Mahendra Mariadassou

151
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Publications

Publications

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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 et al.
ISME Communications, 2024, 4 (1), pp.ycae095. ⟨10.1093/ismeco/ycae095⟩
Article dans une revue hal-04668230 v1

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

Cédric Midoux , Olivier Rué , Olivier Chapleur , Ariane Bize , Valentin Loux et al.
Journal of Open Source Software, 2024, 9 (103), pp.6704. ⟨10.21105/joss.06704⟩
Article dans une revue hal-04785149 v1
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Insight into the Role of Gut Microbiota in Duchenne Muscular Dystrophy

Maxence Jollet , Mahendra Mariadassou , Olivier Rué , Laurence Pessemesse , Vincent Ollendorff et al.
American Journal of Pathology, 2024, 194 (2), pp.264-279. ⟨10.1016/j.ajpath.2023.10.010⟩
Article dans une revue hal-04383411 v1
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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 et al.
Animal Microbiome, 2023, 5 (1), pp.32. ⟨10.1186/s42523-023-00252-w⟩
Article dans une revue hal-04126196 v1
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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⟩
Article dans une revue hal-04072108 v1
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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 , Gregory Bouchaud et al.
Frontiers in Immunology, 2022, 12, pp.745535. ⟨10.3389/fimmu.2021.745535⟩
Article dans une revue hal-03578742 v1
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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 et al.
Cancer Epidemiology, Biomarkers and Prevention, 2022, 31 (2), pp. 305-314. ⟨10.1158/1055-9965.EPI-21-0188⟩
Article dans une revue hal-03625845 v1
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Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Daniel Richter , Romain Watteaux , Thomas Vannier , Jade Leconte , Paul Frémont et al.
eLife, 2022, 11, pp.e78129. ⟨10.7554/eLife.78129⟩
Article dans une revue hal-02399723 v2
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The Rhinobiome of Exacerbated Wheezers and Asthmatics: Insights From a German Pediatric Exacerbation Network

Malik Aydin , Cornelius Weisser , Olivier Rué , Mahendra Mariadassou , Sandra Maaß et al.
Frontiers in Allergy, 2021, 2, ⟨10.3389/falgy.2021.667562⟩
Article dans une revue hal-03244864 v1
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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 et al.
Frontiers in Immunology, 2021, 12, ⟨10.3389/fimmu.2021.742584⟩
Article dans une revue hal-03634400 v1
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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-03323846 v1

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 et al.
Journal of Environmental Management, 2021, 291, pp.112631. ⟨10.1016/j.jenvman.2021.112631⟩
Article dans une revue hal-03211333 v1
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Nitric Oxide Impacts Human Gut Microbiota Diversity and Functionalities

Marion Leclerc , Cassandre Bedu-Ferrari , Lucie Etienne-Mesmin , Mahendra Mariadassou , Lucie Lebreuilly et al.
mSystems, 2021, 6 (5), ⟨10.1128/mSystems.00558-21⟩
Article dans une revue hal-03413913 v1
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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 et al.
Nutrients, 2021, 13 (11), ⟨10.3390/nu13113865⟩
Article dans une revue hal-03415988 v1
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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⟩
Article dans une revue hal-03215628 v1
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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 et al.
Microbiome, 2021, 9 (1), pp.153. ⟨10.1186/s40168-021-01051-8⟩
Article dans une revue hal-03287263 v1
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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 et al.
BMC Genomics, 2021, 22, ⟨10.1186/s12864-021-07471-y⟩
Article dans une revue hal-03176011 v1
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Unraveling the history of the genus Gallus through whole genome sequencing

Mahendra Mariadassou , Marie Suez , Sanbadam Sathyakumar , Alain Vignal , Mariangela Arca et al.
Molecular Phylogenetics and Evolution, 2021, 158, pp.107044. ⟨10.1016/j.ympev.2020.107044⟩
Article dans une revue hal-03155990 v1
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Detection of selection signatures in Limousin cattle using whole‐genome resequencing

M. Mariadassou , Y. Ramayo‐caldas , M. Charles , M. Féménia , G. Renand et al.
Animal Genetics, 2020, 51 (5), pp.815-819. ⟨10.1111/age.12982⟩
Article dans une revue hal-03285327 v1

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⟩
Article dans une revue hal-02622770 v1
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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 et al.
Nutrients, 2020, 12 (2), ⟨10.3390/nu12020287⟩
Article dans une revue hal-02503303 v1
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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 et al.
Behavioural Brain Research, 2020, 384, ⟨10.1016/j.bbr.2020.112549⟩
Article dans une revue hal-02503302 v1
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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 et al.
Frontiers in Microbiology, 2020, 11, ⟨10.3389/fmicb.2020.01093⟩
Article dans une revue hal-02790980 v1
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SimkaMin: fast and resource frugal de novo comparative metagenomics

Gaëtan Benoit , Mahendra Mariadassou , Stéphane Robin , Sophie Schbath , Pierre Peterlongo et al.
Bioinformatics, 2020, 36 (4), pp.1-2. ⟨10.1093/bioinformatics/btz685⟩
Article dans une revue hal-02308101 v1
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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⟩
Article dans une revue hal-04380551 v1
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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⟩
Article dans une revue hal-01511960 v3
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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 et al.
Frontiers in Behavioral Neuroscience, 2020, 14, ⟨10.3389/fnbeh.2020.581296⟩
Article dans une revue hal-03225018 v1
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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⟩
Article dans une revue hal-02635268 v1
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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 et al.
Frontiers in Microbiology, 2020, 11, ⟨10.3389/fmicb.2020.584163⟩
Article dans une revue hal-03019865 v1
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Optimize the plant microbiota to increase plant growth and health

Matthieu Barret , P. Dufour , Mylène Durand-Tardif , Mahendra Mariadassou , Christophe Mougel et al.
Consortium Biocontrôle et GIS Biotechnologies Vertes , 2019, ⟨10.15454/1fve-e105⟩
Article dans une revue hal-03297096 v1

Comparative metatranscriptomic analysis of anaerobic digesters treating anionic surfactant contaminated wastewater

Tiago P. Delforno , Thais Z. Macedo , Cedric Midoux , Gileno V. Lacerda , Olivier Rué et al.
Science of the Total Environment, 2019, 2019 (649), pp.482-494. ⟨10.1016/j.scitotenv.2018.08.328⟩
Article dans une revue hal-01888286 v1
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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 et al.
BMC Genomics, 2019, 20 (1), ⟨10.1186/s12864-019-6188-x⟩
Article dans une revue hal-02392205 v1
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Gut bacteria are critical for optimal muscle functiona potential link with glucose homeostasis

Kevin Nay , Maxence Jollet , Benedicte Goustard , Narjes Baati , Barbara Vernus et al.
AJP - Endocrinology and Metabolism, 2019, 317 (1), pp.E158-E171. ⟨10.1152/ajpendo.00521.2018⟩
Article dans une revue hal-02152871 v1

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 et al.
FASEB Journal, 2019, 33 (6), pp.7126-7142. ⟨10.1096/fj.201801526RR⟩
Article dans une revue hal-02191008 v1
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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 et al.
Cahier des Techniques de l'INRA, 2019, 97, pp.46-69
Article dans une revue (article de synthèse) hal-02311421 v1
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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 et al.
Nutrients, 2019, 71, pp.72-88. ⟨10.1016/j.nutres.2019.09.004⟩
Article dans une revue hal-02503316 v1
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FROGS: Find, Rapidly, OTUs with Galaxy Solution

Frédéric Escudié , Lucas Auer , Maria Bernard , Mahendra Mariadassou , Laurent Cauquil et al.
Bioinformatics, 2018, 34 (8), pp.1287-1294. ⟨10.1093/bioinformatics/btx791⟩
Article dans une revue hal-02626808 v1

Inference of Adaptive Shifts for Multivariate Correlated Traits

Paul Bastide , Céline Ané , Stephane Robin , Mahendra Mariadassou
Systematic Biology, 2018, 67, ⟨10.1093/sysbio/syy005⟩
Article dans une revue hal-01608932 v1
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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 et al.
Microbiome, 2018, 6 (1), 14 p. ⟨10.1186/s40168-018-0452-1⟩
Article dans une revue hal-01774632 v1
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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⟩
Article dans une revue hal-01941270 v1

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⟩
Article dans une revue (data paper) hal-01605865 v1
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Unprecedented large inverted repeats at the replication terminus of circular bacterial chromosomes suggest a novel mode of chromosome rescue

Hela El Kafsi , Valentin Loux , Mahendra Mariadassou , Camille Blin , Hélène Chiapello et al.
Scientific Reports, 2017, 7, pp.1-11. ⟨10.1038/srep44331⟩
Article dans une revue hal-01509688 v1

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 et al.
Journal of Molecular Biology, 2017, 26 p. ⟨10.1016/j.jmb.2017.07.017⟩
Article dans une revue hal-01602647 v1
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Identification of proteins involved in the anti-inflammatory properties of Propionibacterium freudenreichii by means of a multi-strain study

Stéphanie-Marie Deutsch , Mahendra Mariadassou , Pierre Nicolas , Sandrine Parayre , Rozenn Le Guellec et al.
Scientific Reports, 2017, 7, pp.46409. ⟨10.1038/srep46409⟩
Article dans une revue hal-01510019 v1

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⟩
Article dans une revue hal-01551071 v1

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 et al.
Environmental Microbiology, 2016, 18 (5), pp.1484-1497. ⟨10.1111/1462-2920.13181⟩
Article dans une revue istex hal-03372071 v1
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Multiple comparative metagenomics using multiset k -mer counting

Gaëtan Benoit , Pierre Peterlongo , Mahendra Mariadassou , Erwan Drezen , Sophie Schbath et al.
PeerJ Computer Science, 2016, 2 (14), 25 p. ⟨10.7717/peerj-cs.94⟩
Article dans une revue hal-01397150 v1

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⟩
Article dans une revue istex hal-02631286 v1
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Olfactory epithelium changes in germfree mice

Adrien François , Denise Grebert , Moez Rhimi , Mahendra Mariadassou , Laurent Naudon et al.
Scientific Reports, 2016, 6 (1), pp.24687. ⟨10.1038/srep24687⟩
Article dans une revue hal-03371054 v1
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Convergence of the groups posterior distribution in latent or stochastic block models

Mahendra Mariadassou , Catherine Matias
Bernoulli, 2015, 21 (1), pp.537-573
Article dans une revue hal-00713120 v2
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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
Article dans une revue hal-02088216 v1

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 R. Haag et al.
Evolution - International Journal of Organic Evolution, 2015, 69 (10), pp.2747-2756. ⟨10.1111/evo.12770⟩
Article dans une revue istex hal-02634111 v1
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Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii

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

Quantitative prediction of genome-wide resource allocation in bacteria

Anne Goelzer , Jan Muntel , Victor Chubukov , Matthieu Jules , Eric Prestel et al.
Metabolic Engineering, 2015, 32, pp.232-243. ⟨10.1016/j.ymben.2015.10.003⟩
Article dans une revue hal-01536511 v1

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⟩
Article dans une revue istex hal-02631330 v1

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⟩
Article dans une revue hal-02630250 v1
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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 et al.
PLoS ONE, 2014, 9 (1), pp.1-8. ⟨10.1371/journal.pone.0085923⟩
Article dans une revue hal-01204288 v1
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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⟩
Article dans une revue hal-02645508 v1
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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⟩
Article dans une revue hal-02642639 v1
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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⟩
Article dans une revue hal-01191212 v1
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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⟩
Article dans une revue hal-01197514 v1

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⟩
Article dans une revue istex hal-00410872 v1

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⟩
Article dans une revue hal-00312860 v1

Uncovering structure in biological networks

J.J. Daudin , Vincent Lacroix , M. Mariadassou , V. Miele , Franck Picard et al.
incollection, 2006, --, pp.471-483
Article dans une revue hal-00427936 v1
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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
Communication dans un congrès hal-04611225 v1
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Zero-inflation in the MPLN Family

Bastien Batardière , Julien Chiquet , François Gindraud , Mahendra Mariadassou
55èmes journées de la statistique, May 2024, Bordeaux, France
Communication dans un congrès hal-04738587 v1

Drivers of microbial diversity in French Protected designation of Origin (PDO) cheeses

Francoise Irlinger , Mahendra Mariadassou , Eric Dugat-Bony , Cécile Neuvéglise , Olivier Rué et al.
IDF World Dairy Science, Oct 2024, Paris, France
Communication dans un congrès hal-04820075 v1

Milk microbiota: potential allies for mammary gland health

Coralie Goetz , Lucie Rault , Marion Boutinaud , Christine Citti , Hélène Falentin et al.
ADSA annual meeting 2023, American Dairy Science Association, Jun 2023, Ottawa, Canada. pp.146
Communication dans un congrès hal-04164763 v1
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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 et al.
15. Congress of the international society for the study of fatty acids and lipids (ISSFAL), Jul 2023, Nantes, France
Communication dans un congrès hal-04155652 v1

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 et al.
FORUM ON FERMENTED FOODS, COST PIMENTO, May 2023, Lyon, France
Communication dans un congrès hal-04221356 v1

Origins and rate of mutations in bacteriophage Lambda

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

Microbial transfers at the crossroads of agro-ecological transitions in dairy systems

Nicolas Chemidlin Prévost-Bouré , Anne-Laure Abraham , Annick Bernalier Donadille , Juliette Bloor , Matthieu Bouchon et al.
Carrefours de l’innovation agronomique (CIAG) Les indicateurs de qualité des sols et leur usage dans un contexte de transitions agricoles, Nov 2022, Orléans, France
Communication dans un congrès hal-04826247 v1

Nitric Oxide impacts human gut microbiota diversity and functionalities

Nalini Ramarao , Cassandre Bedu-Ferrari , Lucie Etienne-Mesmin , Mahendra Mariadassou , Lucie Lebreuilly et al.
9. Microbiome and probiotics R & D and business collaboration, Oct 2021, Rotterdam, Netherlands
Communication dans un congrès hal-03739679 v1
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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 et al.
Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2021, Paris, France
Communication dans un congrès hal-03451266 v1

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
Communication dans un congrès hal-02790841 v1

Is skeletal muscle remodeling associated with gut microbiota signature?

Maxence Jollet , Barbara Vernus , Anne Bonnieu , Mahendra Mariadassou , Olivier Rué et al.
6th World Congress on Targeting Microbiota, Oct 2018, Porto, Portugal. pp.1
Communication dans un congrès hal-02736948 v1

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 et al.
15. Congrès de la Société Française de Microbiologie (SFM), Société Française de Microbiologie (SFM). FRA., Sep 2019, Paris, France
Communication dans un congrès hal-02789388 v1

Membre du comité d'organisation scientifique

Danielle Canceill , Virginie Bourion , Mahendra Mariadassou , Milka Popova , C Roger-Gaillard, et al.
Séminaire de lancement du métaprogramme HOLOFLUX, Nov 2019, Nantes, France
Communication dans un congrès hal-03229623 v1

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
Communication dans un congrès hal-02735800 v1
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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 et al.
MD 2019 : 5th International Conference on Microbial Diversity, Sep 2019, Catania, Italy
Communication dans un congrès hal-04416628 v1

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
Communication dans un congrès hal-04382269 v1
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A metagenomic tool for cheese ecosystems

Anne-Laure Abraham , Quentin Cavaillé , Thibaut Guirimand , Pierre Renault , Sandra Derozier et 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-02789036 v1
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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⟩
Communication dans un congrès hal-02737108 v1
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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
Communication dans un congrès hal-01510994 v1

Genomics of Chicken Domestication

Mahendra Mariadassou , Marie Suez , Pierre Nicolas , Diane Esquerré , Alain Vignal et al.
10. European Symposium on Poultry Genetics, Jun 2017, Saint Malo, France
Communication dans un congrès hal-02785437 v1

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 et al.
2017 Scientific MEM days: Journées scientifiques MEM (Métaomiques et écosystèmes microbiens), Jan 2017, Paris, France
Communication dans un congrès hal-01608159 v1
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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⟩
Communication dans un congrès hal-02736013 v1
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Food-Microbiomes Transfert, a shotgun metagenomic tool and a database to analyze cheese ecosystems

Thibaut Guirimand , Anne-Laure Abraham , Sandra Derozier , Charlie Pauvert , Mahendra Mariadassou et al.
JOBIM 2017 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2017, Lille, France
Communication dans un congrès hal-02788899 v1

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
Communication dans un congrès hal-02740156 v1
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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
Communication dans un congrès hal-01440084 v1
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Quantitative prediction of genome-wide resource allocation in bacteria

Anne Goelzer , Jan Muntel , Victor Chubukov , Matthieu Jules , Eric Prestel et al.
ISGSB 2016: International Study Group for Systems Biology, Oct 2016, Jena, Germany
Communication dans un congrès hal-02798691 v1

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 et al.
Phages On Marseille, Nov 2016, Marseille, France. pp.1
Communication dans un congrès hal-01531724 v1

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
Communication dans un congrès hal-02793616 v1

Find Rapidly OTU with Galaxy Solution

Frédéric Escudie , Lucas Auer , Maria Bernard , Laurent Cauquil , Katia Vidal et al.
JOBIM 2015 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France
Communication dans un congrès hal-01535378 v1

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
Communication dans un congrès hal-02744122 v1

Dominant Species are Specialists

Mahendra Mariadassou
ECMTB14 - European Conference on Mathematical and Theoretical Biology, Jun 2014, Gôteborg, Sweden. pp.1
Communication dans un congrès hal-02793165 v1
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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
Communication dans un congrès hal-02798419 v1
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Influence function for robust phylogenetic reconstruction

Mahendra Mariadassou , Avner A. Bar-Hen
JOBIM 2011, Jun 2011, Paris, France. pp.422
Communication dans un congrès hal-02746361 v1
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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
Communication dans un congrès hal-02802815 v1
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Fonction d'influence pour la reconstruction de phylogénies robustes

Mahendra Mariadassou , Avner Bar-Hen
42èmes Journées de Statistique, 2010, Marseille, France. pp.USB-key
Communication dans un congrès inria-00494834 v1

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 et al.
FORUM ON FERMENTED FOODS, May 2023, Lyon, France
Poster de conférence hal-04221437 v1

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 et al.
https://www.adsa.org/Meetings/2023-Annual-Meeting. ADSA annual meeting 2023, Jun 2023, Ottawa, Canada. , 2023
Poster de conférence hal-04164713 v1
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Rôle du microbiote dans la relation entre activité physique, santé et bien-être

Benedicte Goustard , Barbara Vernus , Olivier Rué , Mahendra Mariadassou , Laurence Pessemesse et al.
Journées d'Animation Scientifiques, May 2022, Poitiers, France. 317, pp.E158 - E171
Poster de conférence hal-04804882 v1
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Plateforme bioinformatique MIGALE

Mouhamadou Ba , Hélène Chiapello , Christelle Hennequet-Antier , Valentin Loux , Mahendra Mariadassou et al.
Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2022, Rennes, France. 2022
Poster de conférence hal-04176761 v1

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 et al.
3rd International Conference on Holobionts, Jul 2022, Lyon, France. 2022
Poster de conférence hal-04176902 v1
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Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics

Vuong Quoc Hoang Ngo , François Enault , Cédric Midoux , Mahendra Mariadassou , Olivier Chapleur et al.
ISME18, 18th International Symposium on Microbial Ecology, Aug 2022, Lausanne, Switzerland.
Poster de conférence hal-04359643 v1

Gut microbiota and skeletal muscle crosstalk : lessons from muscle remarkable phenotypes.

Maxence Jollet , Kévin Nay , Mahendra Mariadassou , Olivier Rué , A Chopard et al.
19th Congress of Association of Researchers in Physical and Sport Activities ACAPS, Nov 2021, Montpellier, France
Poster de conférence hal-04829963 v1
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Plateforme bioinformatique MIGALE

Mouhamadou Ba , Hélène Chiapello , Christelle Hennequet-Antier , Valentin Loux , Mahendra Mariadassou et al.
Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2021, Paris, France. 2021
Poster de conférence hal-04176768 v1
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A bioinformatic pipeline to elucidate the links between viruses and their hosts in microbial communities, applied to viruses in anaerobic digestion processes

Vuong Quoc Hoang Ngo , Cédric Midoux , Mahendra Mariadassou , Valentin Loux , François Enault et al.
JOBIM 2021 (JOBIM (Journées Ouvertes en Biologie, Informatique et Mathématiques), Jul 2021, Paris, France.
Poster de conférence hal-04359920 v1
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New insights into cow holobiont in relation to heath

Sergine Even , Mahendra Mariadassou , Xavier Nouvel , Fabienne F. Constant , Diego Morgavi et al.
16e congres national de la SFM-MICROBES 2021, Sep 2021, Nantes, France
Poster de conférence hal-03361039 v1
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Plateforme bioinformatique MIGALE

Mouhamadou Ba , Damien Berry , David Christiany , Hélène Chiapello , Olivier Inizan et al.
Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jun 2020, Montpellier, France. 2020
Poster de conférence hal-04176782 v1

New insights into cow holobiont in relation to health

Mahendra Mariadassou , Laurent-Xavier Nouvel , Diego Morgavi , Lucie Rault , Sophie Schbath et al.
Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jun 2020, Montpellier, France. , 2020
Poster de conférence hal-02962468 v1
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A shotgun metagenomics analysis applied to the ecological engineering of anaerobic microbial communities for the production of hydrogen from Citrus Peel Waste

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

Benoit Goutorbe , Anne-Laure Abraham , Mahendra Mariadassou , Valentin Loux , Olivier Rué et al.
JOBIM, Jun 2020, Montpellier, France.
Poster de conférence hal-03451271 v1
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Plateforme bioinformatique MIGALE

Hélène Chiapello , Sandra Dérozier , Olivier Inizan , Mahendra Mariadassou , Véronique Martin et al.
Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2019, Nantes, France. 2019
Poster de conférence hal-04176805 v1
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Detection of an archaeal-specific viral family, previously thought to infect exclusively hyperthermophiles, in human gut metaviromes

Vuong Quoc Hoang Ngo , Cédric Midoux , Olivier Rué , Mahendra Mariadassou , Violette Da Cunha et al.
Phages in Grenoble, Oct 2019, Grenoble, France.
Poster de conférence hal-04360160 v1
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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 et al.
AD16 (16th IWA World Conference on Anaerobic Digestion), Jun 2019, Delft, Netherlands
Poster de conférence hal-04361137 v1
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Feedback on a c omparative metatranscriptomic analysis

Cedric Midoux , Tiago P. Delforno , Thais Z. Macedo , Gileno V. Lacerda , Olivier Rué et al.
JOBIM 2019 : Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. , 2019, JOBIM 2019
Poster de conférence hal-02735859 v1
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Easy16S : a user-friendly Shiny interface for analysis and visualization of metagenomic data

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

Design de communautés bactériennes pour fermenter un nouvel aliment associant lait et légumineuse

Valérie Gagnaire , Fanny Canon , Mahendra Mariadassou , Hélène Falentin , Sandrine Parayre et al.
RFL2, 2e Rencontres Francophones sur les Légumineuses, Oct 2018, Toulouse, France. , 2018
Poster de conférence hal-01902837 v1

New insights into cow holobiont in relation to health

Laurent-Xavier Nouvel , Diego Morgavi , Lucie Rault , Mahendra Mariadassou , Sophie Schbath et al.
Pathobiome 2018 "Pathogens in Microbiotas in Hosts", Jan 2018, Ajaccio, France
Poster de conférence hal-03299131 v1

Simka: large scale de novo comparative metagenomics

Gaëtan Benoit , Pierre Peterlongo , Mahendra Mariadassou , Erwan Drezen , Sophie Schbath et al.
JOBIM 2017 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2017, Lille, France. , pp.234, 2017, JOBIM 2017 LILLE
Poster de conférence hal-01595071 v1
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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
Poster de conférence hal-01563604 v1

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 et al.
4. International Conference on Microbial Diversity 2017, Oct 2017, Bari, Italy. 2017
Poster de conférence hal-01628088 v1
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Cheese ecosystems insights with shotgun metagenomics and a metadata extended genomics database.

Thibaut Guirimand , Charlie Pauvert , Sandra Derozier , Anne-Laure Abraham , Mahendra Mariadassou et al.
JOBIM 2016 : Journées ouvertes de biologie informatique et mathématiques, Jun 2016, Lyon, France. , 2016
Poster de conférence hal-01512085 v1

Accurate taxonomy assignments in cheeses ecosystems via a metagenomic approach

Charlie Pauvert , Anne-Laure Abraham , Mathieu Almeida , Nicolas Pons , Mahendra Mariadassou et al.
JOBIM 2015 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. , pp.1, 2015
Poster de conférence hal-01204484 v1
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FROGS : Find Rapidly OTUs with Galaxy Solution

Frédéric Escudie , Lucas Auer , Maria Bernard , Laurent Cauquil , Katia Vidal et al.
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
Poster de conférence hal-01886389 v1

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 Delbès , Eric Dugat-Bony et al.
JOBIM 16. Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. , 2015
Poster de conférence hal-01195512 v1

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

Valentin Loux , Mahendra Mariadassou , Sintia Almeida da Silva , Helene Chiapello , Amal Hammami et 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-01209851 v1

Approche génomique de la domestication du poulet

Michèle Tixier-Boichard , Mahendra Mariadassou , Xavier X Rognon , Pierre Nicolas , Francois Rodolphe et al.
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
Poster de conférence hal-01535349 v1

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 et al.
20. Colloque du Club des Bactéries Lactiques, Jun 2015, Lille, France. , 2015
Poster de conférence hal-01170054 v1
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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 et al.
14. European Poultry Conference, Jun 2014, Stavanger, Norway. 2014
Poster de conférence hal-01193928 v1

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 et al.
Journées des Microbiologistes de l'INRA 2012, Nov 2012, L'Isle-sur-la-Sorgue, France. 2012
Poster de conférence hal-01209410 v1

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 et al.
Journées ouvertes en biologie informatique mathématiques, Jul 2012, Rennes, France. , 2012
Poster de conférence hal-01209420 v1

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
Chapitre d'ouvrage hal-04688958 v1
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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
Chapitre d'ouvrage hal-04033421 v1

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⟩
Chapitre d'ouvrage hal-02484863 v1
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Robustess of Phylogenetic Trees

Mahendra Mariadassou
Mathematics [math]. Université Paris Sud - Paris XI, 2009. English. ⟨NNT : ⟩
Thèse tel-00472052 v1
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FROGS Training on Galaxy : Metagenomics November 2017

Frédéric Escudié , Lucas Auer , Maria Bernard , Laurent Cauquil , Sarah Maman et al.
Formation Métagénomique avec le logiciel FROGS (Find, Rapidly, Otus with Galaxy Solution), 2017, 270 p
Cours hal-02791696 v1
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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
Cours hal-02788316 v1