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Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility.

Denise R, Abby SS, Rocha EPC.

PLoS Biol. 2019 Jul 19;17(7):e3000390. doi: 10.1371/journal.pbio.3000390. eCollection 2019 Jul.


Bacteriophages benefit from generalized transduction.

Fillol-Salom A, Alsaadi A, Sousa JAM, Zhong L, Foster KR, Rocha EPC, Penadés JR, Ingmer H, Haaber J.

PLoS Pathog. 2019 Jul 5;15(7):e1007888. doi: 10.1371/journal.ppat.1007888. eCollection 2019 Jul.


Emergence profile customization technique during implant transfer.

Dos Santos PH, Suzuki TYU, Martini AP, de Oliveira Reis B, Assunção WG, Rocha EP.

J Indian Prosthodont Soc. 2019 Apr-Jun;19(2):197-200. doi: 10.4103/jips.jips_35_19.


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

Remigi P, Masson-Boivin C, Rocha EPC.

Trends Microbiol. 2019 Jul;27(7):623-634. doi: 10.1016/j.tim.2019.02.003. Epub 2019 Mar 23. Review.


A matter of background: DNA repair pathways as a possible cause for the sparse distribution of CRISPR-Cas systems in bacteria.

Bernheim A, Bikard D, Touchon M, Rocha EPC.

Philos Trans R Soc Lond B Biol Sci. 2019 May 13;374(1772):20180088. doi: 10.1098/rstb.2018.0088.


Ultrafast search of all deposited bacterial and viral genomic data.

Bradley P, den Bakker HC, Rocha EPC, McVean G, Iqbal Z.

Nat Biotechnol. 2019 Feb;37(2):152-159. doi: 10.1038/s41587-018-0010-1. Epub 2019 Feb 4.


Influence of resin cement thickness and temperature variation on mechanical behavior of dental ceramic fragment restoration.

Martini AP, de Souza FI, Anchieta RB, de Almeida EO, Freitas Junior AC, Rocha EP.

Comput Methods Biomech Biomed Engin. 2019 Mar;22(4):409-417. doi: 10.1080/10255842.2018.1560428. Epub 2019 Feb 4.


Genetic exchanges are more frequent in bacteria encoding capsules.

Rendueles O, de Sousa JAM, Bernheim A, Touchon M, Rocha EPC.

PLoS Genet. 2018 Dec 21;14(12):e1007862. doi: 10.1371/journal.pgen.1007862. eCollection 2018 Dec.


HflXr, a homolog of a ribosome-splitting factor, mediates antibiotic resistance.

Duval M, Dar D, Carvalho F, Rocha EPC, Sorek R, Cossart P.

Proc Natl Acad Sci U S A. 2018 Dec 26;115(52):13359-13364. doi: 10.1073/pnas.1810555115. Epub 2018 Dec 13.


Host Range and Genetic Plasticity Explain the Coexistence of Integrative and Extrachromosomal Mobile Genetic Elements.

Cury J, Oliveira PH, de la Cruz F, Rocha EPC.

Mol Biol Evol. 2018 Nov 1;35(11):2850. doi: 10.1093/molbev/msy182. No abstract available.


Author Correction: Parallels between experimental and natural evolution of legume symbionts.

Clerissi C, Touchon M, Capela D, Tang M, Cruveiller S, Genthon C, Lopez-Roques C, Parker MA, Moulin L, Masson-Boivin C, Rocha EPC.

Nat Commun. 2018 Nov 2;9(1):4641. doi: 10.1038/s41467-018-07205-x.


Acute kidney injury in elderly patients: narrative review on incidence, risk factors, and mortality.

Yokota LG, Sampaio BM, Rocha EP, Balbi AL, Sousa Prado IR, Ponce D.

Int J Nephrol Renovasc Dis. 2018 Aug 14;11:217-224. doi: 10.2147/IJNRD.S170203. eCollection 2018. Review.


Serum Uric Acid Levels as an Indicator for Metabolically Unhealthy Obesity in Children and Adolescents.

Rocha EPAA, Vogel M, Stanik J, Pietzner D, Willenberg A, Körner A, Kiess W.

Horm Res Paediatr. 2018;90(1):19-27. doi: 10.1159/000490113. Epub 2018 Jul 27.


Host range and genetic plasticity explain the co-existence of integrative and extrachromosomal mobile genetic elements.

Cury J, Oliveira PH, de la Cruz F, Rocha EPC.

Mol Biol Evol. 2018 Jun 14. doi: 10.1093/molbev/msy123. [Epub ahead of print] Erratum in: Mol Biol Evol. 2018 Nov 1;35(11):2850.


Urinary Neutrophil Gelatinase-Associated Lipocalin Is Excellent Predictor of Acute Kidney Injury in Septic Elderly Patients.

da Rocha EP, Yokota LG, Sampaio BM, Cardoso Eid KZ, Dias DB, de Freitas FM, Balbi AL, Ponce D.

Aging Dis. 2018 Apr 1;9(2):182-191. doi: 10.14336/AD.2017.0307. eCollection 2018 Apr.


Parallels between experimental and natural evolution of legume symbionts.

Clerissi C, Touchon M, Capela D, Tang M, Cruveiller S, Genthon C, Lopez-Roques C, Parker MA, Moulin L, Masson-Boivin C, Rocha EPC.

Nat Commun. 2018 Jun 11;9(1):2264. doi: 10.1038/s41467-018-04778-5. Erratum in: Nat Commun. 2018 Nov 2;9(1):4641.


Soluble epoxide hydrolase inhibitor promotes immunomodulation to inhibit bone resorption.

Napimoga MH, Rocha EP, Trindade-da-Silva CA, Demasi APD, Martinez EF, Macedo CG, Abdalla HB, Bettaieb A, Haj FG, Clemente-Napimoga JT, Inceoglu B, Hammock BD.

J Periodontal Res. 2018 Oct;53(5):743-749. doi: 10.1111/jre.12559. Epub 2018 May 31.


CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins.

Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Néron B, Rocha EPC, Vergnaud G, Gautheret D, Pourcel C.

Nucleic Acids Res. 2018 Jul 2;46(W1):W246-W251. doi: 10.1093/nar/gky425.


Neutral Theory, Microbial Practice: Challenges in Bacterial Population Genetics.

Rocha EPC.

Mol Biol Evol. 2018 Jun 1;35(6):1338-1347. doi: 10.1093/molbev/msy078.


Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement.

Borriss R, Danchin A, Harwood CR, Médigue C, Rocha EPC, Sekowska A, Vallenet D.

Microb Biotechnol. 2018 Jan;11(1):3-17. doi: 10.1111/1751-7915.13043.


Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria.

Bernheim A, Calvo-Villamañán A, Basier C, Cui L, Rocha EPC, Touchon M, Bikard D.

Nat Commun. 2017 Dec 12;8(1):2094. doi: 10.1038/s41467-017-02350-1.


The chromosomal organization of horizontal gene transfer in bacteria.

Oliveira PH, Touchon M, Cury J, Rocha EPC.

Nat Commun. 2017 Oct 10;8(1):841. doi: 10.1038/s41467-017-00808-w.


Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter.

Garcia-Garcera M, Touchon M, Brisse S, Rocha EPC.

Environ Microbiol. 2017 Dec;19(12):5010-5024. doi: 10.1111/1462-2920.13949. Epub 2017 Dec 1.


Integrative and conjugative elements and their hosts: composition, distribution and organization.

Cury J, Touchon M, Rocha EPC.

Nucleic Acids Res. 2017 Sep 6;45(15):8943-8956. doi: 10.1093/nar/gkx607.


A widespread family of polymorphic toxins encoded by temperate phages.

Jamet A, Touchon M, Ribeiro-Gonçalves B, Carriço JA, Charbit A, Nassif X, Ramirez M, Rocha EPC.

BMC Biol. 2017 Aug 29;15(1):75. doi: 10.1186/s12915-017-0415-1.


Microencapsulation of sacha inchi oil using emulsion-based delivery systems.

Vicente J, de Souza Cezarino T, Pereira LJB, da Rocha EP, Sá GR, Gamallo OD, de Carvalho MG, Garcia-Rojas EE.

Food Res Int. 2017 Sep;99(Pt 1):612-622. doi: 10.1016/j.foodres.2017.06.039. Epub 2017 Jun 20.


Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens.

Rendueles O, Garcia-Garcerà M, Néron B, Touchon M, Rocha EPC.

PLoS Pathog. 2017 Jul 24;13(7):e1006525. doi: 10.1371/journal.ppat.1006525. eCollection 2017 Jul.


Comparative genomic analysis of Acinetobacter strains isolated from murine colonic crypts.

Saffarian A, Touchon M, Mulet C, Tournebize R, Passet V, Brisse S, Rocha EPC, Sansonetti PJ, Pédron T.

BMC Genomics. 2017 Jul 11;18(1):525. doi: 10.1186/s12864-017-3925-x.


Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder.

Abby SS, Rocha EPC.

Methods Mol Biol. 2017;1615:1-21. doi: 10.1007/978-1-4939-7033-9_1.


Erratum: Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity.

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.

Nat Genet. 2017 May 26;49(6):970. doi: 10.1038/ng0617-970d. No abstract available.


Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain.

Perrin A, Larsonneur E, Nicholson AC, Edwards DJ, Gundlach KM, Whitney AM, Gulvik CA, Bell ME, Rendueles O, Cury J, Hugon P, Clermont D, Enouf V, Loparev V, Juieng P, Monson T, Warshauer D, Elbadawi LI, Walters MS, Crist MB, Noble-Wang J, Borlaug G, Rocha EPC, Criscuolo A, Touchon M, Davis JP, Holt KE, McQuiston JR, Brisse S.

Nat Commun. 2017 May 24;8:15483. doi: 10.1038/ncomms15483.


Recruitment of a Lineage-Specific Virulence Regulatory Pathway Promotes Intracellular Infection by a Plant Pathogen Experimentally Evolved into a Legume Symbiont.

Capela D, Marchetti M, Clérissi C, Perrier A, Guetta D, Gris C, Valls M, Jauneau A, Cruveiller S, Rocha EPC, Masson-Boivin C.

Mol Biol Evol. 2017 Oct 1;34(10):2503-2521. doi: 10.1093/molbev/msx165.


Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer.

Touchon M, Moura de Sousa JA, Rocha EP.

Curr Opin Microbiol. 2017 Aug;38:66-73. doi: 10.1016/j.mib.2017.04.010. Epub 2017 May 17. Review.


Value of NMR Parameters and DFT Calculations for Quantum Information Processing Utilizing Phosphorus Heterocycles.

Lino JBR, Rocha EP, Ramalho TC.

J Phys Chem A. 2017 Jun 15;121(23):4486-4495. doi: 10.1021/acs.jpca.6b12728. Epub 2017 May 4.


Corrigendum: Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity.

Maury MM, Tsai YH, Charlier C, Touchon M, Chenal-Francisque V, Leclercq A, Criscuolo A, Gaultier C, Roussel S, Brisabois A, Disson O, Rocha EP, Brisse S, Lecuit M.

Nat Genet. 2017 Mar 30;49(4):651. doi: 10.1038/ng0417-651b. No abstract available.


Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance.

Loot C, Nivina A, Cury J, Escudero JA, Ducos-Galand M, Bikard D, Rocha EP, Mazel D.

MBio. 2017 Mar 28;8(2). pii: e02296-16. doi: 10.1128/mBio.02296-16.


Metabolic diversity of the emerging pathogenic lineages of Klebsiella pneumoniae.

Blin C, Passet V, Touchon M, Rocha EPC, Brisse S.

Environ Microbiol. 2017 May;19(5):1881-1898. doi: 10.1111/1462-2920.13689. Epub 2017 Mar 3.


Sealing the Screw Access Channel with Polytetrafluoroethylene Tape: Advantages of the Technique.

Maluly-Proni AT, Anchieta RB, Suzuki TY, Garcia de Oliveira F, Guedes AP, Rocha EP, Assunção WG, Dos Santos PH.

Int J Oral Maxillofac Implants. 2017 September/October;32(5):1132–1134. doi: 10.11607/jomi.5347. Epub 2017 Feb 7.


Genetic and life-history traits associated with the distribution of prophages in bacteria.

Touchon M, Bernheim A, Rocha EP.

ISME J. 2016 Nov;10(11):2744-2754. doi: 10.1038/ismej.2016.47. Epub 2016 Mar 25.


Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes.

Moura A, Criscuolo A, Pouseele H, Maury MM, Leclercq A, Tarr C, Björkman JT, Dallman T, Reimer A, Enouf V, Larsonneur E, Carleton H, Bracq-Dieye H, Katz LS, Jones L, Touchon M, Tourdjman M, Walker M, Stroika S, Cantinelli T, Chenal-Francisque V, Kucerova Z, Rocha EP, Nadon C, Grant K, Nielsen EM, Pot B, Gerner-Smidt P, Lecuit M, Brisse S.

Nat Microbiol. 2016 Oct 10;2:16185. doi: 10.1038/nmicrobiol.2016.185.


Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis.

Breurec S, Criscuolo A, Diancourt L, Rendueles O, Vandenbogaert M, Passet V, Caro V, Rocha EP, Touchon M, Brisse S.

Sci Rep. 2016 Jul 27;6:30379. doi: 10.1038/srep30379.


Assessment of Satisfaction Level of Edentulous Patients Rehabilitated with Implant-Supported Prostheses.

de Souza FI, de Souza Costa A, Dos Santos Pereira R, Dos Santos PH, de Brito RB Jr, Rocha EP.

Int J Oral Maxillofac Implants. 2016 Jul-Aug;31(4):884-90. doi: 10.11607/jomi.4267.


Epidemiological Data and Survival Rate of Removable Partial Dentures.

Moreno A, Haddad MF, Goiato MC, Rocha EP, Assunção WG, Filho HG, Santos EG, Sonego MV, Santos DM.

J Clin Diagn Res. 2016 May;10(5):ZC84-7. doi: 10.7860/JCDR/2016/16638.7816. Epub 2016 May 1.


Regulation of genetic flux between bacteria by restriction-modification systems.

Oliveira PH, Touchon M, Rocha EP.

Proc Natl Acad Sci U S A. 2016 May 17;113(20):5658-63. doi: 10.1073/pnas.1603257113. Epub 2016 May 2.


Identification and analysis of integrons and cassette arrays in bacterial genomes.

Cury J, Jové T, Touchon M, Néron B, Rocha EP.

Nucleic Acids Res. 2016 Jun 2;44(10):4539-50. doi: 10.1093/nar/gkw319. Epub 2016 Apr 29.


Molecular Docking, Metal Substitution and Hydrolysis Reaction of Chiral Substrates of Phosphotriesterase.

de Castro AA, Caetano MS, Silva TC, Mancini DT, Rocha EP, da Cunha EF, Ramalho TC.

Comb Chem High Throughput Screen. 2016;19(4):334-44.


Using Sex to Cure the Genome.

Rocha EP.

PLoS Biol. 2016 Mar 17;14(3):e1002417. doi: 10.1371/journal.pbio.1002417. eCollection 2016 Mar.


Identification of protein secretion systems in bacterial genomes.

Abby SS, Cury J, Guglielmini J, Néron B, Touchon M, Rocha EP.

Sci Rep. 2016 Mar 16;6:23080. doi: 10.1038/srep23080.


The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography.

Lapierre M, Blin C, Lambert A, Achaz G, Rocha EP.

Mol Biol Evol. 2016 Jul;33(7):1711-25. doi: 10.1093/molbev/msw048. Epub 2016 Mar 1.

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