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Items: 1 to 50 of 67

1.

Author Correction: The chromosomal organization of horizontal gene transfer in bacteria.

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

Nat Commun. 2020 Feb 26;11(1):1155. doi: 10.1038/s41467-020-15091-5.

2.

Epigenomic characterization of Clostridioides difficile finds a conserved DNA methyltransferase that mediates sporulation and pathogenesis.

Oliveira PH, Ribis JW, Garrett EM, Trzilova D, Kim A, Sekulovic O, Mead EA, Pak T, Zhu S, Deikus G, Touchon M, Lewis-Sandari M, Beckford C, Zeitouni NE, Altman DR, Webster E, Oussenko I, Bunyavanich S, Aggarwal AK, Bashir A, Patel G, Wallach F, Hamula C, Huprikar S, Schadt EE, Sebra R, van Bakel H, Kasarskis A, Tamayo R, Shen A, Fang G.

Nat Microbiol. 2020 Jan;5(1):166-180. doi: 10.1038/s41564-019-0613-4. Epub 2019 Nov 25.

PMID:
31768029
3.

Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements.

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

Nucleic Acids Res. 2020 Jan 24;48(2):748-760. doi: 10.1093/nar/gkz1091.

PMID:
31745554
4.

CRISPRCasdb a successor of CRISPRdb containing CRISPR arrays and cas genes from complete genome sequences, and tools to download and query lists of repeats and spacers.

Pourcel C, Touchon M, Villeriot N, Vernadet JP, Couvin D, Toffano-Nioche C, Vergnaud G.

Nucleic Acids Res. 2020 Jan 8;48(D1):D535-D544. doi: 10.1093/nar/gkz915.

PMID:
31624845
5.

A simple, reproducible and cost-effective procedure to analyse gut phageome: from phage isolation to bioinformatic approach.

d'Humières C, Touchon M, Dion S, Cury J, Ghozlane A, Garcia-Garcera M, Bouchier C, Ma L, Denamur E, P C Rocha E.

Sci Rep. 2019 Aug 5;9(1):11331. doi: 10.1038/s41598-019-47656-w.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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. Erratum in: Nat Commun. 2020 Feb 26;11(1):1155.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

PMID:
28546578
19.

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.

20.

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.

PMID:
28527384
21.

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.

PMID:
28358126
22.

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.

PMID:
28181409
23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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. 2016 Mar;48(3):308-313. doi: 10.1038/ng.3501. Epub 2016 Feb 1. Erratum in: Nat Genet. 2017 Mar 30;49(4):651. Nat Genet. 2017 May 26;49(6):970.

30.

Coevolution of the Organization and Structure of Prokaryotic Genomes.

Touchon M, Rocha EP.

Cold Spring Harb Perspect Biol. 2016 Jan 4;8(1):a018168. doi: 10.1101/cshperspect.a018168. Review.

31.

Clonogrouping, a Rapid Multiplex PCR Method for Identification of Major Clones of Listeria monocytogenes.

Chenal-Francisque V, Maury MM, Lavina M, Touchon M, Leclercq A, Lecuit M, Brisse S.

J Clin Microbiol. 2015 Oct;53(10):3355-8. doi: 10.1128/JCM.00738-15. Epub 2015 Jul 29.

32.

Bacteria in Ostreococcus tauri cultures - friends, foes or hitchhikers?

Abby SS, Touchon M, De Jode A, Grimsley N, Piganeau G.

Front Microbiol. 2014 Nov 7;5:505. doi: 10.3389/fmicb.2014.00505. eCollection 2014.

33.

Origin in Acinetobacter guillouiae and dissemination of the aminoglycoside-modifying enzyme Aph(3')-VI.

Yoon EJ, Goussard S, Touchon M, Krizova L, Cerqueira G, Murphy C, Lambert T, Grillot-Courvalin C, Nemec A, Courvalin P.

mBio. 2014 Oct 21;5(5):e01972-14. doi: 10.1128/mBio.01972-14.

34.

MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems.

Abby SS, Néron B, Ménager H, Touchon M, Rocha EP.

PLoS One. 2014 Oct 17;9(10):e110726. doi: 10.1371/journal.pone.0110726. eCollection 2014.

35.

The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences.

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.

Genome Biol Evol. 2014 Oct 13;6(10):2866-82. doi: 10.1093/gbe/evu225.

36.

The chromosomal accommodation and domestication of mobile genetic elements.

Touchon M, Bobay LM, Rocha EP.

Curr Opin Microbiol. 2014 Dec;22:22-9. doi: 10.1016/j.mib.2014.09.010. Epub 2014 Oct 8. Review.

37.

The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts.

Oliveira PH, Touchon M, Rocha EP.

Nucleic Acids Res. 2014;42(16):10618-31. doi: 10.1093/nar/gku734. Epub 2014 Aug 12.

38.

Pervasive domestication of defective prophages by bacteria.

Bobay LM, Touchon M, Rocha EP.

Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):12127-32. doi: 10.1073/pnas.1405336111. Epub 2014 Aug 4.

39.

A PNPase dependent CRISPR System in Listeria.

Sesto N, Touchon M, Andrade JM, Kondo J, Rocha EP, Arraiano CM, Archambaud C, Westhof É, Romby P, Cossart P.

PLoS Genet. 2014 Jan;10(1):e1004065. doi: 10.1371/journal.pgen.1004065. Epub 2014 Jan 9.

40.

Manipulating or superseding host recombination functions: a dilemma that shapes phage evolvability.

Bobay LM, Touchon M, Rocha EP.

PLoS Genet. 2013;9(9):e1003825. doi: 10.1371/journal.pgen.1003825. Epub 2013 Sep 26.

41.

From the Flavobacterium genus to the phylum Bacteroidetes: genomic analysis of dnd gene clusters.

Barbier P, Lunazzi A, Fujiwara-Nagata E, Avendaño-Herrera R, Bernardet JF, Touchon M, Duchaud E.

FEMS Microbiol Lett. 2013 Nov;348(1):26-35. doi: 10.1111/1574-6968.12239. Epub 2013 Sep 6.

42.

The adaptation of temperate bacteriophages to their host genomes.

Bobay LM, Rocha EP, Touchon M.

Mol Biol Evol. 2013 Apr;30(4):737-51. doi: 10.1093/molbev/mss279. Epub 2012 Dec 12.

43.

Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements.

Touchon M, Charpentier S, Pognard D, Picard B, Arlet G, Rocha EP, Denamur E, Branger C.

Microbiology. 2012 Dec;158(12):2997-3004. doi: 10.1099/mic.0.060814-0.

PMID:
28206908
44.

Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria.

Nogueira T, Touchon M, Rocha EP.

PLoS One. 2012;7(11):e49403. doi: 10.1371/journal.pone.0049403. Epub 2012 Nov 26.

45.

Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements.

Touchon M, Charpentier S, Pognard D, Picard B, Arlet G, Rocha EP, Denamur E, Branger C.

Microbiology. 2012 Dec;158(Pt 12):2997-3004. doi: 10.1099/mic.0.060814-0. Epub 2012 Oct 11.

PMID:
23059972
46.

Characterization of novel phages isolated in coagulase-negative staphylococci reveals evolutionary relationships with Staphylococcus aureus phages.

Deghorain M, Bobay LM, Smeesters PR, Bousbata S, Vermeersch M, Perez-Morga D, Drèze PA, Rocha EP, Touchon M, Van Melderen L.

J Bacteriol. 2012 Nov;194(21):5829-39. doi: 10.1128/JB.01085-12. Epub 2012 Aug 24.

47.

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

Barbier P, Houel A, Loux V, Poulain J, Bernardet JF, Touchon M, Duchaud E.

J Bacteriol. 2012 Jun;194(11):3024-5. doi: 10.1128/JB.00420-12.

48.

Investment in rapid growth shapes the evolutionary rates of essential proteins.

Vieira-Silva S, Touchon M, Abby SS, Rocha EP.

Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):20030-5. doi: 10.1073/pnas.1110972108. Epub 2011 Nov 30.

49.

Complete genome sequence of the fish pathogen Flavobacterium branchiophilum.

Touchon M, Barbier P, Bernardet JF, Loux V, Vacherie B, Barbe V, Rocha EP, Duchaud E.

Appl Environ Microbiol. 2011 Nov;77(21):7656-62. doi: 10.1128/AEM.05625-11. Epub 2011 Sep 16.

50.

CRISPR distribution within the Escherichia coli species is not suggestive of immunity-associated diversifying selection.

Touchon M, Charpentier S, Clermont O, Rocha EP, Denamur E, Branger C.

J Bacteriol. 2011 May;193(10):2460-7. doi: 10.1128/JB.01307-10. Epub 2011 Mar 18.

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