• 2024
  Manuel Ares-Arroyo, Amandine Nucci, Eduardo Rocha, Expanding the diversity of origin of transfer-containing sequences in mobilizable plasmids, Nature Microbiology, In press, ⟨10.1038/s41564-024-01844-1⟩.
• 2024
  Mazzamurro F, Chirakadavil JB, Durieux I, Poiré L, Plantade J, Ginevra C, Jarraud S, Wilharm G, Charpentier X, P C Rocha E, Intragenomic conflicts with plasmids and chromosomal mobile genetic elements drive the evolution of natural transformation within species., PLoS Biol 2024 Oct; 22(10): e3002814.
• 2024
  Audebert L, Feuerbach F, Zedan M, Schürch AP, Decourty L, Namane A, Permal E, Weis K, Badis G, Saveanu C, RNA degradation triggered by decapping is largely independent of initial deadenylation., EMBO J 2024 Sep; (): .
• 2024
  Anjou C, Royer M, Bertrand É, Bredon M, Le Bris J, Salgueiro IA, Caulat LC, Dupuy B, Barbut F, Morvan C, Rolhion N, Martin-Verstraete I, Adaptation mechanisms of Clostridioides difficile to auranofin and its impact on human gut microbiota., NPJ Biofilms Microbiomes 2024 Sep; 10(1): 86.
• 2024
  Zeitler L, Goldar A, Denby Wilkes C, Soutourina J, The next-generation sequencing-chess problem., NAR Genom Bioinform 2024 Sep; 6(4): lqae144.
• 2024
  Cury J, Haudiquet M, Hernandez Trejo V, Mordret E, Hanouna A, Rotival M, Tesson F, Bonhomme D, Ofir G, Quintana-Murci L, Benaroch P, Poirier EZ, Bernheim A, Conservation of antiviral systems across domains of life reveals immune genes in humans., Cell Host Microbe 2024 Aug; (): .
• 2024
  Burman N, Belukhina S, Depardieu F, Wilkinson RA, Skutel M, Santiago-Frangos A, Graham AB, Livenskyi A, Chechenina A, Morozova N, Zahl T, Henriques WS, Buyukyoruk M, Rouillon C, Saudemont B, Shyrokova L, Kurata T, Hauryliuk V, Severinov K, Groseille J, Thierry A, Koszul R, Tesson F, Bernheim A, Bikard D, Wiedenheft B, Isaev A, A virally-encoded tRNA neutralizes the PARIS antiviral defence system., Nature 2024 Aug; (): .
• 2024
  Serizay J, Koszul R, Epigenomics coverage data extraction and aggregation in R with tidyCoverage., Bioinformatics 2024 Aug; 40(8): .
• 2024
  Benz F, Camara-Wilpert S, Russel J, Wandera KG, Čepaitė R, Ares-Arroyo M, Gomes-Filho JV, Englert F, Kuehn JA, Gloor S, Mestre MR, Cuénod A, Aguilà-Sans M, Maccario L, Egli A, Randau L, Pausch P, Rocha EPC, Beisel CL, Madsen JS, Bikard D, Hall AR, Sørensen SJ, Pinilla-Redondo R, Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans., Cell Host Microbe 2024 May; (): .
• 2024
  Bastié N, Chapard C, Cournac A, Nejmi S, Mboumba H, Gadal O, Thierry A, Beckouët F, Koszul R, Sister chromatid cohesion halts DNA loop expansion., Mol Cell 2024 Mar; 84(6): 1139-1148.e5.
• 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.
• 2024
  Matthieu Haudiquet, Julie Le Bris, Amandine Nucci, Rémy A Bonnin, Pilar Domingo-Calap, Eduardo P C Rocha, Olaya Rendueles, Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency, Nature Communications, 2024, 15 (1), pp.2032. ⟨10.1038/s41467-024-46147-5⟩.
• 2024
  Pfeifer E, Rocha EPC, Phage-plasmids promote recombination and emergence of phages and plasmids., Nat Commun 2024 Feb; 15(1): 1545.
• 2024
  Serizay J, Matthey-Doret C, Bignaud A, Baudry L, Koszul R, Orchestrating chromosome conformation capture analysis with Bioconductor., Nat Commun 2024 Feb; 15(1): 1072.
• 2024
  Egill Richard, Baptiste Darracq, Eloi Littner, Claire Vit, Clémence Whiteway, Julia Bos, Florian Fournes, Geneviève Garriss, Valentin Conte, Delphine Lapaillerie, Vincent Parissi, François Rousset, Ole Skovgaard, David Bikard, Eduardo P. C. Rocha, Didier Mazel, Céline Loot, Cassette recombination dynamics within chromosomal integrons are regulated by toxin-antitoxin systems., Science Advances , 2024, 10 (2), pp.eadj3498. ⟨10.1126/sciadv.adj3498⟩.
• 2024
  Bignaud A, Cockram C, Borde C, Groseille J, Allemand E, Thierry A, Marbouty M, Mozziconacci J, Espéli O, Koszul R, Transcription-induced domains form the elementary constraining building blocks of bacterial chromosomes., Nat Struct Mol Biol 2024 Jan; (): .
• 2024
  Loot C, Millot GA, Richard E, Littner E, Vit C, Lemoine F, Néron B, Cury J, Darracq B, Niault T, Lapaillerie D, Parissi V, Rocha EPC, Mazel D, Integron cassettes integrate into bacterial genomes via widespread non-classical attG sites., Nat Microbiol 2024 Jan; 9(1): 228-240.
• 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): .
• 2023
  Amandine Nucci, Eduardo P C Rocha, Olaya Rendueles, Latent evolution of biofilm formation depends on life-history and genetic background, npj Biofilms and Microbiomes, 2023, 9 (1), pp.53. ⟨10.1038/s41522-023-00422-3⟩.
• 2023
  Gedeon A, Ayoub N, Brûlé S, Raynal B, Karimova G, Gelin M, Mechaly A, Haouz A, Labesse G, Munier-Lehmann H, Insight into the role of the Bateman domain at the molecular and physiological levels through engineered IMPDHs., Protein Sci 2023 Jun; (): e4703.
• 2023
  Lamy-Besnier Q, Bignaud A, Garneau JR, Titecat M, Conti DE, Von Strempel A, Monot M, Stecher B, Koszul R, Debarbieux L, Marbouty M, Chromosome folding and prophage activation reveal specific genomic architecture for intestinal bacteria., Microbiome 2023 May; 11(1): 111.
• 2023
  Rendueles O, de Sousa JAM, Rocha EPC, Competition between lysogenic and sensitive bacteria is determined by the fitness costs of the different emerging phage-resistance strategies., Elife 2023 Mar; 12(): .
• 2023
  de Sousa JAM, Fillol-Salom A, Penadés JR, Rocha EPC, Identification and characterization of thousands of bacteriophage satellites across bacteria., Nucleic Acids Res 2023 Mar; (): .
• 2023
  Larotonda L, Mornico D, Khanna V, Bernal-Bayard J, Ghigo JM, Val ME, Comerci D, Mazel D, Soler-Bistué A, Chromosomal Position of Ribosomal Protein Genes Affects Long-Term Evolution of Vibrio cholerae., mBio 2023 Apr; 14(2): e0343222.
• 2023
  López-Igual R, Dorado-Morales P, Mazel D, , Increasing the Scalability of Toxin-Intein Orthogonal Combinations., ACS Synth Biol 2023 Jan; (): .
• 2022
  Vertti-Quintero N, Levien E, Poggi L, Amir A, Richard GF, Baroud CN, , Time-resolved microfluidics unravels individual cellular fates during double-strand break repair., BMC Biol 2022 Dec; 20(1): 269.
• 2022
  Ares-Arroyo M, Coluzzi C, P C Rocha E, , Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation., Nucleic Acids Res 2022 Nov; (): .
• 2021
  Poggi L, Emmenegger L, Descorps-Declère S, Dumas B, Richard GF, , Differential efficacies of Cas nucleases on microsatellites involved in human disorders and associated off-target mutations., Nucleic Acids Res 2021 08; 49(14): 8120-8134.