Rocha Eduardo

Publications

Article dans une revue (140)

Plug-and-play evolution of the Klebsiella pneumoniae capsule locus enables serotype exchange across genetic backgrounds Julie Le Bris,Hugo Varet,Eduardo P C Rocha,Olaya Rendueles PLoS Biology, 2026, 24 (3), pp.e3003724. ⟨10.1371/journal.pbio.3003724⟩ Article dans une revue pasteur-05576808v1
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
Phenotypic heterogeneity of capsule production across opportunistic pathogens Amandine Nucci,Julie Le Bris,Sara Diaz-Diaz,Lilibeth Torres-Elizalde,Eduardo P C Rochaet al. mBio, In press, pp.e0180725. ⟨10.1128/mbio.01807-25⟩ Article dans une revue hal-05245555v1
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
Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems Baptiste Darracq,Eloi Littner,Manon Brunie,Julia Bos,Pierre Alexandre Kaminskiet al. Science, 2025, 388 (6747), pp.eads0768. ⟨10.1126/science.ads0768⟩ Article dans une revue pasteur-05262023v1
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
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
The pathway to resolve dimeric forms distinguishes plasmids from megaplasmids in Enterobacteriaceae Florian Fournes,Manuel Campos,Jean Cury,Caroline Schiavon,Carine Pagèset al. Nucleic Acids Research, 2025, 53 (2), pp.gkae1300. ⟨10.1093/nar/gkae1300⟩ Article dans une revue hal-04888819v1
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
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 Deniséet al. Cell Reports, 2025, 44 (8), pp.116020. ⟨10.1016/j.celrep.2025.116020⟩ Article dans une revue pasteur-05262007v1
Bacterial natural transformation drives cassette shuffling and simplifies recombination in chromosomal integrons Kevin Debatisse,Manon Brunie,Baptiste Darracq,Elia Bandini,Eloi Littneret al. Nucleic Acids Research, 2025, Genome integrity, repair and replication, 53 (21), pp.gkaf1162. ⟨10.1093/nar/gkaf1162⟩ Article dans une revue pasteur-05379590v1
Adaptive genomic plasticity in large-genome, broad-host-range vibrio phages Charles Bernard,Yannick Labreuche,Carine Diarra,Pauline Daszkowski,Karine Cahieret al. The International Society of Microbiologial Ecology Journal, 2025, 19 (1), pp.wraf063. ⟨10.1093/ismejo/wraf063⟩ Article dans une revue hal-05043618v1
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 Bhayaet al. Bioinformatics, 2024, 40, pp.i58 - i67. ⟨10.1093/bioinformatics/btae224⟩ Article dans une revue pasteur-04778741v1
Belt and braces: Two escape ways to maintain the cassette reservoir of large chromosomal integrons Egill Richard,Baptiste Darracq,Eloi Littner,Gael Millot,Valentin Conteet al. PLoS Genetics, 2024, 20 (4), pp.e1011231. ⟨10.1371/journal.pgen.1011231⟩ Article dans une revue pasteur-04305445v1
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
Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency Matthieu Haudiquet,Julie Le Bris,Amandine Nucci,Rémy A Bonnin,Pilar Domingo-Calapet al. Nature Communications, 2024, 15 (1), pp.2032. ⟨10.1038/s41467-024-46147-5⟩ Article dans une revue hal-04492345v1
Spread of carbapenemase-producing Morganella spp from 2013 to 2021: a comparative genomic study Rémy Bonnin,Elodie Creton,Amandine Perrin,Delphine Girlich,Cecile Emeraudet al. The Lancet Microbe, 2024, 5 (6), pp.e547-e558. ⟨10.1016/S2666-5247(23)00407-X⟩ Article dans une revue hal-04629647v1
Tail assembly interference is a common strategy in bacterial antiviral defenses Lingchen He,Laura Miguel-Romero,Jonasz B Patkowski,Nasser Alqurainy,Eduardo P C Rochaet al. Nature Communications, 2024, 15, pp.7539. ⟨10.1038/s41467-024-51915-4⟩ Article dans une revue pasteur-04778725v1
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 Čepaitėet al. Cell Host & Microbe, 2024, 32 (6), pp.875-886.e9. ⟨10.1016/j.chom.2024.04.016⟩ Article dans une revue pasteur-04785210v1
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 Gauliardet al. Microbiome, 2024, 12 (1), pp.50. ⟨10.1186/s40168-023-01746-0⟩ Article dans une revue hal-04582235v1
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
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 Huntemannet al. Nucleic Acids Research, 2024, 52 (D1), pp.D164-D173. ⟨10.1093/nar/gkad964⟩ Article dans une revue pasteur-04778701v1
Assembly of a unique membrane complex in type VI secretion systems of Bacteroidota Thibault Bongiovanni,Casey Latario,Youn Le Cras,Evan Trus,Sophie Robitailleet 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 Laporteet al. Nature Microbiology, 2024, 9, pp.3345-3361. ⟨10.1038/s41564-024-01859-8⟩ Article dans une revue pasteur-04804169v1
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 Rochaet 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
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 Plantadeet al. PLoS Biology, 2024, 22 (10), pp.e3002814. ⟨10.1371/journal.pbio.3002814⟩ Article dans une revue pasteur-04778731v1
Integron cassettes commonly integrate into bacterial genomes via widespread non-classical attG sites Céline Loot,Gael A Millot,Egill Richard,Eloi Littner,Claire Vitet al. Nature Microbiology, 2024, 9 (1), pp.228-240. ⟨10.1038/s41564-023-01548-y⟩ Article dans une revue pasteur-04384854v1
Cassette recombination dynamics within chromosomal integrons are regulated by toxin-antitoxin systems Egill Richard,Baptiste Darracq,Eloi Littner,Claire Vit,Clémence Whitewayet al. Science Advances , 2024, 10 (2), pp.eadj3498. ⟨10.1126/sciadv.adj3498⟩ Article dans une revue hal-04397951v1
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
Evo‐Scope : Fully automated assessment of correlated evolution on phylogenetic trees Maxime Godfroid,Charles Coluzzi,Amaury Lambert,Philippe Glaser,Eduardo P C Rochaet al. Methods in Ecology and Evolution, 2024, 15 (2), pp.282 - 289. ⟨10.1111/2041-210x.14190⟩ Article dans une revue pasteur-04778723v1
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 Marboutyet al. Nature Communications, 2024, 15 (1), pp.664. ⟨10.1038/s41467-024-44965-1⟩ Article dans une revue hal-04413133v1
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. Rochaet al. Cell Host & Microbe, 2023, 31 (1), pp.69-82.e5. ⟨10.1016/j.chom.2022.12.001⟩ Article dans une revue 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⟩ Article dans une revue pasteur-04177373v1
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
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 Godfroidet al. Molecular Biology and Evolution, 2023, 40 (10), pp.msad217. ⟨10.1093/molbev/msad217⟩ Article dans une revue hal-04281854v1
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
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
Antimicrobial resistance level and conjugation permissiveness shape plasmid distribution in clinical enterobacteria Aida Alonso-del Valle,Laura Toricelestino,Anna Quirant,Carles Tardio Pi,Javier Delafuenteet 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
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
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
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
MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes Bertrand Néron,Rémi Denise,Charles Coluzzi,Marie Touchon,Eduardo P.C. Rochaet al. Peer Community Journal, 2023, 3, pp.e28. ⟨10.24072/pcjournal.250⟩ Article dans une revue (article de synthèse) pasteur-04060331v2
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
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
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
Phage-host coevolution in natural populations Damien Piel,Maxime Bruto,Yannick Labreuche,François Blanquart,David Goudenègeet al. Nature Microbiology, 2022, 7 (7), pp.1075-1086. ⟨10.1038/s41564-022-01157-1⟩ Article dans une revue hal-03738913v2
Phages and their satellites encode hotspots of antiviral systems François Rousset,Florence Depardieu,Solange Miele,Julien Dowding,Anne-Laure Lavalet al. Cell Host & Microbe, 2022, 30 (5), pp.740 - 753.e5. ⟨10.1016/j.chom.2022.02.018⟩ Article dans une revue 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⟩ Article dans une revue pasteur-03952614v1
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
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
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 Curyet al. Microorganisms, 2022, 10 (4), pp.700. ⟨10.3390/microorganisms10040700⟩ Article dans une revue 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⟩ Article dans une revue pasteur-04075979v1
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
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
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 Clermontet al. Nature Microbiology, 2021, 6 (3), pp.301-312. ⟨10.1038/s41564-020-00839-y⟩ Article dans une revue 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⟩ Article dans une revue 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 Rendueleset al. Nature Communications, 2021, 12 (1), 13 p. ⟨10.1038/s41467-021-26041-0⟩ Article dans une revue pasteur-03364094v1
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
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
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
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
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
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 Sismeiroet al. BMC Biology, 2020, 18 (1), pp.43. ⟨10.1186/s12915-020-00777-5⟩ Article dans une revue pasteur-02562489v1
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
PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph Guillaume Gautreau,Adelme Bazin,Mathieu Gachet,Rémi Planel,Laura Burlotet al. PLoS Computational Biology, 2020, ⟨10.1371/journal.pcbi.1007732⟩ Article dans une revue hal-03089210v1
Un siècle de recherche sur les bactériophages Mireille Ansaldi,Pascale Boulanger,Charlotte Brives,Laurent Debarbieux,Nicolas Dufouret al. Virologie, 2020, 24 (1), pp.9-22. ⟨10.1684/vir.2020.0809⟩ Article dans une revue (article de synthèse) hal-02530997v1
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 Siguieret al. Journal of Molecular Biology, 2020, 432 (3), pp.745-761. ⟨10.1016/j.jmb.2019.11.027⟩ Article dans une revue hal-02392007v1
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. Matthewset al. Journal of Biological Chemistry, 2020, 295 (19), pp.6594-6604. ⟨10.1074/jbc.RA120.013316⟩ Article dans une revue pasteur-03015795v1
A synthesis of bacterial and archaeal phenotypic trait data Joshua S. Madin,Daniel A. Nielsen,Maria Brbic,Ross Corkrey,David Dankoet al. Scientific Data , 2020, 7 (1), pp.170. ⟨10.1038/s41597-020-0497-4⟩ Article dans une revue pasteur-03015782v1
Phylogenetic background and habitat drive the genetic diversification of Escherichia coli Marie Touchon,Amandine Perrin,Jorge A Moura de Sousa,Belinda Vangchhia,Samantha Burnet al. PLoS Genetics, 2020, 16 (6), pp.e1008866. ⟨10.1371/journal.pgen.1008866⟩ Article dans une revue pasteur-02866790v2
Les applications antibactériennes des bactériophages Mireille Ansaldi,Pascale Boulanger,Charlotte Brives,Claire Le Hénaff,Laurent Debarbieuxet al. Virologie, 2020, 24 (1), pp.23-36. ⟨10.1684/vir.2019.0805⟩ Article dans une revue (article de synthèse) hal-02530998v1
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 Vielvaet al. Nature Communications, 2020, 11 (1), pp.3602. ⟨10.1038/s41467-020-17278-2⟩ Article dans une revue pasteur-03015777v1
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
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
Unlinked rRNA genes are widespread among Bacteria and Archaea Tess E Brewer,Mads Albertsen,Arwyn Edwards,Rasmus H Kirkegaard,Eduardo P C Rochaet al. The International Society of Microbiologial Ecology Journal, 2020, ⟨10.1038/s41396-019-0552-3⟩ Article dans une revue hal-02363135v1
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
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 Ghozlaneet al. Scientific Reports, 2019, ⟨10.1038/s41598-019-47656-w⟩ Article dans une revue hal-02329655v1
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
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
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
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⟩ Article dans une revue hal-02329753v1
Bacteriophages benefit from generalized transduction Alfred Fillol-Salom,Ahlam Alsaadi,Jorge A Moura de Sousa,Li Zhong,Kevin R Fosteret al. PLoS Pathogens, 2019, 15 (7), pp.e1007888. ⟨10.1371/journal.ppat.1007888⟩ Article dans une revue pasteur-04076056v1
Bacteriophages benefit from generalized transduction Alfred Fillol-Salom,Alsaadiid Ahlam,Jorge Moura de Sousa,Li Zhong,Kevin R Fosteridet al. PLoS Pathogens, 2019, ⟨10.1371/journal.ppat.1007888⟩ Article dans une revue 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⟩ Article dans une revue hal-02329742v1
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
Author Correction : Parallels between experimental and natural evolution of legume symbionts (vol 9, 2264, 2018) Camille Clerissi,Marie Touchon,Delphine Capela,Mingxing Tang,Stéphane Cruveilleret al. Nature Communications, 2018, 9, ⟨10.1038/s41467-018-07205-x⟩ Article dans une revue hal-02617830v1
Parallels between experimental and natural evolution of legume symbionts Camille Clerissi,Marie Touchon,Delphine Capela,Mingxing Tang,Stéphane Cruveilleret al. Nature Communications, 2018, 9 (1), pp.2264. ⟨10.1038/s41467-018-04778-5⟩ Article dans une revue 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⟩ Article dans une revue pasteur-02098387v1
HflXr mediates a novel antibiotic resistance mechanism 1 2 Mélodie Duval,Daniel Dar,Filipe Carvalho,Eduardo P C Rocha,Rotem Soreket 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
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
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 Michaliket al. Nucleic Acids Research, 2018, 46 (W1), pp.W246-W251. ⟨10.1093/nar/gky425⟩ Article dans une revue pasteur-02098389v1
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
Bacillus subtilis, the model Gram-positive bacterium: 20years of annotation refinement Rainer Borriss,Antoine Danchin,Colin R. Harwood,Claudine Médigue,Eduardo P. C. Rochaet al. Microbial Biotechnology, 2018, 11 (1), pp.3-17. ⟨10.1111/1751-7915.13043⟩ Article dans une revue cea-02291345v1
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
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
Metabolic diversity of the emerging pathogenic lineages of&lt;i&gt;Klebsiella pneumoniae&lt;/i&gt; 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
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
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-Galandet al. mBio, 2017, 8 (2), pp.e02296-16. ⟨10.1128/mBio.02296-16⟩ Article dans une revue pasteur-01689524v1
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 Rochaet al. Nature Communications, 2017, 8, pp.2094. ⟨10.1038/s41467-017-02350-1⟩ Article dans une revue pasteur-01967501v1
Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain Amandine Perrin,Elise Larsonneur,Ainsley Nicholson,David Edwards,Kristin Gundlachet al. Nature Communications, 2017, 8 (1), pp.15483. ⟨10.1038/ncomms15483⟩ Article dans une revue hal-02613118v1
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 Guettaet al. Molecular Biology and Evolution, 2017, 34 (10), pp.2503-2521. ⟨10.1093/molbev/msx165⟩ Article dans une revue hal-02620519v1
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
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 Bouchezet al. Molecular Ecology, 2017, 26 (7), pp.1818-1831. ⟨10.1111/mec.13895⟩ Article dans une revue hal-01607703v1
A widespread family of polymorphic toxins encoded by temperate phages Anne Jamet,Marie Touchon,Bruno Goncalves,João André Carriço,Alain Charbitet al. BMC Biology, 2016, 15 (1), pp.75. ⟨10.1186/s12915-017-0415-1⟩ Article dans une revue inserm-01580852v1
Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity Mylène M Maury,Yu-Huan Tsai,Caroline Charlier,Marie Touchon,Viviane Chenal-Francisqueet al. Nature Genetics, 2016, 48 (3), pp.308-313. ⟨10.1038/ng.3501⟩ Article dans une revue pasteur-02170775v1
Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis Sebastien Breurec,Alexis Criscuolo,Laure Diancourt,Olaya Rendueles,Mathias Vandenbogaertet al. Scientific Reports, 2016, 6, pp.30379. ⟨10.1038/srep30379⟩ Article dans une revue hal-02613124v1
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
Identification of protein secretion systems in bacterial genomes Sophie S. Abby,Jean Cury,Julien Guglielmini,Bertrand Néron,Marie Touchonet al. Scientific Reports, 2016, 6, ⟨10.1038/srep23080⟩ Article dans une revue pasteur-01374967v1
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
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
Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes Alexandra Moura,Alexis Criscuolo,Hannes Pouseele,Mylène M. Maury,Alexandre Leclercqet al. Nature Microbiology, 2016, 2, pp.16185. ⟨10.1038/nmicrobiol.2016.185⟩ Article dans une revue pasteur-01415883v1
Insights on the emergence of Mycobacterium tuberculosis from the analysis of Mycobacterium kansasii. Joyce Wang,Fiona Mcintosh,Nicolas Radomski,Ken Dewar,Roxane Simeoneet al. Genome Biology and Evolution, 2015, 7 (3), pp.856-70. ⟨10.1093/gbe/evv035⟩ Article dans une revue pasteur-01352692v1
Common Cell Shape Evolution of Two Nasopharyngeal Pathogens. Frédéric J Veyrier,Nicolas Biais,Pablo Morales,Nouria Belkacem,Cyril Guilhenet al. PLoS Genetics, 2015, 11 (7), pp.e1005338. ⟨10.1371/journal.pgen.1005338⟩ Article dans une revue pasteur-01352679v1
Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations Hong Xue,Otto X. Cordero,Francisco M. Camas,William Trimble,Folker Meyeret al. mBio, 2015, 6 (3), ⟨10.1128/mBio.00552-15⟩ Article dans une revue pasteur-01374963v1
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
Transient Hypermutagenesis Accelerates the Evolution of Legume Endosymbionts following Horizontal Gene Transfer Philippe Remigi,Delphine Capela,Camille Clerissi,Léna Tasse,Rachel Torchetet al. PLoS Biology, 2014, 12 (9), ⟨10.1371/journal.pbio.1001942⟩ Article dans une revue pasteur-01374959v1
The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences. Marie Touchon,Jean Cury,Eun-Jeong Yoon,Lenka Krizova,Gustavo C Cerqueiraet al. Genome Biology and Evolution, 2014, 6 (10), pp.2866-82. ⟨10.1093/gbe/evu225⟩ Article dans une revue pasteur-01132634v1
A PNPase dependent CRISPR System in Listeria. Nina Sesto,Marie Touchon,José Marques Andrade,Jiro Kondo,Eduardo P C Rochaet al. PLoS Genetics, 2014, 10 (1), pp.e1004065. ⟨10.1371/journal.pgen.1004065⟩ Article dans une revue pasteur-01145428v1
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 Maréchalet al. PLoS Neglected Tropical Diseases, 2014, 8 (11), pp.e3308. ⟨10.1371/journal.pntd.0003308⟩ Article dans une revue hal-01342968v1
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
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
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
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
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
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
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
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
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
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
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
Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. Marie Touchon,Claire Hoede,Olivier Tenaillon,Valérie Barbe,Simon Baeriswylet 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 Touchonet al. Antimicrobial Agents and Chemotherapy, 2009, 53 (6), pp.2283-2288. ⟨10.1128/AAC.00123-09⟩ Article dans une revue hal-03612468v1
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
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
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
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
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
The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis Isabelle Chambaud,Roland Heilig,Stephane Ferris,Valérie Barbe,Delphine Samsonet al. Nucleic Acids Research, 2001, 29 (10), pp.2145-2153. ⟨10.1093/nar/29.10.2145⟩ Article dans une revue hal-02679458v1
The complete genome sequence of the gram-positive bacterium Bacillus subtilis Frank Kunst,N. Ogasawara,Ivan Moszer,A.M. Albertini,G. Alloniet al. Nature, 1997, 390 (6657), pp.249-256. ⟨10.1038/36786⟩ Article dans une revue hal-02694553v1

Communication dans un congrès (9)

PPanGGOLiN: Depicting microbial diversity via a Partitioned Pangenome Graph Guillaume Gautreau,Christophe Ambroise,Catherine Matias,Amandine Perrin,Rémi Planelet al. Genome Informatics 2018, Sep 2018, Hinxton, Cambridge, United Kingdom Communication dans un congrès hal-04356757v1
PPanGGOLiN: Depicting microbial diversity via a Partitioned Pangenome Graph Guillaume Gautreau,Christophe Ambroise,Catherine Matias,Amandine Perrin,Rémi Planelet al. JOBIM 2018 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France Communication dans un congrès hal-04355945v1
Genomic diversity of Flavobacterium species. Éric Duchaud,Paul Barbier,Jean-François Bernardet,Christian Michel,Céline Chantry-Darmonet 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 Chantryet 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 Daruvardet al. 15th Congress of the Intern Organization for Mycoplasmology, 2006, Athens, United States. pp.Inconnu Communication dans un congrès hal-02815906v1
MolliGen: a database dedicated to the comparative genomics of mollicutes A Barre,Pascal P. Sirand-Pugnet,Xavier Foissac,Eduardo Rocha,A de Daruvardet 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
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

Poster de conférence (2)

MacSyFinder v2: An improved search engine to model and identify molecular systems in genomes Bertrand Néron,Rémi Denise,Charles Coluzzi,Marie Touchon,Eduardo Rochaet 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 Duboiset al. JOBIM 2019 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France Poster de conférence hal-04358380v1

Chapitre d'ouvrage (4)

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
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

Pré-publication, Document de travail (13)

Logan: Planetary-Scale Genome Assembly Surveys Life’s Diversity Rayan Chikhi,Téo Lemane,Raphaël Loll-Krippleber,Mercè Montoliu-Nerin,Brice Raffestinet al. 2025 Pré-publication, Document de travail hal-05446815v1
Serotype swapping in &lt;i&gt;Klebsiella&lt;/i&gt; spp. by plug-and-play Julie Le Bris,Hugo Varet,Eduardo P.C. Rocha,Olaya Rendueles 2025 Pré-publication, Document de travail hal-05361868v1
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 Coluzziet al. 2024 Pré-publication, Document de travail pasteur-04612996v1
Sedentary chromosomal integrons as biobanks of bacterial anti-phage defence systems Baptiste Darracq,Eloi Littner,Manon Brunie,Julia Bos,Pierre Alexandre Kaminskiet al. 2024 Pré-publication, Document de travail hal-04783441v1
YraN is a helicase-associated nuclease fostering extended recombination events by natural transformation Léo Hardy,Julie Plantade,Violette Morales,Fanny Mazzamuro,Eduardo Rochaet al. 2024 Pré-publication, Document de travail hal-04983173v1
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
A new route for integron cassette dissemination among bacterial genomes Céline Loot,Gael A Millot,Egill Richard,Claire Vit,Baptiste Darracqet al. 2022 Pré-publication, Document de travail 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 Pré-publication, Document de travail hal-03824239v1
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
Genetic drivers of chromosomal integron stability Egill Richard,Baptiste Darracq,Eloi Littner,Claire Vit,Clémence Whitewayet al. 2022 Pré-publication, Document de travail pasteur-03824759v1
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
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
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 Rechet al. 2019 Pré-publication, Document de travail hal-02366139v1

Logiciel (3)

MacSyLib Bertrand Néron,Sophie Abby,Eduardo Rocha 2025, ⟨swh:1:dir:ab0579d9d9fea3b32750df4ccd076ddde3bbce6a;origin=https://github.com/gem-pasteur/macsylib;visit=swh:1:snp:12363be7b9e43518ba1945d24152d3b89b915f6d;anchor=swh:1:rel:54d76b45afdc0bbf3178753ce34003442b2a9afc⟩ Logiciel hal-05421770v1
MacSyFinder Bertrand Néron,Sophie Abby,Eduardo Rocha 2024, ⟨swh:1:dir:a33618de0c3738daa75c2b1bc3e302df450a3987;origin=https://github.com/gem-pasteur/macsyfinder;visit=swh:1:snp:c8f689b846b5ddaff789ace1e17a2e6ad56e6d0e;anchor=swh:1:rel:2371db752dab111a56fe281675e7176c4da9983d⟩ Logiciel hal-04668349v3
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⟩ Logiciel hal-04603009v1