CV Hal

Julien Chiquet, Mahendra Mariadassou, Stéphane Robin. The Poisson-Lognormal Model as a Versatile Framework for the Joint Analysis of Species Abundances. Frontiers in Ecology and Evolution, Frontiers Media S.A, 2021, 9, ⟨10.3389/fevo.2021.588292⟩. ⟨hal-03215628⟩

Franciele Pereira Camargo, Isabel Kimiko Sakamoto, Tiago Palladino Delforno, Mahendra Mariadassou, Valentin Loux, et al.. Microbial and functional characterization of an allochthonous consortium applied to hydrogen production from Citrus Peel Waste in batch reactor in optimized conditions. Journal of Environmental Management, Elsevier, 2021, 291, pp.112631. ⟨10.1016/j.jenvman.2021.112631⟩. ⟨hal-03211333⟩

E. Lejal, J. Chiquet, J. Aubert, S. Robin, A. Estrada-Peña, et al.. Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions. Microbiome, BioMed Central, 2021, 9 (1), pp.153. ⟨10.1186/s40168-021-01051-8⟩. ⟨hal-03287263⟩

Maria Bernard, Olivier Rué, Mahendra Mariadassou, Géraldine Pascal. FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers. Briefings in Bioinformatics, Oxford University Press (OUP), 2021, ⟨10.1093/bib/bbab318⟩. ⟨hal-03323846⟩

Mahendra Mariadassou, Malik Aydin, Cornelius Weisser, Olivier Rué, Sandra Maaß, et al.. The Rhinobiome of Exacerbated Wheezers and Asthmatics: Insights From a German Pediatric Exacerbation Network. Frontiers in Allergy, 2021, 2, ⟨10.3389/falgy.2021.667562⟩. ⟨hal-03244864⟩

Mahendra Mariadassou, Marie Suez, Sanbadam Sathyakumar, Alain Vignal, Mariangela Arca, et al.. Unraveling the history of the genus Gallus through whole genome sequencing. Molecular Phylogenetics and Evolution, Elsevier, 2021, 158, pp.107044. ⟨10.1016/j.ympev.2020.107044⟩. ⟨hal-03155990⟩

Ariane Bize, Cédric Midoux, Mahendra Mariadassou, Sophie Schbath, Patrick Forterre, et al.. Exploring short k-mer profiles in cells and mobile elements from Archaea highlights the major influence of both the ecological niche and evolutionary history. BMC Genomics, 2021, 22, ⟨10.1186/s12864-021-07471-y⟩. ⟨hal-03176011⟩

M. Mariadassou, Y. Ramayo‐caldas, M. Charles, M. Féménia, G. Renand, et al.. Detection of selection signatures in Limousin cattle using whole‐genome resequencing. Animal Genetics, Wiley-Blackwell, 2020, 51 (5), pp.815-819. ⟨10.1111/age.12982⟩. ⟨hal-03285327⟩

Antoine Bichat, Jonathan Plassais, Christophe Ambroise, Mahendra Mariadassou. Incorporating Phylogenetic Information in Microbiome Differential Abundance Studies Has No Effect on Detection Power and FDR Control. Frontiers in Microbiology, Frontiers Media, 2020, 11, ⟨10.3389/fmicb.2020.00649⟩. ⟨hal-02635268⟩

Zahra Safari, Aurelia Bruneau, Magali Monnoye, Mahendra Mariadassou, Catherine Philippe, et al.. Murine genetic background overcomes gut microbiota changes to explain metabolic response to high-fat diet. Nutrients, MDPI, 2020, 12 (2), ⟨10.3390/nu12020287⟩. ⟨hal-02503303⟩

Bénédicte Wenden, Mahendra Mariadassou, Frank-M Chmielewski, Yann Vitasse. Shifts in the temperature-sensitive periods for spring phenology in European beech and pedunculate oak clones across latitudes and over recent decades.. Global Change Biology, Wiley, 2020, 26, pp.1808-1819. ⟨10.1111/gcb.14918⟩. ⟨hal-02622770⟩

Emilie Lejal, Agustin Estrada-Peña, Maud Marsot, Jean-Francois Cosson, Olivier Rué, et al.. Taxon appearance from extraction and amplification steps demonstrates the value of multiple controls in tick microbiome analysis. Frontiers in Microbiology, Frontiers Media, 2020, 11, ⟨10.3389/fmicb.2020.01093⟩. ⟨hal-02790980⟩

Valérie Daugé, Catherine Philippe, Mahendra Mariadassou, Olivier Rué, Jean-Charles Martin, et al.. A Probiotic Mixture Induces Anxiolytic- and Antidepressive-Like Effects in Fischer and Maternally Deprived Long Evans Rats. Frontiers in Behavioral Neuroscience, Frontiers, 2020, 14, ⟨10.3389/fnbeh.2020.581296⟩. ⟨hal-03225018⟩

Laurent Naudon, Adrien François, Mahendra Mariadassou, Magali Monnoye, Catherine Philippe, et al.. First step of odorant detection in the olfactory epithelium and olfactory preferences differ according to the microbiota profile in mice. Behavioural Brain Research, Elsevier, 2020, 384, ⟨10.1016/j.bbr.2020.112549⟩. ⟨hal-02503302⟩

Gaëtan Benoit, Mahendra Mariadassou, Stéphane Robin, Sophie Schbath, Pierre Peterlongo, et al.. SimkaMin: fast and resource frugal de novo comparative metagenomics. Bioinformatics, Oxford University Press (OUP), 2020, 36 (4), pp.1-2. ⟨10.1093/bioinformatics/btz685⟩. ⟨hal-02308101⟩

Vincent Brault, Christine Keribin, Mahendra Mariadassou. Consistency and Asymptotic Normality of Latent Blocks Model Estimators. Electronic Journal of Statistics , Shaker Heights, OH : Institute of Mathematical Statistics, 2020, 14 (1), pp.1234-1268. ⟨10.1214/20-EJS1695⟩. ⟨hal-01511960v3⟩

Fanny Canon, Mahendra Mariadassou, Marie-Bernadette Maillard, Hélène Falentin, Sandrine Parayre, et al.. Function-Driven Design of Lactic Acid Bacteria Co-cultures to Produce New Fermented Food Associating Milk and Lupin. Frontiers in Microbiology, Frontiers Media, 2020, 11, ⟨10.3389/fmicb.2020.584163⟩. ⟨hal-03019865⟩

Tiago P. Delforno, Thais Z. Macedo, Cedric Midoux, Gileno V. Lacerda, Olivier Rué, et al.. Comparative metatranscriptomic analysis of anaerobic digesters treating anionic surfactant contaminated wastewater. Science of the Total Environment, Elsevier, 2019, 2019 (649), pp.482-494. ⟨10.1016/j.scitotenv.2018.08.328⟩. ⟨hal-01888286⟩

Matthieu Barret, P. Dufour, Mylène Durand-Tardif, Mahendra Mariadassou, Christophe Mougel, et al.. Optimize the plant microbiota to increase plant growth and health. Consortium Biocontrôle et GIS Biotechnologies Vertes , 2019, ⟨10.15454/1fve-e105⟩. ⟨hal-03297096⟩

Zahra Safari, Magali Monnoye, Peter M. Abuja, Mahendra Mariadassou, Karl Kashofer, et al.. Steatosis and gut microbiota dysbiosis induced by high-fat diet are reversed by 1-week chow diet administration. Nutrients, MDPI, 2019, 71, pp.72-88. ⟨10.1016/j.nutres.2019.09.004⟩. ⟨hal-02503316⟩

Xufei Zhang, Alexandra Grosfeld, Edek Williams, Daniel Vasiliauskas, Sharon Barretto, et al.. Fructose malabsorption induces cholecystokinin expression in the ileum and cecum by changing microbiota composition and metabolism. FASEB Journal, Federation of American Society of Experimental Biology, 2019, 33 (6), pp.7126-7142. ⟨10.1096/fj.201801526RR⟩. ⟨hal-02191008⟩

Kevin Nay, Maxence Jollet, Benedicte Goustard, Narjes Baati, Barbara Vernus, et al.. Gut bacteria are critical for optimal muscle functiona potential link with glucose homeostasis. AJP - Endocrinology and Metabolism, American Physiological Society, 2019, 317 (1), pp.E158-E171. ⟨10.1152/ajpendo.00521.2018⟩. ⟨hal-02152871⟩

Hélène Falentin, Lucas Auer, Mahendra Mariadassou, Géraldine Pascal, Olivier Rué, et al.. Guide pratique à destination des biologistes, bioinformaticiens et statisticiens qui souhaitent s’initier aux analyses métabarcoding : Partage de pratiques et retours d'expérience des membres du pôle métagénomique du PEPI IBIS. Cahiers des Techniques de l'INRA, INRA, 2019, 2019 (97), pp.1-23. ⟨hal-02311421⟩

Méryl Vila Nova, Kévin Durimel, Kévin La, Arnaud Felten, Philippe Bessieres, et al.. Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale. BMC Genomics, BioMed Central, 2019, 20 (1), ⟨10.1186/s12864-019-6188-x⟩. ⟨hal-02392205⟩

Jeffrey K. Cornuault, Marie-Agnès Petit, Mahendra Mariadassou, Leandro Benevides, Elisabeth Moncaut, et al.. Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes. Microbiome, BioMed Central, 2018, 6 (1), 14 p. ⟨10.1186/s40168-018-0452-1⟩. ⟨hal-01774632⟩

Julien Chiquet, Mahendra Mariadassou, Stephane Robin. Variational inference for probabilistic Poisson PCA. Annals of Applied Statistics, Institute of Mathematical Statistics, 2018, 12 (4), pp.2674-2698. ⟨10.1214/18-AOAS1177⟩. ⟨hal-01941270⟩

Paul Bastide, Céline Ané, Stephane Robin, Mahendra Mariadassou. Inference of Adaptive Shifts for Multivariate Correlated Traits. Systematic Biology, Oxford University Press (OUP), 2018, 67, ⟨10.1093/sysbio/syy005⟩. ⟨hal-01608932⟩

Frédéric Escudié, Lucas Auer, Maria Bernard, Mahendra Mariadassou, Laurent Cauquil, et al.. FROGS: Find, Rapidly, OTUs with Galaxy Solution. Bioinformatics, Oxford University Press (OUP), 2018, 34 (8), pp.1287-1294. ⟨10.1093/bioinformatics/btx791⟩. ⟨hal-02626808⟩

Lucas Auer, Mahendra Mariadassou, Michael O'Donohue, Christophe Klopp, Guillermina Hernandez-Raquet. Analysis of large 16S rRNA Illumina datasets: impact of singleton read filtering on microbial community description. Molecular Ecology Resources, Wiley/Blackwell, 2017, ⟨10.1111/1755-0998.12700⟩. ⟨hal-01605865⟩

Paul Bastide, Mahendra Mariadassou, Stephane Robin. Detection of adaptive shifts on phylogenies by using shifted stochastic processes on a tree. Journal of the Royal Statistical Society: Series B, Royal Statistical Society, 2017, ⟨10.1111/rssb.12206⟩. ⟨hal-01551071⟩

Hela El Kafsi, Valentin Loux, Mahendra Mariadassou, Camille Blin, Hélène Chiapello, et al.. Unprecedented large inverted repeats at the replication terminus of circular bacterial chromosomes suggest a novel mode of chromosome rescue. Scientific Reports, Nature Publishing Group, 2017, 7, pp.44331. ⟨10.1038/srep44331⟩. ⟨hal-01509688⟩

Danilo Segovia, Ahmed Haouz, Dario Porley, Natalia Olivero, Mariano Martinez, et al.. OH1 from Orf virus: a new tyrosine phosphatase that displays distinct structural features and triple substrate specificity. Journal of Molecular Biology, Elsevier, 2017, 26 p. ⟨10.1016/j.jmb.2017.07.017.⟩. ⟨hal-01602647⟩

Stéphanie-Marie Deutsch, Mahendra Mariadassou, Pierre Nicolas, Sandrine Parayre, Rozenn Le Guellec, et al.. Identification of proteins involved in the anti-inflammatory properties of Propionibacterium freudenreichii by means of a multi-strain study. Scientific Reports, Nature Publishing Group, 2017, 7, pp.46409. ⟨10.1038/srep46409⟩. ⟨hal-01510019⟩

Jeanne Alard, Véronique Lehrter, Moez Rhimi, Irène Mangin, Véronique Peucelle, et al.. Beneficial metabolic effects of selected probiotics on diet-induced obesity and insulin resistance in mice are associated with improvement of dysbiotic gut microbiota. Environmental Microbiology, Society for Applied Microbiology and Wiley-Blackwell, 2016, 18 (5), pp.1484-1497. ⟨10.1111/1462-2920.13181⟩. ⟨hal-01532556⟩

Cesar M. J. A. Metzger, Pepijn Luijckx, Gilberto Bento, Mahendra Mariadassou, Dieter Ebert. The Red Queen lives: Epistasis between linked resistance loci. Evolution - International Journal of Organic Evolution, Wiley, 2016, 70 (2), pp.480-487. ⟨10.1111/evo.12854⟩. ⟨hal-02631286⟩

Gaëtan Benoit, Pierre Peterlongo, Mahendra Mariadassou, Erwan Drezen, Sophie Schbath, et al.. Multiple comparative metagenomics using multiset k -mer counting. PeerJ Computer Science, PeerJ, 2016, 2 (14), 25 p. ⟨10.7717/peerj-cs.94⟩. ⟨hal-01397150⟩

Adrien François, Denise Grebert, Moez Rhimi, Mahendra Mariadassou, Laurent Naudon, et al.. Olfactory epithelium changes in germfree mice. Scientific Reports, Nature Publishing Group, 2016, 6, pp.24687. ⟨10.1038/srep24687⟩. ⟨hal-01353286⟩

Anne C Roulin, Mahendra Mariadassou, Matthew D Hall, Jean-Claude Walser, Christoph Haag, et al.. High genetic variation in resting-stage production in a metapopulation: Is there evidence for local adaptation?. Evolution - International Journal of Organic Evolution, Wiley, 2015, 69 (10), pp.2747-56. ⟨10.1111/evo.12770⟩. ⟨hal-02634111⟩

Vincent Brault, Mahendra Mariadassou. Co-clustering through Latent Bloc Model: a Review. Journal de la Société Française de Statistique, Société Française de Statistique et Société Mathématique de France, 2015, 156 (3), pp.120-139. ⟨hal-02088216⟩

Mahendra Mariadassou, Catherine Matias. Convergence of the groups posterior distribution in latent or stochastic block models. Bernoulli, Bernoulli Society for Mathematical Statistics and Probability, 2015, 21 (1), pp.537-573. ⟨hal-00713120v2⟩

Anne Goelzer, Jan Muntel, Victor Chubukov, Matthieu Jules, Eric Prestel, et al.. Quantitative prediction of genome-wide resource allocation in bacteria. Metabolic Engineering, Elsevier, 2015, 32, pp.232-243. ⟨10.1016/j.ymben.2015.10.003⟩. ⟨hal-01536511⟩

Mahendra Mariadassou, Samuel Pichon, Dieter Ebert. Microbial ecosystems are dominated by specialist taxa.. Ecology Letters, Wiley, 2015, 18 (9), pp.974-82. ⟨10.1111/ele.12478⟩. ⟨hal-02631330⟩

Valentin Loux, Mahendra Mariadassou, Sintia Almeida, Hélène Chiapello, Amal Hammani, et al.. Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii. BMC Genomics, BioMed Central, 2015, 16 (1), pp.35. ⟨10.1186/s12864-015-1467-7⟩. ⟨hal-01142363⟩

Clarissa Santos Rocha, Ana Cristina Gomes-Santos, Thais Garcias Moreira, Marcela de Azevedo, Tessalia Diniz Luerce, et al.. Local and Systemic Immune Mechanisms Underlying the Anti-Colitis Effects of the Dairy Bacterium Lactobacillus delbrueckii.. PLoS ONE, Public Library of Science, 2014, 9 (1), pp.1-8. ⟨10.1371/journal.pone.0085923⟩. ⟨hal-01204288⟩

Mahendra Mariadassou, Francois-Xavier Pellay. Identification of amino acids in mitochondrially encoded proteins that correlate with lifespan.. Experimental Gerontology, Elsevier, 2014, 56, pp.53-58. ⟨10.1016/j.exger.2014.03.009⟩. ⟨hal-02630250⟩

Jean-François Gibrat, Mahendra Mariadassou, Pierre Boudinot, Bernard Delmas. 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.. BMC Evolutionary Biology, BioMed Central, 2013, 13, pp.3-17. ⟨10.1186/1471-2148-13-154⟩. ⟨hal-02645508⟩

Mahendra Mariadassou, Avner Bar-Hen, Hirohisa Kishino. Taxon influence index: assessing taxon-induced incongruities in phylogenetic inference. Systematic Biology, Oxford University Press (OUP), 2012, 61 (2), pp.337-345. ⟨10.1093/sysbio/syr129⟩. ⟨hal-02642639⟩

Agnieszka K. Szczepankowska, Eric Prestel, Mahendra Mariadassou, Jacek K. Bardowski, Elena Bidnenko. Phylogenetic and complementation analysis of a single-stranded dna binding protein family from lactococcal phages indicates a non-bacterial origin. PLoS ONE, Public Library of Science, 2011, 6 (11), ⟨10.1371/journal.pone.0026942⟩. ⟨hal-01191212⟩

Mahendra Mariadassou, Stephane Robin, Corinne Vacher. Uncovering latent structure in valued graphs: a variational approach. Annals of Applied Statistics, Institute of Mathematical Statistics, 2010, 4 (2), pp.715-742. ⟨10.1214/10-AOAS361⟩. ⟨hal-01197514⟩

Mahendra Mariadassou, Avner Bar-Hen. Concentration inequality for evolutionary trees. Journal of Multivariate Analysis, Elsevier, 2009, pp.2055-2064. ⟨10.1016/j.jmva.2009.02.015⟩. ⟨hal-00410872⟩

Avner Bar-Hen, Mahendra Mariadassou, Marie-Anne Poursat, Philippe Vandenkoornhuyse. Influence function for robust phylogenetic reconstructions.. Molecular Biology and Evolution, Oxford University Press (OUP), 2008, 25 (5), pp.869-873. ⟨10.1093/molbev/msn030⟩. ⟨hal-00312860⟩

J.J. Daudin, Vincent Lacroix, M. Mariadassou, V. Miele, Franck Picard, et al.. Uncovering structure in biological networks. incollection, 2006, --, pp.471-483. ⟨hal-00427936⟩

Stephane Chaillou, Eric Dugat-Bony, Julien Lossouarn, Marie Agnès Petit, Mahendra Mariadassou, et al.. Caractérisation et modélisation des populations de bactériophages de la croûte de fromages (type époisses) sous différentes conditions environnementales d’affinage. 15. Congrès de la Société Française de Microbiologie (SFM), Société Française de Microbiologie (SFM). FRA., Sep 2019, Paris, France. ⟨hal-02789388⟩

Bénédicte Wenden, Mahendra Mariadassou, Frank-M Chmielewski, Yann Vitasse. Shifts in the temperature sensitivity periods for two forest tree species under warming climatic conditions. EGU General Assembly 2019, Apr 2019, Vienna, Austria. ⟨hal-02790841⟩

Julien Chiquet, Mahendra Mariadassou, Stephane Robin. Variational Inference for sparse network reconstruction from count data. ICML 2019 International Conference on Machine Learning, Jun 2019, Long Beach, United States. ⟨hal-02735800⟩

Danielle Canceill, Virginie Bourion, Mahendra Mariadassou, Milka Popova, C Roger-Gaillard,, et al.. Membre du comité d'organisation scientifique. Séminaire de lancement du métaprogramme HOLOFLUX, Nov 2019, Nantes, France. ⟨hal-03229623⟩

Anne-Laure Abraham, Quentin Cavaillé, Thibaut Guirimand, Pierre Renault, Sandra Derozier, et al.. A metagenomic tool for cheese ecosystems. 17. European Conference on Computational Biology (ECCB 2018, Workshop "Recent Computational Advances in Metagenomics (RCAM)", Sep 2018, Athenes, Greece. ⟨hal-02789036⟩

Maxence Jollet, Barbara Vernus, Anne Bonnieu, Mahendra Mariadassou, Olivier Rué, et al.. Is skeletal muscle remodeling associated with gut microbiota signature?. 6th World Congress on Targeting Microbiota, Oct 2018, Porto, Portugal. pp.1. ⟨hal-02736948⟩

Bénédicte Wenden, Mahendra Mariadassou, José Antonio Campoy, José Quero-Garcia, Elisabeth Dirlewanger. Statistical analysis of trends in sweet cherry flowering data across Europe. 10. International Symposium on Modelling in Fruit Research and Orchard Management, 2017, Leuven, Belgium. ⟨10.17660/ActaHortic.2017.1160.31⟩. ⟨hal-02737108⟩

Bénédicte Wenden, Mahendra Mariadassou. Sweet cherry phenology in the context of climate change: a systems biology approach. 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⟩. ⟨hal-02736013⟩

Vincent Brault, Christine Keribin, Mahendra Mariadassou. Équivalence asymptotique des vraisemblances observée et complète dans le modèle de blocs latents. XXIV èmes Rencontres de la Société Francophone de Classification, Société Francophone de Classification, Jun 2017, Lyon, France. ⟨hal-01510994⟩

Eric Dugat-Bony, Philippine de Barbeyrac, Mahendra Mariadassou, Cecile Callon, Pascal Bonnarme, et al.. FORTRESS : Impact of microbial diversity on the barrier effect against an exogenous species. 2017 Scientific MEM days: Journées scientifiques MEM (Métaomiques et écosystèmes microbiens), Jan 2017, Paris, France. ⟨hal-01608159⟩

Anne-Laure Abraham, Thibaut Guirimand, Charlie Pauvert, Sandra Derozier, Mahendra Mariadassou, et al.. Food-Microbiomes Transfert, a shotgun metagenomic tool and a database to analyze cheese ecosystems. JOBIM 2017 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2017, Lille, France. ⟨hal-02788899⟩

Mahendra Mariadassou, Marie Suez, Pierre Nicolas, Diane Esquerré, Alain Vignal, et al.. Genomics of Chicken Domestication. 10. European Symposium on Poultry Genetics, Jun 2017, Saint Malo, France. ⟨hal-02785437⟩

Marianne de Paepe, Eric Dugat-Bony, Jérôme Hamelin, Mahendra Mariadassou, Kim Milferstedt, et al.. Accessing virus genomes out of metagenomic data: improving statistical and bioinformatics analytic tools to better assess the contribution of phages on microbial ecosystems. Phages On Marseille, Nov 2016, Marseille, France. pp.1. ⟨hal-01531724⟩

Mahendra Mariadassou, Vincent Brault, Christine Keribin. Normalité asymptotique de l’estimateur du maximum de vraisemblance dans le modèle de blocs latents. 48èmes Journées de Statistique de la SFdS, May 2016, Montpellier, France. ⟨hal-01440084⟩

Bénédicte Wenden, Mahendra Mariadassou, José Antonio Campoy, José Quero-Garcia, Elisabeth Dirlewanger. Flowering time response to temperature in sweet cherry across Europe: multi-cultivar and multi-environment analysis. 8. International Rosaceae Genomics Conference (RGC8), Jun 2016, Angers, France. ⟨hal-02740156⟩

Anne Goelzer, Jan Muntel, Victor Chubukov, Matthieu Jules, Eric Prestel, et al.. Quantitative prediction of genome-wide resource allocation in bacteria. ISGSB 2016: International Study Group for Systems Biology, Oct 2016, Jena, Germany. ⟨hal-02798691⟩

Bénédicte Wenden, Mahendra Mariadassou, José Antonio Campoy, José Quero-Garcia, Elisabeth Dirlewanger. Analyse statistique de données multisites de floraison pour le cerisier doux. Colloque Francophone Phénologie, Nov 2015, Clermont Ferrand, France. ⟨hal-02744122⟩

Bénédicte Wenden, Mahendra Mariadassou, José Antonio Campoy, José Quero-Garcia, Elisabeth Dirlewanger. Statistical analysis of trends in Sweet Cherry flowering data across Europe. 10. International Symposium on Modelling in Fruit Research and Orchard Management, Jun 2015, Montpellier, France. ⟨hal-02793616⟩

Frédéric Escudie, Lucas Auer, Maria Bernard, Laurent Cauquil, Katia Vidal, et al.. Find Rapidly OTU with Galaxy Solution. JOBIM 2015 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. ⟨hal-01535378⟩

Charlie Pauvert, Anne-Laure Abraham, Mathieu Almeida, Nicolas Pons, Mahendra Mariadassou, et al.. Accurate taxonomy assignments in cheeses ecosystems via a metagenomic approach. JOBIM 2015 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. pp.1. ⟨hal-01204484⟩

Mahendra Mariadassou, Dieter Ebert, Samuel Pichon. The specificity - abundance relationship in microbial communities. ECMTB14 - European Conference on Mathematical and Theoretical Biology, Jun 2014, Gothenburg, Sweden. pp.1. ⟨hal-02798419⟩

Mahendra Mariadassou. Dominant Species are Specialists. ECMTB14 - European Conference on Mathematical and Theoretical Biology, Jun 2014, Gôteborg, Sweden. pp.1. ⟨hal-02793165⟩

Mahendra Mariadassou, Avner Bar-Hen. Influence function for robust phylogenetic reconstruction. JOBIM 2011, Jun 2011, Paris, France. pp.422. ⟨hal-02746361⟩

Mahendra Mariadassou, Stephane Robin, Corinne Vacher. Uncovering latent structure in valued graphs: a variational approach. Probability and Discrete Mathematics in Mathematical Biology, May 2011, Singapore, Singapore. 47 diapos. ⟨hal-02802815⟩

Mahendra Mariadassou, Avner Bar-Hen. Fonction d'influence pour la reconstruction de phylogénies robustes. 42èmes Journées de Statistique, 2010, Marseille, France. pp.USB-key. ⟨inria-00494834⟩

Cedric Midoux, Franciele Camargo, Olivier Rué, Mahendra Mariadassou, Valentin Loux, et al.. A shotgun metagenomics analysis applied to the ecological engineering of anaerobic microbial communities for the production of hydrogen from Citrus Peel Waste. JOBIM, Jun 2020, Montpellier, France. ⟨hal-02902758⟩

Mahendra Mariadassou, Laurent-Xavier Nouvel, Diego Morgavi, Lucie Rault, Sophie Schbath, et al.. New insights into cow holobiont in relation to health. Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jun 2020, Montpellier, France. 2020. ⟨hal-02962468⟩

Cedric Midoux, Tiago P. Delforno, Thais Z. Macedo, Gileno V. Lacerda, Olivier Rué, et al.. Feedback on a c omparative metatranscriptomic analysis. JOBIM 2019 : Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. 2019, JOBIM 2019. ⟨hal-02735859⟩

Cedric Midoux, Olivier Rué, Olivier Chapleur, Mahendra Mariadassou, Théodore Bouchez, et al.. Easy16S : a user-friendly Shiny interface for analysis and visualization of metagenomic data. JOBIM 2018 : Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. 2018, JOBIM 2018. ⟨hal-02737257⟩

Laurent-Xavier Nouvel, Diego Morgavi, Lucie Rault, Mahendra Mariadassou, Sophie Schbath, et al.. New insights into cow holobiont in relation to health. Pathobiome 2018 "Pathogens in Microbiotas in Hosts", Jan 2018, Ajaccio, France. ⟨hal-03299131⟩

Valérie Gagnaire, Fanny Canon, Mahendra Mariadassou, Hélène Falentin, Sandrine Parayre, et al.. Design de communautés bactériennes pour fermenter un nouvel aliment associant lait et légumineuse. RFL2, 2e Rencontres Francophones sur les Légumineuses, Oct 2018, Toulouse, France. 2018. ⟨hal-01902837⟩

Sophie Schbath, Mahendra Mariadassou, Julie Lao. Comparison of statistical methods of inference of cooccurrence networks within micro- bial ecosystems from metagenomics data. JOBIM 2017 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2017, Lille, France. pp.234, 2017, JOBIM 2017. ⟨hal-01563604⟩

Laurent-Xavier Nouvel, Diego Morgavi, Lucie Rault, Mahendra Mariadassou, Sophie Schbath, et al.. New insights into cow holobiont in relation to health. Jounées du métaprogramme MEM, Jan 2017, Paris, France. ⟨hal-03299117⟩

Gaëtan Benoit, Pierre Peterlongo, Mahendra Mariadassou, Erwan Drezen, Sophie Schbath, et al.. Simka: large scale de novo comparative metagenomics. JOBIM 2017 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2017, Lille, France. pp.234, 2017, JOBIM 2017 LILLE. ⟨hal-01595071⟩

Fanny Canon, Mahendra Mariadassou, Hélène Falentin, Sandrine Parayre, Marie-Bernadette Maillard, et al.. Design of bacterial consortia for fermentation of novel food mixing milk and lupin flour. 4. International Conference on Microbial Diversity 2017, Oct 2017, Bari, Italy. 2017. ⟨hal-01628088⟩

Thibaut Guirimand, Charlie Pauvert, Sandra Derozier, Anne-Laure Abraham, Mahendra Mariadassou, et al.. Cheese ecosystems insights with shotgun metagenomics and a metadata extended genomics database.. JOBIM 2016 : Journées ouvertes de biologie informatique et mathématiques, Jun 2016, Lyon, France. 2016. ⟨hal-01512085⟩

Lucas Auer, Laurent Cauquil, Stephane Chaillou, Céline Delbes, Eric Dugat-Bony, et al.. How to design an efficient and robust pipeline for 16S rRNA-gene sequence analysis to improve our understanding on microbial communities?. JOBIM 16. Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. 2015. ⟨hal-01195512⟩

Michele Tixier-Boichard, Mahendra Mariadassou, Xavier Rognon, Pierre Nicolas, Francois Rodolphe, et al.. Approche génomique de la domestication du poulet. 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. ⟨hal-01535349⟩

Frédéric Escudie, Lucas Auer, Maria Bernard, Laurent Cauquil, Katia Vidal, et al.. FROGS : Find Rapidly OTUs with Galaxy Solution. 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. ⟨hal-01886389⟩

Valentin Loux, Mahendra Mariadassou, Sintia Almeida da Silva, Hélène Chiapello, Amal Hammami, et al.. Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii. 20. Colloque du Club des Bactéries Lactiques, Jun 2015, Lille, France. 2015. ⟨hal-01170054⟩

Valentin Loux, Mahendra Mariadassou, Sintia Almeida da Silva, Helene Chiapello, Amal Hammami, et al.. Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of [i]Propionibacterium freudenreichii[/i]. JOBIM 16.Journées Ouvertes de Biologie, Informatique et Mathématiques, Jul 2015, Clermont-Ferrand, France. 2015. ⟨hal-01209851⟩

Mahendra Mariadassou, Bertrand Bed'Hom, Pierre Nicolas, Jean-Luc Coville, Félicie Lahalle-Faucon, et al.. Insight in the genetic diversity of wild and domestic [i]Gallus[/i]. 14. European Poultry Conference, Jun 2014, Stavanger, Norway. 2014. ⟨hal-01193928⟩

Caroline Le Maréchal, Mahendra Mariadassou, Valentin Loux, Amal Plaudet Hammani, Julien Buratti, et al.. Combination of in silico and proteomic approaches to identify candidate genes responsible for the immunomodulatory properties of Propionibacterium freudenreichii. Journées des Microbiologistes de l'INRA 2012, Nov 2012, L'Isle-sur-la-Sorgue, France. 2012. ⟨hal-01209410⟩

Caroline Le Maréchal, Mahendra Mariadassou, Valentin Loux, Amal Plaudet Hammani, Julien Buratti, et al.. Combination of in silico and proteomic approaches to identify candidate genes responsible for the immunomodulatory properties of[i] Propionibacterium freudenreichii[/i]. Journées ouvertes en biologie informatique mathématiques, Jul 2012, Rennes, France. 2012. ⟨hal-01209420⟩

Mahendra Mariadassou, Avner Bar-Hen, Hirohisa Kishino. Tree Evaluation and Robustness Testing. Encyclopedia of Bioinformatics and Computational Biology, 2, Elsevier, pp.736-745, 2019, ⟨10.1016/B978-0-12-809633-8.20259-8⟩. ⟨hal-02484863⟩

Frédéric Escudie, Lucas Auer, Maria Bernard, Mahendra Mariadassou, Laurent Cauquil, et al.. FROGS : Find Rapidly OTU with Galaxy Solution. 2017. ⟨hal-01886442⟩

Daniel Richter, Romain Watteaux, Thomas Vannier, Jade Leconte, Paul Frémont, et al.. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems. 2020. ⟨hal-02399723⟩

Gaëtan Benoit, Pierre Peterlongo, Mahendra Mariadassou, Erwan Drezen, Sophie Schbath, et al.. Multiple Comparative Metagenomics using Multiset k-mer Counting. 2016. ⟨hal-01300485⟩

Mahendra Mariadassou, Avner Bar-Hen. Assessing the Distribution Consistency of Sequential Data. 2009. ⟨hal-00391682⟩

Julien Chiquet, Mahendra Mariadassou, Stephane Robin. Variational inference for probabilistic Poisson PCA. [University works] auto-saisine. 2017. ⟨hal-01608912⟩

Vincent Brault, Christine Keribin, Mahendra Mariadassou. Équivalence asymptotique des vraisemblances observée et complète dans le modèle de blocs latents. [Travaux universitaires] auto-saisine. 2017. ⟨hal-01603137⟩

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

Maria Bernard, Géraldine Pascal, Mahendra Mariadassou, Laurent Cauquil, Stephane Chaillou. FROGS Training on Galaxy : Statistics to Explore Metagenomics. Training on Galaxy : Statistics to Explore Metagenomics - FROGS (Find, Rapidly, Otus with Galaxy Solution), 2017, 116 p. ⟨hal-02788316⟩

Frédéric Escudié, Lucas Auer, Maria Bernard, Laurent Cauquil, Sarah Maman, et al.. FROGS Training on Galaxy : Metagenomics November 2017. Formation Métagénomique avec le logiciel FROGS (Find, Rapidly, Otus with Galaxy Solution), 2017, 270 p. ⟨hal-02791696⟩