• 2025
  Coluzzi C, Rocha EPC, The Spread of Antibiotic Resistance Is Driven by Plasmids Among the Fastest Evolving and of Broadest Host Range., Mol Biol Evol 2025 Mar; 42(3): .
• 2024
  Hafner L, Gadin E, Huang L, Frouin A, Laporte F, Gaultier C, Vieira A, Maudet C, Varet H, Moura A, Bracq-Dieye H, Tessaud-Rita N, Maury M, Dazas M, Legendre R, Gastineau P, Tsai YH, Coppée JY, Charlier C, Patin E, Chikhi R, Rocha EPC, Leclercq A, Disson O, Aschard H, Lecuit M, Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes., Nat Microbiol 2024 Dec; 9(12): 3345-3361.
• 2024
  Manuel Ares-Arroyo, Amandine Nucci, Eduardo Rocha, Expanding the diversity of origin of transfer-containing sequences in mobilizable plasmids, Nature Microbiology, In press, ⟨10.1038/s41564-024-01844-1⟩.
• 2024
  Mazzamurro F, Chirakadavil JB, Durieux I, Poiré L, Plantade J, Ginevra C, Jarraud S, Wilharm G, Charpentier X, P C Rocha E, Intragenomic conflicts with plasmids and chromosomal mobile genetic elements drive the evolution of natural transformation within species., PLoS Biol 2024 Oct; 22(10): e3002814.
• 2024
  Benz F, Camara-Wilpert S, Russel J, Wandera KG, Čepaitė R, Ares-Arroyo M, Gomes-Filho JV, Englert F, Kuehn JA, Gloor S, Mestre MR, Cuénod A, Aguilà-Sans M, Maccario L, Egli A, Randau L, Pausch P, Rocha EPC, Beisel CL, Madsen JS, Bikard D, Hall AR, Sørensen SJ, Pinilla-Redondo R, Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans., Cell Host Microbe 2024 May; (): .
• 2024
  d'Humières C, Delavy M, Alla L, Ichou F, Gauliard E, Ghozlane A, Levenez F, Galleron N, Quinquis B, Pons N, Mullaert J, Bridier-Nahmias A, Condamine B, Touchon M, Rainteau D, Lamazière A, Lesnik P, Ponnaiah M, Lhomme M, Sertour N, Devente S, Docquier JD, Bougnoux ME, Tenaillon O, Magnan M, Ruppé E, Grall N, Duval X, Ehrlich D, Mentré F, Denamur E, Rocha EPC, Le Chatelier E, Burdet C, Perturbation and resilience of the gut microbiome up to 3 months after β-lactams exposure in healthy volunteers suggest an important role of microbial β-lactamases., Microbiome 2024 Mar; 12(1): 50.
• 2024
  Matthieu Haudiquet, Julie Le Bris, Amandine Nucci, Rémy A Bonnin, Pilar Domingo-Calap, Eduardo P C Rocha, Olaya Rendueles, Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency, Nature Communications, 2024, 15 (1), pp.2032. ⟨10.1038/s41467-024-46147-5⟩.
• 2024
  Pfeifer E, Rocha EPC, Phage-plasmids promote recombination and emergence of phages and plasmids., Nat Commun 2024 Feb; 15(1): 1545.
• 2024
  Egill Richard, Baptiste Darracq, Eloi Littner, Claire Vit, Clémence Whiteway, Julia Bos, Florian Fournes, Geneviève Garriss, Valentin Conte, Delphine Lapaillerie, Vincent Parissi, François Rousset, Ole Skovgaard, David Bikard, Eduardo P. C. Rocha, Didier Mazel, Céline Loot, Cassette recombination dynamics within chromosomal integrons are regulated by toxin-antitoxin systems., Science Advances , 2024, 10 (2), pp.eadj3498. ⟨10.1126/sciadv.adj3498⟩.
• 2024
  Loot C, Millot GA, Richard E, Littner E, Vit C, Lemoine F, Néron B, Cury J, Darracq B, Niault T, Lapaillerie D, Parissi V, Rocha EPC, Mazel D, Integron cassettes integrate into bacterial genomes via widespread non-classical attG sites., Nat Microbiol 2024 Jan; 9(1): 228-240.
• 2023
  Coluzzi C, Guillemet M, Mazzamurro F, Touchon M, Godfroid M, Achaz G, Glaser P, Rocha EPC, Chance Favors the Prepared Genomes: Horizontal Transfer Shapes the Emergence of Antibiotic Resistance Mutations in Core Genes., Mol Biol Evol 2023 Oct; 40(10): .
• 2023
  Amandine Nucci, Eduardo P C Rocha, Olaya Rendueles, Latent evolution of biofilm formation depends on life-history and genetic background, npj Biofilms and Microbiomes, 2023, 9 (1), pp.53. ⟨10.1038/s41522-023-00422-3⟩.
• 2023
  Rendueles O, de Sousa JAM, Rocha EPC, Competition between lysogenic and sensitive bacteria is determined by the fitness costs of the different emerging phage-resistance strategies., Elife 2023 Mar; 12(): .
• 2023
  de Sousa JAM, Fillol-Salom A, Penadés JR, Rocha EPC, Identification and characterization of thousands of bacteriophage satellites across bacteria., Nucleic Acids Res 2023 Mar; (): .
• 2022
  Ares-Arroyo M, Coluzzi C, P C Rocha E, , Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation., Nucleic Acids Res 2022 Nov; (): .
• 2022
  Felipe-Ruiz A, Marina A, Rocha EPC, , Structural and Genomic Evolution of RRNPPA Systems and Their Pheromone Signaling., mBio 2022 Oct; (): e0251422.
• 2022
  Pfeifer E, Bonnin RA, Rocha EPC, , Phage-Plasmids Spread Antibiotic Resistance Genes through Infection and Lysogenic Conversion., mBio 2022 Sep; (): e0185122.
• 2022
  Nucci A, Rocha EPC, Rendueles O, , Adaptation to novel spatially-structured environments is driven by the capsule and alters virulence-associated traits., Nat Commun 2022 Aug; 13(1): 4751.
• 2022
  Coluzzi C, Garcillán-Barcia MP, de la Cruz F, Rocha EPC, , Evolution of Plasmid Mobility: Origin and Fate of Conjugative and Nonconjugative Plasmids., Mol Biol Evol 2022 Jun; 39(6): .
• 2022
  Rousset F, Depardieu F, Miele S, Dowding J, Laval AL, Lieberman E, Garry D, Rocha EPC, Bernheim A, Bikard D, Phages and their satellites encode hotspots of antiviral systems., Cell Host Microbe 2022 May; 30(5): 740-753.e5.
• 2022
  Moura de Sousa JA, Rocha EPC, , To catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites., Philos Trans R Soc Lond B Biol Sci 2022 Jan; 377(1842): 20200475.
• 2021
  Haudiquet M, Buffet A, Rendueles O, Rocha EPC, , Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of the nosocomial pathogen Klebsiella pneumoniae., PLoS Biol 2021 Jul; 19(7): e3001276.
• 2021
  Pfeifer E, Moura de Sousa JA, Touchon M, Rocha EPC, , Bacteria have numerous distinctive groups of phage-plasmids with conserved phage and variable plasmid gene repertoires., Nucleic Acids Res 2021 03; 49(5): 2655-2673.
• 2021
  Amandine Buffet , Eduardo P. C. Rocha and Olaya Rendueles, Nutrient conditions are primary drivers of bacterial capsule maintenance in Klebsiella, Proc. R. Soc. B.288:20202876.
• 2021
  Rousset F, Cabezas-Caballero J, Piastra-Facon F, Fernández-Rodríguez J, Clermont O, Denamur E, Rocha EPC, Bikard D, , The impact of genetic diversity on gene essentiality within the Escherichia coli species., Nat Microbiol 2021 03; 6(3): 301-312.
• 2021
  de Sousa JAM, Pfeifer E, Touchon M, Rocha EPC, , Causes and consequences of bacteriophage diversification via genetic exchanges across lifestyles and bacterial taxa., Mol Biol Evol 2021 Feb; (): .
• 2020
  Jorge A. Moura de Sousa, Amandine Buffet, Matthieu Haudiquet, Eduardo P.C. Rocha & Olaya Rendueles, Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation, ISME J (2020). https://doi.org/10.1038/s41396-020-0726-z.
• 2020
  Redondo-Salvo S, Fernández-López R, Ruiz R, Vielva L, de Toro M, Rocha EPC, Garcillán-Barcia MP, de la Cruz F, , Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids., Nat Commun 2020 07; 11(1): 3602.
• 2020
  Madin JS, Nielsen DA, Brbic M, Corkrey R, Danko D, Edwards K, Engqvist MKM, Fierer N, Geoghegan JL, Gillings M, Kyrpides NC, Litchman E, Mason CE, Moore L, Nielsen SL, Paulsen IT, Price ND, Reddy TBK, Richards MA, Rocha EPC, Schmidt TM, Shaaban H, Shukla M, Supek F, Tetu SG, Vieira-Silva S, Wattam AR, Westfall DA, Westoby M, , A synthesis of bacterial and archaeal phenotypic trait data., Sci Data 2020 06; 7(1): 170.
• 2020
  Touchon M, Perrin A, de Sousa JAM, Vangchhia B, Burn S, O'Brien CL, Denamur E, Gordon D, Rocha EP, , Phylogenetic background and habitat drive the genetic diversification of Escherichia coli., PLoS Genet. 2020 Jun; 16(6): e1008866.
• 2020
  Sheppard D, Berry JL, Denise R, Rocha EPC, Matthews S, Pelicic V, , The major subunit of widespread competence pili exhibits a novel and conserved type IV pilin fold., J. Biol. Chem. 2020 May; 295(19): 6594-6604.
• 2020
  Denise R, Abby SS, Rocha EPC, , The Evolution of Protein Secretion Systems by Co-option and Tinkering of Cellular Machineries., Trends Microbiol. 2020 May; 28(5): 372-386.
• 2020
  Soler-Bistué A, Aguilar-Pierlé S, Garcia-Garcerá M, Val ME, Sismeiro O, Varet H, Sieira R, Krin E, Skovgaard O, Comerci DJ, Rocha EPC, Mazel D, Macromolecular crowding links ribosomal protein gene dosage to growth rate in Vibrio cholerae., BMC Biol 2020 Apr; 18(1): 43.
• 2020
  Planchenault C, Pons MC, Schiavon C, Siguier P, Rech J, Guynet C, Dauverd-Girault J, Cury J, Rocha EPC, Junier I, Cornet F, Espéli O, , Intracellular Positioning Systems Limit the Entropic Eviction of Secondary Replicons Toward the Nucleoid Edges in Bacterial Cells., J. Mol. Biol. 2020 02; 432(3): 745-761.
• 2020
  Garcia-Garcera M, Rocha EPC, , Community diversity and habitat structure shape the repertoire of extracellular proteins in bacteria., Nat Commun 2020 02; 11(1): 758.
• 2020
  Brewer TE, Albertsen M, Edwards A, Kirkegaard RH, Rocha EPC, Fierer N, , Unlinked rRNA genes are widespread among bacteria and archaea., ISME J 2020 02; 14(2): 597-608.
• 2020
  Bernheim A, Bikard D, Touchon M, Rocha EPC, Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements, Nucleic Acids Res. 2020 Jan;48(2):748-760.
• 2020
  Cury J, Abby SS, Doppelt-Azeroual O, Néron B, Rocha EPC, , Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan., Methods Mol. Biol. 2020 ; 2075(): 265-283.
• 2019
  Denise R, Abby SS, Rocha EPC, Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility, PLoS Biol. 2019 Jul;17(7):e3000390.
• 2019
  Bernheim A, Bikard D, Touchon M, Rocha EPC, A matter of background: DNA repair pathways as a possible cause for the sparse distribution of CRISPR-Cas systems in bacteria, Philos. Trans. R. Soc. Lond., B, Biol. Sci. 2019 May;374(1772):20180088.
• 2019
  Bradley P, den Bakker HC, Rocha EPC, McVean G, Iqbal Z, Ultrafast search of all deposited bacterial and viral genomic data, Nat. Biotechnol. 2019 Feb;37(2):152-159.
• 2018
  Rendueles O, de Sousa JAM, Bernheim A, Touchon M, Rocha EPC, Genetic exchanges are more frequent in bacteria encoding capsules, PLoS Genet. 2018 12;14(12):e1007862.
• 2018
  Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Néron B, Rocha EPC, Vergnaud G, Gautheret D, Pourcel C, CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins, Nucleic Acids Res. 2018 Jul;46(W1):W246-W251.
• 2018
  Cury J, Oliveira PH, de la Cruz F, Rocha EPC, Host range and genetic plasticity explain the co-existence of integrative and extrachromosomal mobile genetic elements, Mol. Biol. Evol. 2018 Jun;.
• 2018
  Clerissi C, Touchon M, Capela D, Tang M, Cruveiller S, Genthon C, Lopez-Roques C, Parker MA, Moulin L, Masson-Boivin C, Rocha EPC, Parallels between experimental and natural evolution of legume symbionts, Nat Commun 2018 06;9(1):2264.
• 2018
  Rocha EPC, Neutral Theory, Microbial Practice: Challenges in Bacterial Population Genetics, Mol. Biol. Evol. 2018 Jun;35(6):1338-1347.
• 2018
  Borriss R, Danchin A, Harwood CR, Médigue C, Rocha EPC, Sekowska A, Vallenet D, Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement, Microb Biotechnol 2018 01;11(1):3-17.
• 2017
  Aude Bernheim, Alicia Calvo Villamanan, Clovis Basier, Lun Cui, Eduardo P. C. Rocha, Marie Touchon, David Bikard, Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria, Nature Communications 8, 2094..
• 2017
  Oliveira PH, Touchon M, Cury J, Rocha EPC, The chromosomal organization of horizontal gene transfer in bacteria, Nat Commun 2017 Oct;8(1):841.
• 2017
  Garcia-Garcera M, Touchon M, Brisse S, Rocha EPC, Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter, Environ. Microbiol. 2017 Oct;.
• 2017
  Capela D, Marchetti M, Clérissi C, Perrier A, Guetta D, Gris C, Valls M, Jauneau A, Cruveiller S, Rocha EPC, Masson-Boivin C., Recruitment of a lineage-specific virulence regulatory pathway promotes intracellular infection by a plant pathogen experimentally evolved into a legume symbiont., Mol Biol Evol. 2017 May 23. doi: 10.1093/molbev/msx165.
• 2017
  Cury J, Touchon M, Rocha EPC, Integrative and conjugative elements and their hosts: composition, distribution and organization, Nucleic Acids Res. 2017 Sep;45(15):8943-8956.
• 2017
  Jamet A, Touchon M, Ribeiro-Gonçalves B, Carriço JA, Charbit A, Nassif X, Ramirez M, Rocha EPC, A widespread family of polymorphic toxins encoded by temperate phages, BMC Biol. 2017 Aug;15(1):75.
• 2017
  Rendueles O, Garcia-Garcerà M, Néron B, Touchon M, Rocha EPC, Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens, PLoS Pathog. 2017 Jul;13(7):e1006525.
• 2017
  Touchon M, Moura de Sousa JA, Rocha EPC, Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer, Curr Opin Microbiol. 2017 May 17;38:66-73.
• 2017
  Céline Loot, Aleksandra Nivina, Jean Cury, José Antonio Escudero, Magaly Ducos-Galand, David Bikard, Eduardo P C Rocha, Didier Mazel, Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance., mBio, 2017, 8 (2), pp.e02296-16. ⟨10.1128/mBio.02296-16⟩.
• 2017
  Abby SS, Rocha EPC, Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder, Methods Mol Biol. 2017;1615:1-21.
• 2016
  Breurec S, Criscuolo A, Diancourt L, Rendueles O, Vandenbogaert M, Passet V, Caro V, Rocha EP, Touchon M, Brisse S, Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis, Sci Rep 2016;6:30379.
• 2016
  Pedro H. Oliveira, Marie Touchon, and Eduardo P. C. Rocha, Regulation of genetic flux between bacteria by restriction-modification systems., Proc Natl Acad Sci U S A. 2016 May 17;113(20):5658-63. doi: 10.1073/pnas.1603257113. .
• 2016
  Jean Cury, Thomas Jové, Marie Touchon, Bertrand Néron, and Eduardo PC Rocha, Identification and analysis of integrons and cassette arrays in bacterial genomes., Nucleic Acids Res. 2016 Apr 29. pii: gkw319..
• 2016
  Touchon M, Bernheim A, Rocha EPC, Genetic and life-history traits associated with the distribution of prophages in bacteria., ISME J. 2016 Mar 25. doi: 10.1038/ismej.2016.47. .
• 2016
  Eduardo PC Rocha, Using Sex to Cure the Genome, PLoS Biol 14(3): e1002417. doi:10.1371/ journal.pbio.1002417.
• 2016
  Sophie S. Abby, Jean Cury, Julien Guglielmini, Bertrand Néron, Marie Touchon & Eduardo P. C. Rocha, Identification of protein secretion systems in bacterial genomes, Scientific Reports 6, 23080 (2016).
• 2016
  Maury MM, Tsai YH, Charlier C, Touchon M, Chenal-Francisque V, Leclercq A, Criscuolo A, Gaultier C, Roussel S, Brisabois A, Disson O, Rocha EPC, Brisse S, Lecuit M, , Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity., Nat Genet 2016 Mar; 48(3): 308-313.
• 2016
  Marguerite Lapierre, Camille Blin, Amaury Lambert, Guillaume Achaz and Eduardo P. C. Rocha, The impact of selection, gene conversion, and biased sampling on the assessment of microbial demography, Mol Biol Evol (2016) doi: 10.1093/molbev/msw048 .
• 2016
  Touchon M, Rocha EPC, Coevolution of the Organization and Structure of Prokaryotic Genomes., Cold Spring Harb Perspect Biol. 2016 Jan 4;8(1).
• 2015
  Xue H, Cordero OX, Camas FM, Trimble W, Meyer F, Guglielmini J, Rocha EP, Polz MF, Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations, MBio 2015;6(3):e00552-15.
• 2015
  Wang J, McIntosh F, Radomski N, Dewar K, Simeone R, Enninga J, Brosch R, Rocha EP, Veyrier FJ, Behr MA, Insights on the emergence of Mycobacterium tuberculosis from the analysis of Mycobacterium kansasii, Genome Biol Evol 2015 Mar;7(3):856-70.
• 2014
  Khan ME, Borde C, Rocha EP, Mériaux V, Maréchal V, Escoll P, Goyard S, Cavaillon JM, Manoury B, Doyen N, TLR9 activation is triggered by the excess of stimulatory versus inhibitory motifs present in Trypanosomatidae DNA, PLoS Negl Trop Dis 2014 Nov;8(11):e3308.
• 2014
  Abby SS, Néron B, Ménager H, Touchon M, Rocha EP, MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems, PLoS ONE 2014;9(10):e110726.
• 2014
  Touchon M, Cury J, Yoon EJ, Krizova L, Cerqueira GC, Murphy C, Feldgarden M, Wortman J, Clermont D, Lambert T, Grillot-Courvalin C, Nemec A, Courvalin P, Rocha EP, , The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences., Genome Biol Evol 2014 Oct; 6(10): 2866-82.
• 2014
  Touchon M, Bobay LM, Rocha EP, The chromosomal accommodation and domestication of mobile genetic elements, Curr. Opin. Microbiol. 2014 Dec;22:22-9.
• 2014
  Remigi P, Capela D, Clerissi C, Tasse L, Torchet R, Bouchez O, Batut J, Cruveiller S, Rocha EP, Masson-Boivin C, Transient hypermutagenesis accelerates the evolution of legume endosymbionts following horizontal gene transfer, PLoS Biol. 2014 Sep;12(9):e1001942.
• 2014
  Oliveira PH, Touchon M, Rocha EP, The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts, Nucleic Acids Res. 2014;42(16):10618-31.
• 2014
  Bobay LM, Touchon M, Rocha EP, Pervasive domestication of defective prophages by bacteria, Proc. Natl. Acad. Sci. U.S.A. 2014 Aug;111(33):12127-32.
• 2014
  Guglielmini J, Néron B, Abby SS, Garcillán-Barcia MP, de la Cruz F, Rocha EP, Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion, Nucleic Acids Res. 2014 May;42(9):5715-27.
• 2014
  Sesto N, Touchon M, Andrade JM, Kondo J, Rocha EP, Arraiano CM, Archambaud C, Westhof É, Romby P, Cossart P, A PNPase dependent CRISPR System in Listeria, PLoS Genet. 2014 Jan;10(1):e1004065.
• 2013
  Bobay LM, Touchon M, Rocha EP, Manipulating or superseding host recombination functions: a dilemma that shapes phage evolvability, PLoS Genet. 2013;9(9):e1003825.
• 2013
  Machado LS, de Oliveira FG, Rocha EP, dos Santos PH, Briso AL, Sundefeld ML, Sundfeld RH, Clinical trial evaluating color change and tooth sensitivity throughout and following in-office bleaching, Int J Periodontics Restorative Dent 2013 Mar-Apr;33(2):209-15.
• 2013
  Rocha EP, Evolution. With a little help from prokaryotes, Science 2013 Mar;339(6124):1154-5.
• 2013
  Nuñez PA, Romero H, Farber MD, Rocha EP, Natural selection for operons depends on genome size, Genome Biol Evol 2013;5(11):2242-54.
• 2013
  Brito PH, Rocha EP, Xavier KB, Gordo I, Natural genome diversity of AI-2 quorum sensing in Escherichia coli: conserved signal production but labile signal reception, Genome Biol Evol 2013;5(1):16-30.
• 2012
  Bobay LM, Rocha EP, Touchon M, The adaptation of temperate bacteriophages to their host genomes, Mol. Biol. Evol. 2013 Apr;30(4):737-51.
• 2012
  Nogueira T, Touchon M, Rocha EP, Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria, PLoS ONE 2012;7(11):e49403.
• 2012
  Viana LV, Leitão CB, Grillo Mde F, Rocha EP, Brenner JK, Friedman R, Gross JL, Are diabetes management guidelines applicable in ‘real life’?, Diabetol Metab Syndr 2012;4(1):47.
• 2012
  Martini AP, Barros RM, Júnior AC, Rocha EP, de Almeida EO, Ferraz CC, Pellegrin MC, Anchieta RB, Influence of platform and abutment angulation on peri-implant bone. A three-dimensional finite element stress analysis, J Oral Implantol 2013 Dec;39(6):663-9.
• 2012
  Touchon M, Charpentier S, Pognard D, Picard B, Arlet G, Rocha EP, Denamur E, Branger C, Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements, Microbiology (Reading, Engl.) 2012 Dec;158(Pt 12):2997-3004.
• 2012
  Abby SS, Rocha EP, The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems, PLoS Genet. 2012 Sep;8(9):e1002983.
• 2012
  Guglielmini J, de la Cruz F, Rocha EP, Evolution of conjugation and type IV secretion systems, Mol. Biol. Evol. 2013 Feb;30(2):315-31.
• 2012
  Deghorain M, Bobay LM, Smeesters PR, Bousbata S, Vermeersch M, Perez-Morga D, Drèze PA, Rocha EP, Touchon M, Van Melderen L, Characterization of novel phages isolated in coagulase-negative staphylococci reveals evolutionary relationships with Staphylococcus aureus phages, J. Bacteriol. 2012 Nov;194(21):5829-39.
• 2012
  Nickerson NN, Abby SS, Rocha EP, Chami M, Pugsley AP, A Single Amino Acid Substitution Changes the Self-Assembly Status of a Type IV Piliation Secretin, J. Bacteriol. 2012 Sep;194(18):4951-8.
• 2012
  Namouchi A, Didelot X, Schöck U, Gicquel B, Rocha EP, After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection, Genome Res. 2012 Apr;22(4):721-34.
• 2012
  Gama JA, Abby SS, Vieira-Silva S, Dionisio F, Rocha EP, Immune subversion and quorum-sensing shape the variation in infectious dose among bacterial pathogens, PLoS Pathog. 2012 Feb;8(2):e1002503.
• 2011
  Vieira-Silva S, Touchon M, Abby SS, Rocha EP, Investment in rapid growth shapes the evolutionary rates of essential proteins, Proc. Natl. Acad. Sci. U.S.A. 2011 Dec;108(50):20030-5.
• 2011
  Touchon M, Barbier P, Bernardet JF, Loux V, Vacherie B, Barbe V, Rocha EP, Duchaud E, Complete genome sequence of the fish pathogen Flavobacterium branchiophilum, Appl. Environ. Microbiol. 2011 Nov;77(21):7656-62.
• 2011
  Guglielmini J, Quintais L, Garcillán-Barcia MP, de la Cruz F, Rocha EP, The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation, PLoS Genet. 2011 Aug;7(8):e1002222.
• 2011
  Touchon M, Charpentier S, Clermont O, Rocha EP, Denamur E, Branger C, CRISPR distribution within the Escherichia coli species is not suggestive of immunity-associated diversifying selection, J. Bacteriol. 2011 May;193(10):2460-7.
• 2011
  Warnecke T, Rocha EP, Function-specific accelerations in rates of sequence evolution suggest predictable epistatic responses to reduced effective population size, Mol. Biol. Evol. 2011 Aug;28(8):2339-49.
• 2011
  Treangen TJ, Rocha EP, Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes, PLoS Genet. 2011;7(1):e1001284.
• 2010
  Rocha EP, Feil EJ, Mutational patterns cannot explain genome composition: Are there any neutral sites in the genomes of bacteria?, PLoS Genet. 2010 Sep;6(9):e1001104.
• 2010
  Smillie C, Garcillán-Barcia MP, Francia MV, Rocha EP, de la Cruz F, Mobility of plasmids, Microbiol. Mol. Biol. Rev. 2010 Sep;74(3):434-52.
• 2010
  Touchon M, Rocha EP, The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella, PLoS ONE 2010;5(6):e11126.
• 2010
  Vieira-Silva S, Touchon M, Rocha EP, No evidence for elemental-based streamlining of prokaryotic genomes, Trends Ecol. Evol. (Amst.) 2010 Jun;25(6):319-20; author reply 320-1.
• 2010
  Rankin DJ, Rocha EP, Brown SP, What traits are carried on mobile genetic elements, and why?, Heredity (Edinb) 2011 Jan;106(1):1-10.
• 2010
  Vieira-Silva S, Rocha EP, The systemic imprint of growth and its uses in ecological (meta)genomics, PLoS Genet. 2010 Jan;6(1):e1000808.
• 2009
  Mil-Homens D, Rocha EP, Fialho AM, Genome-wide analysis of DNA repeats in Burkholderia cenocepacia J2315 identifies a novel adhesin-like gene unique to epidemic-associated strains of the ET-12 lineage, Microbiology (Reading, Engl.) 2010 Apr;156(Pt 4):1084-96.
• 2009
  Nogueira T, Rankin DJ, Touchon M, Taddei F, Brown SP, Rocha EP, Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence, Curr. Biol. 2009 Nov;19(20):1683-91.
• 2009
  Abraham AL, Pothier J, Rocha EP, Alternative to homo-oligomerisation: the creation of local symmetry in proteins by internal amplification, J. Mol. Biol. 2009 Dec;394(3):522-34.
• 2009
  Treangen TJ, Abraham AL, Touchon M, Rocha EP, Genesis, effects and fates of repeats in prokaryotic genomes, FEMS Microbiol. Rev. 2009 May;33(3):539-71.
• 2009
  Treangen TJ, Darling AE, Achaz G, Ragan MA, Messeguer X, Rocha EP, A novel heuristic for local multiple alignment of interspersed DNA repeats, IEEE/ACM Trans Comput Biol Bioinform 2009 Apr-Jun;6(2):180-9.
• 2009
  Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O, Calteau A, Chiapello H, Clermont O, Cruveiller S, Danchin A, Diard M, Dossat C, Karoui ME, Frapy E, Garry L, Ghigo JM, Gilles AM, Johnson J, Le Bouguénec C, Lescat M, Mangenot S, Martinez-Jéhanne V, Matic I, Nassif X, Oztas S, Petit MA, Pichon C, Rouy Z, Ruf CS, Schneider D, Tourret J, Vacherie B, Vallenet D, Médigue C, Rocha EP, Denamur E, Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths, PLoS Genet. 2009 Jan;5(1):e1000344.
• 2008
  Balbi KJ, Rocha EP, Feil EJ, The temporal dynamics of slightly deleterious mutations in Escherichia coli and Shigella spp, Mol. Biol. Evol. 2009 Feb;26(2):345-55.
• 2008
  Holden MT, Seth-Smith HM, Crossman LC, Sebaihia M, Bentley SD, Cerdeño-Tárraga AM, Thomson NR, Bason N, Quail MA, Sharp S, Cherevach I, Churcher C, Goodhead I, Hauser H, Holroyd N, Mungall K, Scott P, Walker D, White B, Rose H, Iversen P, Mil-Homens D, Rocha EP, Fialho AM, Baldwin A, Dowson C, Barrell BG, Govan JR, Vandamme P, Hart CA, Mahenthiralingam E, Parkhill J, The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients, J. Bacteriol. 2009 Jan;191(1):261-77.
• 2008
  Rocha EP, Evolutionary patterns in prokaryotic genomes, Curr. Opin. Microbiol. 2008 Oct;11(5):454-60.
• 2008
  Vieira-Silva S, Rocha EP, An assessment of the impacts of molecular oxygen on the evolution of proteomes, Mol. Biol. Evol. 2008 Sep;25(9):1931-42.
• 2008
  Abraham AL, Rocha EP, Pothier J, Swelfe: a detector of internal repeats in sequences and structures, Bioinformatics 2008 Jul;24(13):1536-7.
• 2008
  Assunção WG, Tabata LF, Barão VA, Rocha EP, Comparison of stress distribution between complete denture and implant-retained overdenture-2D FEA, J Oral Rehabil 2008 Oct;35(10):766-74.
• 2008
  Treangen TJ, Ambur OH, Tonjum T, Rocha EP, The impact of the neisserial DNA uptake sequences on genome evolution and stability, Genome Biol. 2008;9(3):R60.
• 2008
  Fang G, Rocha EP, Danchin A, Persistence drives gene clustering in bacterial genomes, BMC Genomics 2008;9:4.
• 2008
  Rocha EP, The organization of the bacterial genome, Annu. Rev. Genet. 2008;42:211-33.
• 2007
  Touchon M, Rocha EP, From GC skews to wavelets: a gentle guide to the analysis of compositional asymmetries in genomic data, Biochimie 2008 Apr;90(4):648-59.
• 2007
  Bailly-Bechet M, Vergassola M, Rocha E, Causes for the intriguing presence of tRNAs in phages, Genome Res. 2007 Oct;17(10):1486-95.
• 2007
  Gómez-Valero L, Rocha EP, Latorre A, Silva FJ, Reconstructing the ancestor of Mycobacterium leprae: the dynamics of gene loss and genome reduction., Genome Res 2007 Aug; 17(8): 1178-85.
• 2007
  Touchon M, Rocha EP, Causes of insertion sequences abundance in prokaryotic genomes, Mol. Biol. Evol. 2007 Apr;24(4):969-81.
• 2007
  Ochman H, Liu R, Rocha EP, Erosion of interaction networks in reduced and degraded genomes, J. Exp. Zool. B Mol. Dev. Evol. 2007 Jan;308(1):97-103.
• 2006
  Rocha EP, Touchon M, Feil EJ, Similar compositional biases are caused by very different mutational effects, Genome Res. 2006 Dec;16(12):1537-47.
• 2006
  Achaz G, Boyer F, Rocha EP, Viari A, Coissac E, Repseek, a tool to retrieve approximate repeats from large DNA sequences, Bioinformatics 2007 Jan;23(1):119-21.
• 2006
  Hurst LD, Feil EJ, Rocha EP, Protein evolution: causes of trends in amino-acid gain and loss, Nature 2006 Aug;442(7105):E11-2; discussion E12.
• 2006
  Iverson-Cabral SL, Astete SG, Cohen CR, Rocha EP, Totten PA, Intrastrain heterogeneity of the mgpB gene in Mycoplasma genitalium is extensive in vitro and in vivo and suggests that variation is generated via recombination with repetitive chromosomal sequences, Infect. Immun. 2006 Jul;74(7):3715-26.
• 2006
  Rocha EP, The quest for the universals of protein evolution, Trends Genet. 2006 Aug;22(8):412-6.
• 2006
  Swidan F, Rocha EP, Shmoish M, Pinter RY, An integrative method for accurate comparative genome mapping, PLoS Comput. Biol. 2006 Aug;2(8):e75.
• 2006
  Fischer G, Rocha EP, Brunet F, Vergassola M, Dujon B, Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages, PLoS Genet. 2006 Mar;2(3):e32.
• 2006
  Couturier E, Rocha EP, Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes, Mol. Microbiol. 2006 Mar;59(5):1506-18.
• 2005
  Rocha EP, Inference and analysis of the relative stability of bacterial chromosomes, Mol. Biol. Evol. 2006 Mar;23(3):513-22.
• 2005
  Rocha EP, Smith JM, Hurst LD, Holden MT, Cooper JE, Smith NH, Feil EJ, Comparisons of dN/dS are time dependent for closely related bacterial genomes, J. Theor. Biol. 2006 Mar;239(2):226-35.
• 2005
  Médigue C, Krin E, Pascal G, Barbe V, Bernsel A, Bertin PN, Cheung F, Cruveiller S, D'Amico S, Duilio A, Fang G, Feller G, Ho C, Mangenot S, Marino G, Nilsson J, Parrilli E, Rocha EP, Rouy Z, Sekowska A, Tutino ML, Vallenet D, von Heijne G, Danchin A, Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125, Genome Res. 2005 Oct;15(10):1325-35.
• 2005
  Rocha EP, Cornet E, Michel B, Comparative and evolutionary analysis of the bacterial homologous recombination systems, PLoS Genet. 2005 Aug;1(2):e15.
• 2005
  Fang G, Rocha E, Danchin A, How essential are nonessential genes?, Mol. Biol. Evol. 2005 Nov;22(11):2147-56.
• 2005
  Figueiredo LM, Rocha EP, Mancio-Silva L, Prevost C, Hernandez-Verdun D, Scherf A, , The unusually large Plasmodium telomerase reverse-transcriptase localizes in a discrete compartment associated with the nucleolus., Nucleic Acids Res 2005 ; 33(3): 1111-22.
• 2004
  Rocha EP, Codon usage bias from tRNA’s point of view: redundancy, specialization, and efficient decoding for translation optimization, Genome Res. 2004 Nov;14(11):2279-86.
• 2004
  Rocha EP, Order and disorder in bacterial genomes, Curr. Opin. Microbiol. 2004 Oct;7(5):519-27.
• 2004
  Wang Y, Rocha EP, Leung FC, Danchin A, Cytosine methylation is not the major factor inducing CpG dinucleotide deficiency in bacterial genomes, J. Mol. Evol. 2004 Jun;58(6):692-700.
• 2004
  Rocha EP, The replication-related organization of bacterial genomes, Microbiology (Reading, Engl.) 2004 Jun;150(Pt 6):1609-27.
• 2003
  Rocha EP, Danchin A, Gene essentiality determines chromosome organisation in bacteria, Nucleic Acids Res. 2003 Nov;31(22):6570-7.
• 2003
  Rocha EP, DNA repeats lead to the accelerated loss of gene order in bacteria, Trends Genet. 2003 Nov;19(11):600-3.
• 2003
  Rocha EP, Danchin A, An analysis of determinants of amino acids substitution rates in bacterial proteins, Mol. Biol. Evol. 2004 Jan;21(1):108-16.
• 2003
  Achaz G, Coissac E, Netter P, Rocha EP, Associations between inverted repeats and the structural evolution of bacterial genomes, Genetics 2003 Aug;164(4):1279-89.
• 2003
  Rocha EP, Fralick J, Vediyappan G, Danchin A, Norris V, A strand-specific model for chromosome segregation in bacteria, Mol. Microbiol. 2003 Aug;49(4):895-903.
• 2003
  Rocha EP, Danchin A, Essentiality, not expressiveness, drives gene-strand bias in bacteria, Nat. Genet. 2003 Aug;34(4):377-8.
• 2003
  Rocha EP, An appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: from duplications to genome reduction, Genome Res. 2003 Jun;13(6A):1123-32.
• 2002
  Rocha EP, Pradillon O, Bui H, Sayada C, Denamur E, A new family of highly variable proteins in the Chlamydophila pneumoniae genome, Nucleic Acids Res. 2002 Oct;30(20):4351-60.
• 2002
  Rocha E, Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes?, Trends Microbiol. 2002 Sep;10(9):393-5.
• 2002
  Achaz G, Rocha EP, Netter P, Coissac E, Origin and fate of repeats in bacteria, Nucleic Acids Res. 2002 Jul;30(13):2987-94.
• 2002
  Rocha EP, Danchin A, Base composition bias might result from competition for metabolic resources, Trends Genet. 2002 Jun;18(6):291-4.
• 2002
  Rocha EP, Blanchard A, Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution, Nucleic Acids Res. 2002 May;30(9):2031-42.
• 2002
  Rocha EP, Matic I, Taddei F, Over-representation of repeats in stress response genes: a strategy to increase versatility under stressful conditions?, Nucleic Acids Res. 2002 May;30(9):1886-94.
• 2001
  Rocha EP, Danchin A, Ongoing evolution of strand composition in bacterial genomes, Mol. Biol. Evol. 2001 Sep;18(9):1789-99.
• 2001
  Rocha EP, Danchin A, Viari A, Evolutionary role of restriction/modification systems as revealed by comparative genome analysis, Genome Res. 2001 Jun;11(6):946-58.
• 2001
  Chambaud I, Heilig R, Ferris S, Barbe V, Samson D, Galisson F, Moszer I, Dybvig K, Wróblewski H, Viari A, Rocha EP, Blanchard A, The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis, Nucleic Acids Res. 2001 May;29(10):2145-53.
• 2000
  Rocha EP, Danchin A, Viari A, The DB case: pattern matching evidence is not significant, Mol. Microbiol. 2000 Jul;37(1):216-8.
• 2000
  Rocha EP, Sekowska A, Danchin A, Sulphur islands in the Escherichia coli genome: markers of the cell’s architecture?, FEBS Lett. 2000 Jun;476(1-2):8-11.
• 2000
  Rocha EP, Guerdoux-Jamet P, Moszer I, Viari A, Danchin A, Implication of gene distribution in the bacterial chromosome for the bacterial cell factory, J. Biotechnol. 2000 Mar;78(3):209-19.
• 1999
  Rocha EP, Danchin A, Viari A, Functional and evolutionary roles of long repeats in prokaryotes, Res. Microbiol. 1999 Nov-Dec;150(9-10):725-33.
• 1999
  Moszer I, Rocha EP, Danchin A, Codon usage and lateral gene transfer in Bacillus subtilis, Curr. Opin. Microbiol. 1999 Oct;2(5):524-8.
• 1999
  Rocha EP, Danchin A, Viari A, Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in Bacillus subtilis and other competent prokaryotes, Mol. Biol. Evol. 1999 Sep;16(9):1219-30.
• 1999
  Rocha EP, Danchin A, Viari A, Translation in Bacillus subtilis: roles and trends of initiation and termination, insights from a genome analysis, Nucleic Acids Res. 1999 Sep;27(17):3567-76.
• 1999
  Rocha EP, Danchin A, Viari A, Bacterial DNA strand compositional asymmetry: response, Trends Microbiol. 1999 Aug;7(8):308.
• 1999
  Rocha EP, Danchin A, Viari A, Universal replication biases in bacteria, Mol. Microbiol. 1999 Apr;32(1):11-6.
• 1998
  Rocha EP, Viari A, Danchin A, Oligonucleotide bias in Bacillus subtilis: general trends and taxonomic comparisons, Nucleic Acids Res. 1998 Jun;26(12):2971-80.