Olivier Rué

Publications

Article dans une revue (47)

Validation of a representative sampling protocol for studying grape berry microbiota at the plot scale Gabriela Pinto Miguel,Olivier Rué,Martine Pradal,Evelyne Aguera,Cécile Neuvéglise Journal of Microbiological Methods, 2026, 241, pp.107376. ⟨10.1016/j.mimet.2025.107376⟩ Article dans une revue hal-05489027v1
From process to flavor: Microbial and sensory characterization of traditional Kaak and its artisanal production methods Rachelle Alhosry,Lucie Arnould,Olivier Rué,Rosette Daoud,Pierre Abi Nakhoulet al. Food Microbiology, 2026, 136, pp.104999. ⟨10.1016/j.fm.2025.104999⟩ Article dans une revue hal-05583049v1
Micro-RNA expression data from common carp brain cells infected by Cyvirus cyprinidallo3 at permissive and non-permissive temperatures Olivier Rué,Nurul Novelia Fuandila,Saliha Hammoumi,Christine Gaspin,Jean-Christophe Avarre Data in Brief, 2025, 61, pp.111800. ⟨10.1016/j.dib.2025.111800⟩ Article dans une revue (data paper) hal-05142154v1
Ancient Microbiomes as Mirrored by DNA Extracted From Century‐Old Herbarium Plants and Associated Soil Gianluca Grasso,Régis Debruyne,Martino Adamo,Olivier Rué,Franck Lejzerowiczet al. Molecular Ecology Resources, 2025, 25 (7), pp.e14122. ⟨10.1111/1755-0998.14122⟩ Article dans une revue hal-05122326v1
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
Insights into the microbial species diversity and specific making techniques behind Lebanese sourdough breads Pamela Bechara,Lucie Arnould,Olivier Rué,Rabih El Rammouz,Pierre Abi-Nakhoulet al. Journal of Applied Microbiology, 2025, 136 (11), ⟨10.1093/jambio/lxaf266⟩ Article dans une revue hal-05583006v1
Gut microbiota dysfunction in Crohn’s disease Sylvie Buffet-Bataillon,Gabriela Durão,Isabelle Luron Le Huërou-Luron,Olivier Rué,Yann Le Cunffet al. Frontiers in Cellular and Infection Microbiology, 2025, 15, pp.1540352. ⟨10.3389/fcimb.2025.1540352⟩ Article dans une revue hal-04973386v1
The cutting type of vegetables influences the spontaneous fermentation rate Florence Valence,Romane Junker,Céline Baty,Olivier Rué,Mahendra Mariadassouet al. Peer Community In Microbiology, 2025, ⟨10.24072/pcjournal.553⟩ Article dans une revue hal-04701063v3
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
Insight into the Role of Gut Microbiota in Duchenne Muscular Dystrophy Maxence Jollet,Mahendra Mariadassou,Olivier Rué,Laurence Pessemesse,Vincent Ollendorffet al. American Journal of Pathology, 2024, 194 (2), pp.264-279. ⟨10.1016/j.ajpath.2023.10.010⟩ Article dans une revue hal-04383411v1
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
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
Microbiota members from body sites of dairy cows are largely shared within individual hosts throughout lactation but sharing is limited in the herd Mahendra Mariadassou,Laurent-Xavier Nouvel,Fabienne Constant,Diego P. Morgavi,Lucie Raultet al. Animal Microbiome, 2023, 5 (1), pp.32. ⟨10.1186/s42523-023-00252-w⟩ Article dans une revue hal-04126196v1
Holistic integration of omics data reveals the drivers that shape the ecology of microbial meat spoilage scenarios Simon Poirier,Gwendoline Coeuret,Marie-Christine Champomier-Vergès,Marie-Hélène Desmonts,Dalal Werneret al. Frontiers in Microbiology, 2023, 14, ⟨10.3389/fmicb.2023.1286661⟩ Article dans une revue hal-04282392v1
Artisanal and farmer bread making practices differently shape fungal species community composition in French sourdoughs Elisa Michel,Estelle Masson,Sandrine Bubbendorf,Léocadie Lapicque,Thibault Nideletet al. Peer Community Journal, 2023, 3, pp.e11. ⟨10.24072/pcjournal.237⟩ Article dans une revue hal-04206586v1
Comparative analysis of bacterial diversity in clouds and aerosols Raphaëlle Péguilhan,Florent Rossi,Olivier Rué,Muriel Joly,Pierre Amato Atmospheric Environment, 2023, 298, pp.119635. ⟨10.1016/j.atmosenv.2023.119635⟩ Article dans une revue hal-04042603v1
Microbial communities of a variety of 75 homemade fermented vegetables Anne Thierry,Marie-Noelle Madec,Victoria Chuat,Anne-Sophie Bage,Olivier Picardet al. Frontiers in Microbiology, 2023, 14, pp.1323424. ⟨10.3389/fmicb.2023.1323424⟩ Article dans une revue hal-04350660v1
Microbial community dispersal from wheat grains to sourdoughs : a contribution of participatory research Lucas von Gastrow,Elisa Michel,Judith Legrand,Rémy Amelot,Diego Segondet al. Molecular Ecology, 2023, 32 (10), pp.2413-2427. ⟨10.1111/mec.16630⟩ Article dans une revue hal-03741463v2
The ileal fungal microbiota is altered in Crohn's disease and is associated with the disease course Maya Olaisen,Mathias Richard,Vidar Beisvåg,Atle van Beelen Granlund,Elin Røysetet al. Frontiers in Medicine, 2022, 9, pp.868812. ⟨10.3389/fmed.2022.868812⟩ Article dans une revue hal-04007387v1
Comparison of Fecal Sample Collection Methods for Microbial Analysis Embedded within Colorectal Cancer Screening Programs Semi Zouiouich,Mahendra Mariadassou,Olivier Rué,Emily Vogtmann,Inge Huybrechtset al. Cancer Epidemiology, Biomarkers and Prevention, 2022, 31 (2), pp. 305-314. ⟨10.1158/1055-9965.EPI-21-0188⟩ Article dans une revue hal-03625845v1
Investigation of the Phageome and Prophages in French Cider, a Fermented Beverage Pierre Ledormand,Nathalie Desmasures,Cédric Midoux,Olivier Rué,Marion Dalmasso Microorganisms, 2022, 10 (6), pp.1203. ⟨10.3390/microorganisms10061203⟩ Article dans une revue hal-03693766v1
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
Virulent Phages Isolated from a Smear-Ripened Cheese Are Also Detected in Reservoirs of the Cheese Factory Thomas Paillet,Julien Lossouarn,Clarisse Figueroa,Cédric Midoux,Olivier Ruéet al. Viruses, 2022, 14 (8), pp.1620. ⟨10.3390/v14081620⟩ Article dans une revue hal-03738602v1
Mining the equine gut metagenome: poorly-characterized taxa associated with cardiovascular fitness in endurance athletes Núria Mach,Cédric Midoux,Sébastien Leclercq,Samuel Pennarun,Laurence Le Moyecet al. Communications Biology, 2022, 5, pp.1032. ⟨10.1038/s42003-022-03977-7⟩ Article dans une revue hal-03794437v2
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
Diversity and dynamics of bacterial and fungal communities in cider for distillation B. Misery,Patrick Legendre,Olivier Rué,Valérie Bouchart,H. Guichardet al. International Journal of Food Microbiology, 2021, 339, pp.108987. ⟨10.1016/j.ijfoodmicro.2020.108987⟩ Article dans une revue hal-03287173v1
FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers Maria Bernard,Olivier Rué,Mahendra Mariadassou,Géraldine Pascal Briefings in Bioinformatics, 2021, 22 (6), ⟨10.1093/bib/bbab318⟩ Article dans une revue hal-03323846v1
The Rhinobiome of Exacerbated Wheezers and Asthmatics: Insights From a German Pediatric Exacerbation Network Malik Aydin,Cornelius Weisser,Olivier Rué,Mahendra Mariadassou,Sandra Maaßet al. Frontiers in Allergy, 2021, 2, ⟨10.3389/falgy.2021.667562⟩ Article dans une revue hal-03244864v1
Nitric Oxide Impacts Human Gut Microbiota Diversity and Functionalities Marion Leclerc,Cassandre Bedu-Ferrari,Lucie Etienne-Mesmin,Mahendra Mariadassou,Lucie Lebreuillyet al. mSystems, 2021, 6 (5), ⟨10.1128/mSystems.00558-21⟩ Article dans une revue hal-03413913v1
A Yarrowia lipolytica Strain Engineered for Pyomelanin Production Macarena Larroude,Djamila Onésime,Olivier Rué,Jean-Marc Nicaud,Tristan Rossignol Microorganisms, 2021, 9 (4), pp.838. ⟨10.3390/microorganisms9040838⟩ Article dans une revue hal-03274344v1
Does Physical Inactivity Induce Significant Changes in Human Gut Microbiota? New Answers Using the Dry Immersion Hypoactivity Model Maxence Jollet,Kevin Nay,Angèle Chopard,Marie-Pierre Bareille,Arnaud Becket al. Nutrients, 2021, 13 (11), ⟨10.3390/nu13113865⟩ Article dans une revue hal-03415988v1
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
First step of odorant detection in the olfactory epithelium and olfactory preferences differ according to the microbiota profile in mice Laurent Naudon,Adrien François,Mahendra Mariadassou,Magali Monnoye,Catherine Philippeet al. Behavioural Brain Research, 2020, 384, ⟨10.1016/j.bbr.2020.112549⟩ Article dans une revue hal-02503302v1
Taxon appearance from extraction and amplification steps demonstrates the value of multiple controls in tick microbiome analysis Emilie Lejal,Agustin Estrada-Peña,Maud Marsot,Jean-Francois J.-F. Cosson,Olivier Ruéet al. Frontiers in Microbiology, 2020, 11, ⟨10.3389/fmicb.2020.01093⟩ Article dans une revue hal-02790980v1
Lactococcus lactis Diversity Revealed by Targeted Amplicon Sequencing of purR Gene, Metabolic Comparisons and Antimicrobial Properties in an Undefined Mixed Starter Culture Used for Soft-Cheese Manufacture Sabrina Saltaji,Olivier Rué,Valérie Sopena,Sophie Sablé,Fatoumata Tambadouet al. Foods, 2020, 9 (5), pp.622. ⟨10.3390/foods9050622⟩ Article dans une revue hal-03516147v1
A Probiotic Mixture Induces Anxiolytic- and Antidepressive-Like Effects in Fischer and Maternally Deprived Long Evans Rats Valérie Daugé,Catherine Philippe,Mahendra Mariadassou,Olivier Rué,Jean-Charles Martinet al. Frontiers in Behavioral Neuroscience, 2020, 14, ⟨10.3389/fnbeh.2020.581296⟩ Article dans une revue hal-03225018v1
Assessing the quality of fresh Whitemouth croaker (Micropogonias furnieri) meat based on micro‐organism and histamine analysis using NGS, qPCR and HPLC‐DAD Alessandra Danile de Lira,Caroline Isabel Kothe,Olivier Rué,Cédric Midoux,Michele Bertoni Mannet al. Journal of Applied Microbiology, 2020, 128 (5), pp.1448-1459. ⟨10.1111/jam.14566⟩ Article dans une revue hal-02903118v1
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
Gut bacteria are critical for optimal muscle functiona potential link with glucose homeostasis Kevin Nay,Maxence Jollet,Benedicte Goustard,Narjes Baati,Barbara Vernuset al. AJP - Endocrinology and Metabolism, 2019, 317 (1), pp.E158-E171. ⟨10.1152/ajpendo.00521.2018⟩ Article dans une revue hal-02152871v1
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
Guide pratique à destination des biologistes, bioinformaticiens et statisticiens qui souhaitent s’initier aux analyses métabarcoding Hélène Falentin,Lucas Auer,Mahendra Mariadassou,Géraldine Pascal,Olivier Ruéet al. Cahier des Techniques de l'INRA, 2019, 97, pp.46-69 Article dans une revue (article de synthèse) hal-02311421v1
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
Oak genome reveals facets of long lifespan Christophe Plomion,Jean-Marc Aury,Joelle Amselem,Thibault Leroy,Florent Muratet al. Nature Plants, 2018, 4 (7), pp.440-452. ⟨10.1038/s41477-018-0172-3⟩ Article dans une revue hal-01820559v1
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
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
Ingredients for in silico miRNA identification and annotation Christine Gaspin,Olivier Rué,Matthias Zytnicki JSM Biotechnology and Biomedical Engineering, 2016, 3 (5), pp.1-5 Article dans une revue (article de synthèse) hal-01607400v1
Characterization of an extensive rainbow trout miRNA transcriptome by next generation sequencing Amélie Juanchich,Philippe Bardou,Olivier Rué,Jean-Charles Gabillard,Christine Gaspinet al. BMC Genomics, 2016, 17:164 (1), pp.1-12. ⟨10.1186/s12864-016-2505-9⟩ Article dans une revue hal-01509042v1

Communication dans un congrès (26)

LEAP - Learn and Evaluate Affiliation databanks on an online Platform Olivier Rué,Maria Bernard,Lucas Auer,Gabryelle Agoutin,Maelle Pomieset al. FROGSDays, FROGS team, Dec 2025, Toulouse, France Communication dans un congrès hal-05397586v1
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
Rétrospective FROGS 2015–2025 Géraldine Pascal,Maria Bernard,Olivier Rué,Mahendra Mariadassou,Frédéric Escudiéet al. Symposium FROGSDays, INRAE Toulouse, Dec 2025, Castanet Tolosan, France Communication dans un congrès hal-05492401v1
FROGS5 - News Olivier Rué,Maelle Pomies,Maria Bernard,Lucas Auer,Gabryelle Agoutinet al. FROGSDays, FROGS team, Dec 2025, Toulouse, France Communication dans un congrès hal-05397597v1
Impact of superchilling technique on the microbiological quality of fresh salmon Pierre Collin,Maud Darsonval,Olivier Rué,Fatou Toutie Ndoye,Graciela Alvarezet al. FoodMicro 2024, ICFMH, Jul 2024, Burgos, Spain Communication dans un congrès hal-04760035v1
Présentation du service d'analyse de données Olivier Rué Migale & Vous, May 2024, Jouy-en-Josas (FR), France Communication dans un congrès hal-04963446v1
Microbiome, disease-resistant varieties, and wine quality Gabriela Pinto Miguel,Martine Pradal,Olivier Rué,Evelyne Aguera,Cécile Neuvéglise 45. World Congress of Vine and Wine, Oct 2024, Dijon, France. ⟨10.58233/d4ACq14T⟩ Communication dans un congrès hal-04954449v1
News about FROGS Olivier Rué,Lucas Auer,Gabryelle Agoutin,Maria Bernard,Géraldine Pascal PEPI IBIS, Nov 2024, Virtuel, France Communication dans un congrès hal-04786277v1
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
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
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
Transcriptomic and proteomic response of a Liquorilactobacillus mali strain from cider to a lytic phage infection Pierre Ledormand,Nathalie Desmasures,Benoit Bernay,Olivier Rué,Cédric Midouxet al. Société Francaise Microbiologie, 2021, Nantes, France Communication dans un congrès hal-03896401v1
Élément du portfolio - projet METABARFOOD Olivier Rué visite HCERES unité MaIAGE, Dec 2024, Jouy-En-Josas, France. ⟨10.1093/bib/bbab318⟩ Communication dans un congrès hal-04963473v1
Baker’s bread-making practices and house microbiota shape fungal species diversity in french sourdoughs Delphine Sicard,Elisa Michel,Judith Legrand,Estelle Masson,Sandrine Bubendorffet al. Harlan III, Jun 2019, Montpellier, France Communication dans un congrès hal-02950822v1
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
Domestication of microbial communities for bread making: insights from a participatory research project Elisa Michel,Judith Legrand,Estelle Masson,Sandrine Bubendorff,Stephane Guezenecet al. The 2019 Congress of the European Society for Evolutionary Biology, ESEB, Aug 2019, Turku, Finland Communication dans un congrès hal-02950758v1
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
Is skeletal muscle remodeling associated with gut microbiota signature? Maxence Jollet,Barbara Vernus,Anne Bonnieu,Mahendra Mariadassou,Olivier Ruéet al. 6th World Congress on Targeting Microbiota, Oct 2018, Porto, Portugal. pp.1 Communication dans un congrès hal-02736948v1
Deciphering intra-species bacterial diversity using gyrB amplicon sequencing Olivier Rué JOBIM 2019, Société Française de Bio-Informatique (SFBI). FRA.; Centre National de la Recherche Scientifique (CNRS). FRA.; Institut Français de Bioinformatique (IFB). FRA., Jul 2019, Nantes, France. 422 p Communication dans un congrès hal-02266901v1
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
An integrated information system dedicated to oak genomics and genetics Joëlle Amselem,Nicolas Francillonne,Célia Michotey,Thomas Letellier,Jean-Marc Auryet al. PAG XXVI Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.27 slides Communication dans un congrès hal-01839185v1
Domestication of microbial community in action : a participatory research and multidisciplinary study of sourdough bread Elisa Michel,Maria Belen Carbonetto,Charlotte Urien,Emilie Lhomme,Stephane Guezenecet al. Second Joint Congress on Evolutionary Biology (EVOLUTION 2018), Aug 2018, Montpellier, France Communication dans un congrès hal-02008729v1
Annotation of the oak genome sequence and associated bioinformatic resources Joelle J. Amselem,Jean Marc Aury,Nicolas Francillonne,Tina Alaeitabar,Corinne da Silvaet al. IUFRO Genomics and Forest Tree Genetics, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., May 2016, Arcachon, France. 134 p Communication dans un congrès hal-02741128v1
Biomechanical evaluation for the identification of free kick determinants in soccer Guillaume Nicolas,Benoit Bideau,Richard Kulpa,Olivier Rué,Maxime Billienet al. European Workshop On Movement Science, 2009, Lisbon, Portugal Communication dans un congrès hal-04783543v1

Poster de conférence (31)

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
LEAP: Learn and Evaluate Affiliation databanks on an online Platform Olivier Rué,Gabryelle Agoutin,Lucas Auer,Lynn Bekaï,Maria Bernardet al. JOBIM, Jul 2025, Bordeaux, France Poster de conférence hal-05143055v1
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
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
Exploration of dairy cow holobiont revealed an important sharing of microbes between anatomic sites within individual hosts throughout lactation but sharing was limited in the herd Mahendra Mariadassou,Laurent-Xavier Nouvel,Fabienne Constant,Diego Morgavi,Lucie Raultet al. https://www.adsa.org/Meetings/2023-Annual-Meeting. ADSA annual meeting 2023, Jun 2023, Ottawa, Canada. , 2023 Poster de conférence hal-04164713v1
Exploring the microbiota of resistant varieties in organic farming Evelyne Aguera,Romain Maindron,Erick Casalta,Laurent Deliere,Aarti Jaswaet al. PYYF8 - 8. Conference on Physiology of Yeasts and Filamentous Fungi, Jun 2023, Cork, Ireland. Poster de conférence hal-04665549v1
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
Rôle du microbiote dans la relation entre activité physique, santé et bien-être Benedicte Goustard,Barbara Vernus,Olivier Rué,Mahendra Mariadassou,Laurence Pessemesseet al. Journées d'Animation Scientifiques du Département PHASE, May 2022, Poitiers, France. 317, pp.E158 - E171 Poster de conférence hal-04804882v1
FROGSFUNC: Smart integration of PICRUSt2 software into FROGS pipeline Vincent Darbot,Moussa Samb,Maria Bernard,Olivier Rué,Géraldine Pascal JOBIM 2022, Jul 2022, Rennes, France. Poster de conférence hal-03806133v1
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
Bacteriophages infecting surface bacteria from a smear-ripened cheese are persistent and contaminate the dairy plant Thomas Paillet,Julien Lossouarn,Clarisse Figueroa,Inès Pedros,Cédric Midouxet al. Viruses of Microbes (VoM) 2022, Jul 2022, Guimarães, Portugal Poster de conférence hal-04416527v1
Exploring the microbiota of resistant varieties in organic farming Evelyne Aguera,Romain Maindron,Marine Touret,Laurent Deliere,Aarti Jaswaet al. Montpellier Vine & WIne sciences - International seminar: Sharing knowledge & designing research programs to address key challenges of the vine-wine sector, Oct 2022, Montpellier, France Poster de conférence hal-04667137v1
Le cidre est une matrice délicate pour l’étude des bactériophages et des phageomes. Pierre Ledormand,Nathalie Desmasures,Céline Caillard,Erwan Renard,Didier Gouxet al. Société Française de Microbiologie 2022, 2022, Nantes, France Poster de conférence hal-03896438v1
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
Gut microbiota and skeletal muscle crosstalk : lessons from muscle remarkable phenotypes. Maxence Jollet,Kévin Nay,Mahendra Mariadassou,Olivier Rué,A Chopardet al. 19. Congress of Association of Researchers in Physical and Sport Activities ACAPS, Nov 2021, Montpellier, France Poster de conférence hal-04829963v1
Bacteriophage ecology of cider, an alcoholic fermented beverage: phages, are you there? Pierre Ledormand,Nathalie Desmasures,Didier Goux,Cédric Midoux,Olivier Ruéet al. LAB symposium, 2021, Egmond aan Zee, Netherlands Poster de conférence hal-03896414v1
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
New virulent bacteriophages isolated from the surface of Epoisses cheese infect ripening bacteria Thomas Paillet,Julien Lossouarn,Inès Pedros,Cédric Midoux,Olivier Ruéet al. Sixth symposium of the French PHAGE Network, Oct 2021, Roscoff, France Poster de conférence hal-03441698v1
New insights into cow holobiont in relation to heath Sergine Even,Mahendra Mariadassou,Xavier Nouvel,Fabienne F. Constant,Diego Morgaviet al. 16e congres national de la SFM-MICROBES 2021, Sep 2021, Nantes, France Poster de conférence hal-03361039v1
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
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
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
Des solutions informatiques innovantes pour l’utilisation et le développement de biomarqueurs de diversité du microbiote. Maria Bernard,Olivier Rué,Malo Le Boulch,Jean Mainguy,Laurent Cauquilet al. DefisPHASE 2019, 2019, Rennes, France Poster de conférence hal-03851900v1
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
Plateforme bioinformatique MIGALE Hélène Chiapello,Sandra Dérozier,Olivier Inizan,Mahendra Mariadassou,Véronique Martinet al. Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2019, Nantes, France. 2019 Poster de conférence hal-04176805v1
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
Mining anaerobic digestion data with Deep-omics, a new digital environmental engineering platform for omics data Cédric Midoux,Guillaume Perréal,Manon Prédhumeau,Olivier Rué,Yannick Fayolleet al. AD16 (16th IWA World Conference on Anaerobic Digestion), Jun 2019, Delft, Netherlands Poster de conférence hal-04361137v1
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
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

Pré-publication, Document de travail (3)

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
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
Experimental and methodological framework for the assessment of nucleic acids in airborne microorganisms Raphaëlle Péguilhan,Florent Rossi,Olivier Rué,Muriel Joly,Pierre Amato 2024 Pré-publication, Document de travail hal-04271307v1

Mémoire d'étudiant (1)

Extracting and displaying information from the databanks used for metabarcoding Lynn Bekai,Olivier Rué,Géraldine Pascal Bio-Informatique, Biologie Systémique [q-bio.QM]. 2024 Mémoire d'étudiant hal-04786236v2

Logiciel (3)

FROGS Géraldine Pascal,Maria Bernard,Olivier Rué,Frédéric Escudié,Vincent Darbotet al. 2024, ⟨swh:1:dir:1f2728ab804b46ba8080e6530c5100f1daf37eb7;origin=https://github.com/geraldinepascal/FROGS;visit=swh:1:snp:bf5bd90e285971eead69ea9ad93aa61c0a9f0db2;anchor=swh:1:rev:1f61d660e1281c65f4160b49b10bb11855849cd2⟩ Logiciel hal-04384514v1
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
Repository containing source code and scripts used for the METABARFOOD project Olivier Rué 2023, ⟨swh:1:dir:82af0d07097206f20464df2f1f3782608196bd93;origin=https://hal.archives-ouvertes.fr/hal-04212255;visit=swh:1:snp:1128716d438ad454e56e802489faafb03a17163d;anchor=swh:1:rel:649e46468e38ae7732dd9fc2dc238c48e08acc7f;path=/⟩ Logiciel hal-04212255v1