• 2025
  Pfeifer E, d'Humières C, Lamy-Besnier Q, Oñate FP, Denisé R, Dion S, Condamine B, Touchon M, Ma L, Burdet C, Mentré F, Denamur E, Rocha EPC, Antibiotic perturbation of the human gut phageome preserves its individuality and promotes blooms of virulent phages., Cell Rep 2025 Aug; 44(8): 116020.
• 2025
  Mazzamurro F, Touchon M, Charpentier X, Rocha EPC, Impact of Natural Transformation on the Acquisition of Novel Genes in Bacteria., Mol Biol Evol 2025 Jul; 42(8): .
• 2025
  , Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems, Science, 388, 6747, (2025)..
• 2025
  Darracq B, Littner E, Brunie M, Bos J, Kaminski PA, Depardieu F, Slesak W, Debatisse K, Touchon M, Bernheim A, Bikard D, Le Roux F, Mazel D, Rocha EPC, Loot C, Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems., Science, 2025 May; 388(6747): eads0768.
• 2024
  d'Humières C, Delavy M, Alla L, Ichou F, Gauliard E, Ghozlane A, Levenez F, Galleron N, Quinquis B, Pons N, Mullaert J, Bridier-Nahmias A, Condamine B, Touchon M, Rainteau D, Lamazière A, Lesnik P, Ponnaiah M, Lhomme M, Sertour N, Devente S, Docquier JD, Bougnoux ME, Tenaillon O, Magnan M, Ruppé E, Grall N, Duval X, Ehrlich D, Mentré F, Denamur E, Rocha EPC, Le Chatelier E, Burdet C, Perturbation and resilience of the gut microbiome up to 3 months after β-lactams exposure in healthy volunteers suggest an important role of microbial β-lactamases., Microbiome 2024 Mar; 12(1): 50.
• 2023
  Coluzzi C, Guillemet M, Mazzamurro F, Touchon M, Godfroid M, Achaz G, Glaser P, Rocha EPC, Chance Favors the Prepared Genomes: Horizontal Transfer Shapes the Emergence of Antibiotic Resistance Mutations in Core Genes., Mol Biol Evol 2023 Oct; 40(10): .
• 2021
  Pfeifer E, Moura de Sousa JA, Touchon M, Rocha EPC, , Bacteria have numerous distinctive groups of phage-plasmids with conserved phage and variable plasmid gene repertoires., Nucleic Acids Res 2021 03; 49(5): 2655-2673.
• 2021
  de Sousa JAM, Pfeifer E, Touchon M, Rocha EPC, , Causes and consequences of bacteriophage diversification via genetic exchanges across lifestyles and bacterial taxa., Mol Biol Evol 2021 Feb; (): .
• 2020
  Aude Bernheim, David Bikard, Marie Touchon, Eduardo Rocha, Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements, Nucleic Acids Research, 2020, 48, pp.748 - 760. ⟨10.1093/nar/gkz1091⟩.
• 2019
  Aude Bernheim, David Bikard, Marie Touchon, Eduardo P C Rocha, A matter of background: DNA repair pathways as a possible cause for the sparse distribution of CRISPR-Cas systems in bacteria, Philosophical Transactions of the Royal Society B: Biological Sciences, 2019, 374 (1772), pp.20180088. ⟨10.1098/rstb.2018.0088⟩.
• 2018
  Rendueles O, de Sousa JAM, Bernheim A, Touchon M, Rocha EPC, Genetic exchanges are more frequent in bacteria encoding capsules, PLoS Genet. 2018 12;14(12):e1007862.
• 2018
  David Couvin, Aude Bernheim, Claire Toffano-Nioche, Marie Touchon, Juraj Michalik, Bertrand Néron, Eduardo P C Rocha, Gilles Vergnaud, Daniel Gautheret, Christine Pourcel, CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins, Nucleic Acids Research, 2018, 46 (W1), pp.W246-W251. ⟨10.1093/nar/gky425⟩.
• 2018
  Clerissi C, Touchon M, Capela D, Tang M, Cruveiller S, Genthon C, Lopez-Roques C, Parker MA, Moulin L, Masson-Boivin C, Rocha EPC, Parallels between experimental and natural evolution of legume symbionts, Nat Commun 2018 06;9(1):2264.
• 2017
  Aude Bernheim, Alicia Calvo Villamanan, Clovis Basier, Lun Cui, Eduardo P. C. Rocha, Marie Touchon, David Bikard, Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria, Nature Communications 8, 2094..
• 2017
  Oliveira PH, Touchon M, Cury J, Rocha EPC, The chromosomal organization of horizontal gene transfer in bacteria, Nat Commun 2017 Oct;8(1):841.
• 2017
  Garcia-Garcera M, Touchon M, Brisse S, Rocha EPC, Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter, Environ. Microbiol. 2017 Oct;.
• 2017
  Cury J, Touchon M, Rocha EPC, Integrative and conjugative elements and their hosts: composition, distribution and organization, Nucleic Acids Res. 2017 Sep;45(15):8943-8956.
• 2017
  Jamet A, Touchon M, Ribeiro-Gonçalves B, Carriço JA, Charbit A, Nassif X, Ramirez M, Rocha EPC, A widespread family of polymorphic toxins encoded by temperate phages, BMC Biol. 2017 Aug;15(1):75.
• 2017
  Rendueles O, Garcia-Garcerà M, Néron B, Touchon M, Rocha EPC, Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens, PLoS Pathog. 2017 Jul;13(7):e1006525.
• 2017
  Touchon M, Moura de Sousa JA, Rocha EPC, Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer, Curr Opin Microbiol. 2017 May 17;38:66-73.
• 2016
  Breurec S, Criscuolo A, Diancourt L, Rendueles O, Vandenbogaert M, Passet V, Caro V, Rocha EP, Touchon M, Brisse S, Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis, Sci Rep 2016;6:30379.
• 2016
  Pedro H. Oliveira, Marie Touchon, and Eduardo P. C. Rocha, Regulation of genetic flux between bacteria by restriction-modification systems., Proc Natl Acad Sci U S A. 2016 May 17;113(20):5658-63. doi: 10.1073/pnas.1603257113. .
• 2016
  Jean Cury, Thomas Jové, Marie Touchon, Bertrand Néron, and Eduardo PC Rocha, Identification and analysis of integrons and cassette arrays in bacterial genomes., Nucleic Acids Res. 2016 Apr 29. pii: gkw319..
• 2016
  Touchon M, Bernheim A, Rocha EPC, Genetic and life-history traits associated with the distribution of prophages in bacteria., ISME J. 2016 Mar 25. doi: 10.1038/ismej.2016.47. .
• 2016
  Sophie S. Abby, Jean Cury, Julien Guglielmini, Bertrand Néron, Marie Touchon & Eduardo P. C. Rocha, Identification of protein secretion systems in bacterial genomes, Scientific Reports 6, 23080 (2016).
• 2016
  Maury MM, Tsai YH, Charlier C, Touchon M, Chenal-Francisque V, Leclercq A, Criscuolo A, Gaultier C, Roussel S, Brisabois A, Disson O, Rocha EPC, Brisse S, Lecuit M, , Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity., Nat Genet 2016 Mar; 48(3): 308-313.
• 2016
  Touchon M, Rocha EPC, Coevolution of the Organization and Structure of Prokaryotic Genomes., Cold Spring Harb Perspect Biol. 2016 Jan 4;8(1).