Mahendra Mariadassou

144

Documents

Publications

	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 Neuvéglise ISME Communications, inPress, 4 (1), pp.ycae095. ⟨10.1093/ismeco/ycae095⟩ Journal articles hal-04668230v1
	Insight into the Role of Gut Microbiota in Duchenne Muscular Dystrophy Maxence Jollet , Mahendra Mariadassou , Olivier Rué , Laurence Pessemesse , Vincent Ollendorff American Journal of Pathology, 2024, 194 (2), pp.264-279. ⟨10.1016/j.ajpath.2023.10.010⟩ Journal articles hal-04383411v1
	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 Rault Animal Microbiome, 2023, 5 (1), pp.32. ⟨10.1186/s42523-023-00252-w⟩ Journal articles hal-04126196v1
	Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems Daniel Richter , Romain Watteaux , Thomas Vannier , Jade Leconte , Paul Frémont eLife, 2022, 11, pp.e78129. ⟨10.7554/eLife.78129⟩ Journal articles hal-02399723v2
	Hierarchical correction of p-values via an ultrametric tree running Ornstein-Uhlenbeck process Antoine Bichat , Christophe Ambroise , Mahendra Mariadassou Computational Statistics, 2022, 37 (3), pp.995-1013. ⟨10.1007/s00180-021-01148-6⟩ Journal articles hal-04072108v1
	Prebiotic Supplementation During Gestation Induces a Tolerogenic Environment and a Protective Microbiota in Offspring Mitigating Food Allergy Amandine Selle , Carole Brosseau , Wieneke Dijk , Angéline Duval , Grégory Bouchaud Frontiers in Immunology, 2022, 12, pp.745535. ⟨10.3389/fimmu.2021.745535⟩ Journal articles hal-03578742v1
	Comparison of Fecal Sample Collection Methods for Microbial Analysis Embedded within Colorectal Cancer Screening Programs Semi Zouiouich , Mahendra Mariadassou , Olivier Rué , Emily Vogtmann , Inge Huybrechts Cancer Epidemiology, Biomarkers and Prevention, 2022, 31 (2), pp. 305-314. ⟨10.1158/1055-9965.EPI-21-0188⟩ Journal articles hal-03625845v1
	Exploring short k-mer profiles in cells and mobile elements from Archaea highlights the major influence of both the ecological niche and evolutionary history Ariane Bize , Cédric Midoux , Mahendra Mariadassou , Sophie Schbath , Patrick Forterre BMC Genomics, 2021, 22, ⟨10.1186/s12864-021-07471-y⟩ Journal articles hal-03176011v1
	Unraveling the history of the genus Gallus through whole genome sequencing Mahendra Mariadassou , Marie Suez , Sanbadam Sathyakumar , Alain Vignal , Mariangela Arca Molecular Phylogenetics and Evolution, 2021, 158, pp.107044. ⟨10.1016/j.ympev.2020.107044⟩ Journal articles hal-03155990v1
	Microbial and functional characterization of an allochthonous consortium applied to hydrogen production from Citrus Peel Waste in batch reactor in optimized conditions Franciele Pereira Camargo , Isabel Kimiko Sakamoto , Tiago Palladino Delforno , Mahendra Mariadassou , Valentin Loux Journal of Environmental Management, 2021, 291, pp.112631. ⟨10.1016/j.jenvman.2021.112631⟩ Journal articles hal-03211333v1
	Glucose but Not Fructose Alters the Intestinal Paracellular Permeability in Association With Gut Inflammation and Dysbiosis in Mice Magali Monnoye , Xufei Zhang , Mahendra Mariadassou , Fabienne Beguet-Crespel , Nicolas Lapaque Frontiers in Immunology, 2021, 12, ⟨10.3389/fimmu.2021.742584⟩ Journal articles hal-03634400v1
	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⟩ Journal articles 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 Maaß Frontiers in Allergy, 2021, 2, ⟨10.3389/falgy.2021.667562⟩ Journal articles hal-03244864v1
	Nitric Oxide Impacts Human Gut Microbiota Diversity and Functionalities Marion Leclerc , Cassandre Bedu-Ferrari , Lucie Etienne-Mesmin , Mahendra Mariadassou , Lucie Lebreuilly mSystems, 2021, 6 (5), ⟨10.1128/mSystems.00558-21⟩ Journal articles hal-03413913v1
	The Poisson-Lognormal Model as a Versatile Framework for the Joint Analysis of Species Abundances Julien Chiquet , Mahendra Mariadassou , Stéphane Robin Frontiers in Ecology and Evolution, 2021, 9, ⟨10.3389/fevo.2021.588292⟩ Journal articles hal-03215628v1
	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 Beck Nutrients, 2021, 13 (11), ⟨10.3390/nu13113865⟩ Journal articles hal-03415988v1
	Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions E. Lejal , J. Chiquet , J. Aubert , S. Robin , A. Estrada-Peña Microbiome, 2021, 9 (1), pp.153. ⟨10.1186/s40168-021-01051-8⟩ Journal articles hal-03287263v1
	Shifts in the temperature-sensitive periods for spring phenology in European beech and pedunculate oak clones across latitudes and over recent decades. Bénédicte Wenden , Mahendra Mariadassou , Frank-M Chmielewski , Yann Vitasse Global Change Biology, 2020, 26, pp.1808-1819. ⟨10.1111/gcb.14918⟩ Journal articles hal-02622770v1
	Detection of selection signatures in Limousin cattle using whole‐genome resequencing M. Mariadassou , Y. Ramayo‐caldas , M. Charles , M. Féménia , G. Renand Animal Genetics, 2020, 51 (5), pp.815-819. ⟨10.1111/age.12982⟩ Journal articles hal-03285327v1
	Consistency and Asymptotic Normality of Latent Blocks Model Estimators Vincent Brault , Christine Keribin , Mahendra Mariadassou Electronic Journal of Statistics , 2020, 14 (1), pp.1234-1268. ⟨10.1214/20-EJS1695⟩ Journal articles hal-01511960v3
	Incorporating Phylogenetic Information in Microbiome Differential Abundance Studies Has No Effect on Detection Power and FDR Control Antoine Bichat , Jonathan Plassais , Christophe Ambroise , Mahendra Mariadassou Frontiers in Microbiology, 2020, 11, ⟨10.3389/fmicb.2020.00649⟩ Journal articles hal-02635268v1
	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 Martin Frontiers in Behavioral Neuroscience, 2020, 14, ⟨10.3389/fnbeh.2020.581296⟩ Journal articles hal-03225018v1
	Murine genetic background overcomes gut microbiota changes to explain metabolic response to high-fat diet Zahra Safari , Aurelia Bruneau , Magali Monnoye , Mahendra Mariadassou , Catherine Philippe Nutrients, 2020, 12 (2), ⟨10.3390/nu12020287⟩ Journal articles hal-02503303v1
	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 Philippe Behavioural Brain Research, 2020, 384, ⟨10.1016/j.bbr.2020.112549⟩ Journal articles 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 Rué Frontiers in Microbiology, 2020, 11, ⟨10.3389/fmicb.2020.01093⟩ Journal articles hal-02790980v1
	Consistency and asymptotic normality of stochastic block models estimators from sampled data Mahendra Mariadassou , Timothée Tabouy Electronic Journal of Statistics , 2020, 14 (2), pp.3672-3704. ⟨10.1214/20-ejs1750⟩ Journal articles hal-04380551v1
	SimkaMin: fast and resource frugal de novo comparative metagenomics Gaëtan Benoit , Mahendra Mariadassou , Stéphane Robin , Sophie Schbath , Pierre Peterlongo Bioinformatics, 2020, 36 (4), pp.1-2. ⟨10.1093/bioinformatics/btz685⟩ Journal articles hal-02308101v1
	Function-Driven Design of Lactic Acid Bacteria Co-cultures to Produce New Fermented Food Associating Milk and Lupin Fanny Canon , Mahendra Mariadassou , Marie-Bernadette Maillard , Hélène Falentin , Sandrine Parayre Frontiers in Microbiology, 2020, 11, ⟨10.3389/fmicb.2020.584163⟩ Journal articles hal-03019865v1
	Optimize the plant microbiota to increase plant growth and health Matthieu Barret , P. Dufour , Mylène Durand-Tardif , Mahendra Mariadassou , Christophe Mougel Consortium Biocontrôle et GIS Biotechnologies Vertes , 2019, ⟨10.15454/1fve-e105⟩ Journal articles hal-03297096v1
	Comparative metatranscriptomic analysis of anaerobic digesters treating anionic surfactant contaminated wastewater Tiago P. Delforno , Thais Z. Macedo , Cedric Midoux , Gileno V. Lacerda , Olivier Rué Science of the Total Environment, 2019, 2019 (649), pp.482-494. ⟨10.1016/j.scitotenv.2018.08.328⟩ Journal articles hal-01888286v1
	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 Rué Cahier des Techniques de l'INRA, 2019, 97, pp.46-69 Journal articles hal-02311421v1
	Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale Méryl Vila Nova , Kévin Durimel , Kévin La , Arnaud Felten , Philippe Bessieres BMC Genomics, 2019, 20 (1), ⟨10.1186/s12864-019-6188-x⟩ Journal articles hal-02392205v1
	Gut bacteria are critical for optimal muscle functiona potential link with glucose homeostasis Kevin Nay , Maxence Jollet , Benedicte Goustard , Narjes Baati , Barbara Vernus AJP - Endocrinology and Metabolism, 2019, 317 (1), pp.E158-E171. ⟨10.1152/ajpendo.00521.2018⟩ Journal articles hal-02152871v1
	Fructose malabsorption induces cholecystokinin expression in the ileum and cecum by changing microbiota composition and metabolism Xufei Zhang , Alexandra Grosfeld , Edek Williams , Daniel Vasiliauskas , Sharon Barretto FASEB Journal, 2019, 33 (6), pp.7126-7142. ⟨10.1096/fj.201801526RR⟩ Journal articles hal-02191008v1
	Steatosis and gut microbiota dysbiosis induced by high-fat diet are reversed by 1-week chow diet administration Zahra Safari , Magali Monnoye , Peter M. Abuja , Mahendra Mariadassou , Karl Kashofer Nutrients, 2019, 71, pp.72-88. ⟨10.1016/j.nutres.2019.09.004⟩ Journal articles hal-02503316v1
	FROGS: Find, Rapidly, OTUs with Galaxy Solution Frédéric Escudié , Lucas Auer , Maria Bernard , Mahendra Mariadassou , Laurent Cauquil Bioinformatics, 2018, 34 (8), pp.1287-1294. ⟨10.1093/bioinformatics/btx791⟩ Journal articles hal-02626808v1
	Inference of Adaptive Shifts for Multivariate Correlated Traits Paul Bastide , Céline Ané , Stephane Robin , Mahendra Mariadassou Systematic Biology, 2018, 67, ⟨10.1093/sysbio/syy005⟩ Journal articles hal-01608932v1
	Variational inference for probabilistic Poisson PCA Julien Chiquet , Mahendra Mariadassou , Stephane Robin Annals of Applied Statistics, 2018, 12 (4), pp.2674-2698. ⟨10.1214/18-AOAS1177⟩ Journal articles hal-01941270v1
	Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes Jeffrey K. Cornuault , Marie-Agnès Petit , Mahendra Mariadassou , Leandro Benevides , Elisabeth Moncaut Microbiome, 2018, 6 (1), 14 p. ⟨10.1186/s40168-018-0452-1⟩ Journal articles hal-01774632v1
	OH1 from Orf virus: a new tyrosine phosphatase that displays distinct structural features and triple substrate specificity Danilo Segovia , Ahmed Haouz , Dario Porley , Natalia Olivero , Mariano Martinez Journal of Molecular Biology, 2017, 26 p. ⟨10.1016/j.jmb.2017.07.017⟩ Journal articles hal-01602647v1
	Identification of proteins involved in the anti-inflammatory properties of Propionibacterium freudenreichii by means of a multi-strain study Stéphanie-Marie Deutsch , Mahendra Mariadassou , Pierre Nicolas , Sandrine Parayre , Rozenn Le Guellec Scientific Reports, 2017, 7, pp.46409. ⟨10.1038/srep46409⟩ Journal articles hal-01510019v1
	Detection of adaptive shifts on phylogenies by using shifted stochastic processes on a tree Paul Bastide , Mahendra Mariadassou , Stephane Robin Journal of the Royal Statistical Society: Series B, 2017, ⟨10.1111/rssb.12206⟩ Journal articles hal-01551071v1
	Analysis of large 16S rRNA Illumina datasets: impact of singleton read filtering on microbial community description Lucas Auer , Mahendra Mariadassou , Michael O'Donohue , Christophe Klopp , Guillermina Hernandez-Raquet Molecular Ecology Resources, 2017, ⟨10.1111/1755-0998.12700⟩ Journal articles hal-01605865v1
	Unprecedented large inverted repeats at the replication terminus of circular bacterial chromosomes suggest a novel mode of chromosome rescue Hela El Kafsi , Valentin Loux , Mahendra Mariadassou , Camille Blin , Hélène Chiapello Scientific Reports, 2017, 7, pp.1-11. ⟨10.1038/srep44331⟩ Journal articles hal-01509688v1
	Beneficial metabolic effects of selected probiotics on diet-induced obesity and insulin resistance in mice are associated with improvement of dysbiotic gut microbiota Jeanne Alard , Véronique Lehrter , Moez Rhimi , Irène Mangin , Véronique Peucelle Environmental Microbiology, 2016, 18 (5), pp.1484-1497. ⟨10.1111/1462-2920.13181⟩ Journal articles hal-03372071v1
	The Red Queen lives: Epistasis between linked resistance loci Cesar M. J. A. Metzger , Pepijn Luijckx , Gilberto Bento , Mahendra Mariadassou , Dieter Ebert Evolution - International Journal of Organic Evolution, 2016, 70 (2), pp.480-487. ⟨10.1111/evo.12854⟩ Journal articles hal-02631286v1
	Multiple comparative metagenomics using multiset k -mer counting Gaëtan Benoit , Pierre Peterlongo , Mahendra Mariadassou , Erwan Drezen , Sophie Schbath PeerJ Computer Science, 2016, 2 (14), 25 p. ⟨10.7717/peerj-cs.94⟩ Journal articles hal-01397150v1
	Olfactory epithelium changes in germfree mice Adrien François , Denise Grebert , Moez Rhimi , Mahendra Mariadassou , Laurent Naudon Scientific Reports, 2016, 6 (1), pp.24687. ⟨10.1038/srep24687⟩ Journal articles hal-03371054v1
	Convergence of the groups posterior distribution in latent or stochastic block models Mahendra Mariadassou , Catherine Matias Bernoulli, 2015, 21 (1), pp.537-573 Journal articles hal-00713120v2
	Co-clustering through Latent Bloc Model: a Review Vincent Brault , Mahendra Mariadassou Journal de la Société Française de Statistique, 2015, 156 (3), pp.120-139 Journal articles hal-02088216v1
	High genetic variation in resting-stage production in a metapopulation: Is there evidence for local adaptation? Anne C Roulin , Mahendra Mariadassou , Matthew D Hall , Jean-Claude Walser , Christoph Haag Evolution - International Journal of Organic Evolution, 2015, 69 (10), pp.2747-56. ⟨10.1111/evo.12770⟩ Journal articles hal-02634111v1
	Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii Valentin Loux , Mahendra Mariadassou , Sintia Almeida , Hélène Chiapello , Amal Hammani BMC Genomics, 2015, 16 (1), pp.35. ⟨10.1186/s12864-015-1467-7⟩ Journal articles hal-01142363v1
	Quantitative prediction of genome-wide resource allocation in bacteria Anne Goelzer , Jan Muntel , Victor Chubukov , Matthieu Jules , Eric Prestel Metabolic Engineering, 2015, 32, pp.232-243. ⟨10.1016/j.ymben.2015.10.003⟩ Journal articles hal-01536511v1
	Microbial ecosystems are dominated by specialist taxa. Mahendra Mariadassou , Samuel Pichon , Dieter Ebert Ecology Letters, 2015, 18 (9), pp.974-82. ⟨10.1111/ele.12478⟩ Journal articles hal-02631330v1
	Identification of amino acids in mitochondrially encoded proteins that correlate with lifespan. Mahendra Mariadassou , Francois-Xavier Pellay Experimental Gerontology, 2014, 56, pp.53-58. ⟨10.1016/j.exger.2014.03.009⟩ Journal articles hal-02630250v1
	Local and systemic Immune mechanisms underlying the Anti-Colitis effects of the dairy Bacterium Lactobacillus delbrueckii. Clarissa Santos Rocha , Ana Cristina Gomes-Santos , Thais Garcias Moreira , Marcela de Azevedo , Tessalia Diniz Luerce PLoS ONE, 2014, 9 (1), pp.1-8. ⟨10.1371/journal.pone.0085923⟩ Journal articles hal-01204288v1
	Analyses of the radiation of birnaviruses from diverse host phyla and of their evolutionary affinities with other double-stranded RNA and positive strand RNA viruses using robust structure-based multiple sequence alignments and advanced phylogenetic methods. Jean-François Gibrat , Mahendra Mariadassou , Pierre Boudinot , Bernard B. Delmas BMC Evolutionary Biology, 2013, 13, pp.3-17. ⟨10.1186/1471-2148-13-154⟩ Journal articles hal-02645508v1
	Taxon influence index: assessing taxon-induced incongruities in phylogenetic inference Mahendra Mariadassou , Avner Bar-Hen , Hirohisa Kishino Systematic Biology, 2012, 61 (2), pp.337-345. ⟨10.1093/sysbio/syr129⟩ Journal articles hal-02642639v1
	Phylogenetic and complementation analysis of a single-stranded dna binding protein family from lactococcal phages indicates a non-bacterial origin Agnieszka K. Szczepankowska , Eric Prestel , Mahendra Mariadassou , Jacek K. Bardowski , Elena Bidnenko PLoS ONE, 2011, 6 (11), ⟨10.1371/journal.pone.0026942⟩ Journal articles hal-01191212v1
	Uncovering latent structure in valued graphs: a variational approach Mahendra Mariadassou , Stephane Robin , Corinne Vacher Annals of Applied Statistics, 2010, 4 (2), pp.715-742. ⟨10.1214/10-AOAS361⟩ Journal articles hal-01197514v1
	Concentration inequality for evolutionary trees Mahendra Mariadassou , Avner Bar-Hen Journal of Multivariate Analysis, 2009, pp.2055-2064. ⟨10.1016/j.jmva.2009.02.015⟩ Journal articles hal-00410872v1
	Influence function for robust phylogenetic reconstructions. Avner Bar-Hen , Mahendra Mariadassou , Marie-Anne Poursat , Philippe Vandenkoornhuyse Molecular Biology and Evolution, 2008, 25 (5), pp.869-873. ⟨10.1093/molbev/msn030⟩ Journal articles hal-00312860v1
	Uncovering structure in biological networks J.J. Daudin , Vincent Lacroix , M. Mariadassou , V. Miele , Franck Picard incollection, 2006, --, pp.471-483 Journal articles hal-00427936v1

	Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data Cédric Midoux , Mahendra Mariadassou Rencontres R, Société Française de Statistique, Jun 2024, Vannes, France Conference papers hal-04611225v1
	Origins and rate of mutations in bacteriophage Lambda Julien Lopez , Mahendra Mariadassou , Valentin Loux , Rafael Sanjuán , Marina Elez Phages in Lyon 2023, phages.fr, Nov 2023, Lyon, France Conference papers hal-04321371v1
	Milk microbiota: potential allies for mammary gland health Coralie Goetz , Lucie Rault , Marion Boutinaud , Christine Citti , Hélène Falentin ADSA annual meeting 2023, American Dairy Science Association, Jun 2023, Ottawa, Canada. pp.146 Conference papers hal-04164763v1
	MetaPDOcheese : investigation of the drivers of microbial communities from French PDO milks and cheeses Francoise Irlinger , Mahendra Mariadassou , Eric Dugat-Bony , Cécile Neuvéglise , Olivier Rué FORUM ON FERMENTED FOODS, COST PIMENTO, May 2023, Lyon, France Conference papers hal-04221356v1
	Addition of dairy lipids and probiotic in infant formulas modulates gut microbiota and intestinal physiology with long-term consequences; a preclinical study in a minipig model Marion Lemaire , Mahendra Mariadassou , Laurence Le Normand , Gwenaelle Randuineau , Véronique Rome 15. Congress of the international society for the study of fatty acids and lipids (ISSFAL), Jul 2023, Nantes, France Conference papers hal-04155652v1
	Nitric Oxide impacts human gut microbiota diversity and functionalities Nalini Ramarao , Cassandre Bedu-Ferrari , Lucie Etienne-Mesmin , Mahendra Mariadassou , Lucie Lebreuilly 9. Microbiome and probiotics R & D and business collaboration, Oct 2021, Rotterdam, Netherlands Conference papers hal-03739679v1
	Shallow Shotgun Metagenomics as a cost-effective and accurate alternative to WGS for taxonomic profiling and clinical diagnosis Benoit Goutorbe , Anne-Laure Abraham , Mahendra Mariadassou , Anne Plauzolles , Ghislain Bidaut Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2021, Paris, France Conference papers hal-03451266v1
	Caractérisation et modélisation des populations de bactériophages de la croûte de fromages (type époisses) sous différentes conditions environnementales d’affinage Stephane Chaillou , Eric Dugat-Bony , Julien Lossouarn , Marie-Agnès Petit , Mahendra Mariadassou 15. Congrès de la Société Française de Microbiologie (SFM), Société Française de Microbiologie (SFM). FRA., Sep 2019, Paris, France Conference papers hal-02789388v1
	Membre du comité d'organisation scientifique Danielle Canceill , Virginie Bourion , Mahendra Mariadassou , Milka Popova , C Roger-Gaillard, Séminaire de lancement du métaprogramme HOLOFLUX, Nov 2019, Nantes, France Conference papers hal-03229623v1
	Variational Inference for sparse network reconstruction from count data Julien Chiquet , Mahendra Mariadassou , Stephane Robin ICML 2019 International Conference on Machine Learning, Jun 2019, Long Beach, United States Conference papers hal-02735800v1
	Ecological modelling of phage, bacterial and yeast populations structure in Epoisses cheese under changing ripening conditions using factorial experimental design and metavirome analysis Eric Dugat-Bony , Julien Lossouarn , Mahendra Mariadassou , Daniel Picque , Marie-Agnès Petit MD 2019 : 5th International Conference on Microbial Diversity, Sep 2019, Catania, Italy Conference papers hal-04416628v1
	Shifts in the temperature sensitivity periods for two forest tree species under warming climatic conditions Bénédicte Wenden , Mahendra Mariadassou , Frank-M Chmielewski , Yann Vitasse EGU General Assembly 2019, Apr 2019, Vienna, Austria Conference papers hal-02790841v1
	A Walk Along Models for Count Data in Microbial Ecology Mahendra Mariadassou , Julien Chiquet , Stéphane Robin Recent Computational Advances in Metagenomics (RCAM) 2018, Sep 2018, Athènes, Greece Conference papers hal-04382269v1
	Is skeletal muscle remodeling associated with gut microbiota signature? Maxence Jollet , Barbara Vernus , Anne Bonnieu , Mahendra Mariadassou , Olivier Rué 6th World Congress on Targeting Microbiota, Oct 2018, Porto, Portugal. pp.1 Conference papers hal-02736948v1
	A metagenomic tool for cheese ecosystems Anne-Laure Abraham , Quentin Cavaillé , Thibaut Guirimand , Pierre Renault , Sandra Derozier 17. European Conference on Computational Biology (ECCB 2018, Workshop "Recent Computational Advances in Metagenomics (RCAM)", Sep 2018, Athenes, Greece Conference papers hal-02789036v1
	Équivalence asymptotique des vraisemblances observée et complète dans le modèle de blocs latents Vincent Brault , Christine Keribin , Mahendra Mariadassou XXIV èmes Rencontres de la Société Francophone de Classification, Société Francophone de Classification, Jun 2017, Lyon, France Conference papers hal-01510994v1
	Statistical analysis of trends in sweet cherry flowering data across Europe Bénédicte Wenden , Mahendra Mariadassou , José Antonio Campoy , José Quero-Garcia , Elisabeth Dirlewanger 10. International Symposium on Modelling in Fruit Research and Orchard Management, 2017, Leuven, Belgium. ⟨10.17660/ActaHortic.2017.1160.31⟩ Conference papers hal-02737108v1
	Food-Microbiomes Transfert, a shotgun metagenomic tool and a database to analyze cheese ecosystems Thibaut Guirimand , Anne-Laure Abraham , Sandra Derozier , Charlie Pauvert , Mahendra Mariadassou JOBIM 2017 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2017, Lille, France Conference papers hal-02788899v1
	Sweet cherry phenology in the context of climate change: a systems biology approach Bénédicte Wenden , Mahendra Mariadassou COST Cherry FA1104 Working Group 2 Cherry Phenology, Modelling and Climate Change, International Society for Horticultural Science (ISHS). INT., 2017, Ullensvang, Norway. ⟨10.17660/ActaHortic.2017.1162.6⟩ Conference papers hal-02736013v1
	Genomics of Chicken Domestication Mahendra Mariadassou , Marie Suez , Pierre Nicolas , Diane Esquerré , Alain Vignal 10. European Symposium on Poultry Genetics, Jun 2017, Saint Malo, France Conference papers hal-02785437v1
	FORTRESS : Impact of microbial diversity on the barrier effect against an exogenous species Eric Dugat-Bony , Philippine de Barbeyrac , Mahendra Mariadassou , Cecile Callon , Pascal Bonnarme 2017 Scientific MEM days: Journées scientifiques MEM (Métaomiques et écosystèmes microbiens), Jan 2017, Paris, France Conference papers hal-01608159v1
	Flowering time response to temperature in sweet cherry across Europe: multi-cultivar and multi-environment analysis Bénédicte B. Wenden , Mahendra Mariadassou , José Antonio Campoy , José Quero-Garcia , Elisabeth Dirlewanger 8. International Rosaceae Genomics Conference (RGC8), Jun 2016, Angers, France Conference papers hal-02740156v1
	Normalité asymptotique de l’estimateur du maximum de vraisemblance dans le modèle de blocs latents Mahendra Mariadassou , Vincent Brault , Christine Keribin 48èmes Journées de Statistique de la SFdS, May 2016, Montpellier, France Conference papers hal-01440084v1
	Quantitative prediction of genome-wide resource allocation in bacteria Anne Goelzer , Jan Muntel , Victor Chubukov , Matthieu Jules , Eric Prestel ISGSB 2016: International Study Group for Systems Biology, Oct 2016, Jena, Germany Conference papers hal-02798691v1
	Accessing virus genomes out of metagenomic data: improving statistical and bioinformatics analytic tools to better assess the contribution of phages on microbial ecosystems Marianne de Paepe , Eric Dugat-Bony , Jérôme Hamelin , Mahendra Mariadassou , Kim Milferstedt Phages On Marseille, Nov 2016, Marseille, France. pp.1 Conference papers hal-01531724v1
	Analyse statistique de données multisites de floraison pour le cerisier doux Bénédicte B. Wenden , Mahendra Mariadassou , José Antonio Campoy , José Quero-Garcia , Elisabeth Dirlewanger Colloque Francophone Phénologie, Nov 2015, Clermont Ferrand, France Conference papers hal-02744122v1
	Statistical analysis of trends in Sweet Cherry flowering data across Europe Bénédicte B. Wenden , Mahendra Mariadassou , José Antonio Campoy , José Quero-Garcia , Elisabeth Dirlewanger 10. International Symposium on Modelling in Fruit Research and Orchard Management, Jun 2015, Montpellier, France Conference papers hal-02793616v1
	Find Rapidly OTU with Galaxy Solution Frédéric Escudie , Lucas Auer , Maria Bernard , Laurent Cauquil , Katia Vidal JOBIM 2015 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France Conference papers hal-01535378v1
	Dominant Species are Specialists Mahendra Mariadassou ECMTB14 - European Conference on Mathematical and Theoretical Biology, Jun 2014, Gôteborg, Sweden. pp.1 Conference papers hal-02793165v1
	The specificity - abundance relationship in microbial communities Mahendra Mariadassou , Dieter Ebert , Samuel Pichon ECMTB14 - European Conference on Mathematical and Theoretical Biology, Jun 2014, Gothenburg, Sweden. pp.1 Conference papers hal-02798419v1
	Influence function for robust phylogenetic reconstruction Mahendra Mariadassou , Avner A. Bar-Hen JOBIM 2011, Jun 2011, Paris, France. pp.422 Conference papers hal-02746361v1
	Uncovering latent structure in valued graphs: a variational approach Mahendra Mariadassou , Stephane S. Robin , Corinne C. Vacher Probability and Discrete Mathematics in Mathematical Biology, May 2011, Singapore, Singapore. 47 diapos Conference papers hal-02802815v1
	Fonction d'influence pour la reconstruction de phylogénies robustes Mahendra Mariadassou , Avner Bar-Hen 42èmes Journées de Statistique, 2010, Marseille, France. pp.USB-key Conference papers inria-00494834v1

	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 Rault https://www.adsa.org/Meetings/2023-Annual-Meeting. ADSA annual meeting 2023, Jun 2023, Ottawa, Canada. , 2023 Conference poster hal-04164713v1
	Microbial transfers across a food chain: from grassland to cheese using metagenetic high-throughput sequencing approaches Anne-Laure Abraham , Juliette Bloor , Céline Delbès , Annick Bernalier Donadille , Matthieu Bouchon FORUM ON FERMENTED FOODS, May 2023, Lyon, France Conference poster hal-04221437v1
	Plateforme bioinformatique MIGALE Mouhamadou Ba , Hélène Chiapello , Christelle Hennequet-Antier , Valentin Loux , Mahendra Mariadassou Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2022, Rennes, France. 2022 Conference poster hal-04176761v1
	Combining marker genes in amplicon sequencing: a novel approach enhancing taxonomic profiling of microbial ecosystems Benoît Goutorbe , Anne-Laure Abraham , Mahendra Mariadassou , Marion Bonnet , Anne Plauzolles 3rd International Conference on Holobionts, Jul 2022, Lyon, France. 2022 Conference poster hal-04176902v1
	Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics Vuong Quoc Hoang Ngo , François Enault , Cédric Midoux , Mahendra Mariadassou , Olivier Chapleur ISME18, 18th International Symposium on Microbial Ecology, Aug 2022, Lausanne, Switzerland. Conference poster hal-04359643v1
	Plateforme bioinformatique MIGALE Mouhamadou Ba , Hélène Chiapello , Christelle Hennequet-Antier , Valentin Loux , Mahendra Mariadassou Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2021, Paris, France. 2021 Conference poster hal-04176768v1
	A bioinformatic pipeline to elucidate the links between viruses and their hosts in microbial communities, applied to viruses in anaerobic digestion processes Vuong Quoc Hoang Ngo , Cédric Midoux , Mahendra Mariadassou , Valentin Loux , François Enault JOBIM 2021 (JOBIM (Journées Ouvertes en Biologie, Informatique et Mathématiques), Jul 2021, Paris, France. Conference poster hal-04359920v1
	New insights into cow holobiont in relation to heath Sergine Even , Mahendra Mariadassou , Xavier Nouvel , Fabienne F. Constant , Diego Morgavi 16e congres national de la SFM-MICROBES 2021, Sep 2021, Nantes, France Conference poster hal-03361039v1
	Shallow sequencing: a cost-effective and accurate alternative to WGS for taxonomic profiling ? Benoit Goutorbe , Anne-Laure Abraham , Mahendra Mariadassou , Valentin Loux , Olivier Rué JOBIM, Jun 2020, Montpellier, France. Conference poster 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 Loux JOBIM, Jun 2020, Montpellier, France Conference poster hal-02902758v1
	Plateforme bioinformatique MIGALE Mouhamadou Ba , Damien Berry , David Christiany , Hélène Chiapello , Olivier Inizan Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jun 2020, Montpellier, France. 2020 Conference poster hal-04176782v1
	New insights into cow holobiont in relation to health Mahendra Mariadassou , Laurent-Xavier Nouvel , Diego Morgavi , Lucie Rault , Sophie Schbath Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jun 2020, Montpellier, France. , 2020 Conference poster hal-02962468v1
	Detection of an archaeal-specific viral family, previously thought to infect exclusively hyperthermophiles, in human gut metaviromes Vuong Quoc Hoang Ngo , Cédric Midoux , Olivier Rué , Mahendra Mariadassou , Violette Da Cunha Phages in Grenoble, Oct 2019, Grenoble, France. Conference poster hal-04360160v1
	Plateforme bioinformatique MIGALE Hélène Chiapello , Sandra Dérozier , Olivier Inizan , Mahendra Mariadassou , Véronique Martin Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2019, Nantes, France. 2019 Conference poster hal-04176805v1
	Feedback on a c omparative metatranscriptomic analysis Cedric Midoux , Tiago P. Delforno , Thais Z. Macedo , Gileno V. Lacerda , Olivier Rué JOBIM 2019 : Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. , 2019, JOBIM 2019 Conference poster hal-02735859v1
	Mining anaerobic digestion data with Deep-omics, a new digital environmental engineering platform for omics data Cédric Midoux , Guillaume Perréal , Marion Predhumeau , Olivier Rué , Yannick Fayolle AD16 (16th IWA World Conference on Anaerobic Digestion), Jun 2019, Delft, Netherlands Conference poster hal-04361137v1
	Easy16S : a user-friendly Shiny interface for analysis and visualization of metagenomic data Cedric Midoux , Olivier Rué , Olivier Chapleur , Mahendra Mariadassou , Théodore Bouchez JOBIM 2018 : Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. , 2018, JOBIM 2018 Conference poster hal-02737257v1
	Design de communautés bactériennes pour fermenter un nouvel aliment associant lait et légumineuse Valérie Gagnaire , Fanny Canon , Mahendra Mariadassou , Hélène Falentin , Sandrine Parayre RFL2, 2e Rencontres Francophones sur les Légumineuses, Oct 2018, Toulouse, France. , 2018 Conference poster hal-01902837v1
	New insights into cow holobiont in relation to health Laurent-Xavier Nouvel , Diego Morgavi , Lucie Rault , Mahendra Mariadassou , Sophie Schbath Pathobiome 2018 "Pathogens in Microbiotas in Hosts", Jan 2018, Ajaccio, France Conference poster hal-03299131v1
	Design of bacterial consortia for fermentation of novel food mixing milk and lupin flour Fanny Canon , Mahendra Mariadassou , Hélène Falentin , Sandrine Parayre , Marie-Bernadette Maillard 4. International Conference on Microbial Diversity 2017, Oct 2017, Bari, Italy. 2017 Conference poster hal-01628088v1
	Simka: large scale de novo comparative metagenomics Gaëtan Benoit , Pierre Peterlongo , Mahendra Mariadassou , Erwan Drezen , Sophie Schbath JOBIM 2017 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2017, Lille, France. , pp.234, 2017, JOBIM 2017 LILLE Conference poster hal-01595071v1
	Comparison of statistical methods of inference of cooccurrence networks within micro- bial ecosystems from metagenomics data Sophie Schbath , Mahendra Mariadassou , Julie Lao JOBIM 2017 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2017, Lille, France. , pp.234, 2017, JOBIM 2017 Conference poster hal-01563604v1
	Cheese ecosystems insights with shotgun metagenomics and a metadata extended genomics database. Thibaut Guirimand , Charlie Pauvert , Sandra Derozier , Anne-Laure Abraham , Mahendra Mariadassou JOBIM 2016 : Journées ouvertes de biologie informatique et mathématiques, Jun 2016, Lyon, France. , 2016 Conference poster hal-01512085v1
	Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii Valentin Loux , Mahendra Mariadassou , Sintia Almeida da Silva , Hélène Chiapello , Amal Hammami 20. Colloque du Club des Bactéries Lactiques, Jun 2015, Lille, France. , 2015 Conference poster hal-01170054v1
	Approche génomique de la domestication du poulet Michèle Tixier-Boichard , Mahendra Mariadassou , Xavier X Rognon , Pierre Nicolas , Francois Rodolphe 11. Journées de la Recherches Avicole et Palmipèdes à Foie Gras, Mar 2015, Tours, France. , 2015, Onzièmes Journées de la Recherche Avicole et Palmipèdes à Foie Gras Conference poster hal-01535349v1
	FROGS : Find Rapidly OTUs with Galaxy Solution Frédéric Escudie , Lucas Auer , Maria Bernard , Laurent Cauquil , Katia Vidal Colloque d'Écologie Microbienne organisé par l'Association Française d'Écologie Microbienne (AFEM), Nov 2015, Anglet, France. Oxford University Press, 34, 7 p., 2015, Bioinformatics Conference poster hal-01886389v1
	Accurate taxonomy assignments in cheeses ecosystems via a metagenomic approach Charlie Pauvert , Anne-Laure Abraham , Mathieu Almeida , Nicolas Pons , Mahendra Mariadassou JOBIM 2015 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. , pp.1, 2015 Conference poster hal-01204484v1
	Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii Valentin Loux , Mahendra Mariadassou , Sintia Almeida da Silva , Helene Chiapello , Amal Hammami JOBIM 16. Journées Ouvertes de Biologie, Informatique et Mathématiques, Jul 2015, Clermont-Ferrand, France. , 2015, ⟨10.1186/s12864-015-1467-7⟩ Conference poster hal-01209851v1
	How to design an efficient and robust pipeline for 16S rRNA-gene sequence analysis to improve our understanding on microbial communities? Lucas Auer , Laurent Cauquil , Stephane Chaillou , Céline Delbes , Eric Dugat-Bony JOBIM 16. Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. , 2015 Conference poster hal-01195512v1
	Insight in the genetic diversity of wild and domestic [i]Gallus[/i] Mahendra Mariadassou , Bertrand Bed'Hom , Pierre Nicolas , Jean-Luc Coville , Félicie Lahalle-Faucon 14. European Poultry Conference, Jun 2014, Stavanger, Norway. 2014 Conference poster hal-01193928v1
	Combination of in silico and proteomic approaches to identify candidate genes responsible for the immunomodulatory properties of[i] Propionibacterium freudenreichii[/i] Caroline Le Maréchal , Mahendra Mariadassou , Valentin Loux , Amal Plaudet Hammani , Julien Buratti Journées ouvertes en biologie informatique mathématiques, Jul 2012, Rennes, France. , 2012 Conference poster hal-01209420v1
	Combination of in silico and proteomic approaches to identify candidate genes responsible for the immunomodulatory properties of Propionibacterium freudenreichii Caroline Le Maréchal , Mahendra Mariadassou , Valentin Loux , Amal Plaudet Hammani , Julien Buratti Journées des Microbiologistes de l'INRA 2012, Nov 2012, L'Isle-sur-la-Sorgue, France. 2012 Conference poster hal-01209410v1

	Le modèle Poisson log-normal pour l’analyse de distributions jointes d’abondance Julien Chiquet , Marie-Josée Cros , Mahendra Mariadassou , Nathalie Peyrard , Stéphane Robin Nathalie Peyrard; Olivier Gimenez. Approches statistiques pour les variables cachées en écologie, ISTE Éditions, 2022, 9781789480474 Book sections hal-04033421v1
	The Poisson Log-Normal Model: A Generic Framework for Analyzing Joint Abundance Distributions Julien Chiquet , Marie-Josée Cros , Mahendra Mariadassou , Nathalie Peyrard , Stéphane Robin Nathalie Peyrard; Olivier Gimenez. Statistical approaches for hidden variables in ecology, Wiley, 2022 Book sections hal-04688958v1
	Tree Evaluation and Robustness Testing Mahendra Mariadassou , Avner Bar-Hen , Hirohisa Kishino Encyclopedia of Bioinformatics and Computational Biology, 2, Elsevier, pp.736-745, 2019, ⟨10.1016/B978-0-12-809633-8.20259-8⟩ Book sections hal-02484863v1

	FROGS : Find Rapidly OTU with Galaxy Solution Frédéric Escudie , Lucas Auer , Maria Bernard , Mahendra Mariadassou , Laurent Cauquil 2017 Other publications hal-01886442v1

	OneNet – One network to rule them all: consensus network inference from microbiome data Camille Champion , Raphaelle Momal , Emmanuelle Le Chatelier , Mahendra Mariadassou , Magali Berland 2024 Preprints, Working Papers, ... hal-04381703v1
	The cutting type of spontaneously fermented vegetables impacts their fermentation rate Florence Valence , Romane Junker , Céline Baty , Olivier Rué , Mahendra Mariadassou 2024 Preprints, Working Papers, ... hal-04701063v1
	Characterizing the limits of shallow shotgun metagenomics for taxonomic profiling of human gut microbiota in clinical studies Benoit Goutorbe , Anne-Laure Abraham , Mahendra Mariadassou , Anne Plauzolles , Ghislain Bidaut 2022 Preprints, Working Papers, ... hal-04316615v1
	Multiple Comparative Metagenomics using Multiset k-mer Counting Gaëtan Benoit , Pierre Peterlongo , Mahendra Mariadassou , Erwan Drezen , Sophie Schbath 2016 Preprints, Working Papers, ... hal-01300485v1
	Assessing the Distribution Consistency of Sequential Data Mahendra Mariadassou , Avner Bar-Hen 2009 Preprints, Working Papers, ... hal-00391682v1

	Équivalence asymptotique des vraisemblances observée et complète dans le modèle de blocs latents Vincent Brault , Christine Keribin , Mahendra Mariadassou [Travaux universitaires] auto-saisine. 2017 Reports hal-01603137v1
	Variational inference for probabilistic Poisson PCA Julien Chiquet , Mahendra Mariadassou , Stephane Robin [University works] auto-saisine. 2017 Reports hal-01608912v1

	Robustess of Phylogenetic Trees Mahendra Mariadassou Mathematics [math]. Université Paris Sud - Paris XI, 2009. English. ⟨NNT : ⟩ Theses tel-00472052v1

	FROGS Training on Galaxy : Statistics to Explore Metagenomics Maria Bernard , Géraldine Pascal , Mahendra Mariadassou , Laurent Cauquil , Stephane Chaillou Training on Galaxy : Statistics to Explore Metagenomics - FROGS (Find, Rapidly, Otus with Galaxy Solution), 2017, 116 p Lectures hal-02788316v1
	FROGS Training on Galaxy : Metagenomics November 2017 Frédéric Escudié , Lucas Auer , Maria Bernard , Laurent Cauquil , Sarah Maman Formation Métagénomique avec le logiciel FROGS (Find, Rapidly, Otus with Galaxy Solution), 2017, 270 p Lectures hal-02791696v1

	Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome Cédric Midoux , Mahendra Mariadassou 2023, ⟨swh:1:dir:1828e5d3e367f8dbb972a1dc6684fc4aebe04825⟩ Software hal-04304559v1
	PLNmodels: Poisson lognormal models Julien Chiquet , Mahendra Mariadassou , Stephane S. Robin , François Gindraud 2019, ⟨swh:1:dir:cfa1e1e06bbff34b4203820ebe23d1a1b54e713f;origin=https://github.com/PLN-team/PLNmodels;visit=swh:1:snp:33650f3635758717aa9ed6d1c6150f6e00711181;anchor=swh:1:rev:afad5560c704d29ff5704df4993bb471bd971f6c⟩ Software hal-04440660v1

Mahendra Mariadassou

Publications

A comprehensive, large-scale analysis of “terroir” cheese and milk microbiota reveals profiles strongly shaped by both geographical and human factors

Insight into the Role of Gut Microbiota in Duchenne Muscular Dystrophy

Microbiota members from body sites of dairy cows are largely shared within individual hosts throughout lactation but sharing is limited in the herd

Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Hierarchical correction of p-values via an ultrametric tree running Ornstein-Uhlenbeck process

Prebiotic Supplementation During Gestation Induces a Tolerogenic Environment and a Protective Microbiota in Offspring Mitigating Food Allergy

Comparison of Fecal Sample Collection Methods for Microbial Analysis Embedded within Colorectal Cancer Screening Programs

Exploring short k-mer profiles in cells and mobile elements from Archaea highlights the major influence of both the ecological niche and evolutionary history

Unraveling the history of the genus Gallus through whole genome sequencing

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

Glucose but Not Fructose Alters the Intestinal Paracellular Permeability in Association With Gut Inflammation and Dysbiosis in Mice

FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers

The Rhinobiome of Exacerbated Wheezers and Asthmatics: Insights From a German Pediatric Exacerbation Network

Nitric Oxide Impacts Human Gut Microbiota Diversity and Functionalities

The Poisson-Lognormal Model as a Versatile Framework for the Joint Analysis of Species Abundances

Does Physical Inactivity Induce Significant Changes in Human Gut Microbiota? New Answers Using the Dry Immersion Hypoactivity Model

Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions

Shifts in the temperature-sensitive periods for spring phenology in European beech and pedunculate oak clones across latitudes and over recent decades.

Detection of selection signatures in Limousin cattle using whole‐genome resequencing

Consistency and Asymptotic Normality of Latent Blocks Model Estimators

Incorporating Phylogenetic Information in Microbiome Differential Abundance Studies Has No Effect on Detection Power and FDR Control

A Probiotic Mixture Induces Anxiolytic- and Antidepressive-Like Effects in Fischer and Maternally Deprived Long Evans Rats

Murine genetic background overcomes gut microbiota changes to explain metabolic response to high-fat diet

First step of odorant detection in the olfactory epithelium and olfactory preferences differ according to the microbiota profile in mice

Taxon appearance from extraction and amplification steps demonstrates the value of multiple controls in tick microbiome analysis

Consistency and asymptotic normality of stochastic block models estimators from sampled data

SimkaMin: fast and resource frugal de novo comparative metagenomics

Function-Driven Design of Lactic Acid Bacteria Co-cultures to Produce New Fermented Food Associating Milk and Lupin

Optimize the plant microbiota to increase plant growth and health

Comparative metatranscriptomic analysis of anaerobic digesters treating anionic surfactant contaminated wastewater

Guide pratique à destination des biologistes, bioinformaticiens et statisticiens qui souhaitent s’initier aux analyses métabarcoding

Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale

Gut bacteria are critical for optimal muscle functiona potential link with glucose homeostasis

Fructose malabsorption induces cholecystokinin expression in the ileum and cecum by changing microbiota composition and metabolism

Steatosis and gut microbiota dysbiosis induced by high-fat diet are reversed by 1-week chow diet administration

FROGS: Find, Rapidly, OTUs with Galaxy Solution

Inference of Adaptive Shifts for Multivariate Correlated Traits

Variational inference for probabilistic Poisson PCA

Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes

OH1 from Orf virus: a new tyrosine phosphatase that displays distinct structural features and triple substrate specificity

Identification of proteins involved in the anti-inflammatory properties of Propionibacterium freudenreichii by means of a multi-strain study

Detection of adaptive shifts on phylogenies by using shifted stochastic processes on a tree

Analysis of large 16S rRNA Illumina datasets: impact of singleton read filtering on microbial community description

Unprecedented large inverted repeats at the replication terminus of circular bacterial chromosomes suggest a novel mode of chromosome rescue

Beneficial metabolic effects of selected probiotics on diet-induced obesity and insulin resistance in mice are associated with improvement of dysbiotic gut microbiota

The Red Queen lives: Epistasis between linked resistance loci

Multiple comparative metagenomics using multiset k -mer counting

Olfactory epithelium changes in germfree mice

Convergence of the groups posterior distribution in latent or stochastic block models

Co-clustering through Latent Bloc Model: a Review

High genetic variation in resting-stage production in a metapopulation: Is there evidence for local adaptation?

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

Quantitative prediction of genome-wide resource allocation in bacteria

Microbial ecosystems are dominated by specialist taxa.

Identification of amino acids in mitochondrially encoded proteins that correlate with lifespan.

Local and systemic Immune mechanisms underlying the Anti-Colitis effects of the dairy Bacterium Lactobacillus delbrueckii.

Analyses of the radiation of birnaviruses from diverse host phyla and of their evolutionary affinities with other double-stranded RNA and positive strand RNA viruses using robust structure-based multiple sequence alignments and advanced phylogenetic methods.

Taxon influence index: assessing taxon-induced incongruities in phylogenetic inference

Phylogenetic and complementation analysis of a single-stranded dna binding protein family from lactococcal phages indicates a non-bacterial origin

Uncovering latent structure in valued graphs: a variational approach

Concentration inequality for evolutionary trees

Influence function for robust phylogenetic reconstructions.

Uncovering structure in biological networks

Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data

Origins and rate of mutations in bacteriophage Lambda

Milk microbiota: potential allies for mammary gland health

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

Addition of dairy lipids and probiotic in infant formulas modulates gut microbiota and intestinal physiology with long-term consequences; a preclinical study in a minipig model

Nitric Oxide impacts human gut microbiota diversity and functionalities

Shallow Shotgun Metagenomics as a cost-effective and accurate alternative to WGS for taxonomic profiling and clinical diagnosis

Caractérisation et modélisation des populations de bactériophages de la croûte de fromages (type époisses) sous différentes conditions environnementales d’affinage

Membre du comité d'organisation scientifique

Variational Inference for sparse network reconstruction from count data

Ecological modelling of phage, bacterial and yeast populations structure in Epoisses cheese under changing ripening conditions using factorial experimental design and metavirome analysis

Shifts in the temperature sensitivity periods for two forest tree species under warming climatic conditions

A Walk Along Models for Count Data in Microbial Ecology

Is skeletal muscle remodeling associated with gut microbiota signature?

A metagenomic tool for cheese ecosystems