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Complete Nucleotide Sequence of Two Multidrug-Resistant IncR Plasmids from Klebsiella pneumoniae

 Fabrice Compain , L. Frangeul , Laurence Drieux , Charlotte Verdet , Sylvain Brisse , et al.
Antimicrobial Agents and Chemotherapy, 2014, 58 (7), pp.4207-4210. ⟨10.1128/AAC.02773-13⟩
Article dans une revue pasteur-03252020v1
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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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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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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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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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Mobility of Plasmids

 C. Smillie , M. P. Garcillan-Barcia , M. V. Francia , Eduardo P.C. Rocha , F. de La Cruz
Microbiology and Molecular Biology Reviews, 2010, 74 (3), pp.434 - 452. ⟨10.1128/MMBR.00020-10⟩
Article dans une revue pasteur-01374958v1
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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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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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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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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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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 Clermont , et al.
Nature Microbiology, 2021, 6 (3), pp.301-312. ⟨10.1038/s41564-020-00839-y⟩
Article dans une revue pasteur-03264663v1
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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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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
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Genetic drivers of chromosomal integron stability

 Egill Richard , Baptiste Darracq , Eloi Littner , Claire Vit , Clémence Whiteway , et al.
2022
Pré-publication, Document de travail pasteur-03824759v1
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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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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
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The Adaptation of Temperate Bacteriophages to Their Host Genomes

 M. Bobay , E. P. C. Rocha , M. Touchon
Molecular Biology and Evolution, 2013, 30 (4), pp.737 - 751. ⟨10.1093/molbev/mss279⟩
Article dans une revue pasteur-01374945v1

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 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
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Cassette recombination dynamics within chromosomal integrons are regulated by toxin-antitoxin systems

 Egill Richard , Baptiste Darracq , Eloi Littner , Claire Vit , Clémence Whiteway , et al.
Science Advances , 2024, 10 (2), pp.eadj3498. ⟨10.1126/sciadv.adj3498⟩
Article dans une revue hal-04397951v1
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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 Rocha , et 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
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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 Plantade , et al.
PLoS Biology, 2024, 22 (10), pp.e3002814. ⟨10.1371/journal.pbio.3002814⟩
Article dans une revue pasteur-04778731v1
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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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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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Development of a multiplex PCR assay for identification of Klebsiella pneumoniae hypervirulent clones of capsular serotype K2

 Suzanne Bialek-Davenet , Alexis Criscuolo , Florent Ailloud , Virginie Passet , Marie-Hélène Nicolas-Chanoine , et al.
Journal of Medical Microbiology, 2014, 63 (12), pp.1608-1614. ⟨10.1099/jmm.0.081448-0⟩
Article dans une revue hal-04575045v1

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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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
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Pervasive domestication of defective prophages by bacteria

 M. Bobay , M. Touchon , E. P. C. Rocha
Proceedings of the National Academy of Sciences of the United States of America, 2014, 111 (33), pp.12127 - 12132. ⟨10.1073/pnas.1405336111⟩
Article dans une revue pasteur-01374961v1
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