Overview

I am mainly interested in evolutionary genomics with a special interest in robust phylogenetic inferrence, outlier detection in evolutionary studies (rogue taxa/influent sites), phylogenetic comparative methods. I'm also interested in metagenomics, with a special interest in statistical models for multivariate count data, such as encountered in metagenomics studies.

Software

Here are some softwares / scripts I developed or contributed to:

2017
PLNmodels project
R package to analyze multivariate count using the Poisson Log-Normal distribution. Includes PCA, Network Inference, LDA, Mixture Models, etc.
2016
FROGSwebsite, project
Python-based pipeline to reconstruct OTU count table from raw sequence reads
2015
PhylogeneticEM package, project
R package to detect adaptive shifts on phylogenies
2015
Local specifity index scripts (includes a vignette)
R scripts to compute the Local Specifity Index, as used in Mariadassou et al. (2015)
2012
Taxon Influence Index scripts
R scripts to compute Taxon Influence Index, as used in Mariadassou et al. (2012)


Publications

Under construction!

Some references and/or preprint may be missing.


  1. Mahendra Mariadassou, Avner Bar-Hen, and Hirohisa Kishino. Tree Evaluation and Robustness Testing. In: Ranganathan, S., Gribskov, M., Nakai, K., and Schönbach, C. (eds.) Encyclopedia of Bioinformatics and Computational Biology, pp. 736–745, Academic Press, Oxford, 2019.

  2. Tiago P. Delforno, Thais Z. Macedo, Cédric Midoux, Gileno V. Lacerda, Olivier Rué, Mahendra Mariadassou, Valentin Loux, Maria B.A. Varesche, Théodore Bouchez, Ariane Bize, and Valéria M. Oliveira. Comparative metatranscriptomic analysis of anaerobic digesters treating anionic surfactant contaminated wastewater. Science of The Total Environment, 649 :482–494, 2019.

  3. Frédéric Escudié, Lucas Auer, Maria Bernard, Mahendra Mariadassou, Laurent Cauquil, Katia Vidal, Sarah Maman, Guillermina Hernandez-Raquet, Sylvie Combes, and Géraldine Pascal. FROGS: Find, Rapidly, OTUs with Galaxy Solution. Bioinformatics, 34(8) :1287–1294, 2018.

  4. Jeffrey K. Cornuault, Marie-Agnès Petit, Mahendra Mariadassou, Leandro Benevides, Elisabeth Moncaut, Philippe Langella, Harry Sokol, and Marianne De Paepe. Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes. Microbiome, 6 :65, 2018.

  5. Julien Chiquet, Mahendra Mariadassou, and Stéphane Robin. Variational inference for probabilistic Poisson PCA. Ann. Appl. Stat., In press :np, 2018.

  6. Paul Bastide, Cécile Ané, Stéphane Robin, and Mahendra Mariadassou. Inference of Adaptive Shifts for Multivariate Correlated Traits. Systematic Biology, 67(4) :662–680, 2018.

  7. Bénédicte Wenden and M Mariadassou. Sweet cherry phenology in the context of climate change: A systems biology approach. In: Acta Horticulturae, pp. 31–38 2017.

  8. Danilo Segovia, Ahmed Haouz, Darío Porley, Natalia Olivero, Mariano Martínez, Mahendra Mariadassou, Mabel Berois, Gwenaëlle André-Leroux, and Andrea Villarino. OH1 from Orf Virus: A New Tyrosine Phosphatase that Displays Distinct Structural Features and Triple Substrate Specificity. Journal of Molecular Biology, 429(18) :2816–2824, 2017.

  9. Hela El Kafsi, Valentin Loux, Mahendra Mariadassou, Camille Blin, Hélène Chiapello, Anne-Laure Abraham, Emmanuelle Maguin, and Maarten van de Guchte. Unprecedented large inverted repeats at the replication terminus of circular bacterial chromosomes suggest a novel mode of chromosome rescue. Scientific Reports, 7 :44331, 2017.

  10. Stéphanie-Marie Deutsch, Mahendra Mariadassou, Pierre Nicolas, Sandrine Parayre, Rozenn Le Guellec, Victoria Chuat, Vincent Peton, Caroline Le Maréchal, Julien Burati, Valentin Loux, Valérie Briard-Bion, Julien Jardin, Coline Plé, Benoît Foligné, Gwénaël Jan, and Hélène Falentin. Identification of proteins involved in the anti-inflammatory properties of Propionibacterium freudenreichii by means of a multi-strain study. Scientific Reports, 7 :46409, 2017.

  11. Paul Bastide, Mahendra Mariadassou, and Stéphane Robin. Detection of adaptive shifts on phylogenies by using shifted stochastic processes on a tree. Journal of the Royal Statistical Society: Series B (Statistical Methodology), 79(4) :1067–1093, 2017.

  12. Lucas Auer, Mahendra Mariadassou, Michael O’Donohue, Christophe Klopp, and Guillermina Hernandez-Raquet. Analysis of large 16S rRNA Illumina data sets: Impact of singleton read filtering on microbial community description. Molecular Ecology Resources, 17(6) :e122–e132, 2017.

  13. César M. J. A. Metzger, Pepijn Luijckx, Gilberto Bento, Mahendra Mariadassou, and Dieter Ebert. The Red Queen lives: Epistasis between linked resistance loci. Evolution, 70(2) :480–487, 2016.

  14. Adrien François, Denise Grebert, Moez Rhimi, Mahendra Mariadassou, Laurent Naudon, Sylvie Rabot, and Nicolas Meunier. Olfactory epithelium changes in germfree mice. Scientific Reports, 6 :24687, 2016.

  15. Gaëtan Benoit, Pierre Peterlongo, Mahendra Mariadassou, Erwan Drezen, Sophie Schbath, Dominique Lavenier, and Claire Lemaitre. Multiple comparative metagenomics using multiset \textitk-mer counting. PeerJ Computer Science, 2 :e94, 2016.

  16. Jeanne Alard, Véronique Lehrter, Moez Rhimi, Irène Mangin, Véronique Peucelle, Anne-Laure Abraham, Mahendra Mariadassou, Emmanuelle Maguin, Anne-Judith Waligora-Dupriet, Bruno Pot, Isabelle Wolowczuk, and Corinne Grangette. 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, 18(5) :1484–1497, 2016.

  17. Anne C. Roulin, Mahendra Mariadassou, Matthew D. Hall, Jean-Claude Walser, Christoph Haag, and Dieter Ebert. High genetic variation in resting-stage production in a metapopulation: Is there evidence for local adaptation? Evolution, 69(10) :2747–2756, 2015.

  18. Mahendra Mariadassou, Samuel Pichon, and Dieter Ebert. Microbial ecosystems are dominated by specialist taxa. Ecology Letters, 18(9) :974–982, 2015.

  19. Mahendra Mariadassou and Catherine Matias. Convergence of the groups posterior distribution in latent or stochastic block models. Bernoulli, 21(1) :537–573, 2015.

  20. Valentin Loux, Mahendra Mariadassou, Sintia Almeida, Hélène Chiapello, Amal Hammani, Julien Buratti, Annie Gendrault, Valérie Barbe, Jean-Marc Aury, Stéphanie-Marie Deutsch, Sandrine Parayre, Marie-Noëlle Madec, Victoria Chuat, Gwenaël Jan, Pierre Peterlongo, Vasco Azevedo, Yves Le Loir, and Hélène Falentin. Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii. BMC Genomics, 16(1) :296, 2015.

  21. Anne Goelzer, Jan Muntel, Victor Chubukov, Matthieu Jules, Eric Prestel, Rolf Nölker, Mahendra Mariadassou, Stéphane Aymerich, Michael Hecker, Philippe Noirot, Dörte Becher, and Vincent Fromion. Quantitative prediction of genome-wide resource allocation in bacteria. Metabolic Engineering, 32 :232–243, 2015.

  22. Vincent Brault and Mahendra Mariadassou. Co-clustering through Latent Bloc Model: a Review. Journal de la SFdS, 156(3) :120–139, 2015.

  23. Clarissa Santos Rocha, Ana Cristina Gomes-Santos, Thais Garcias Moreira, Marcela de Azevedo, Tessalia Diniz Luerce, Mahendra Mariadassou, Ana Paula Longaray Delamare, Philippe Langella, Emmanuelle Maguin, Vasco Azevedo, Ana Maria Caetano de Faria, Anderson Miyoshi, and Maarten van de Guchte. Local and Systemic Immune Mechanisms Underlying the Anti-Colitis Effects of the Dairy Bacterium \textitLactobacillus delbrueckii. PLoS ONE, 9(1) :e85923, 2014.

  24. Mahendra Mariadassou and François-Xavier Pellay. Identification of amino acids in mitochondrially encoded proteins that correlate with lifespan. Exp Gerontol, 56 :53–58, 2014.


  1. Tiago P. Delforno, Thais Z. Macedo, Cédric Midoux, Gileno V. Lacerda, Olivier Rué, Mahendra Mariadassou, Valentin Loux, Maria B.A. Varesche, Théodore Bouchez, Ariane Bize, and Valéria M. Oliveira. Comparative metatranscriptomic analysis of anaerobic digesters treating anionic surfactant contaminated wastewater. Science of The Total Environment, 649 :482–494, 2019.

  2. Frédéric Escudié, Lucas Auer, Maria Bernard, Mahendra Mariadassou, Laurent Cauquil, Katia Vidal, Sarah Maman, Guillermina Hernandez-Raquet, Sylvie Combes, and Géraldine Pascal. FROGS: Find, Rapidly, OTUs with Galaxy Solution. Bioinformatics, 34(8) :1287–1294, 2018.

  3. Jeffrey K. Cornuault, Marie-Agnès Petit, Mahendra Mariadassou, Leandro Benevides, Elisabeth Moncaut, Philippe Langella, Harry Sokol, and Marianne De Paepe. Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes. Microbiome, 6 :65, 2018.

  4. Julien Chiquet, Mahendra Mariadassou, and Stéphane Robin. Variational inference for probabilistic Poisson PCA. Ann. Appl. Stat., In press :np, 2018.

  5. Paul Bastide, Cécile Ané, Stéphane Robin, and Mahendra Mariadassou. Inference of Adaptive Shifts for Multivariate Correlated Traits. Systematic Biology, 67(4) :662–680, 2018.

  6. Danilo Segovia, Ahmed Haouz, Darío Porley, Natalia Olivero, Mariano Martínez, Mahendra Mariadassou, Mabel Berois, Gwenaëlle André-Leroux, and Andrea Villarino. OH1 from Orf Virus: A New Tyrosine Phosphatase that Displays Distinct Structural Features and Triple Substrate Specificity. Journal of Molecular Biology, 429(18) :2816–2824, 2017.

  7. Hela El Kafsi, Valentin Loux, Mahendra Mariadassou, Camille Blin, Hélène Chiapello, Anne-Laure Abraham, Emmanuelle Maguin, and Maarten van de Guchte. Unprecedented large inverted repeats at the replication terminus of circular bacterial chromosomes suggest a novel mode of chromosome rescue. Scientific Reports, 7 :44331, 2017.

  8. Stéphanie-Marie Deutsch, Mahendra Mariadassou, Pierre Nicolas, Sandrine Parayre, Rozenn Le Guellec, Victoria Chuat, Vincent Peton, Caroline Le Maréchal, Julien Burati, Valentin Loux, Valérie Briard-Bion, Julien Jardin, Coline Plé, Benoît Foligné, Gwénaël Jan, and Hélène Falentin. Identification of proteins involved in the anti-inflammatory properties of Propionibacterium freudenreichii by means of a multi-strain study. Scientific Reports, 7 :46409, 2017.

  9. Paul Bastide, Mahendra Mariadassou, and Stéphane Robin. Detection of adaptive shifts on phylogenies by using shifted stochastic processes on a tree. Journal of the Royal Statistical Society: Series B (Statistical Methodology), 79(4) :1067–1093, 2017.

  10. Lucas Auer, Mahendra Mariadassou, Michael O’Donohue, Christophe Klopp, and Guillermina Hernandez-Raquet. Analysis of large 16S rRNA Illumina data sets: Impact of singleton read filtering on microbial community description. Molecular Ecology Resources, 17(6) :e122–e132, 2017.

  11. César M. J. A. Metzger, Pepijn Luijckx, Gilberto Bento, Mahendra Mariadassou, and Dieter Ebert. The Red Queen lives: Epistasis between linked resistance loci. Evolution, 70(2) :480–487, 2016.

  12. Adrien François, Denise Grebert, Moez Rhimi, Mahendra Mariadassou, Laurent Naudon, Sylvie Rabot, and Nicolas Meunier. Olfactory epithelium changes in germfree mice. Scientific Reports, 6 :24687, 2016.

  13. Gaëtan Benoit, Pierre Peterlongo, Mahendra Mariadassou, Erwan Drezen, Sophie Schbath, Dominique Lavenier, and Claire Lemaitre. Multiple comparative metagenomics using multiset \textitk-mer counting. PeerJ Computer Science, 2 :e94, 2016.

  14. Jeanne Alard, Véronique Lehrter, Moez Rhimi, Irène Mangin, Véronique Peucelle, Anne-Laure Abraham, Mahendra Mariadassou, Emmanuelle Maguin, Anne-Judith Waligora-Dupriet, Bruno Pot, Isabelle Wolowczuk, and Corinne Grangette. 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, 18(5) :1484–1497, 2016.

  15. Anne C. Roulin, Mahendra Mariadassou, Matthew D. Hall, Jean-Claude Walser, Christoph Haag, and Dieter Ebert. High genetic variation in resting-stage production in a metapopulation: Is there evidence for local adaptation? Evolution, 69(10) :2747–2756, 2015.

  16. Mahendra Mariadassou, Samuel Pichon, and Dieter Ebert. Microbial ecosystems are dominated by specialist taxa. Ecology Letters, 18(9) :974–982, 2015.

  17. Mahendra Mariadassou and Catherine Matias. Convergence of the groups posterior distribution in latent or stochastic block models. Bernoulli, 21(1) :537–573, 2015.

  18. Valentin Loux, Mahendra Mariadassou, Sintia Almeida, Hélène Chiapello, Amal Hammani, Julien Buratti, Annie Gendrault, Valérie Barbe, Jean-Marc Aury, Stéphanie-Marie Deutsch, Sandrine Parayre, Marie-Noëlle Madec, Victoria Chuat, Gwenaël Jan, Pierre Peterlongo, Vasco Azevedo, Yves Le Loir, and Hélène Falentin. Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii. BMC Genomics, 16(1) :296, 2015.

  19. Anne Goelzer, Jan Muntel, Victor Chubukov, Matthieu Jules, Eric Prestel, Rolf Nölker, Mahendra Mariadassou, Stéphane Aymerich, Michael Hecker, Philippe Noirot, Dörte Becher, and Vincent Fromion. Quantitative prediction of genome-wide resource allocation in bacteria. Metabolic Engineering, 32 :232–243, 2015.

  20. Vincent Brault and Mahendra Mariadassou. Co-clustering through Latent Bloc Model: a Review. Journal de la SFdS, 156(3) :120–139, 2015.

  21. Clarissa Santos Rocha, Ana Cristina Gomes-Santos, Thais Garcias Moreira, Marcela de Azevedo, Tessalia Diniz Luerce, Mahendra Mariadassou, Ana Paula Longaray Delamare, Philippe Langella, Emmanuelle Maguin, Vasco Azevedo, Ana Maria Caetano de Faria, Anderson Miyoshi, and Maarten van de Guchte. Local and Systemic Immune Mechanisms Underlying the Anti-Colitis Effects of the Dairy Bacterium \textitLactobacillus delbrueckii. PLoS ONE, 9(1) :e85923, 2014.

  22. Mahendra Mariadassou and François-Xavier Pellay. Identification of amino acids in mitochondrially encoded proteins that correlate with lifespan. Exp Gerontol, 56 :53–58, 2014.

  23. Jean-François Gibrat, Mahendra Mariadassou, Pierre Boudinot, and 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 Evol Biol, 13 :154, 2013.

  24. Mahendra Mariadassou, Avner Bar-Hen, and Hirohisa Kishino. Taxon influence index: assessing taxon-induced incongruities in phylogenetic inference. Syst Biol, 61(2) :337–345, 2012.

  25. Agnieszka K Szczepankowska, Eric Prestel, Mahendra Mariadassou, Jacek K Bardowski, and Elena Bidnenko. Phylogenetic and complementation analysis of a single-stranded DNA binding protein family from lactococcal phages indicates a non-bacterial origin. PLoS One, 6(11) :e26942, 2011.

  26. Mahendra Mariadassou, Stéphane Robin, and Corinne Vacher. Uncovering latent structure in valued graphs: A variational approach. Ann. Appl. Stat., 4(2) :715–742, 2010.

  27. Mahendra Mariadassou and A. Bar-Hen. Concentration inequality for evolutionary trees. Journal of Multivariate Analysis, 100 :2055–2064, 2009.

  28. Avner Bar-Hen, Mahendra Mariadassou, Marie-Anne Poursat, and Philippe Vandenkoornhuyse. Influence function for robust phylogenetic reconstructions. Mol Biol Evol, 25(5) :869–873, 2008.


  1. Mahendra. Mariadassou, Julien. Chiquet, and Stéphane. Robin. Probabilistic PCA for count data in microbial ecology. In: Proceedings of the 2018 JOBIM edition, pp. 30–32 JOBIM.

  2. Bénédicte Wenden and M Mariadassou. Sweet cherry phenology in the context of climate change: A systems biology approach. In: Acta Horticulturae, pp. 31–38 2017.


  1. Mahendra Mariadassou, Avner Bar-Hen, and Hirohisa Kishino. Tree Evaluation and Robustness Testing. In: Ranganathan, S., Gribskov, M., Nakai, K., and Schönbach, C. (eds.) Encyclopedia of Bioinformatics and Computational Biology, pp. 736–745, Academic Press, Oxford, 2019.