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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 pasteur-04060331v2
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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⟩
Article dans une revue pasteur-04076056v1
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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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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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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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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⟩
Article dans une revue hal-02363135v1

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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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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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
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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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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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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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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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Role of Klebsiella pneumoniae Type VI secretion system (T6SS) in long-term gastrointestinal colonization

 Thomas Merciecca , Stéphanie Bornes , Laurence Nakusi , Sébastien Theil , Olaya Rendueles , et al.
Scientific Reports, 2022, 12 (1), pp.16968. ⟨10.1038/s41598-022-21396-w⟩
Article dans une revue pasteur-03809977v1
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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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A Single Amino Acid Substitution Changes the Self-Assembly Status of a Type IV Piliation Secretin

 N. N. Nickerson , S. S. Abby , E. P. C. Rocha , M. Chami , A. P. Pugsley
Journal of Bacteriology, 2012, 194 (18), pp.4951 - 4958. ⟨10.1128/JB.00798-12⟩
Article dans une revue pasteur-01374952v1
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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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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

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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1926–2016: 90 Years of listeriology

 Alice Lebreton , Fabrizia Stavru , Sylvain Brisse , Pascale Cossart
Microbes and Infection, 2016, 18 (12), pp.711 - 723. ⟨10.1016/j.micinf.2016.10.009⟩
Article dans une revue hal-01400517v2
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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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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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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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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 hal-02329724v1
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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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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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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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BioConvert: a comprehensive format converter for life sciences

 Hugo Caro , Sulyvan Dollin , Anne Biton , Bryan Brancotte , Dimitri Desvillechabrol , et al.
NAR Genomics and Bioinformatics, 2023, 5 (3), ⟨10.1093/nargab/lqad074⟩
Article dans une revue pasteur-04279554v2
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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 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⟩
Article dans une revue hal-02329655v1
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