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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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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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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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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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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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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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Identification and characterization of thousands of bacteriophage satellites across bacteria

Jorge Moura de Sousa , Alfred Fillol-Salom , José Penadés , Eduardo P.C. Rocha
Nucleic Acids Research, In press, ⟨10.1093/nar/gkad123⟩
Article dans une revue hal-03838678v2
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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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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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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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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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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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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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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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Draft Genome Sequence of Campylobacter coli Strain IPSID-1 Isolated from a Patient with Immunoproliferative Small Intestinal Disease

Alexis Criscuolo , Arnaud de La Blanchardière , Solène Coeuret , Virginie Passet , Virginie Saguet-Rysanek , et al.
Genome Announcements, 2014, 2 (2), pp.e00079-14. ⟨10.1128/genomeA.00079-14⟩
Article dans une revue pasteur-02869569v1
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Listeria monocytogenes sequence type 1 is predominant in ruminant rhombencephalitis

Margaux Dreyer , Lisandra Aguilar-Bultet , Sebastian Rupp , Claudia Guldimann , Roger Stephan , et al.
Scientific Reports, 2016, 6 (1), pp.36419. ⟨10.1038/srep36419⟩
Article dans une revue pasteur-02185472v1
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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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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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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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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
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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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Tools for massive bacterial comparative genomics : Development and Applications

Amandine Perrin
Quantitative Methods [q-bio.QM]. Sorbonne Université, 2022. English. ⟨NNT : 2022SORUS127⟩
Thèse tel-03789655v2
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Complete Genome Sequence of Streptococcus pyogenes emm28 Clinical Isolate M28PF1, Responsible for a Puerperal Fever

Magalie Longo , Mathieu de Jode , Céline Plainvert , Antonin Weckel , Anna Hua , et al.
Genome Announcements, 2015, 3 (4), pp.e00750-15. ⟨10.1128/genomeA.00750-15⟩
Article dans une revue inserm-01179116v1
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“Epidemic Clones” of Listeria monocytogenes Are Widespread and Ancient Clonal Groups

Thomas Cantinelli , Viviane Chenal-Francisque , Laure Diancourt , Lise Frezal , Alexandre Leclercq , et al.
Journal of Clinical Microbiology, 2013, 51 (11), pp.3770-3779. ⟨10.1128/JCM.01874-13⟩
Article dans une revue pasteur-02869829v1

Testing for independence between evolutionary processes

Abdelkader Behdenna , Joël Pothier , Sophie S. Abby , Guillaume Achaz , Amaury Lambert
Systematic Biology, 2016, 65 (5), pp.812-823. ⟨10.1093/sysbio/syw004⟩
Article dans une revue hal-01490961v1
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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, In press, pp.Ahead of Print. ⟨10.1128/aac.00127-23⟩
Article dans une revue pasteur-04027513v1