Rocha Eduardo

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Bacterial natural transformation drives cassette shuffling and simplifies recombination in chromosomal integrons

Kevin Debatisse , Manon Brunie , Baptiste Darracq , Elia Bandini , Eloi Littner et al.

Nucleic Acids Research, 2025, Genome integrity, repair and replication, 53 (21), pp.gkaf1162. ⟨10.1093/nar/gkaf1162⟩

Article dans une revue pasteur-05379590v1
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Antibiotic perturbation of the human gut phageome preserves its individuality and promotes blooms of virulent phages

Eugen Pfeifer , Camille D’humières , Quentin Lamy-Besnier , Florian Plaza Oñate , Remi Denisé et al.

Cell Reports, 2025, 44 (8), pp.116020. ⟨10.1016/j.celrep.2025.116020⟩

Article dans une revue pasteur-05262007v1
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Impact of Natural Transformation on the Acquisition of Novel Genes in Bacteria

Fanny Mazzamurro , Marie Touchon , Xavier Charpentier , Eduardo P C Rocha

Molecular Biology and Evolution, 2025, 42 (8), pp.msaf192. ⟨10.1093/molbev/msaf192⟩

Article dans une revue pasteur-05262000v1
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Adaptive genomic plasticity in large-genome, broad-host-range vibrio phages

Charles Bernard , Yannick Labreuche , Carine Diarra , Pauline Daszkowski , Karine Cahier et al.

The International Society of Microbiologial Ecology Journal, 2025, 19 (1), pp.wraf063. ⟨10.1093/ismejo/wraf063⟩

Article dans une revue hal-05043618v1
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The extended mobility of plasmids

Maria Pilar Garcillán-Barcia , Fernando de la Cruz , Eduardo P Rocha

Nucleic Acids Research, 2025, 53 (14), pp.gkaf652. ⟨10.1093/nar/gkaf652⟩

Article dans une revue pasteur-05262009v1
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Phenotypic heterogeneity of capsule production across opportunistic pathogens

Amandine Nucci , Julie Le Bris , Sara Diaz-Diaz , Lilibeth Torres-Elizalde , Eduardo P C Rocha et al.

mBio, In press, pp.e0180725. ⟨10.1128/mbio.01807-25⟩

Article dans une revue hal-05245555v1
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The Spread of Antibiotic Resistance Is Driven by Plasmids Among the Fastest Evolving and of Broadest Host Range

Charles Coluzzi , Eduardo Rocha

Molecular Biology and Evolution, 2025, 42 (3), pp.msaf060. ⟨10.1093/molbev/msaf060⟩

Article dans une revue pasteur-05262012v1
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Horizontal Gene Transfer and Recombination in Cyanobacteriota

Devaki Bhaya , Gabriel Birzu , Eduardo P.C. Rocha

Annual Review of Microbiology, In press, ⟨10.1146/annurev-micro-041522-100420⟩

Article dans une revue pasteur-05262034v1
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Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems

Baptiste Darracq , Eloi Littner , Manon Brunie , Julia Bos , Pierre Alexandre Kaminski et al.

Science, 2025, 388 (6747), pp.eads0768. ⟨10.1126/science.ads0768⟩

Article dans une revue pasteur-05262023v1
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Genetics, ecology and evolution of phage satellites

José Penadés , Kimberley Seed , John Chen , David Bikard , Eduardo Rocha

Nature Reviews Microbiology, 2025, 23 (7), pp.410-422. ⟨10.1038/s41579-025-01156-z⟩

Article dans une revue (article de synthèse) pasteur-05115370v1
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The pathway to resolve dimeric forms distinguishes plasmids from megaplasmids in Enterobacteriaceae

Florian Fournes , Manuel Campos , Jean Cury , Caroline Schiavon , Carine Pagès et al.

Nucleic Acids Research, 2025, 53 (2), pp.gkae1300. ⟨10.1093/nar/gkae1300⟩

Article dans une revue hal-04888819v1
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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 et al.

Nature Communications, 2024, 15 (1), pp.664. ⟨10.1038/s41467-024-44965-1⟩

Article dans une revue hal-04413133v1
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Expanding the diversity of origin of transfer-containing sequences in mobilizable plasmids

Manuel Ares-Arroyo , Amandine Nucci , Eduardo Rocha

Nature Microbiology, 2024, 9 (12), pp.3240-3253. ⟨10.1038/s41564-024-01844-1⟩

Article dans une revue pasteur-04781480v1
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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 et al.

PLoS Genetics, 2024, 20 (4), pp.e1011231. ⟨10.1371/journal.pgen.1011231⟩

Article dans une revue pasteur-04305445v1
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Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency

Matthieu Haudiquet , Julie Le Bris , Amandine Nucci , Rémy A Bonnin , Pilar Domingo-Calap et al.

Nature Communications, 2024, 15 (1), pp.2032. ⟨10.1038/s41467-024-46147-5⟩

Article dans une revue hal-04492345v1
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Spread of carbapenemase-producing Morganella spp from 2013 to 2021: a comparative genomic study

Rémy Bonnin , Elodie Creton , Amandine Perrin , Delphine Girlich , Cecile Emeraud et al.

The Lancet Microbe, 2024, 5 (6), pp.e547-e558. ⟨10.1016/S2666-5247(23)00407-X⟩

Article dans une revue hal-04629647v1
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Reference-free structural variant detection in microbiomes via long-read co-assembly graphs

Kristen D Curry , Feiqiao Brian Yu , Summer E Vance , Santiago Segarra , Devaki Bhaya et al.

Bioinformatics, 2024, 40, pp.i58 - i67. ⟨10.1093/bioinformatics/btae224⟩

Article dans une revue pasteur-04778741v1
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Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans

Fabienne Benz , Sarah Camara-Wilpert , Jakob Russel , Katharina Wandera , Rimvydė Čepaitė et al.

Cell Host & Microbe, 2024, 32 (6), pp.875-886.e9. ⟨10.1016/j.chom.2024.04.016⟩

Article dans une revue pasteur-04785210v1
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Tail assembly interference is a common strategy in bacterial antiviral defenses

Lingchen He , Laura Miguel-Romero , Jonasz B Patkowski , Nasser Alqurainy , Eduardo P C Rocha et al.

Nature Communications, 2024, 15, pp.7539. ⟨10.1038/s41467-024-51915-4⟩

Article dans une revue pasteur-04778725v1
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Assembly of a unique membrane complex in type VI secretion systems of Bacteroidota

Thibault Bongiovanni , Casey Latario , Youn Le Cras , Evan Trus , Sophie Robitaille et al.

Nature Communications, 2024, 15 (1), pp.429. ⟨10.1038/s41467-023-44426-1⟩

Article dans une revue hal-04390477v1

Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes

Lukas Hafner , Enzo Gadin , Lei Huang , Arthur Frouin , Fabien Laporte et al.

Nature Microbiology, 2024, 9, pp.3345-3361. ⟨10.1038/s41564-024-01859-8⟩

Article dans une revue pasteur-04804169v1
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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 et al.

Microbiome, 2024, 12 (1), pp.50. ⟨10.1186/s40168-023-01746-0⟩

Article dans une revue hal-04582235v1
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IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata

Antonio Pedro Camargo , Lee Call , Simon Roux , Stephen Nayfach , Marcel Huntemann et al.

Nucleic Acids Research, 2024, 52 (D1), pp.D164-D173. ⟨10.1093/nar/gkad964⟩

Article dans une revue pasteur-04778701v1
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Hijackers, hitchhikers, or co-drivers? The mysteries of mobilizable genetic elements

Manuel Ares-Arroyo , Charles Coluzzi , Jorge A Moura de Sousa , Eduardo P C Rocha

PLoS Biology, 2024, 22 (8), pp.e3002796. ⟨10.1371/journal.pbio.3002796⟩

Article dans une revue pasteur-04778737v2
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Cassette recombination dynamics within chromosomal integrons are regulated by toxin-antitoxin systems

Egill Richard , Baptiste Darracq , Eloi Littner , Claire Vit , Clémence Whiteway et al.

Science Advances , 2024, 10 (2), pp.eadj3498. ⟨10.1126/sciadv.adj3498⟩

Article dans une revue hal-04397951v1
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Intragenomic conflicts with plasmids and chromosomal mobile genetic elements drive the evolution of natural transformation within species

Fanny Mazzamurro , Jason Baby Chirakadavil , Isabelle Durieux , Ludovic Poiré , Julie Plantade et al.

PLoS Biology, 2024, 22 (10), pp.e3002814. ⟨10.1371/journal.pbio.3002814⟩

Article dans une revue pasteur-04778731v1
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Phage-plasmids promote recombination and emergence of phages and plasmids

Eugen Pfeifer , Eduardo P C Rocha

Nature Communications, 2024, 15 (1), pp.1545. ⟨10.1038/s41467-024-45757-3⟩

Article dans une revue pasteur-04778718v1
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Integron cassettes commonly integrate into bacterial genomes via widespread non-classical attG sites

Céline Loot , Gael A Millot , Egill Richard , Eloi Littner , Claire Vit et al.

Nature Microbiology, 2024, 9 (1), pp.228-240. ⟨10.1038/s41564-023-01548-y⟩

Article dans une revue pasteur-04384854v1
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Manipulation of natural transformation by AbaR-type islands promotes fixation of antibiotic resistance in Acinetobacter baumannii

Rémi Tuffet , Gabriel Carvalho , Anne-Sophie Godeux , Fanny Mazzamurro , Eduardo P C Rocha et al.

Proceedings of the National Academy of Sciences of the United States of America, 2024, 121 (39), pp.e2409843121. ⟨10.1073/pnas.2409843121⟩

Article dans une revue pasteur-04778734v1
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Evo‐Scope : Fully automated assessment of correlated evolution on phylogenetic trees

Maxime Godfroid , Charles Coluzzi , Amaury Lambert , Philippe Glaser , Eduardo P C Rocha et al.

Methods in Ecology and Evolution, 2024, 15 (2), pp.282 - 289. ⟨10.1111/2041-210x.14190⟩

Article dans une revue pasteur-04778723v1
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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⟩

Article dans une revue pasteur-04057813v1
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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 et al.

Molecular Biology and Evolution, 2023, 40 (10), pp.msad217. ⟨10.1093/molbev/msad217⟩

Article dans une revue hal-04281854v1
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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, 2023, 4, pp.uqad038. ⟨10.1093/femsml/uqad038⟩

Article dans une revue pasteur-04225506v1
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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⟩

Article dans une revue pasteur-04177373v1
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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 et al.

Cell Host & Microbe, 2023, 31 (1), pp.69-82.e5. ⟨10.1016/j.chom.2022.12.001⟩

Article dans une revue pasteur-03952543v2
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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⟩

Article dans une revue pasteur-04236062v1
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Antimicrobial resistance level and conjugation permissiveness shape plasmid distribution in clinical enterobacteria

Aida Alonso-del Valle , Laura Toricelestino , Anna Quirant , Carles Tardio Pi , Javier Delafuente et al.

Proceedings of the National Academy of Sciences of the United States of America, 2023, 120 (51), pp.e2314135120. ⟨10.1073/pnas.2314135120⟩

Article dans une revue pasteur-04778706v1
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Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with bacterial hosts

Bogna J Smug , Krzysztof Szczepaniak , Eduardo P. C. Rocha , Stanislaw Dunin-Horkawicz , Rafał J Mostowy

Nature Communications, 2023, 14 (1), pp.7460. ⟨10.1038/s41467-023-43236-9⟩

Article dans une revue pasteur-04778709v1
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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, 2023, 67 (4), pp.e00127-23. ⟨10.1128/aac.00127-23⟩

Article dans une revue (data paper) pasteur-04027513v1
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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⟩

Article dans une revue hal-03838678v2
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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 et al.

Peer Community Journal, 2023, 3, pp.e28. ⟨10.24072/pcjournal.250⟩

Article dans une revue (article de synthèse) pasteur-04060331v2
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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⟩

Article dans une revue pasteur-03818031v1
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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⟩

Article dans une revue pasteur-03684736v1
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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⟩

Article dans une revue pasteur-03684761v2
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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⟩

Article dans une revue pasteur-03690954v1
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Phage-host coevolution in natural populations

Damien Piel , Maxime Bruto , Yannick Labreuche , François Blanquart , David Goudenège et al.

Nature Microbiology, 2022, 7 (7), pp.1075-1086. ⟨10.1038/s41564-022-01157-1⟩

Article dans une revue hal-03738913v2
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When bacteria are phage playgrounds: interactions between viruses, cells, and mobile genetic elements

Eugen Pfeifer , Jorge A Moura de Sousa , Marie Touchon , Eduardo Pc Rocha

Current Opinion in Microbiology, 2022, 70, pp.102230. ⟨10.1016/j.mib.2022.102230⟩

Article dans une revue hal-04604548v1
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Phages and their satellites encode hotspots of antiviral systems

François Rousset , Florence Depardieu , Solange Miele , Julien Dowding , Anne-Laure Laval et al.

Cell Host & Microbe, 2022, 30 (5), pp.740 - 753.e5. ⟨10.1016/j.chom.2022.02.018⟩

Article dans une revue pasteur-04075930v1
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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⟩

Article dans une revue pasteur-03952614v1
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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 et al.

Microorganisms, 2022, 10 (4), pp.700. ⟨10.3390/microorganisms10040700⟩

Article dans une revue hal-03655020v1
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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⟩

Article dans une revue pasteur-03818036v1
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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⟩

Article dans une revue pasteur-04075979v1
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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⟩

Article dans une revue pasteur-03794548v1
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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 et al.

Nature Microbiology, 2021, 6 (3), pp.301-312. ⟨10.1038/s41564-020-00839-y⟩

Article dans une revue pasteur-03264663v1
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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⟩

Article dans une revue hal-03357362v1
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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 et al.

Nature Communications, 2021, 12 (1), 13 p. ⟨10.1038/s41467-021-26041-0⟩

Article dans une revue pasteur-03364094v1
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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⟩

Article dans une revue pasteur-03818042v1
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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⟩

Article dans une revue hal-03357352v1
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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⟩

Article dans une revue hal-03281367v1
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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⟩

Article dans une revue pasteur-03158282v1
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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⟩

Article dans une revue hal-03357369v1
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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⟩

Article dans une revue pasteur-02626502v1
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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 et al.

Journal of Biological Chemistry, 2020, 295 (19), pp.6594-6604. ⟨10.1074/jbc.RA120.013316⟩

Article dans une revue pasteur-03015795v1
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A synthesis of bacterial and archaeal phenotypic trait data

Joshua S. Madin , Daniel A. Nielsen , Maria Brbic , Ross Corkrey , David Danko et al.

Scientific Data , 2020, 7 (1), pp.170. ⟨10.1038/s41597-020-0497-4⟩

Article dans une revue pasteur-03015782v1
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Intracellular Positioning Systems Limit the Entropic Eviction of Secondary Replicons Toward the Nucleoid Edges in Bacterial Cells

Julie Dauverd -Girault , Charlène Planchenault , Marine C Pons , Caroline Schiavon , Patricia Siguier et al.

Journal of Molecular Biology, 2020, 432 (3), pp.745-761. ⟨10.1016/j.jmb.2019.11.027⟩

Article dans une revue hal-02392007v1
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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 et al.

BMC Biology, 2020, 18 (1), pp.43. ⟨10.1186/s12915-020-00777-5⟩

Article dans une revue pasteur-02562489v1
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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⟩

Article dans une revue pasteur-02991081v1
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Un siècle de recherche sur les bactériophages

Mireille Ansaldi , Pascale Boulanger , Charlotte Brives , Laurent Debarbieux , Nicolas Dufour et al.

Virologie, 2020, 24 (1), pp.9-22. ⟨10.1684/vir.2020.0809⟩

Article dans une revue (article de synthèse) hal-02530997v1
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PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph

Guillaume Gautreau , Adelme Bazin , Mathieu Gachet , Rémi Planel , Laura Burlot et al.

PLoS Computational Biology, 2020, ⟨10.1371/journal.pcbi.1007732⟩

Article dans une revue hal-03089210v1
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Phylogenetic background and habitat drive the genetic diversification of Escherichia coli

Marie Touchon , Amandine Perrin , Jorge A Moura de Sousa , Belinda Vangchhia , Samantha Burn et al.

PLoS Genetics, 2020, 16 (6), pp.e1008866. ⟨10.1371/journal.pgen.1008866⟩

Article dans une revue pasteur-02866790v2
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Les applications antibactériennes des bactériophages

Mireille Ansaldi , Pascale Boulanger , Charlotte Brives , Claire Le Hénaff , Laurent Debarbieux et al.

Virologie, 2020, 24 (1), pp.23-36. ⟨10.1684/vir.2019.0805⟩

Article dans une revue (article de synthèse) hal-02530998v1
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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 et al.

Nature Communications, 2020, 11 (1), pp.3602. ⟨10.1038/s41467-020-17278-2⟩

Article dans une revue pasteur-03015777v1
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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⟩

Article dans une revue pasteur-02626487v1
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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⟩

Article dans une revue pasteur-02626815v1
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Unlinked rRNA genes are widespread among Bacteria and Archaea

Tess E Brewer , Mads Albertsen , Arwyn Edwards , Rasmus H Kirkegaard , Eduardo P C Rocha et al.

The International Society of Microbiologial Ecology Journal, 2020, ⟨10.1038/s41396-019-0552-3⟩

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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⟩

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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⟩

Article dans une revue pasteur-02263349v1
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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⟩

Article dans une revue pasteur-02098383v1
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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 et al.

Scientific Reports, 2019, ⟨10.1038/s41598-019-47656-w⟩

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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⟩

Article dans une revue (article de synthèse) hal-02329724v1
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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⟩

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Bacteriophages benefit from generalized transduction

Alfred Fillol-Salom , Ahlam Alsaadi , Jorge A Moura de Sousa , Li Zhong , Kevin R Foster et al.

PLoS Pathogens, 2019, 15 (7), pp.e1007888. ⟨10.1371/journal.ppat.1007888⟩

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Bacteriophages benefit from generalized transduction

Alfred Fillol-Salom , Alsaadiid Ahlam , Jorge Moura de Sousa , Li Zhong , Kevin R Fosterid et al.

PLoS Pathogens, 2019, ⟨10.1371/journal.ppat.1007888⟩

Article dans une revue hal-02329705v1

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⟩

Article dans une revue hal-01677379v1
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Bacillus subtilis, the model Gram-positive bacterium: 20years of annotation refinement

Rainer Borriss , Antoine Danchin , Colin R. Harwood , Claudine Médigue , Eduardo P. C. Rocha et al.

Microbial Biotechnology, 2018, 11 (1), pp.3-17. ⟨10.1111/1751-7915.13043⟩

Article dans une revue cea-02291345v1
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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⟩

Article dans une revue hal-02329762v1
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Parallels between experimental and natural evolution of legume symbionts

Camille Clerissi , Marie Touchon , Delphine Capela , Mingxing Tang , Stéphane Cruveiller et al.

Nature Communications, 2018, 9 (1), pp.2264. ⟨10.1038/s41467-018-04778-5⟩

Article dans une revue cea-01880286v1
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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 et al.

Nature Communications, 2018, 9, ⟨10.1038/s41467-018-07205-x⟩

Article dans une revue hal-02617830v1
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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⟩

Article dans une revue pasteur-02098387v1
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HflXr mediates a novel antibiotic resistance mechanism 1 2

Mélodie Duval , Daniel Dar , Filipe Carvalho , Eduardo P C Rocha , Rotem Sorek et al.

Proceedings of the National Academy of Sciences of the United States of America, 2018, 115 (52), pp.13359-13364. ⟨10.1073/pnas.1810555115⟩

Article dans une revue hal-02329775v1
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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⟩

Article dans une revue pasteur-02012595v1
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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 et al.

Nucleic Acids Research, 2018, 46 (W1), pp.W246-W251. ⟨10.1093/nar/gky425⟩

Article dans une revue pasteur-02098389v1

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 et al.

Molecular Ecology, 2017, 26 (7), pp.1818-1831. ⟨10.1111/mec.13895⟩

Article dans une revue hal-01607703v1
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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⟩

Article dans une revue pasteur-04076019v1
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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⟩

Article dans une revue pasteur-03111100v1

Metabolic diversity of the emerging pathogenic lineages of<i>Klebsiella pneumoniae</i>

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⟩

Article dans une revue pasteur-04076001v1
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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⟩

Article dans une revue hal-04325283v1
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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 et al.

mBio, 2017, 8 (2), pp.e02296-16. ⟨10.1128/mBio.02296-16⟩

Article dans une revue pasteur-01689524v1
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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 et al.

Nature Communications, 2017, 8, pp.2094. ⟨10.1038/s41467-017-02350-1⟩

Article dans une revue pasteur-01967501v1
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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 et al.

Nature Communications, 2017, 8 (1), pp.15483. ⟨10.1038/ncomms15483⟩

Article dans une revue hal-02613118v1
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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⟩

Article dans une revue 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 et al.

Molecular Biology and Evolution, 2017, 34 (10), pp.2503-2521. ⟨10.1093/molbev/msx165⟩

Article dans une revue hal-02620519v1
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Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes

Alexandra Moura , Alexis Criscuolo , Hannes Pouseele , Mylène M. Maury , Alexandre Leclercq et al.

Nature Microbiology, 2016, 2, pp.16185. ⟨10.1038/nmicrobiol.2016.185⟩

Article dans une revue pasteur-01415883v1
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Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity

Mylène M Maury , Yu-Huan Tsai , Caroline Charlier , Marie Touchon , Viviane Chenal-Francisque et al.

Nature Genetics, 2016, 48 (3), pp.308-313. ⟨10.1038/ng.3501⟩

Article dans une revue pasteur-02170775v1
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A widespread family of polymorphic toxins encoded by temperate phages

Anne Jamet , Marie Touchon , Bruno Goncalves , João André Carriço , Alain Charbit et al.

BMC Biology, 2016, 15 (1), pp.75. ⟨10.1186/s12915-017-0415-1⟩

Article dans une revue inserm-01580852v1
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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⟩

Article dans une revue pasteur-01374969v1
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Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis

Sebastien Breurec , Alexis Criscuolo , Laure Diancourt , Olaya Rendueles , Mathias Vandenbogaert et al.

Scientific Reports, 2016, 6, pp.30379. ⟨10.1038/srep30379⟩

Article dans une revue hal-02613124v1
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Identification of protein secretion systems in bacterial genomes

Sophie S. Abby , Jean Cury , Julien Guglielmini , Bertrand Néron , Marie Touchon et al.

Scientific Reports, 2016, 6, ⟨10.1038/srep23080⟩

Article dans une revue pasteur-01374967v1
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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⟩

Article dans une revue pasteur-01374966v1
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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⟩

Article dans une revue pasteur-01374968v1
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Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations

Hong Xue , Otto X. Cordero , Francisco M. Camas , William Trimble , Folker Meyer et al.

mBio, 2015, 6 (3), ⟨10.1128/mBio.00552-15⟩

Article dans une revue pasteur-01374963v1
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Insights on the emergence of Mycobacterium tuberculosis from the analysis of Mycobacterium kansasii.

Joyce Wang , Fiona Mcintosh , Nicolas Radomski , Ken Dewar , Roxane Simeone et al.

Genome Biology and Evolution, 2015, 7 (3), pp.856-70. ⟨10.1093/gbe/evv035⟩

Article dans une revue pasteur-01352692v1
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Common Cell Shape Evolution of Two Nasopharyngeal Pathogens.

Frédéric J Veyrier , Nicolas Biais , Pablo Morales , Nouria Belkacem , Cyril Guilhen et al.

PLoS Genetics, 2015, 11 (7), pp.e1005338. ⟨10.1371/journal.pgen.1005338⟩

Article dans une revue pasteur-01352679v1
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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⟩

Article dans une revue pasteur-01122287v1
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The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences.

Marie Touchon , Jean Cury , Eun-Jeong Yoon , Lenka Krizova , Gustavo C Cerqueira et al.

Genome Biology and Evolution, 2014, 6 (10), pp.2866-82. ⟨10.1093/gbe/evu225⟩

Article dans une revue pasteur-01132634v1
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Transient Hypermutagenesis Accelerates the Evolution of Legume Endosymbionts following Horizontal Gene Transfer

Philippe Remigi , Delphine Capela , Camille Clerissi , Léna Tasse , Rachel Torchet et al.

PLoS Biology, 2014, 12 (9), ⟨10.1371/journal.pbio.1001942⟩

Article dans une revue pasteur-01374959v1
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A PNPase dependent CRISPR System in Listeria.

Nina Sesto , Marie Touchon , José Marques Andrade , Jiro Kondo , Eduardo P C Rocha et al.

PLoS Genetics, 2014, 10 (1), pp.e1004065. ⟨10.1371/journal.pgen.1004065⟩

Article dans une revue pasteur-01145428v1
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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 et al.

PLoS Neglected Tropical Diseases, 2014, 8 (11), pp.e3308. ⟨10.1371/journal.pntd.0003308⟩

Article dans une revue hal-01342968v1
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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⟩

Article dans une revue pasteur-01080418v1
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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⟩

Article dans une revue pasteur-01374951v1
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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⟩

Article dans une revue pasteur-01374955v1
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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⟩

Article dans une revue pasteur-01374947v1
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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⟩

Article dans une revue pasteur-00655553v1
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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⟩

Article dans une revue pasteur-00578535v1
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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⟩

Article dans une revue pasteur-00647077v1
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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⟩

Article dans une revue pasteur-00488678v1
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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⟩

Article dans une revue pasteur-01374940v1
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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⟩

Article dans une revue pasteur-00578536v1

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⟩

Article dans une revue hal-02319387v1

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⟩

Article dans une revue (article de synthèse) hal-02319386v1
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Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths.

Marie Touchon , Claire Hoede , Olivier Tenaillon , Valérie Barbe , Simon Baeriswyl et al.

PLoS Genetics, 2009, 5 (1), pp.e1000344. ⟨10.1371/journal.pgen.1000344⟩

Article dans une revue 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 et al.

Antimicrobial Agents and Chemotherapy, 2009, 53 (6), pp.2283-2288. ⟨10.1128/AAC.00123-09⟩

Article dans une revue hal-03612468v1
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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⟩

Article dans une revue pasteur-00336123v1
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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⟩

Article dans une revue pasteur-00336121v1
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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⟩

Article dans une revue pasteur-00336122v1
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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⟩

Article dans une revue hal-02683075v1
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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. ⟨10.1093/nar/30.9.2031⟩

Article dans une revue hal-02676514v1
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The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis

Isabelle Chambaud , Roland Heilig , Stephane Ferris , Valérie Barbe , Delphine Samson et al.

Nucleic Acids Research, 2001, 29 (10), pp.2145-2153. ⟨10.1093/nar/29.10.2145⟩

Article dans une revue hal-02679458v1
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The complete genome sequence of the gram-positive bacterium Bacillus subtilis

Frank Kunst , N. Ogasawara , Ivan Moszer , A.M. Albertini , G. Alloni et al.

Nature, 1997, 390 (6657), pp.249-256. ⟨10.1038/36786⟩

Article dans une revue hal-02694553v1

PPanGGOLiN: Depicting microbial diversity via a Partitioned Pangenome Graph

Guillaume Gautreau , Christophe Ambroise , Catherine Matias , Amandine Perrin , Rémi Planel et al.

JOBIM 2018 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France

Communication dans un congrès hal-04355945v1

PPanGGOLiN: Depicting microbial diversity via a Partitioned Pangenome Graph

Guillaume Gautreau , Christophe Ambroise , Catherine Matias , Amandine Perrin , Rémi Planel et al.

Genome Informatics 2018, Sep 2018, Hinxton, Cambridge, United Kingdom

Communication dans un congrès hal-04356757v1

Genomic diversity of Flavobacterium species.

Éric Duchaud , Paul Barbier , Jean-François Bernardet , Christian Michel , Céline Chantry-Darmon et al.

Flavobacterium 2012, 2012, Turku, Finland

Communication dans un congrès hal-02746549v1

Bactéries pathogènes des poissons du genre Flavobacterium

Éric Duchaud , Jean-François Bernardet , Brigitte Kerouault , Christian Michel , Céline Chantry et al.

2. Journées de la Recherche Filière Piscicole, Jul 2009, Paris, France. 1 p

Communication dans un congrès 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 et al.

15th Congress of the Intern Organization for Mycoplasmology, 2006, Athens, United States. pp.Inconnu

Communication dans un congrès hal-02815906v1

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

Communication dans un congrès hal-02825759v1

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

Communication dans un congrès hal-02825689v1

MolliGen: a database dedicated to the comparative genomics of mollicutes

A Barre , Pascal P. Sirand-Pugnet , Xavier Foissac , Eduardo Rocha , A de Daruvard et al.

European conference on Computational Biology, 2003, Paris, France. pp.Inconnu

Communication dans un congrès hal-02826789v1

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

Communication dans un congrès hal-02825310v1
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MacSyFinder v2: An improved search engine to model and identify molecular systems in genomes

Bertrand Néron , Rémi Denise , Charles Coluzzi , Marie Touchon , Eduardo Rocha et al.

JOBIM, Jul 2022, Rennes (Campus de Beaulieu), France. , https://jobim2022.sciencesconf.org/data/pages/JOBIM2022_proceedings_posters_demos.pdf

Poster de conférence pasteur-04583571v1

PanGBank: depicting microbial species diversity via PPanGGOLiN

Guillaume Gautreau , Adelme Bazin , Rémi Planel , Mathieu Gachet , Mathieu Dubois et al.

JOBIM 2019 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France

Poster de conférence hal-04358380v1

Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder Version 2

Sophie Abby , Rémi Denise , Eduardo P. C. Rocha

Bacterial Secretion Systems: methods and protocols [second edition], 2715, Springer, pp.1-25, 2024, Methods in Molecular Biology, 978-1-0716-3445-5 (eBook). ⟨10.1007/978-1-0716-3445-5_1⟩

Chapitre d'ouvrage hal-04886614v1
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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⟩

Chapitre d'ouvrage 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

Chapitre d'ouvrage 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

Chapitre d'ouvrage hal-02827574v1
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Logan: Planetary-Scale Genome Assembly Surveys Life’s Diversity

Rayan Chikhi , Téo Lemane , Raphaël Loll-Krippleber , Mercè Montoliu-Nerin , Brice Raffestin et al.

2025

Pré-publication, Document de travail hal-05446815v1
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Serotype swapping in <i>Klebsiella</i> spp. by plug-and-play

Julie Le Bris , Hugo Varet , Eduardo P.C. Rocha , Olaya Rendueles

2025

Pré-publication, Document de travail hal-05361868v1
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YraN is a helicase-associated nuclease fostering extended recombination events by natural transformation

Léo Hardy , Julie Plantade , Violette Morales , Fanny Mazzamuro , Eduardo Rocha et al.

2024

Pré-publication, Document de travail hal-04983173v1
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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 et al.

2024

Pré-publication, Document de travail pasteur-04612996v1
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Sedentary chromosomal integrons as biobanks of bacterial anti-phage defence systems

Baptiste Darracq , Eloi Littner , Manon Brunie , Julia Bos , Pierre Alexandre Kaminski et al.

2024

Pré-publication, Document de travail hal-04783441v1
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Identification of protein secretion systems in bacterial genomes using MacSyFinder version 2

Sophie S. Abby , Rémi Denise , Eduardo Pc Rocha

2023

Pré-publication, Document de travail hal-04257010v1
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A new route for integron cassette dissemination among bacterial genomes

Céline Loot , Gael A Millot , Egill Richard , Claire Vit , Baptiste Darracq et al.

2022

Pré-publication, Document de travail pasteur-03826688v1
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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

Pré-publication, Document de travail hal-03824239v1
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Competition between phage-resistance mechanisms determines the outcome of bacterial co-existence

Olaya Rendueles , Jorge A Moura de Sousa , Eduardo P.C. Rocha

2022

Pré-publication, Document de travail pasteur-03795539v1
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Genetic drivers of chromosomal integron stability

Egill Richard , Baptiste Darracq , Eloi Littner , Claire Vit , Clémence Whiteway et al.

2022

Pré-publication, Document de travail pasteur-03824759v1
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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

Pré-publication, Document de travail pasteur-02991089v1
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Genome diversification via genetic exchanges between temperate and virulent bacteriophages

Jorge A. Moura de Sousa , Eugen Pfeifer , Marie Touchon , Eduardo P. C. Rocha

2020

Pré-publication, Document de travail hal-02988810v1
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Intracellular positioning systems limit the entropic eviction of secondary replicons toward the nucleoid edges in bacterial cells

Charlene Planchenault , Marine C Pons , Caroline Schiavon , Patricia Siguier , Jérôme Rech et al.

2019

Pré-publication, Document de travail hal-02366139v1