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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⟩
Journal articles hal-02613124v1
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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⟩
Journal articles hal-00390293v1
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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⟩
Journal articles pasteur-01967501v1
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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⟩
Journal articles pasteur-02012595v1
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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
Journal articles ensl-00175517v1

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⟩
Journal articles hal-03612468v1
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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⟩
Journal articles pasteur-01374967v1
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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⟩
Journal articles pasteur-01374955v1
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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
Preprints, Working Papers, ... hal-02988810v1

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

Paul Barbier , Armel A. Houel , Valentin Loux , Julie Poulain , Jean Francois J. F. Bernardet , et al.
Journal of Bacteriology, 2012, 194 (11), pp.3024-3025. ⟨10.1128/JB.00420-12⟩
Journal articles 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⟩
Journal articles pasteur-02098389v1
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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⟩
Journal articles 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⟩
Journal articles pasteur-01145428v1
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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⟩
Journal articles hal-02613118v1
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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⟩
Journal articles pasteur-01374940v1
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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⟩
Journal articles pasteur-02626502v1
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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⟩
Journal articles ensl-00175525v1
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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⟩
Journal articles hal-02329742v1
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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⟩
Journal articles pasteur-01415883v1
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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⟩
Journal articles hal-03357369v1
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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⟩
Journal articles pasteur-01374968v1

Regulation of genetic flux between bacteria by restriction–modification systems

Pedro H. Oliveira , Marie Touchon , Eduardo P. C. Rocha
Proceedings of the National Academy of Sciences of the United States of America, 2016, 113 (20), pp.5658 - 5663. ⟨10.1073/pnas.1603257113⟩
Journal articles pasteur-01374969v1
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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⟩
Journal articles 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⟩
Journal articles pasteur-01578349v1
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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⟩
Journal articles pasteur-04060331v2
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Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer

Marie Touchon , Jorge A Moura de Sousa , Eduardo P. C. Rocha
Current Opinion in Microbiology, 2017, 38, pp.66-73. ⟨10.1016/j.mib.2017.04.010⟩
Journal articles pasteur-03111100v1
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Phylogenetic background and habitat drive the genetic diversification of Escherichia coli

Marie Touchon , Amandine Perrin , Jorge A Moura de Sousa , Belinda Vangchhia , Samantha Burn , et al.
PLoS Genetics, 2020, 16 (6), pp.e1008866. ⟨10.1371/journal.pgen.1008866⟩
Journal articles pasteur-02866790v2
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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⟩
Journal articles cea-01880286v1

Metabolic diversity of the emerging pathogenic lineages ofKlebsiella pneumoniae

Camille Blin , Virginie Passet , Marie Touchon , Eduardo P. C. Rocha , Sylvain Brisse
Environmental Microbiology, 2017, 19 (5), pp.1881 - 1898. ⟨10.1111/1462-2920.13689⟩
Journal articles pasteur-04076001v1
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The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences.

Marie Touchon , Jean Cury , Eun-Jeong Yoon , Lenka Krizova , Gustavo C Cerqueira , et al.
Genome Biology and Evolution, 2014, 6 (10), pp.2866-82. ⟨10.1093/gbe/evu225⟩
Journal articles pasteur-01132634v1