1128/JB.00255-12⟩ Article dans une revue hal-02643377v1
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. Junotet al. Applied Microbiology and Biotechnology, 2011, 91 (5), pp.1409-1423. ⟨10.1007/s00253-011-3481-2⟩ Article dans une revue istex hal-01000029v1
Complete genome sequence of the clinical Streptococcus salivarius strain CCHSS3 Christine C. Delorme,Eric Guédon,Nicolas N. Pons,Corinne Cruaud,Arnaud A. Coulouxet al. Journal of Bacteriology, 2011, 193 (18), pp.5041-5042. ⟨10.1128/JB.05416-11⟩ Article dans une revue hal-01000176v1
Complete genome sequence of the pigmented Streptococcus thermophilus strain JIM8232 Christine C. Delorme,Claire C. Bartholini,Mélanie M. Luraschi,Nicolas N. Pons,Valentin Louxet al. Journal of Bacteriology, 2011, 193 (19), pp.5581-5582. ⟨10.1128/JB.05404-11⟩ Article dans une revue hal-01000180v1
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⟩ Article dans une revue hal-02644023v1
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 Vacherieet al. PLoS ONE, 2010, 5 (11), pp.e15489. ⟨10.1371/journal.pone.0015489⟩ Article dans une revue hal-01195440v1
Complete genome sequence of the probiotic Lactobacillus casei strain BL23 Alain Mazé,Grégory Boël,Manuel Zùniga,Alexa Bourand,Valentin Louxet al. Journal of Bacteriology, 2010, 192 (10), pp.2647-2648. ⟨10.1128/JB.00076-10⟩ Article dans une revue hal-01204245v1
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 Thierryet al. PLoS ONE, 2010, 5 (7), pp.1-12. ⟨10.1371/journal.pone.0011748⟩ Article dans une revue hal-01204238v1
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. Gittonet al. Journal of Proteome Research, 2010, 9 (2), pp.677-688 Article dans une revue hal-02657656v1
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. Langellaet al. Proteomics, 2009, 9 (1), pp.61-73. ⟨10.1002/pmic.200800195⟩ Article dans une revue hal-02663676v1
Identification of brevibacteriaceae by multilocus sequence typing and comparative genomic hybridization analyses. Marie-Pierre Forquin,Hugo Duvergey,Caroline Proux,Valentin Loux,Jérôme Mounieret al. Applied and Environmental Microbiology, 2009, 75 (19), pp.6406-9. ⟨10.1128/AEM.00224-09⟩ Article dans une revue hal-00557018v1
Complete genome sequence of the fish pathogen Flavobacterium psychrophilum Éric Duchaud,Mekki Boussaha,Valentin Loux,Jean-François Bernardet,Christian Michelet al. Nature Biotechnology, 2007, 25 (7), pp.763 - 769. ⟨10.1038/nbt1313⟩ Article dans une revue hal-02666599v1
AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system K. Bryson,Valentin Loux,Robert R. Bossy,P. Nicolas,Stéphane Chaillouet al. Nucleic Acids Research, 2006, 34 (12), pp.3533-3545. ⟨10.1093/nar/gkl471⟩ Article dans une revue hal-02665192v1
The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution Maarten van de Guchte,Stéphanie Penaud,Christine Grimaldi,Valérie Barbe,K. Brysonet al. 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
The complete genome sequence of the meat-borne lactic acid bacterium Lactobacillus sakei 23K Stéphane Chaillou,Marie-Christine Champomier Verges,Monique Cornet,Anne-Marie Crutz-Le Coq,Anne-Marie Dudezet al. Nature Biotechnology, 2005, 23 (12), pp.1527-1533. ⟨10.1038/nbt1160⟩ Article dans une revue hal-02683108v1

Communication dans un congrès (39)

Analyse croisée de données métabarcoding et métagénomiques sur des microbiotes d'hôtes animaux Núria Mach,Maverick Monié--Ibanes,Cédric Midoux,Olivier Rué,Eric Barreyet al. FROGSdays 2025, équipe FROGS INRAe, Dec 2025, Auzeville Tolosan, France Communication dans un congrès hal-05397464v1
Prevalence and diversity of Integrative and Conjugative or Mobilizable Elements carrying antimicrobial resistance genes in Streptococcus suis Manon Dechêne-Tempier,Stéphanie Bougeard,Valentin Loux,Hélène Chiapello,Virginie Libanteet al. International Conference on type IV secretion system, UMR1128 DynAMic; PROPULS', Feb 2025, Nancy, France Communication dans un congrès hal-05286237v1
Drivers of microbial diversity in French Protected designation of Origin (PDO) cheeses Francoise Irlinger,Mahendra Mariadassou,Eric Dugat-Bony,Cécile Neuvéglise,Olivier Ruéet al. IDF World Dairy Science, Oct 2024, Paris, France Communication dans un congrès hal-04820075v1
Metagenomics reveal contrasted and dynamic responses of microbial soil communities to in situ wheat straw amendment in croplands or grasslands Domitille Jarrige,Vincent Tardy,Valentin Loux,Olivier Rué,Abad Chabbiet al. Symposium on Environmental and Agronomical Genomics organisé par France Génomique and the Research Group “Environmental Genomics", Feb 2024, Toulouse, France Communication dans un congrès hal-04654371v1
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
Variable and core functional rhizosphere microbiota associated with seven Medicago truncatula genotypes Zhu, Liya,Olivier Rué,Florence Deau,Julie Cremaschi,Valentin Louxet al. Journée doctorants UMR Agroécologie, Nov 2023, Dijon, France Communication dans un congrès hal-04317070v1
MetaPDOcheese : investigation of the drivers of microbial communities from French PDO milks and cheeses Francoise Irlinger,Mahendra Mariadassou,Eric Dugat-Bony,Cécile Neuvéglise,Olivier Ruéet al. FORUM ON FERMENTED FOODS, COST PIMENTO, May 2023, Lyon, France Communication dans un congrès hal-04221356v1
Origins and rate of mutations in bacteriophage Lambda Julien Lopez,Mahendra Mariadassou,Valentin Loux,Rafael Sanjuán,Marina Elezet al. Phages in Lyon 2023, phages.fr, Nov 2023, Lyon, France Communication dans un congrès hal-04321371v1
Variable and core functional microbiota associated with seven Medicago truncatula genotypes Zhu, Liya,Olivier Rué,Florence Deau,Julie Cremaschi,Valentin Louxet al. 12th International PGPR Workshop 2023, May 2023, Toulouse, France Communication dans un congrès hal-04139303v1
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 Benoitet al. International Scientific Association for Probiotics and Prebiotics Annual Meeting, Jun 2021, Online conference, France Communication dans un congrès hal-04285897v1
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 Libanteet al. Réunion du GDR3546 Eléments transposables, Dec 2021, Paris, France Communication dans un congrès hal-03495840v1
Prebiotics for digestive health and wellness: how to successfully promote the gut microbiome? Cassandre Bedu-Ferrari,Paul Biscarrat,Sarah Vati,Cyril Chaudemanche,Valerie Benoitet al. 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 Lacroixet al. 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
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-Vergèset al. JOBIM 20. Journées Ouvertes Biologie Informatique Mathématiques, Jul 2019, Nantes, France Communication dans un congrès hal-02947091v1
Shotgun metagenomics sequencing of the rhizosphere microbiota associated to seven ecotypes of &lt;em&gt;Medicago truncatula&lt;/em&gt; Julie Cremaschi,Olivier Rué,Florence Deau,Philippe Lemanceau,Valentin Louxet al. Rhizosphere 5, Jul 2019, Saskatoon, Saskatchewan, Canada Communication dans un congrès hal-02735116v1
L'ontologie OntoBiotope pour l'étude de la biodiversité microbienne Claire Nédellec,Estelle Chaix,Robert Bossy,Louise Deleger,Sandra Derozieret al. 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 Louxet al. 3rd MPItM-Labex ARBRE Workshop, Nov 2018, cologne, Germany Communication dans un congrès hal-03339776v1
A metagenomic tool for cheese ecosystems Anne-Laure Abraham,Quentin Cavaillé,Thibaut Guirimand,Pierre Renault,Sandra Derozieret al. 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
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
The journey of a team of engineers in learning packaging technology Laure Quintric,Patrick Durand,Olivier Inizan,Valentin Marcon,Caroline Dussartet al. Galaxy Community Conference - GCC2018, Jun 2018, Portland, United States Communication dans un congrès hal-02784992v1
Florilège: a database gathering microbial phenotypes of food interest Hélène Falentin,Estelle Chaix,Bedis Dridi,Philippe Bessieres,S Buchinet al. 2017 Scientific MEM days: Journées scientifiques MEM (Métaomiques et écosystèmes microbiens), Jan 2017, Paris, France Communication dans un congrès hal-01607327v1
Food-Microbiomes Transfert, a shotgun metagenomic tool and a database to analyze cheese ecosystems Thibaut Guirimand,Anne-Laure Abraham,Sandra Derozier,Charlie Pauvert,Mahendra Mariadassouet al. JOBIM 2017 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2017, Lille, France Communication dans un congrès hal-02788899v1
Représentation systémique multi-échelle des processus biologiques de la bactérie Vincent J. Henry,Arnaud Ferré,Christine Froidevaux,Anne Goelzer,Vincent V. Fromionet al. IC2016 - Ingénierie des Connaissances, Jun 2016, Montpellier, France Communication dans un congrès hal-01442727v1
Représentation systémique multi-échelle des processus biologiques de la bactérie Vincent Henry,Arnaud Ferré,Christine Froidevaux,Anne Goelzer,Vincent Fromionet al. IC201: 27es Journées francophones d'Ingénierie des Connaissances, Jun 2016, Montpellier, France Communication dans un congrès hal-02741418v1
Deciphering why &lt;em&gt;Salmonella&lt;/em&gt; Gallinarum is less invasive in vitro than &lt;em&gt;Salmonella&lt;/em&gt; Enteritidis Aurore Rossignol,Sylvie Roche,Isabelle Virlogeux-Payant,Olivier Grépinet,Nadia Abedet al. 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
Mapping reads on a genomic sequence: a practical comparative analysis Sophie S. Schbath,Veronique V. Martin,Matthias Zytnicki,Julien Fayolle,Valentin Louxet al. Kick-of meeting of PF7 RADIANT project, Jan 2013, Manchester, United Kingdom. 19 diapos Communication dans un congrès hal-02804577v1
Mapping reads on a genomic sequence: a practical comparative analysis Sophie S. Schbath,Veronique V. Martin,Matthias Zytnicki,Julien Fayolle,Valentin Louxet al. 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-Darmonet al. Flavobacterium 2012, 2012, Turku, Finland Communication dans un congrès hal-02746549v1
SURFING: A national project to understand immunomodulatury effects of dairy starters Benoît Foligné,Valentin Loux,Christophe Hervé,Jean-René Kerjean,Denis Matteret al. 2nd International Symposium "Microbes For Health", Dec 2011, Paris, France Communication dans un congrès hal-01190437v1
Genomic diversity of 24 Propionibacterium freudenreichii 1 strains Hélène Falentin,Valentin Loux,Valérie Barbe,Amal Plaudet Hammani,Stéphanie-Marie Deutschet al. 6 Conference on Functional Genomics of Gram-positive Microorganisms 16 International Conference on Bacilli, Jun 2011, Montecatini, Italy Communication dans un congrès hal-01454328v1
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
Web services for microbial genome annotation using data integration Célia Michotey,Ludovic Legrand,Helene H. Chiapello,Valentin Loux,Annie A. Gendrault-Jacquemardet al. JOBIM 2010 : Journées Ouvertes en Biologie, Informatique et Mathématiques, Sep 2010, Montpellier, France Communication dans un congrès hal-02752226v1
Bactéries pathogènes des poissons du genre Flavobacterium Éric Duchaud,Jean-François Bernardet,Brigitte Kerouault,Christian Michel,Céline Chantryet al. 2. Journées de la Recherche Filière Piscicole, Jul 2009, Paris, France. 1 p Communication dans un congrès hal-02823179v1
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
Towards a semi-automatic functional annotation tool based on decision tree techniques Jérôme Azé,L. Gentils,Claire Toffano-Nioche,Valentin Loux,Jean-François Gibratet al. 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 Stéphane Chaillou,Monique Cornet,Anne-Marie A.-M. Le Coq,Anne-Marie Loustau,Robert R. Bossyet al. 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 Stéphane Chaillou,Monique Cornet,Anne-Marie A.-M. Le Coq,Anne-Marie Loustau,Robert R. Bossyet al. 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 Stéphane Chaillou,Monique Cornet,Anne-Marie Loustau,Robert R. Bossy,Valentin Louxet al. 13. Colloque du Club des Bactéries Lactiques, Sep 2004, Nantes, France. 142 p Communication dans un congrès hal-02759825v1

Poster de conférence (61)

Holograph: a generic RDF schema to handle data from agroecological holobionts Marie Lahaye,Alice Mataigne,Edmond Berne,Matéo Boudet,Olivier Dameronet al. SWAT4HCLS, Mar 2026, Amsterdam, France. 2026 Poster de conférence hal-05486358v1
Cell-free genome-wide transcriptomics through machine learning optimization Léa Wagner,An Hoang,Olivier Rue,Olivier Delumeau,Valentin Louxet al. SEED 2025, Jun 2025, Houston, United States Poster de conférence hal-05155548v1
Data stewardship strategy of the Ferments du Futur grand challenge Erwan Le Floch,Agnès Barnabé,Jonathan Duperrier,Thomas Lacroix,Aaron Millan-oropezaet al. Journées Ouvertes Biologie, Informatique, Mathématiques 2025, Jul 2025, Bordeaux, France. 2025 Poster de conférence hal-05149332v2
SIDURI: from an integrative information system to a user-friendly portal for data analysis and visualisation dedicated to fermentation Agnès Barnabé,Erwan Le Floch,Jonathan Duperrier,Mariène Wan,Aaron Millan-oropezaet al. Journées Ouvertes Biologie, Informatique, Mathématiques 2025, Jul 2025, Bordeaux, France. pp.1 Poster de conférence hal-05142051v1
When bacteriophages enter the cheese ripening process: An overview of the PHAGOFROM project Marion Dalmasso,Eric Dugat-Bony,Alicia Bertry,Camille Leneveu,Margareth Renaultet al. Microbes 2025, Sep 2025, Bordeaux, France Poster de conférence hal-05162180v1
Siduri : an integrative information system for next generation fermented foods Mariène Wan,Aaron Millan-oropeza,Thomas Lacroix,Jonathan Mineau-Cesari,Sophie Schbathet al. JOBIM 2024 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2024, Toulouse, France. Poster de conférence hal-04633572v1
Deciphering and cataloging the genomic and functional diversity of the French cheese microbiota Hélène Gardon,Françoise Irlinger,Céline Delbès,Éric Dugat-Bony,Julia Gendreet al. WDS 2024, Oct 2024, Paris, France Poster de conférence hal-05288574v1
HoloOLIGO corpus, a manually annotated text dataset supporting schema-based relational information extraction for mammalian milk oligosaccharide diversity pattern comprehension Mathilde Rumeau,Robert Bossy,Clara Sauvion,Valentin Loux,Mouhamadou Baet al. Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jun 2024, Toulouse, France Poster de conférence hal-04666797v1
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 Libanteet al. 5th International Workshop on Streptococcus suis, Jun 2023, Bangkok / Thailand, Thailand Poster de conférence hal-04232466v1
Different Medicago truncatula genotypes, expressing different phenotypes, modulate microbial functional genes in the rhizosphere Zhu, Liya,Olivier Rué,Florence Deau,Julie Cremaschi,Valentin Louxet al. miCROPe 2022, international Symposium microbe-assisted crop production opportunities, challenges & needs, Jul 2022, Vienne, France Poster de conférence hal-04199757v1
Plateforme bioinformatique MIGALE Mouhamadou Ba,Hélène Chiapello,Christelle Hennequet-Antier,Valentin Loux,Mahendra Mariadassouet al. Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2022, Rennes, France. 2022 Poster de conférence hal-04176761v1
Omnicrobe : une base de données d’habitats et de phénotypes microbiens Hélène Falentin,Olivier Harlé,Sandra Derozier,Louise Deléger,Estelle Chaixet al. 23ème édition du colloque du Club des Bactéries Lactiques, Jun 2022, Rennes, France. , 2022 Poster de conférence hal-03694214v1
Implementing a Text Mining Service Offer on the Migale Bioinformatics Platform Mouhamadou Ba,Véronique Martin,Olivier Rué,Sophie Schbath,Valérie Vidalet al. Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2022, Rennes, France. 2022 Poster de conférence hal-04176740v1
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 Chapleuret al. ISME18, 18th International Symposium on Microbial Ecology, Aug 2022, Lausanne, Switzerland. Poster de conférence hal-04359643v1
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-Bourgoinet al. 5th International Caparica Congress in Antibiotic Resistance (IC2AR 2022), Sep 2022, Caparica, Lisbon, Portugal Poster de conférence hal-04232454v1
Plateforme bioinformatique MIGALE Mouhamadou Ba,Hélène Chiapello,Christelle Hennequet-Antier,Valentin Loux,Mahendra Mariadassouet al. 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 Benoitet al. 12th International Symposium on Gut Microbiology, Oct 2021, Online conference, France Poster de conférence hal-04285893v1
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 Enaultet al. JOBIM 2021 (JOBIM (Journées Ouvertes en Biologie, Informatique et Mathématiques), Jul 2021, Paris, France. Poster de conférence hal-04359920v1
Testing markers to characterize microbial communities in food ecosystems using a metagenomics approach Claire Vincent,Serge Casaregola,Monika Coton,Céline Delbès,Hugo Devillerset al. JOBIM, Jun 2020, Montpellier, France Poster de conférence hal-02914960v1
DeepOmics, a Digital Environmental Engineering Platform for meta-omics data Ariane Bize,Guillaume Perréal,Aurélie Gramusset,Marion Predhumeau,Cédric Midouxet al. Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM2020), Jun 2020, Montpellier, France. Poster de conférence hal-04493150v1
Plateforme bioinformatique MIGALE Mouhamadou Ba,Damien Berry,David Christiany,Hélène Chiapello,Olivier Inizanet al. Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jun 2020, Montpellier, France. 2020 Poster de conférence hal-04176782v1
Florilege, a database gathering microbial habitats, phenotypes and uses Sandra Derozier,Louise Deleger,Estelle Chaix,Reda Mekdad,Mouhamadou Baet al. JOBIM 2020, Jun 2020, Montpellier, France Poster de conférence hal-02904156v1
Shallow sequencing: a cost-effective and accurate alternative to WGS for taxonomic profiling ? Benoit Goutorbe,Anne-Laure Abraham,Mahendra Mariadassou,Valentin Loux,Olivier Ruéet al. JOBIM, Jun 2020, Montpellier, France. Poster de conférence hal-03451271v1
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 Louxet al. JOBIM, Jun 2020, Montpellier, France Poster de conférence hal-02902758v1
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 Cunhaet al. Phages in Grenoble, Oct 2019, Grenoble, France. Poster de conférence hal-04360160v1
Feedback on a c omparative metatranscriptomic analysis Cedric Midoux,Tiago P. Delforno,Thais Z. Macedo,Gileno V. Lacerda,Olivier Ruéet al. JOBIM 2019 : Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. , 2019, JOBIM 2019 Poster de conférence hal-02735859v1
Metagenomic analysis of an african beer ecosystem using Food Microbiome Transfert application Anne-Laure Abraham,Sandra Derozier,Quentin Cavaillé,Thibaut Guirimand,Solange Akaet al. jobim 2019, Jul 2019, Nantes, France. 2019 Poster de conférence hal-02789073v1
MetaFoldScan: a pipeline to scan metagenomes and identify structural homologs using HMM Sandra Derozier,Veronique Martin,Jean-Marc Chatel,Nalini Rama Rao,Valentin Louxet al. JOBIM 2018, Jul 2018, Marseille, France. , 2018, ABSTRACTS JOBIM 2018 Poster de conférence hal-01827944v1
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-Vergeset al. Food Micro 2018, Sep 2018, Berlin, Germany. , 2018 Poster de conférence hal-02786728v1
Easy16S : a user-friendly Shiny interface for analysis and visualization of metagenomic data Cedric Midoux,Olivier Rué,Olivier Chapleur,Mahendra Mariadassou,Théodore Bouchezet al. JOBIM 2018 : Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. , 2018, JOBIM 2018 Poster de conférence hal-02737257v1
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 Blanchetet al. Annual Research in Computational Molecular Biology (RECOMB), Apr 2018, Paris, France. , 2018 Poster de conférence hal-02736501v1
FoodMicrobiome transfert: Web based metagenomic analysis Quentin Cavaillé,Thibaut Guirimand,Sandra Derozier,Anne-Laure Abraham,Bedis Dridiet al. 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 Dussartet al. Jobim (Journées Ouvertes Biologie Informatique Mathématiques), Jul 2018, Marseille, France. , 2018, JOBIM 2018 Poster de conférence hal-02733639v1
FLORILEGE: an integrative database using text mining and ontologies Estelle Chaix,Sandra Derozier,Louise Deleger,Hélène Falentin,Jean-Baptiste Bohuonet al. JOBIM 2018, Jul 2018, Marseille, France. , 2018, ABSTRACTS JOBIM 2018 Poster de conférence hal-01827946v1
Florilege : a database gathering microbial phenotypes of food interest Hélène Falentin,Estelle Chaix,Bedis Dridi,Philippe Bessieres,S Buchinet al. 4. International Conference on Microbial Diversity 2017, Oct 2017, Bari, Italy. , 2017 Poster de conférence hal-01651302v1
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
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
Monoxenic experimental cheese reveals anti-inflammatory effect of Propionibacterium freudenreichii in vivo. Caroline Le Maréchal,Vincent Péton,Coline Plé,Julien Jardin,Valérie Briard-Bionet al. IDF Dairy Science & Technology Symposia 2016 Cheese Science & Technology, Apr 2016, Dublin, Ireland. , 2016 Poster de conférence hal-01512192v1
Cheese ecosystems insights with shotgun metagenomics and a metadata extended genomics database. Thibaut Guirimand,Charlie Pauvert,Sandra Derozier,Anne-Laure Abraham,Mahendra Mariadassouet al. JOBIM 2016 : Journées ouvertes de biologie informatique et mathématiques, Jun 2016, Lyon, France. , 2016 Poster de conférence hal-01512085v1
Food Microbiome-Transfert a database to characterize cheese ecosystems. Thibaut Guirimand,Sandra S. Derozier,Charlie Pauvert,Anne-Laure Abraham,Valentin Louxet al. Journées Bioinformatique Inra, Mar 2016, Toulouse, France. , 2016 Poster de conférence hal-02799027v1
Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of &lt;i&gt;Propionibacterium freudenreichii&lt;/i&gt; Valentin Loux,Mahendra Mariadassou,Sintia Almeida da Silva,Helene Chiapello,Amal Hammamiet al. 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
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 Hammamiet al. 20. Colloque du Club des Bactéries Lactiques, Jun 2015, Lille, France. , 2015 Poster de conférence hal-01170054v1
The multiple-genomes browser of the IFB cloud Marie-Laure Franchinard,Frederic Sapet,Sandra S. Derozier,Franck F. Samson,Valentin Louxet al. Journées SUCCES 2015, Nov 2015, Paris, France. , pp.1, 2015 Poster de conférence hal-02795851v1
An integrative approach of [i]Propionibacterium freudenreichii[/i] immunomodulatory mechanisms Caroline Le Maréchal,Vincent Péton,Julien Jardin,Valérie Briard-Bion,Stéphanie-Marie Deutschet al. 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 Montfortet al. 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 Louxet al. 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-Bionet al. International Scientific Conference on Probiotics and Prebiotics – IPC2014, Jun 2014, Budapest, Hungary. PAMIDA International Ltd, 2014, IPC 2014 Poster de conférence hal-01209657v1
Mapdecode : inventory and benchmark of read mapping tools Jérome Compain,Jullien Renaud,Sivagangari Nandy,Olivier Collin,Jean-François Gibratet al. ECCB'14 : European conference on Computational Biology, Sep 2014, Strasbourg, France. , pp.1, 2014 Poster de conférence hal-02792306v1
Immunomodulatory properties of the probiotic Propionibacterium freudenreichii surface proteome Gwénaël Jan,Benoit Foligne,Stéphanie-Marie Deutsch,Rozenn Le Guellec,Fabien Cousinet al. 19 ième Colloque du Club des bactéries lactiques, Oct 2013, Bordeaux, France. , pp.72, 2013 Poster de conférence hal-01209501v1
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 Montfortet al. Colloque Génomique Environnementale, Nov 2013, Rennes, France. , 2013 Poster de conférence hal-01209535v1
The probiotic[i] Propionibacterium freudenreichii[/i] surface proteome Caroline Le Maréchal,Vincent Péton,Julien Jardin,Valérie Briard-Bion,Christophe Vrolandet al. EUPA 2013, Oct 2013, Saint-Malo, France. , 2013 Poster de conférence hal-01209498v1
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
IGO, Integration from Genomes to Organisms Sandra S. Derozier,Helene H. Chiapello,Thomas Lacroix,Cyprien Guerin Guérin,Valentin Louxet al. JOBIM 2013, Jul 2013, Toulouse, France. , pp.246, 2013, JOBIM TOULOUSE 2013 - RÉSUMÉS COURTS (affiches) Poster de conférence hal-02746442v1
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 Burattiet al. Journées des Microbiologistes de l'INRA 2012, Nov 2012, L'Isle-sur-la-Sorgue, France. 2012 Poster de conférence hal-01209410v1
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 Burattiet al. Journées ouvertes en biologie informatique mathématiques, Jul 2012, Rennes, France. , 2012 Poster de conférence hal-01209420v1
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
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 Janet al. 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
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
Whole-genome sequence of the fish-pathogenic bacterium Flavobacterium psychrophilum Jean-François Bernardet,Éric Duchaud,Mekki Boussaha,Christian Michel,Valentin Louxet al. 2. FEMS Congress of European Microbiologists, Jul 2006, Madrid, Spain. 1 p., 2006 Poster de conférence hal-02812810v1

Chapitre d'ouvrage (3)

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

Autre publication scientifique (2)

F3M_database_V1.1.0 Stéphane Chaillou,Julien Tap,Nacer Mohellibi,Valentin Loux,Colin R. Tinsley 2025 Autre publication scientifique hal-05318537v1
High quality food bacterial genomic ressources from fermented vegetables Elham Karimi,Julien Tap,Julia Gendre,Eric Dugat-Bony,Florence Valence-Bertelet al. 2024, ⟨10.57745/O4OJA2⟩ Autre publication scientifique hal-05306548v1

Pré-publication, Document de travail (6)

A study of the integration by non-homologous end joining (NHEJ) of a trackable DNA cassette with randomly-generated borders into Yarrowia lipolytica genome sheds light on exogenous DNA extremities degradation and confirms the potential of NHEJ-mediated integration for the design of genome-scale insertional mutant libraries in non-conventional yeasts Marie-Noëlle Rossignol,Olivier Rué,Stéphane Thomas,Valentin Loux,Christophe Monnetet al. 2026 Pré-publication, Document de travail (preprint/prepublication) hal-05503909v1
MiCoReCa (Microbiome Community Resource Catalogue) - Towards Centralized Curation And Integration Of Microbiome Bioinformatics Resources Vivek Ashokan,Clara Emery,Agnès Barnabé,Valentin Loux,Christina Pavloudiet al. 2026 Pré-publication, Document de travail hal-05443844v1
Food Microbiome Metabolic Modules (F3M), a tool suite for functional profiling of food microbiomes Julien Tap,Nacer Mohellibi,Colin Tinsley,Valentin Loux,Stéphane Chaillou 2025 Pré-publication, Document de travail hal-05306516v1
Atypical Replication Error Pattern and Limited Repair Efficiency Contribute to Elevated Mutation Rate in Phage lambda Julien Lopez,Magali Ventroux,Valentin Loux,Mahendra Mariadassou,François Lecointeet al. 2025 Pré-publication, Document de travail hal-05289701v1
Cell-free genome-wide transcriptomics through machine learning optimization Léa Wagner,An Hoang,Olivier Rue,Olivier Delumeau,Valentin Louxet al. 2025 Pré-publication, Document de travail hal-05170246v1
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 Chaixet al. 2022 Pré-publication, Document de travail (preprint/prepublication) hal-03828105v1

Rapport (1)

MilkOligoCorpus annotation guidelines Mathilde Rumeau,Marine Courtin,Robert Bossy,Clara Sauvion,Valentin Louxet al. INRAE. 2024 Rapport hal-04830410v1

Logiciel (2)

Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data Cédric Midoux,Olivier Rué,Olivier Chapleur,Ariane Bize,Valentin Louxet al. 2024, ⟨swh:1:rel:35d2caacc87474efa1f1e277f5eb13352962793d⟩ Logiciel hal-04304559v2
Insyght Thomas Lacroix,Valentin Loux,Annie A. Gendrault-Jacquemard,Jean-François Gibrat 2014 Logiciel hal-02795962v1