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Experimental Evolution as a Tool to Investigate Natural Processes and Molecular Functions

Philippe Remigi , Catherine Masson-Boivin , Eduardo P C Rocha
Trends in Microbiology, 2019, 27 (7), pp.623-634. ⟨10.1016/j.tim.2019.02.003⟩
Article dans une revue hal-02329724v1
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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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Transient Hypermutagenesis Accelerates the Evolution of Legume Endosymbionts following Horizontal Gene Transfer

Philippe Remigi , Delphine Capela , Camille Clerissi , Léna Tasse , Rachel Torchet , et al.
PLoS Biology, 2014, 12 (9), ⟨10.1371/journal.pbio.1001942⟩
Article dans une revue pasteur-01374959v1
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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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Multicenter Outbreak of Infections by Saprochaete clavata , an Unrecognized Opportunistic Fungal Pathogen

Sophie Vaux , Alexis Criscuolo , Marie Desnos-Ollivier , Laure Diancourt , Chloé Tarnaud , et al.
mBio, 2014, 5 (6), pp.e02309-14. ⟨10.1128/mBio.02309-14⟩
Article dans une revue hal-01484251v1
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Molecular epidemiology of carbapenem non-susceptible Acinetobacter baumannii in France.

Katy Jeannot , Laure Diancourt , Sophie Vaux , Michelle Thouverez , Amandina Ribeiro , et al.
PLoS ONE, 2013, 9 (12), pp.e115452. ⟨10.1371/journal.pone.0115452⟩
Article dans une revue hal-01114942v1
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The chromosomal organization of horizontal gene transfer in bacteria

Pedro H. Oliveira , Marie Touchon , Jean Cury , Eduardo P C Rocha
Nature Communications, 2017, 8 (1), pp.841. ⟨10.1038/s41467-017-00808-w⟩
Article dans une revue hal-04325283v1
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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

Marker-free plasmids for biotechnological applications – implications and perspectives

Pedro Oliveira , Juergen Mairhofer
Trends in Biotechnology, 2013, 31 (9), pp.539-547. ⟨10.1016/j.tibtech.2013.06.001⟩
Article dans une revue istex hal-04328020v1
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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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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

Biofilms structural diversity of 100 strains of the food-borne pathogen Listeria monocytogenes

Morgan Guilbaud , Pascal Piveteau , Sylvain Brisse , Romain Briandet
BIOFILMS 5, Dec 2012, PARIS, France
Poster hal-01570155v1
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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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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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1926–2016: 90 Years of listeriology

Alice Lebreton , Fabrizia Stavru , Sylvain Brisse , Pascale Cossart
Microbes and Infection, 2016, 18 (12), pp.711 - 723. ⟨10.1016/j.micinf.2016.10.009⟩
Article dans une revue hal-01400517v2
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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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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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Unlinked rRNA genes are widespread among Bacteria and Archaea

Tess E Brewer , Mads Albertsen , Arwyn Edwards , Rasmus H Kirkegaard , Eduardo P C Rocha , et al.
The International Society of Microbiologial Ecology Journal, 2020, ⟨10.1038/s41396-019-0552-3⟩
Article dans une revue hal-02363135v1

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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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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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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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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Real-time search of all bacterial and viral genomic data

Phelim Bradley , Henk C den Bakker , Eduardo P C Rocha , Gil Mcvean , Zamin Iqbal
Nature Biotechnology, 2019, 37 (2), pp.152-159. ⟨10.1038/s41587-018-0010-1⟩
Article dans une revue hal-02329753v1

A Systematic and Functional Classification of Streptococcus pyogenes That Serves as a New Tool for Molecular Typing and Vaccine Development

Martina Sanderson-Smith , David de Oliveira , Julien Guglielmini , David Mcmillan , Therese Vu , et al.
Journal of Infectious Diseases, 2014, 210 (8), pp.1325-1338. ⟨10.1093/infdis/jiu260⟩
Article dans une revue hal-03259577v1
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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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Bacteriophages benefit from generalized transduction

Alfred Fillol-Salom , Ahlam Alsaadi , Jorge A Moura de Sousa , Li Zhong , Kevin R Foster , et al.
PLoS Pathogens, 2019, 15 (7), pp.e1007888. ⟨10.1371/journal.ppat.1007888⟩
Article dans une revue pasteur-04076056v1
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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