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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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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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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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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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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

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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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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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

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

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
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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

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
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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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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
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The absence of surface D-alanylation, localized on lipoteichoic acid, impacts the Clostridioides difficile way of life and antibiotic resistance

 Pierre-Alexandre Lacotte , Sandrine Denis-Quanquin , Eva Chatonnat , Julie Le Bris , David Leparfait , et al.
Frontiers in Microbiology, 2023, 14, ⟨10.3389/fmicb.2023.1267662⟩
Article dans une revue hal-04281897v1
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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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Mining zebrafish microbiota reveals key community-level resistance against fish pathogen infection

 Franziska Stressmann , Joaquin Bernal-Bayard , David Pérez-Pascual , Bianca Audrain , Olaya Rendueles , et al.
2020
Pré-publication, Document de travail pasteur-02873606v1
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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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CRISPRCasdb a successor of CRISPRdb containing CRISPR arrays and cas genes from complete genome sequences, and tools to download and query lists of repeats and spacers

 Christine Pourcel , Marie Touchon , Nicolas Villeriot , Jean-Philippe Vernadet , David Couvin , et al.
Nucleic Acids Research, 2020, 48 (D1), pp.D535-D544. ⟨10.1093/nar/gkz915⟩
Article dans une revue hal-02990278v1

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
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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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Systematic and quantitative view of the antiviral arsenal of prokaryotes

 Florian Tesson , Alexandre Hervé , Ernest Mordret , Marie Touchon , Camille D’humières , et al.
Nature Communications, 2022, 13 (1), pp.2561. ⟨10.1038/s41467-022-30269-9⟩
Article dans une revue hal-03823827v2
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Optimized Multilocus Variable-Number Tandem-Repeat Analysis Assay and Its Complementarity with Pulsed-Field Gel Electrophoresis and Multilocus Sequence Typing for Listeria monocytogenes Clone Identification and Surveillance

 Viviane Chenal-Francisque , Laure Diancourt , Thomas Cantinelli , Virginie Passet , Coralie Tran-Hykes , et al.
Journal of Clinical Microbiology, 2013, 51 (6), pp.1868-1880. ⟨10.1128/JCM.00606-13⟩
Article dans une revue pasteur-02869993v1
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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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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 hal-02530998v1
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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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