Microbial defenses against mobile genetic elements and viruses: Who defends whom from what? von Rocha, Eduardo P C, Bikard, David

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Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes von Treangen, Todd J, Rocha, Eduardo P C

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Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility von Denise, Rémi, Abby, Sophie S, Rocha, Eduardo P C

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The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems von Abby, Sophie S, Rocha, Eduardo P C

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Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids von Redondo-Salvo, Santiago, Fernández-López, Raúl, Ruiz, Raúl, Vielva, Luis, de Toro, María, Rocha, Eduardo P. C., Garcillán-Barcia, M. Pilar, de la Cruz, Fernando

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Genetic and life-history traits associated with the distribution of prophages in bacteria von Touchon, Marie, Bernheim, Aude, Rocha, Eduardo PC

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The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella von Touchon, Marie, Rocha, Eduardo P C

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Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity von Maury, Mylène M, Tsai, Yu-Huan, Charlier, Caroline, Touchon, Marie, Chenal-Francisque, Viviane, Leclercq, Alexandre, Criscuolo, Alexis, Gaultier, Charlotte, Roussel, Sophie, Brisabois, Anne, Disson, Olivier, Rocha, Eduardo P C, Brisse, Sylvain, Lecuit, Marc

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MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems von Abby, Sophie S, Néron, Bertrand, Ménager, Hervé, Touchon, Marie, Rocha, Eduardo P C

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Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of the nosocomial pathogen Klebsiella pneumoniae von Haudiquet, Matthieu, Buffet, Amandine, Rendueles, Olaya, Rocha, Eduardo P. C

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The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation von Guglielmini, Julien, Quintais, Leonor, Garcillán-Barcia, Maria Pilar, de la Cruz, Fernando, Rocha, Eduardo P C

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Pervasive domestication of defective prophages by bacteria von Bobay, Louis-Marie, Touchon, Marie, Rocha, Eduardo P. C.

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The systemic imprint of growth and its uses in ecological (meta)genomics von Vieira-Silva, Sara, Rocha, Eduardo P C

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PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph von Gautreau, Guillaume, Bazin, Adelme, Gachet, Mathieu, Planel, Remi, Burlot, Laura, Dubois, Mathieu, Perrin, Amandine, Medigue, Claudine, Calteau, Alexandra, Cruveiller, Stephane, Matias, Catherine, Ambroise, Christophe, Rocha, Eduardo P. C., Vallenet, David

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Phage-plasmids promote recombination and emergence of phages and plasmids von Pfeifer, Eugen, Rocha, Eduardo P. C.

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The chromosomal organization of horizontal gene transfer in bacteria von Oliveira, Pedro H., Touchon, Marie, Cury, Jean, Rocha, Eduardo P. C.

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Integrative and conjugative elements and their hosts: composition, distribution and organization von Cury, Jean, Touchon, Marie, Rocha, Eduardo P C

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The Evolution of Protein Secretion Systems by Co-option and Tinkering of Cellular Machineries von Denise, Rémi, Abby, Sophie S., Rocha, Eduardo P.C.

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CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins von Couvin, David, Bernheim, Aude, Toffano-Nioche, Claire, Touchon, Marie, Michalik, Juraj, Néron, Bertrand, Rocha, Eduardo P C, Vergnaud, Gilles, Gautheret, Daniel, Pourcel, Christine

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Adaptation to novel spatially-structured environments is driven by the capsule and alters virulence-associated traits von Nucci, Amandine, Rocha, Eduardo P. C., Rendueles, Olaya

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