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Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths.

 Marie Touchon , Claire Hoede , Olivier Tenaillon , Valérie Barbe , Simon Baeriswyl , et al.
PLoS Genetics, 2009, 5 (1), pp.e1000344. ⟨10.1371/journal.pgen.1000344⟩
Article dans une revue hal-00390293v1
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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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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
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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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The Small, Slow and Specialized CRISPR and Anti-CRISPR of Escherichia and Salmonella

 Marie Touchon , Eduardo P. C. Rocha
PLoS ONE, 2010, 5 (6), pp.11126 - 11126. ⟨10.1371/journal.pone.0011126.s006⟩
Article dans une revue pasteur-01374940v1
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Replication-associated strand asymmetries in mammalian genomes: toward detection of replication origins.

 Marie Touchon , Samuel Nicolay , Benjamin Audit , Edward-Benedict Brodie of Brodie , Yves d'Aubenton-Carafa , et al.
Proceedings of the National Academy of Sciences of the United States of America, 2005, 28 (102), pp.9836-41. ⟨10.1073/pnas.0500577102⟩
Article dans une revue ensl-00175525v1
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Comparative genomic analysis of Acinetobacter strains isolated from murine colonic crypts

 Azadeh Saffarian , Marie Touchon , Céline Mulet , Régis R. Tournebize , Virginie Passet , et al.
BMC Genomics, 2017, 18 (1), pp.525. ⟨10.1186/s12864-017-3925-x⟩
Article dans une revue pasteur-01570221v1
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Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens

 Olaya Rendueles , Marc Garcia-Garcerà , Bertrand Néron , Marie Touchon , Eduardo P C Rocha
PLoS Pathogens, 2017, 44, pp.289 - 289. ⟨10.1371/journal.ppat.1006525.s020⟩
Article dans une revue pasteur-01578349v1
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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
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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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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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Epigenomic characterization of Clostridioides difficile finds a conserved DNA methyltransferase that mediates sporulation and pathogenesis

 Pedro Oliveira , John Ribis , Elizabeth Garrett , Dominika Trzilova , Alex Kim , et al.
Nature Microbiology, 2020, 5 (1), pp.166-180. ⟨10.1038/s41564-019-0613-4⟩
Article dans une revue hal-02988691v1
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A PNPase dependent CRISPR System in Listeria.

 Nina Sesto , Marie Touchon , José Marques Andrade , Jiro Kondo , Eduardo P C Rocha , et al.
PLoS Genetics, 2014, 10 (1), pp.e1004065. ⟨10.1371/journal.pgen.1004065⟩
Article dans une revue pasteur-01145428v1

Complete genome sequence of Flavobacterium indicum GPSTA100-9T, isolated from warm spring water

 Paul Barbier , Armel A. Houel , Valentin Loux , Julie Poulain , Jean-François Bernardet , et al.
Journal of Bacteriology, 2012, 194 (11), pp.3024-3025. ⟨10.1128/JB.00420-12⟩
Article dans une revue hal-02643519v1
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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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Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain

 Amandine Perrin , Elise Larsonneur , Ainsley Nicholson , David Edwards , Kristin Gundlach , et al.
Nature Communications, 2017, 8 (1), pp.15483. ⟨10.1038/ncomms15483⟩
Article dans une revue hal-02613118v1
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From DNA sequence analysis to modeling replication in the human genome.

 Edward-Benedict Brodie of Brodie , Samuel Nicolay , Marie Touchon , Benjamin Audit , Yves d'Aubenton-Carafa , et al.
Physical Review Letters, 2005, 24 (94), pp.248103
Article dans une revue ensl-00175517v1
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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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Identification of protein secretion systems in bacterial genomes

 Sophie S. Abby , Jean Cury , Julien Guglielmini , Bertrand Néron , Marie Touchon , et al.
Scientific Reports, 2016, 6, ⟨10.1038/srep23080⟩
Article dans une revue pasteur-01374967v1
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Genome diversification via genetic exchanges between temperate and virulent bacteriophages

 Jorge A. Moura de Sousa , Eugen Pfeifer , Marie Touchon , Eduardo P. C. Rocha
2020
Pré-publication, Document de travail hal-02988810v1
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Genetic exchanges are more frequent in bacteria encoding capsules

 Olaya Rendueles , Jorge a Moura de Sousa , Aude Bernheim , Marie Touchon , Eduardo P C Rocha
PLoS Genetics, 2018, 14 (12), pp.e1007862. ⟨10.1371/journal.pgen.1007862⟩
Article dans une revue pasteur-02012595v1
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Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria

 Aude Bernheim , Alicia Calvo-Villamañán , Clovis Basier , Lun Cui , Eduardo P C Rocha , et al.
Nature Communications, 2017, 8, pp.2094. ⟨10.1038/s41467-017-02350-1⟩
Article dans une revue pasteur-01967501v1

A Module Located at a Chromosomal Integration Hot Spot Is Responsible for the Multidrug Resistance of a Reference Strain from Escherichia coli Clonal Group A

 Mathilde Lescat , Alexandra Calteau , Claire Hoede , Valérie Barbe , Marie Touchon , et al.
Antimicrobial Agents and Chemotherapy, 2009, 53 (6), pp.2283-2288. ⟨10.1128/AAC.00123-09⟩
Article dans une revue hal-03612468v1

Human gene organization driven by the coordination of replication and transcription.

 Maxime Huvet , Samuel Nicolay , Marie Touchon , Benjamin Audit , Yves d'Aubenton-Carafa , et al.
Genome Research, 2007, 17, pp.1278-85. ⟨10.1101/gr.6533407⟩
Article dans une revue ensl-00198451v1
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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

Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity

 Mylène M Maury , Yu-Huan Tsai , Caroline Charlier , Marie Touchon , Viviane Chenal-Francisque , et al.
Nature Genetics, 2016, 48 (3), pp.308-313. ⟨10.1038/ng.3501⟩
Article dans une revue pasteur-02170775v1
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When bacteria are phage playgrounds: interactions between viruses, cells and mobile genetic elements

 Eugen Pfeifer , Jorge de Sousa , Marie Touchon , Eduardo Rocha
2022
Pré-publication, Document de travail hal-03824239v1
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Causes and Consequences of Bacteriophage Diversification via Genetic Exchanges across Lifestyles and Bacterial Taxa

 Jorge A Moura de Sousa , Eugen Pfeifer , Marie Touchon , Eduardo P. C. Rocha
Molecular Biology and Evolution, 2021, 38 (6), pp.2497-2512. ⟨10.1093/molbev/msab044⟩
Article dans une revue hal-03357362v1
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A widespread family of polymorphic toxins encoded by temperate phages

 Anne Jamet , Marie Touchon , Bruno Goncalves , João André Carriço , Alain Charbit , et al.
BMC Biology, 2016, 15 (1), pp.75. ⟨10.1186/s12915-017-0415-1⟩
Article dans une revue inserm-01580852v1
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