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Exploring the diversity of listeria monocytogenes biofilm architecture by high-throughput confocal laser scanning microscopy and the predominance of the honeycomb-like morphotype

 Morgan Guilbaud , Pascal Piveteau , Mickaël Desvaux , Sylvain Brisse , Romain Briandet
Applied and Environmental Microbiology, 2015, 81 (5), pp.1813-1819. ⟨10.1128/AEM.03173-14⟩
Article dans une revue hal-01204409v1
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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

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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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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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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How capsules protect the cell, shape genetic exchanges and drive bacterial evolution

 Matthieu Haudiquet
Human health and pathology. Université Paris Cité, 2022. English. ⟨NNT : 2022UNIP7137⟩
Thèse tel-04076297v2
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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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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
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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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A Genomic Survey of Reb Homologs Suggests Widespread Occurrence of R-Bodies in Proteobacteria

 Kasie Raymann , Louis-Marie Bobay , Thomas G. Doak , Michael Lynch , Simonetta Gribaldo
G3, 2013, 3 (3), pp.505-516. ⟨10.1534/g3.112.005231⟩
Article dans une revue hal-01579027v1
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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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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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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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In Silico Analysis of Usher Encoding Genes in Klebsiella pneumoniae and Characterization of Their Role in Adhesion and Colonization

 Fida Khater , Damien Balestrino , Nicolas Charbonnel , Jean François Dufayard , Sylvain Brisse , et al.
PLoS ONE, 2015, 10 (3), ⟨10.1371/journal.pone.0116215⟩
Article dans une revue hal-01393629v1
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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

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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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

Bacterial toxin-antitoxin systems: Translation inhibitors everywhere

 Julien Guglielmini , Laurence van Melderen
Mobile Genetic Elements, 2014, 1 (4), pp.283-306. ⟨10.4161/mge.18477⟩
Article dans une revue hal-03259584v1

A Systematic and Functional Classification of Streptococcus pyogenes That Serves as a New Tool for Molecular Typing and Vaccine Development

 Martina Sanderson-Smith , David de Oliveira , Julien Guglielmini , David Mcmillan , Therese Vu , et al.
Journal of Infectious Diseases, 2014, 210 (8), pp.1325-1338. ⟨10.1093/infdis/jiu260⟩
Article dans une revue hal-03259577v1
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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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In-vivo loss of carbapenem resistance by extensively drug-resistant Klebsiella pneumoniae during treatment via porin expression modification

 Suzanne Bialek-Davenet , Noémie Mayer , Julia Vergalli , Marion Duprilot , Sylvain Brisse , et al.
Scientific Reports, 2017, 7 (1), ⟨10.1038/s41598-017-06503-6⟩
Article dans une revue hal-01831725v1
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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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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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Impact of antibiotics on the human gut phageome : from method to application

 Camille d'Humières
Life Sciences [q-bio]. Université Paris Cité, 2020. English. ⟨NNT : 2020UNIP7014⟩
Thèse tel-04076281v1
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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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