Rocha Eduardo

139

Documents

Publications

	Assembly of a unique membrane complex in type VI secretion systems of Bacteroidota Thibault Bongiovanni , Casey Latario , Youn Le Cras , Evan Trus , Sophie Robitaille Nature Communications, 2024, 15 (1), pp.429. ⟨10.1038/s41467-023-44426-1⟩ Journal articles hal-04390477v1
	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 Camille D’humières , Margot Delavy , Laurie Alla , Farid Ichou , Emilie Gauliard Microbiome, 2024, 12 (1), pp.50. ⟨10.1186/s40168-023-01746-0⟩ Journal articles hal-04582235v1
	Phage-inducible chromosomal minimalist islands (PICMIs), a novel family of small marine satellites of virulent phages Rubén Barcia-Cruz , David Goudenège , Jorge Moura de Sousa , Damien Piel , Martial Marbouty Nature Communications, 2024, 15 (1), pp.664. ⟨10.1038/s41467-024-44965-1⟩ Journal articles hal-04413133v1
	Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency Matthieu Haudiquet , Julie Le Bris , Amandine Nucci , Rémy A Bonnin , Pilar Domingo-Calap Nature Communications, 2024, 15 (1), pp.2032. ⟨10.1038/s41467-024-46147-5⟩ Journal articles hal-04492345v1
	Belt and braces: Two escape ways to maintain the cassette reservoir of large chromosomal integrons Egill Richard , Baptiste Darracq , Eloi Littner , Gael Millot , Valentin Conte PLoS Genetics, 2024, 20 (4), pp.e1011231. ⟨10.1371/journal.pgen.1011231⟩ Journal articles pasteur-04305445v1
	Cassette recombination dynamics within chromosomal integrons are regulated by toxin-antitoxin systems Egill Richard , Baptiste Darracq , Eloi Littner , Claire Vit , Clémence Whiteway Science Advances , 2024, 10 (2), pp.eadj3498. ⟨10.1126/sciadv.adj3498⟩ Journal articles hal-04397951v1
	Integron cassettes commonly integrate into bacterial genomes via widespread non-classical attG sites Céline Loot , Gael A Millot , Egill Richard , Eloi Littner , Claire Vit Nature Microbiology, 2024, 9 (1), pp.228-240. ⟨10.1038/s41564-023-01548-y⟩ Journal articles pasteur-04384854v1
	A widespread family of phage-inducible chromosomal islands only steals bacteriophage tails to spread in nature Nasser Alqurainy , Laura Miguel-Romero , Jorge Moura de Sousa , John Chen , Eduardo P.C. Rocha Cell Host & Microbe, 2023, 31 (1), pp.69-82.e5. ⟨10.1016/j.chom.2022.12.001⟩ Journal articles pasteur-03952543v2
	Latent evolution of biofilm formation depends on life-history and genetic background Amandine Nucci , Eduardo P C Rocha , Olaya Rendueles npj Biofilms and Microbiomes, 2023, 9 (1), pp.53. ⟨10.1038/s41522-023-00422-3⟩ Journal articles pasteur-04177373v1
	Identification and characterization of thousands of bacteriophage satellites across bacteria Jorge A Moura de Sousa , Alfred Fillol-Salom , José Penadés , Eduardo P.C. Rocha Nucleic Acids Research, 2023, 51 (6), pp.2759-2777. ⟨10.1093/nar/gkad123⟩ Journal articles hal-03838678v2
	MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes Bertrand Néron , Rémi Denise , Charles Coluzzi , Marie Touchon , Eduardo P.C. Rocha Peer Community Journal, 2023, 3, pp.e28. ⟨10.24072/pcjournal.250⟩ Journal articles pasteur-04060331v2
	Restriction-modification systems have shaped the evolution and distribution of plasmids across bacteria Liam Shaw , Eduardo Rocha , R Craig Maclean Nucleic Acids Research, 2023, 51 (13), pp.6806-6818. ⟨10.1093/nar/gkad452⟩ Journal articles pasteur-04236062v1
	The Capsule Increases Susceptibility to Last-Resort Polymyxins, but Not to Other Antibiotics, in Klebsiella pneumoniae Francesca D’angelo , Eduardo Rocha , Olaya Rendueles Antimicrobial Agents and Chemotherapy, In press, pp.Ahead of Print. ⟨10.1128/aac.00127-23⟩ Journal articles pasteur-04027513v1
	Competition between lysogenic and sensitive bacteria is determined by the fitness costs of the different emerging phage-resistance strategies Olaya Rendueles , Jorge Am Moura de Sousa , Eduardo Pc Rocha eLife, 2023, 12, pp.e83479. ⟨10.7554/eLife.83479⟩ Journal articles pasteur-04057813v1
	Chance Favors the Prepared Genomes: Horizontal Transfer Shapes the Emergence of Antibiotic Resistance Mutations in Core Genes Charles Coluzzi , Martin Guillemet , Fanny Mazzamurro , Marie Touchon , Maxime Godfroid Molecular Biology and Evolution, 2023, 40 (10), pp.msad217. ⟨10.1093/molbev/msad217⟩ Journal articles hal-04281854v1
	Emergence of novel non-aggregative variants under negative frequency-dependent selection in Klebsiella variicola Amandine Nucci , Juliette Janaszkiewicz , Eduardo P C Rocha , Olaya Rendueles microLife, inPress, 4, ⟨10.1093/femsml/uqad038⟩ Journal articles pasteur-04225506v1
	Phages and their satellites encode hotspots of antiviral systems François Rousset , Florence Depardieu , Solange Miele , Julien Dowding , Anne-Laure Laval Cell Host & Microbe, 2022, 30 (5), pp.740 - 753.e5. ⟨10.1016/j.chom.2022.02.018⟩ Journal articles pasteur-04075930v1
	Structural and Genomic Evolution of RRNPPA Systems and Their Pheromone Signaling Alonso Felipe-Ruiz , Alberto Marina , Eduardo P C Rocha mBio, 2022, 13 (6), pp.e0251422. ⟨10.1128/mbio.02514-22⟩ Journal articles pasteur-03952614v1
	Adaptation to novel spatially-structured environments is driven by the capsule and alters virulence-associated traits Amandine Nucci , Eduardo Rocha , Olaya Rendueles Nature Communications, 2022, 13 (1), pp.4751. ⟨10.1038/s41467-022-32504-9⟩ Journal articles pasteur-03794548v1
	IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella Bertrand Néron , Eloi Littner , Matthieu Haudiquet , Amandine Perrin , Jean Cury Microorganisms, 2022, 10 (4), pp.700. ⟨10.3390/microorganisms10040700⟩ Journal articles hal-03655020v1
	NAR Breakthrough Article Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation Manuel Ares-Arroyo , Charles Coluzzi , Eduardo P.C. Rocha Nucleic Acids Research, 2022, 51 (7), pp.3001-3016. ⟨10.1093/nar/gkac1079⟩ Journal articles pasteur-04075979v1
	Evolution of Plasmid Mobility: Origin and Fate of Conjugative and Nonconjugative Plasmids Charles Coluzzi , Maria Pilar Garcillán-Barcia , Fernando de la Cruz , Eduardo P.C. Rocha Molecular Biology and Evolution, 2022, 39 (6), pp.msac115. ⟨10.1093/molbev/msac115⟩ Journal articles pasteur-03818036v1
	Phage-Plasmids Spread Antibiotic Resistance Genes through Infection and Lysogenic Conversion Eugen Pfeifer , Rémy A. Bonnin , Eduardo Rocha mBio, 2022, Ahead of print. ⟨10.1128/mbio.01851-22⟩ Journal articles pasteur-03818031v1
	Selfish, promiscuous, and sometimes useful: how mobile genetic elements drive horizontal gene transfer in microbial populations Matthieu Haudiquet , Jorge A Moura de Sousa , Marie Touchon , Eduardo P. C. Rocha Philosophical Transactions of the Royal Society of London. B (1887–1895), 2022, 377 (1861), pp.20210234. ⟨10.1098/rstb.2021.0234⟩ Journal articles pasteur-03684761v2
	Microbial defenses against mobile genetic elements and viruses: Who defends whom from what? Eduardo P. C. Rocha , David Bikard PLoS Biology, 2022, 20 (1), pp.e3001514. ⟨10.1371/journal.pbio.3001514⟩ Journal articles pasteur-03690954v1
	To catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites Jorge A Moura de Sousa , Eduardo P. C. Rocha Philosophical Transactions of the Royal Society B: Biological Sciences, 2022, 377 (1842), pp.20200475. ⟨10.1098/rstb.2020.0475⟩ Journal articles pasteur-03684736v1
	Phage-host coevolution in natural populations Damien Piel , Maxime Bruto , Yannick Labreuche , François Blanquart , David Goudenège Nature Microbiology, 2022, 7 (7), pp.1075-1086. ⟨10.1038/s41564-022-01157-1⟩ Journal articles hal-03738913v2
	PanACoTA: a modular tool for massive microbial comparative genomics Amandine Perrin , Eduardo P. C. Rocha NAR Genomics and Bioinformatics, 2021, 3 (1), pp.lqaa106. ⟨10.1093/nargab/lqaa106⟩ Journal articles hal-03357352v1
	Bacteria have numerous distinctive groups of phage-plasmids with conserved phage and variable plasmid gene repertoires Eugen Pfeifer , Jorge A Moura de Sousa , Marie Touchon , Eduardo P. C. Rocha Nucleic Acids Research, 2021, 49 (5), pp.2655-2673. ⟨10.1093/nar/gkab064⟩ Journal articles hal-03357369v1
	Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of the nosocomial pathogen Klebsiella pneumoniae Matthieu Haudiquet , Amandine Buffet , Olaya Rendueles , Eduardo P. C. Rocha PLoS Biology, 2021, 19 (7), pp.e3001276. ⟨10.1371/journal.pbio.3001276⟩ Journal articles hal-03281367v1
	The impact of genetic diversity on gene essentiality within the E. coli species François Rousset , José Cabezas Caballero , Florence Piastra-Facon , Jesús Fernández-Rodríguez , Olivier Clermont Nature Microbiology, 2021, 6 (3), pp.301-312. ⟨10.1038/s41564-020-00839-y⟩ Journal articles pasteur-03264663v1
	Causes and Consequences of Bacteriophage Diversification via Genetic Exchanges across Lifestyles and Bacterial Taxa Jorge A Moura de Sousa , Eugen Pfeifer , Marie Touchon , Eduardo P. C. Rocha Molecular Biology and Evolution, 2021, 38 (6), pp.2497-2512. ⟨10.1093/molbev/msab044⟩ Journal articles hal-03357362v1
	Human commensal gut Proteobacteria withstand type VI secretion attacks through immunity protein-independent mechanisms Nicolas Flaugnatti , Sandrine Isaac , Leonardo Lemos Rocha , Sandrine Stutzmann , Olaya Rendueles Nature Communications, 2021, 12 (1), 13 p. ⟨10.1038/s41467-021-26041-0⟩ Journal articles pasteur-03364094v1
	Nutrient conditions are primary drivers of bacterial capsule maintenance in Klebsiella Amandine Buffet , Eduardo P C Rocha , Olaya Rendueles Proceedings of the Royal Society B: Biological Sciences, 2021, 288 (1946), pp.20202876. ⟨10.1098/rspb.2020.2876⟩ Journal articles pasteur-03158282v1
	Evolution of ColE1-like plasmids across γ-Proteobacteria: From bacteriocin production to antimicrobial resistance Manuel Ares-Arroyo , Eduardo Rocha , Bruno Gonzalez-Zorn PLoS Genetics, 2021, 17 (11), pp.e1009919. ⟨10.1371/journal.pgen.1009919⟩ Journal articles pasteur-03818042v1
	Unlinked rRNA genes are widespread among Bacteria and Archaea Tess E Brewer , Mads Albertsen , Arwyn Edwards , Rasmus H Kirkegaard , Eduardo P C Rocha The International Society of Microbiologial Ecology Journal, 2020, ⟨10.1038/s41396-019-0552-3⟩ Journal articles hal-02363135v1
	Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids M. Pilar Garcillán-Barcia , Santiago Redondo-Salvo , Raúl Fernández-López , Raúl Ruiz , Luis Vielva Nature Communications, 2020, 11 (1), pp.3602. ⟨10.1038/s41467-020-17278-2⟩ Journal articles pasteur-03015777v1
	Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements Aude Bernheim , David Bikard , Marie Touchon , Eduardo Rocha Nucleic Acids Research, 2020, 48, pp.748 - 760. ⟨10.1093/nar/gkz1091⟩ Journal articles pasteur-02626502v1
	A synthesis of bacterial and archaeal phenotypic trait data Joshua S. Madin , Daniel A. Nielsen , Maria Brbic , Ross Corkrey , David Danko Scientific Data , 2020, 7 (1), pp.170. ⟨10.1038/s41597-020-0497-4⟩ Journal articles pasteur-03015782v1
	The major subunit of widespread competence pili exhibits a novel and conserved type IV pilin fold D. Sheppard , J.L. Berry , R. Denise , Eduardo P C Rocha , S. Matthews Journal of Biological Chemistry, 2020, 295 (19), pp.6594-6604. ⟨10.1074/jbc.RA120.013316⟩ Journal articles pasteur-03015795v1
	Intracellular Positioning Systems Limit the Entropic Eviction of Secondary Replicons Toward the Nucleoid Edges in Bacterial Cells Julie Dauverd -Girault , Charlène Planchenault , Marine Pons , Caroline Schiavon , Patricia Siguier Journal of Molecular Biology, 2020, 432 (3), pp.745-761. ⟨10.1016/j.jmb.2019.11.027⟩ Journal articles hal-02392007v1
	Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation Jorge A. M. de Sousa , Amandine Buffet , Matthieu Haudiquet , Eduardo P. C. Rocha , Olaya Rendueles The International Society of Microbiologial Ecology Journal, 2020, 14 (12), pp.2980-2996. ⟨10.1038/s41396-020-0726-z⟩ Journal articles pasteur-02991081v1
	Macromolecular crowding links ribosomal protein gene dosage to growth rate in Vibrio cholerae Alfonso Soler-Bistué , Sebastián Aguilar-Pierlé , Marc Garcia-Garcerà , Marie-Eve Val , Odile Sismeiro BMC Biology, 2020, 18 (1), pp.43. ⟨10.1186/s12915-020-00777-5⟩ Journal articles pasteur-02562489v1
	Un siècle de recherche sur les bactériophages Mireille Ansaldi , Pascale Boulanger , Charlotte Brives , Laurent Debarbieux , Nicolas Dufour Virologie, 2020, 24 (1), pp.9-22. ⟨10.1684/vir.2020.0809⟩ Journal articles hal-02530997v1
	PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph Guillaume Gautreau , Adelme Bazin , Mathieu Gachet , Rémi Planel , Laura Burlot PLoS Computational Biology, 2020, ⟨10.1371/journal.pcbi.1007732⟩ Journal articles hal-03089210v1
	The evolution of protein secretion systems by co-option and tinkering of cellular machineries Rémi Denise , Sophie S. Abby , Eduardo Rocha Trends in Microbiology, 2020, 28 (5), pp.372-386. ⟨10.1016/j.tim.2020.01.005⟩ Journal articles pasteur-02626815v1
	Community diversity and habitat structure shape the repertoire of extracellular proteins in bacteria Marc Garcia-Garcerà , Eduardo Rocha Nature Communications, 2020, 11 (1), ⟨10.1038/s41467-020-14572-x⟩ Journal articles pasteur-02626487v1
	Phylogenetic background and habitat drive the genetic diversification of Escherichia coli Marie Touchon , Amandine Perrin , Jorge A Moura de Sousa , Belinda Vangchhia , Samantha Burn PLoS Genetics, 2020, 16 (6), pp.e1008866. ⟨10.1371/journal.pgen.1008866⟩ Journal articles pasteur-02866790v2
	Les applications antibactériennes des bactériophages Mireille Ansaldi , Pascale Boulanger , Charlotte Brives , Claire Le Hénaff , Laurent Debarbieux Virologie, 2020, 24 (1), pp.23-36. ⟨10.1684/vir.2019.0805⟩ Journal articles hal-02530998v1
	Experimental Evolution as a Tool to Investigate Natural Processes and Molecular Functions Philippe Remigi , Catherine Masson-Boivin , Eduardo P C Rocha Trends in Microbiology, 2019, 27 (7), pp.623-634. ⟨10.1016/j.tim.2019.02.003⟩ Journal articles hal-02329724v1
	Bacteriophages benefit from generalized transduction Alfred Fillol-Salom , Ahlam Alsaadi , Jorge A Moura de Sousa , Li Zhong , Kevin R Foster PLoS Pathogens, 2019, 15 (7), pp.e1007888. ⟨10.1371/journal.ppat.1007888⟩ Journal articles pasteur-04076056v1
	Real-time search of all bacterial and viral genomic data Phelim Bradley , Henk C den Bakker , Eduardo P C Rocha , Gil Mcvean , Zamin Iqbal Nature Biotechnology, 2019, 37 (2), pp.152-159. ⟨10.1038/s41587-018-0010-1⟩ Journal articles hal-02329753v1
	Bacteriophages benefit from generalized transduction Alfred Fillol-Salom , Alsaadiid Ahlam , Jorge Moura de Sousa , Li Zhong , Kevin R Fosterid PLoS Pathogens, 2019, ⟨10.1371/journal.ppat.1007888⟩ Journal articles hal-02329705v1
	A matter of background: DNA repair pathways as a possible cause for the sparse distribution of CRISPR-Cas systems in bacteria Aude Bernheim , David Bikard , Marie Touchon , Eduardo P C Rocha Philosophical Transactions of the Royal Society B: Biological Sciences, 2019, 374 (1772), pp.20180088. ⟨10.1098/rstb.2018.0088⟩ Journal articles hal-02329742v1
	Environmental structure drives resistance to phages and antibiotics during phage therapy and to invading lysogens during colonisation Jorge A Moura de Sousa , Eduardo P C Rocha Scientific Reports, 2019, 9 (1), pp.3149. ⟨10.1038/s41598-019-39773-3⟩ Journal articles pasteur-02098383v1
	Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility Rémi Denise , Sophie S. Abby , Eduardo P. C. Rocha PLoS Biology, 2019, 17 (7), pp.e3000390. ⟨10.1371/journal.pbio.3000390⟩ Journal articles pasteur-02263349v1
	A simple, reproducible and cost- effective procedure to analyse gut phageome: from phage isolation to bioinformatic approach Camille d'Humières , Marie Touchon , Sara Dion , Jean Cury , Amine Ghozlane Scientific Reports, 2019, ⟨10.1038/s41598-019-47656-w⟩ Journal articles hal-02329655v1
	HflXr mediates a novel antibiotic resistance mechanism 1 2 Mélodie Duval , Daniel Dar , Filipe Carvalho , Eduardo P C Rocha , Rotem Sorek Proceedings of the National Academy of Sciences of the United States of America, 2018, 115 (52), pp.13359-13364. ⟨10.1073/pnas.1810555115⟩ Journal articles hal-02329775v1
	Genetic exchanges are more frequent in bacteria encoding capsules Olaya Rendueles , Jorge a Moura de Sousa , Aude Bernheim , Marie Touchon , Eduardo P C Rocha PLoS Genetics, 2018, 14 (12), pp.e1007862. ⟨10.1371/journal.pgen.1007862⟩ Journal articles pasteur-02012595v1
	Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder. Sophie S. Abby , Eduardo P C Rocha Methods in Molecular Biology, 2018, Bacterial protein secretion systems, 1615, pp.1-21. ⟨10.1007/978-1-4939-7033-9_1⟩ Journal articles hal-01677379v1
	Bacillus subtilis, the model Gram-positive bacterium: 20years of annotation refinement Rainer Borriss , Antoine Danchin , Colin R. Harwood , Claudine Médigue , Eduardo P. C. Rocha Microbial Biotechnology, 2018, 11 (1), pp.3-17. ⟨10.1111/1751-7915.13043⟩ Journal articles cea-02291345v1
	Neutral Theory, Microbial Practice: Challenges in Bacterial Population Genetics Eduardo P C Rocha Molecular Biology and Evolution, 2018, 35 (6), pp.1338-1347. ⟨10.1093/molbev/msy078⟩ Journal articles hal-02329762v1
	CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins David Couvin , Aude Bernheim , Claire Toffano-Nioche , Marie Touchon , Juraj Michalik Nucleic Acids Research, 2018, 46 (W1), pp.W246-W251. ⟨10.1093/nar/gky425⟩ Journal articles pasteur-02098389v1
	Parallels between experimental and natural evolution of legume symbionts Camille Clerissi , Marie Touchon , Delphine Capela , Mingxing Tang , Stéphane Cruveiller Nature Communications, 2018, 9 (1), pp.2264. ⟨10.1038/s41467-018-04778-5⟩ Journal articles cea-01880286v1
	Host Range and Genetic Plasticity Explain the Coexistence of Integrative and Extrachromosomal Mobile Genetic Elements Jean Cury , Pedro De Oliveira , Fernando de La Cruz , Eduardo P C Rocha Molecular Biology and Evolution, 2018, 35 (9), pp.2230-2239. ⟨10.1093/molbev/msy123⟩ Journal articles pasteur-02098387v1
	Author Correction : Parallels between experimental and natural evolution of legume symbionts (vol 9, 2264, 2018) Camille Clerissi , Marie Touchon , Delphine Capela , Mingxing Tang , Stéphane Cruveiller Nature Communications, 2018, 9, ⟨10.1038/s41467-018-07205-x⟩ Journal articles hal-02617830v1
	The chromosomal organization of horizontal gene transfer in bacteria Pedro H. Oliveira , Marie Touchon , Jean Cury , Eduardo P C Rocha Nature Communications, 2017, 8 (1), pp.841. ⟨10.1038/s41467-017-00808-w⟩ Journal articles hal-04325283v1
	Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens Olaya Rendueles , Marc Garcia-Garcerà , Bertrand Néron , Marie Touchon , Eduardo P C Rocha PLoS Pathogens, 2017, 44, pp.289 - 289. ⟨10.1371/journal.ppat.1006525.s020⟩ Journal articles pasteur-01578349v1
	Recruitment of a Lineage-Specific Virulence Regulatory Pathway Promotes Intracellular Infection by a Plant Pathogen Experimentally Evolved into a Legume Symbiont Delphine Capela , Marta Marchetti , Camille Clerissi , Anthony Perrier , Dorian Guetta Molecular Biology and Evolution, 2017, 34 (10), pp.2503-2521. ⟨10.1093/molbev/msx165⟩ Journal articles hal-02620519v1
	Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria Aude Bernheim , Alicia Calvo-Villamañán , Clovis Basier , Lun Cui , Eduardo P C Rocha Nature Communications, 2017, 8, pp.2094. ⟨10.1038/s41467-017-02350-1⟩ Journal articles pasteur-01967501v1
	Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance Céline Loot , Aleksandra Nivina , Jean Cury , José Antonio Escudero , Magaly Ducos-Galand mBio, 2017, 8 (2), pp.e02296-16. ⟨10.1128/mBio.02296-16⟩ Journal articles pasteur-01689524v1
	Experimental evolution of rhizobia may lead to either extra- or intracellular symbiotic adaptation depending on the selection regime Marta Marchetti , Camille Clerissi , Yasmine Yousfi , Carine Gris , Olivier Bouchez Molecular Ecology, 2017, 26 (7), pp.1818-1831. ⟨10.1111/mec.13895⟩ Journal articles hal-01607703v1
	Integrative and conjugative elements and their hosts: composition, distribution and organization Jean Cury , Marie Touchon , Eduardo P. C. Rocha Nucleic Acids Research, 2017, 45 (15), pp.8943 - 8956. ⟨10.1093/nar/gkx607⟩ Journal articles pasteur-04076019v1
	Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain Amandine Perrin , Elise Larsonneur , Ainsley Nicholson , David Edwards , Kristin Gundlach Nature Communications, 2017, 8 (1), pp.15483. ⟨10.1038/ncomms15483⟩ Journal articles hal-02613118v1
	Metabolic diversity of the emerging pathogenic lineages ofKlebsiella pneumoniae Camille Blin , Virginie Passet , Marie Touchon , Eduardo P. C. Rocha , Sylvain Brisse Environmental Microbiology, 2017, 19 (5), pp.1881 - 1898. ⟨10.1111/1462-2920.13689⟩ Journal articles pasteur-04076001v1
	Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer Marie Touchon , Jorge A Moura de Sousa , Eduardo P. C. Rocha Current Opinion in Microbiology, 2017, 38, pp.66-73. ⟨10.1016/j.mib.2017.04.010⟩ Journal articles pasteur-03111100v1
	Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis Sebastien Breurec , Alexis Criscuolo , Laure Diancourt , Olaya Rendueles , Mathias Vandenbogaert Scientific Reports, 2016, 6, pp.30379. ⟨10.1038/srep30379⟩ Journal articles hal-02613124v1
	Identification and analysis of integrons and cassette arrays in bacterial genomes Jean Cury , Thomas Jové , Marie Touchon , Bertrand Néron , Eduardo Pc Rocha Nucleic Acids Research, 2016, 44 (10), pp.4539 - 4550. ⟨10.1093/nar/gkw319⟩ Journal articles pasteur-01374968v1
	Identification of protein secretion systems in bacterial genomes Sophie S. Abby , Jean Cury , Julien Guglielmini , Bertrand Néron , Marie Touchon Scientific Reports, 2016, 6, ⟨10.1038/srep23080⟩ Journal articles pasteur-01374967v1
	Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes Alexandra Moura , Alexis Criscuolo , Hannes Pouseele , Mylène M. Maury , Alexandre Leclercq Nature Microbiology, 2016, 2, pp.16185. ⟨10.1038/nmicrobiol.2016.185⟩ Journal articles pasteur-01415883v1
	Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity Mylène M Maury , Yu-Huan Tsai , Caroline Charlier , Marie Touchon , Viviane Chenal-Francisque Nature Genetics, 2016, 48 (3), pp.308-313. ⟨10.1038/ng.3501⟩ Journal articles pasteur-02170775v1
	A widespread family of polymorphic toxins encoded by temperate phages Anne Jamet , Marie Touchon , Bruno Goncalves , João André Carriço , Alain Charbit BMC Biology, 2016, 15 (1), pp.75. ⟨10.1186/s12915-017-0415-1⟩ Journal articles inserm-01580852v1
	The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography Marguerite Lapierre , Camille Blin , Amaury Lambert , Guillaume Achaz , Eduardo P C Rocha Molecular Biology and Evolution, 2016, 33, pp.1711 - 1725. ⟨10.1093/molbev/msw048⟩ Journal articles pasteur-01374966v1
	Regulation of genetic flux between bacteria by restriction–modification systems Pedro H. Oliveira , Marie Touchon , Eduardo P. C. Rocha Proceedings of the National Academy of Sciences of the United States of America, 2016, 113 (20), pp.5658 - 5663. ⟨10.1073/pnas.1603257113⟩ Journal articles pasteur-01374969v1
	Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations Hong Xue , Otto X. Cordero , Francisco M. Camas , William Trimble , Folker Meyer mBio, 2015, 6 (3), ⟨10.1128/mBio.00552-15⟩ Journal articles pasteur-01374963v1
	Insights on the emergence of Mycobacterium tuberculosis from the analysis of Mycobacterium kansasii. Joyce Wang , Fiona Mcintosh , Nicolas Radomski , Ken Dewar , Roxane Simeone Genome Biology and Evolution, 2015, 7 (3), pp.856-70. ⟨10.1093/gbe/evv035⟩ Journal articles pasteur-01352692v1
	Common Cell Shape Evolution of Two Nasopharyngeal Pathogens. Frédéric J Veyrier , Nicolas Biais , Pablo Morales , Nouria Belkacem , Cyril Guilhen PLoS Genetics, 2015, 11 (7), pp.e1005338. ⟨10.1371/journal.pgen.1005338⟩ Journal articles pasteur-01352679v1
	Transient Hypermutagenesis Accelerates the Evolution of Legume Endosymbionts following Horizontal Gene Transfer Philippe Remigi , Delphine Capela , Camille Clerissi , Léna Tasse , Rachel Torchet PLoS Biology, 2014, 12 (9), ⟨10.1371/journal.pbio.1001942⟩ Journal articles pasteur-01374959v1
	TLR9 Activation Is Triggered by the Excess of Stimulatory versus Inhibitory Motifs Present in Trypanosomatidae DNA Melissa Erin Khan , Chloé Borde , Eduardo P C Rocha , Véronique Mériaux , Vincent Maréchal PLoS Neglected Tropical Diseases, 2014, 8 (11), pp.e3308. ⟨10.1371/journal.pntd.0003308⟩ Journal articles hal-01342968v1
	The chromosomal accommodation and domestication of mobile genetic elements Marie Touchon , Louis-Marie Bobay , Eduardo P C Rocha Current Opinion in Microbiology, 2014, 22, pp.22-29. ⟨10.1016/j.mib.2014.09.010⟩ Journal articles pasteur-01122287v1
	A PNPase dependent CRISPR System in Listeria. Nina Sesto , Marie Touchon , José Marques Andrade , Jiro Kondo , Eduardo P C Rocha PLoS Genetics, 2014, 10 (1), pp.e1004065. ⟨10.1371/journal.pgen.1004065⟩ Journal articles pasteur-01145428v1
	The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences. Marie Touchon , Jean Cury , Eun-Jeong Yoon , Lenka Krizova , Gustavo C Cerqueira Genome Biology and Evolution, 2014, 6 (10), pp.2866-82. ⟨10.1093/gbe/evu225⟩ Journal articles pasteur-01132634v1
	Manipulating or Superseding Host Recombination Functions: A Dilemma That Shapes Phage Evolvability Marie Bobay , Marie Touchon , Eduardo P. C. Rocha PLoS Genetics, 2013, 9 (9), pp.e1003825. ⟨10.1371/journal.pgen.1003825.s010⟩ Journal articles pasteur-01374955v1
	MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems. Sophie S Abby , Bertrand Néron , Hervé Ménager , Marie Touchon , Eduardo P C Rocha PLoS ONE, 2013, 9 (10), pp.e110726. ⟨10.1371/journal.pone.0110726⟩ Journal articles pasteur-01080418v1
	Evolution of Conjugation and Type IV Secretion Systems Julien Guglielmini , Fernando de La Cruz , Eduardo P C Rocha Molecular Biology and Evolution, 2013, 30, pp.315 - 331. ⟨10.1093/molbev/mss221⟩ Journal articles pasteur-01374951v1
	The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems Sophie S. Abby , Eduardo P. C. Rocha PLoS Genetics, 2012, 8 (9), pp.e1002983. ⟨10.1371/journal.pgen.1002983.s017⟩ Journal articles pasteur-01374947v1
	The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation. Julien Guglielmini , Leonor Quintais , Maria Pilar Garcillán-Barcia , Fernando de La Cruz , Eduardo P C Rocha PLoS Genetics, 2011, 7 (8), pp.e1002222. ⟨10.1371/journal.pgen.1002222⟩ Journal articles pasteur-00647077v1
	Investment in rapid growth shapes the evolutionary rates of essential proteins. Sara Vieira-Silva , Marie Touchon , Sophie S Abby , Eduardo P C Rocha Proceedings of the National Academy of Sciences of the United States of America, 2011, 108 (50), pp.20030-5. ⟨10.1073/pnas.1110972108⟩ Journal articles pasteur-00655553v1
	Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. Todd J Treangen , Eduardo P C Rocha PLoS Genetics, 2011, 7 (1), pp.e1001284. ⟨10.1371/journal.pgen.1001284⟩ Journal articles pasteur-00578535v1
	The Small, Slow and Specialized CRISPR and Anti-CRISPR of Escherichia and Salmonella Marie Touchon , Eduardo P. C. Rocha PLoS ONE, 2010, 5 (6), pp.11126 - 11126. ⟨10.1371/journal.pone.0011126.s006⟩ Journal articles pasteur-01374940v1
	The systemic imprint of growth and its uses in ecological (meta)genomics. Sara Vieira-Silva , Eduardo P C Rocha PLoS Genetics, 2010, 6, pp.e1000808. ⟨10.1371/journal.pgen.1000808⟩ Journal articles pasteur-00488678v1
	Mutational patterns cannot explain genome composition: Are there any neutral sites in the genomes of bacteria? Eduardo P C Rocha , Edward J Feil PLoS Genetics, 2010, 6 (9), pp.e1001104. ⟨10.1371/journal.pgen.1001104⟩ Journal articles pasteur-00578536v1
	Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. Marie Touchon , Claire Hoede , Olivier Tenaillon , Valérie Barbe , Simon Baeriswyl PLoS Genetics, 2009, 5 (1), pp.e1000344. ⟨10.1371/journal.pgen.1000344⟩ Journal articles hal-00390293v1
	A Module Located at a Chromosomal Integration Hot Spot Is Responsible for the Multidrug Resistance of a Reference Strain from Escherichia coli Clonal Group A Mathilde Lescat , Alexandra Calteau , Claire Hoede , Valérie Barbe , Marie Touchon Antimicrobial Agents and Chemotherapy, 2009, 53 (6), pp.2283-2288. ⟨10.1128/AAC.00123-09⟩ Journal articles hal-03612468v1
	Genesis, effects and fates of repeats in prokaryotic genomes Todd J. Treangen , Anne-Laure Abraham , Marie Touchon , Eduardo P.C Rocha FEMS Microbiology Reviews, 2009, 33 (3), pp.539-571. ⟨10.1111/j.1574-6976.2009.00169.x⟩ Journal articles hal-02319386v1
	Alternative to homo-oligomerisation: the creation of local symmetry in proteins by internal amplification Anne-Laure Abraham , Joël Pothier , Eduardo P.C Rocha Journal of Molecular Biology, 2009, 394 (3), pp.522-534. ⟨10.1016/j.jmb.2009.09.031⟩ Journal articles hal-02319387v1
	The impact of the neisserial DNA uptake sequences on genome evolution and stability Todd J. Treangen , Ole Herman Ambur , Tone Tonjum , Eduardo P. C. Rocha Genome Biology, 2008, 9 (3), pp.R60. ⟨10.1186/gb-2008-9-3-r60⟩ Journal articles pasteur-00336122v1
	An assessment of the impacts of molecular oxygen on the evolution of proteomes. Sara Vieira-Silva , Eduardo P. C. Rocha Molecular Biology and Evolution, 2008, 25 (9), pp.1931-42. ⟨10.1093/molbev/msn142⟩ Journal articles pasteur-00336121v1
	Swelfe: a detector of internal repeats in sequences and structures. Anne-Laure Abraham , Eduardo P C Rocha , Joël Pothier Bioinformatics, 2008, 24 (13), pp.1536-7. ⟨10.1093/bioinformatics/btn234⟩ Journal articles pasteur-00336123v1
	Comparative and evolutionary analysis of the bacterial homologous recombination systems Eduardo Rocha , Emmanuel Cornet , Bénédicte Michel PLoS Genetics, 2005, 1 (2), pp.e15. ⟨10.1371/journal.pgen.0010015⟩ Journal articles hal-02683075v1
	Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution Eduardo P. C. Rocha , Alain A. Blanchard Nucleic Acids Research, 2002, 30 (9), pp.2031-2042 Journal articles hal-02676514v1
	The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis Isabelle Chambaud , Roland Heilig , Stephane Ferris , Valérie Barbe , Delphine Samson Nucleic Acids Research, 2001, 29 (10), pp.2145-2153. ⟨10.1093/nar/29.10.2145⟩ Journal articles hal-02679458v1

	PPanGGOLiN: Depicting microbial diversity via a Partitioned Pangenome Graph Guillaume Gautreau , Christophe Ambroise , Catherine Matias , Amandine Perrin , Rémi Planel JOBIM 2018 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France Conference papers hal-04355945v1
	PPanGGOLiN: Depicting microbial diversity via a Partitioned Pangenome Graph Guillaume Gautreau , Christophe Ambroise , Catherine Matias , Amandine Perrin , Rémi Planel Genome Informatics 2018, Sep 2018, Hinxton, Cambridge, United Kingdom Conference papers hal-04356757v1
	Genomic diversity of Flavobacterium species. Éric Duchaud , Paul Barbier , Jean-François Bernardet , Christian Michel , Céline Chantry-Darmon Flavobacterium 2012, 2012, Turku, Finland Conference papers hal-02746549v1
	Bactéries pathogènes des poissons du genre Flavobacterium Éric Duchaud , Jean-François Bernardet , Brigitte Kerouault , Christian Michel , Céline Chantry 2. Journées de la Recherche Filière Piscicole, Jul 2009, Paris, France. 1 p Conference papers hal-02823179v1
	MolliGen, a database dedicated to the comparative genomics of mollicutes A Barre , Pascal P. Sirand-Pugnet , Xavier Foissac , Eduardo Rocha , A de Daruvard 15th Congress of the Intern Organization for Mycoplasmology, 2006, Athens, United States. pp.Inconnu Conference papers hal-02815906v1
	Impact de la génomique sur les recherches portant sur les mycoplasmes C Lartigue , Pascal P. Sirand-Pugnet , Joël Renaudin , Eduardo Rocha , Alain A. Blanchard Journées Nationales des Microbiologistes de l'INRA, 2003, Dourdan, France. pp.Inconnu Conference papers hal-02825310v1
	From structural to functional genomics in mycoplasmas Alain A. Blanchard , C Lartigue , A Barre , Eduardo Rocha , Pascal P. Sirand-Pugnet Meeting de Mycoplasmologistes, 2003, Athens, United States. pp.Inconnu Conference papers hal-02825689v1
	Impact of genomics on mycoplasma research Alain A. Blanchard , C Lartigue , Pascal P. Sirand-Pugnet , Eduardo Rocha FEMS Ist congress of European Microbiologists, 2003, Ljubljana, Slovenia. pp.Inconnu Conference papers hal-02825759v1
	MolliGen: a database dedicated to the comparative genomics of mollicutes A Barre , Pascal P. Sirand-Pugnet , Xavier Foissac , Eduardo Rocha , A de Daruvard European conference on Computational Biology, 2003, Paris, France. pp.Inconnu Conference papers hal-02826789v1

	MacSyFinder v2: An improved search engine to model and identify molecular systems in genomes Bertrand Néron , Rémi Denise , Charles Coluzzi , Marie Touchon , Eduardo Rocha JOBIM, Jul 2022, Rennes (Campus de Beaulieu), France. , https://jobim2022.sciencesconf.org/data/pages/JOBIM2022_proceedings_posters_demos.pdf Conference poster pasteur-04583571v1
	PanGBank: depicting microbial species diversity via PPanGGOLiN Guillaume Gautreau , Adelme Bazin , Rémi Planel , Mathieu Gachet , Mathieu Dubois JOBIM 2019 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France Conference poster hal-04358380v1

	Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan Jean Cury , Sophie S. Abby , Olivia Doppelt-Azeroual , Bertrand Néron , Eduardo P C Rocha Fernando de la Cruz. Horizontal Gene Transfer : Methods and Protocols, Springer Science; Business Media, pp.265-283, 2019, 978-1-4939-9876-0. ⟨10.1007/978-1-4939-9877-7_19⟩ Book sections pasteur-02867882v1
	Genome analysis : recombination, repair and recombinational hotspots Eduardo Rocha , Pascal P. Sirand-Pugnet , Alain A. Blanchard Mycoplasmas. Molecular biology, pathogenicity and strategies for control, Horizon Bioscience, 2005, 0-8493-9861-4 Book sections hal-02831395v1
	Genome analysis : recombination, repair and recombinational hotspots Eduardo Rocha , Pascal P. Sirand-Pugnet , Alain A. Blanchard Mycoplasmas: Molecular biology, pathogenicity and strategies for control, Horizon Bioscience, 2005, 0-8493-9861-4 Book sections hal-02827574v1

	Hijackers, hitchhikers, or co-drivers? The mysteries of microbial mobilizable genetic elements Manuel Ares Arroyo , Charles Coluzzi , Jorge A Moura de Sousa , Eduardo P C Rocha 2024 Preprints, Working Papers, ... pasteur-04604601v1
	A type IVB secretion system contributes to the pathogenicity of Yersinia pseudotuberculosis strains responsible for the Far East scarlet-like fever Marion Lemarignier , Cyril Savin , Ines Ruedas Torres , Anne Derbise , Charles Coluzzi 2024 Preprints, Working Papers, ... pasteur-04612996v1
	Identification of protein secretion systems in bacterial genomes using MacSyFinder version 2 Sophie S. Abby , Rémi Denise , Eduardo Pc Rocha 2023 Preprints, Working Papers, ... hal-04257010v1
	A new route for integron cassette dissemination among bacterial genomes Céline Loot , Gael A Millot , Egill Richard , Claire Vit , Baptiste Darracq 2022 Preprints, Working Papers, ... pasteur-03826688v1
	When bacteria are phage playgrounds: interactions between viruses, cells and mobile genetic elements Eugen Pfeifer , Jorge A Moura de Sousa , Marie Touchon , Eduardo Rocha 2022 Preprints, Working Papers, ... hal-03824239v1
	Genetic drivers of chromosomal integron stability Egill Richard , Baptiste Darracq , Eloi Littner , Claire Vit , Clémence Whiteway 2022 Preprints, Working Papers, ... pasteur-03824759v1
	Competition between phage-resistance mechanisms determines the outcome of bacterial co-existence Olaya Rendueles , Jorge A Moura de Sousa , Eduardo P.C. Rocha 2022 Preprints, Working Papers, ... pasteur-03795539v1
	Genome diversification via genetic exchanges between temperate and virulent bacteriophages Jorge A. Moura de Sousa , Eugen Pfeifer , Marie Touchon , Eduardo P. C. Rocha 2020 Preprints, Working Papers, ... hal-02988810v1
	Selection for the bacterial capsule in the absence of biotic and abiotic aggressions depends on growth conditions Amandine Buffet , Eduardo P. C. Rocha , Olaya Rendueles 2020 Preprints, Working Papers, ... pasteur-02991089v1
	Intracellular positioning systems limit the entropic eviction of secondary replicons toward the nucleoid edges in bacterial cells Charlene Planchenault , Marine Pons , Caroline Schiavon , Patricia Siguier , Jérôme Rech 2019 Preprints, Working Papers, ... hal-02366139v1

	Integron_Finder Bertrand Néron , Jean Cury , Eduardo Rocha , Amandine Perrin 2024, ⟨swh:1:dir:6cc5d36f34974f2264a2ea9e195edb1981b2f9ba;origin=https://github.com/gem-pasteur/Integron_Finder;visit=swh:1:snp:f5d82d096a64d390358869946048ca7f801b2ded;anchor=swh:1:rev:0388197211bd9b232082a2dd9275623b62c5599a⟩ Software hal-04603009v1
	macsyfinder Bertrand Néron , Sophie Abby , Eduardo Rocha 2024, ⟨swh:1:dir:1e9ecd3b3b2bff278fac4b2814c56380c01853c9;origin=https://github.com/gem-pasteur/macsyfinder;visit=swh:1:snp:673748faa3f4f15687e2b6eb6d3d30b9eee9e68c;anchor=swh:1:rel:91c37f034f0348980547f788953425c0e490b8ea⟩ Software hal-04668349v1
	MacSyFinder Bertrand Néron , Sophie Abby , Eduardo Rocha 2023, ⟨swh:1:dir:b7595ff8d8bfbb327f63ae0dc8f33314f46c0996;origin=https://github.com/gem-pasteur/macsyfinder;visit=swh:1:snp:d01ecf21ed904146f244bad043bf052f2d2f8d0d;anchor=swh:1:rev:1821de180b026abe24043305cbfbdcf5e63d2881⟩ Software hal-04372564v1

Rocha Eduardo

Publications

Assembly of a unique membrane complex in type VI secretion systems of Bacteroidota

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

Phage-inducible chromosomal minimalist islands (PICMIs), a novel family of small marine satellites of virulent phages

Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency

Belt and braces: Two escape ways to maintain the cassette reservoir of large chromosomal integrons

Cassette recombination dynamics within chromosomal integrons are regulated by toxin-antitoxin systems

Integron cassettes commonly integrate into bacterial genomes via widespread non-classical attG sites

A widespread family of phage-inducible chromosomal islands only steals bacteriophage tails to spread in nature

Latent evolution of biofilm formation depends on life-history and genetic background

Identification and characterization of thousands of bacteriophage satellites across bacteria

MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes

Restriction-modification systems have shaped the evolution and distribution of plasmids across bacteria

The Capsule Increases Susceptibility to Last-Resort Polymyxins, but Not to Other Antibiotics, in Klebsiella pneumoniae

Competition between lysogenic and sensitive bacteria is determined by the fitness costs of the different emerging phage-resistance strategies

Chance Favors the Prepared Genomes: Horizontal Transfer Shapes the Emergence of Antibiotic Resistance Mutations in Core Genes

Emergence of novel non-aggregative variants under negative frequency-dependent selection in Klebsiella variicola

Phages and their satellites encode hotspots of antiviral systems

Structural and Genomic Evolution of RRNPPA Systems and Their Pheromone Signaling

Adaptation to novel spatially-structured environments is driven by the capsule and alters virulence-associated traits

IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella

NAR Breakthrough Article Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation

Evolution of Plasmid Mobility: Origin and Fate of Conjugative and Nonconjugative Plasmids

Phage-Plasmids Spread Antibiotic Resistance Genes through Infection and Lysogenic Conversion

Selfish, promiscuous, and sometimes useful: how mobile genetic elements drive horizontal gene transfer in microbial populations

Microbial defenses against mobile genetic elements and viruses: Who defends whom from what?

To catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites

Phage-host coevolution in natural populations

PanACoTA: a modular tool for massive microbial comparative genomics

Bacteria have numerous distinctive groups of phage-plasmids with conserved phage and variable plasmid gene repertoires

Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of the nosocomial pathogen Klebsiella pneumoniae

The impact of genetic diversity on gene essentiality within the E. coli species

Causes and Consequences of Bacteriophage Diversification via Genetic Exchanges across Lifestyles and Bacterial Taxa

Human commensal gut Proteobacteria withstand type VI secretion attacks through immunity protein-independent mechanisms

Nutrient conditions are primary drivers of bacterial capsule maintenance in Klebsiella

Evolution of ColE1-like plasmids across γ-Proteobacteria: From bacteriocin production to antimicrobial resistance

Unlinked rRNA genes are widespread among Bacteria and Archaea

Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids

Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements

A synthesis of bacterial and archaeal phenotypic trait data

The major subunit of widespread competence pili exhibits a novel and conserved type IV pilin fold

Intracellular Positioning Systems Limit the Entropic Eviction of Secondary Replicons Toward the Nucleoid Edges in Bacterial Cells

Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation

Macromolecular crowding links ribosomal protein gene dosage to growth rate in Vibrio cholerae

Un siècle de recherche sur les bactériophages

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph

The evolution of protein secretion systems by co-option and tinkering of cellular machineries

Community diversity and habitat structure shape the repertoire of extracellular proteins in bacteria

Phylogenetic background and habitat drive the genetic diversification of Escherichia coli

Les applications antibactériennes des bactériophages

Experimental Evolution as a Tool to Investigate Natural Processes and Molecular Functions

Bacteriophages benefit from generalized transduction

Real-time search of all bacterial and viral genomic data

Bacteriophages benefit from generalized transduction

A matter of background: DNA repair pathways as a possible cause for the sparse distribution of CRISPR-Cas systems in bacteria

Environmental structure drives resistance to phages and antibiotics during phage therapy and to invading lysogens during colonisation

Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility

A simple, reproducible and cost- effective procedure to analyse gut phageome: from phage isolation to bioinformatic approach

HflXr mediates a novel antibiotic resistance mechanism 1 2

Genetic exchanges are more frequent in bacteria encoding capsules

Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder.

Bacillus subtilis, the model Gram-positive bacterium: 20years of annotation refinement

Neutral Theory, Microbial Practice: Challenges in Bacterial Population Genetics

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

Parallels between experimental and natural evolution of legume symbionts

Host Range and Genetic Plasticity Explain the Coexistence of Integrative and Extrachromosomal Mobile Genetic Elements

Author Correction : Parallels between experimental and natural evolution of legume symbionts (vol 9, 2264, 2018)

The chromosomal organization of horizontal gene transfer in bacteria

Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens

Recruitment of a Lineage-Specific Virulence Regulatory Pathway Promotes Intracellular Infection by a Plant Pathogen Experimentally Evolved into a Legume Symbiont

Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria

Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance

Experimental evolution of rhizobia may lead to either extra- or intracellular symbiotic adaptation depending on the selection regime

Integrative and conjugative elements and their hosts: composition, distribution and organization

Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain

Metabolic diversity of the emerging pathogenic lineages ofKlebsiella pneumoniae

Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer

Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis

Identification and analysis of integrons and cassette arrays in bacterial genomes