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Items: 1 to 20 of 96

1.

Entering the era of bacterial epigenomics with single molecule real time DNA sequencing.

Davis BM, Chao MC, Waldor MK.

Curr Opin Microbiol. 2013 Apr;16(2):192-8. doi: 10.1016/j.mib.2013.01.011. Epub 2013 Feb 19. Review.

2.

Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing.

Fang G, Munera D, Friedman DI, Mandlik A, Chao MC, Banerjee O, Feng Z, Losic B, Mahajan MC, Jabado OJ, Deikus G, Clark TA, Luong K, Murray IA, Davis BM, Keren-Paz A, Chess A, Roberts RJ, Korlach J, Turner SW, Kumar V, Waldor MK, Schadt EE.

Nat Biotechnol. 2012 Dec;30(12):1232-9. doi: 10.1038/nbt.2432. Epub 2012 Nov 8. Erratum in: Nat Biotechnol. 2013 Jun;31(6):566.

3.

Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic.

Feng Z, Fang G, Korlach J, Clark T, Luong K, Zhang X, Wong W, Schadt E.

PLoS Comput Biol. 2013;9(3):e1002935. doi: 10.1371/journal.pcbi.1002935. Epub 2013 Mar 14.

4.

Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite- sequencing.

Yu M, Ji L, Neumann DA, Chung DH, Groom J, Westpheling J, He C, Schmitz RJ.

Nucleic Acids Res. 2015 Dec 2;43(21):e148. doi: 10.1093/nar/gkv738. Epub 2015 Jul 15.

5.

Direct detection of DNA methylation during single-molecule, real-time sequencing.

Flusberg BA, Webster DR, Lee JH, Travers KJ, Olivares EC, Clark TA, Korlach J, Turner SW.

Nat Methods. 2010 Jun;7(6):461-5. doi: 10.1038/nmeth.1459. Epub 2010 May 9.

6.

Single-molecule, genome-scale analyses of DNA modifications: exposing the epigenome with next-generation technologies.

Zillner K, Németh A.

Epigenomics. 2012 Aug;4(4):403-14. doi: 10.2217/epi.12.30. Review.

PMID:
22920180
7.

Genome-wide methylation patterns in Salmonella enterica Subsp. enterica Serovars.

Pirone-Davies C, Hoffmann M, Roberts RJ, Muruvanda T, Timme RE, Strain E, Luo Y, Payne J, Luong K, Song Y, Tsai YC, Boitano M, Clark TA, Korlach J, Evans PS, Allard MW.

PLoS One. 2015 Apr 10;10(4):e0123639. doi: 10.1371/journal.pone.0123639. eCollection 2015.

8.

Exploring bacterial epigenomics in the next-generation sequencing era: a new approach for an emerging frontier.

Chen P, Jeannotte R, Weimer BC.

Trends Microbiol. 2014 May;22(5):292-300. doi: 10.1016/j.tim.2014.03.005. Epub 2014 Apr 8. Review.

PMID:
24725482
9.

Exploring the roles of DNA methylation in the metal-reducing bacterium Shewanella oneidensis MR-1.

Bendall ML, Luong K, Wetmore KM, Blow M, Korlach J, Deutschbauer A, Malmstrom RR.

J Bacteriol. 2013 Nov;195(21):4966-74. doi: 10.1128/JB.00935-13. Epub 2013 Aug 30.

10.

Role of DNA methyltransferases in epigenetic regulation in bacteria.

Kumar R, Rao DN.

Subcell Biochem. 2013;61:81-102. doi: 10.1007/978-94-007-4525-4_4. Review.

PMID:
23150247
11.

DNA methylation in bacteria: from the methyl group to the methylome.

Sánchez-Romero MA, Cota I, Casadesús J.

Curr Opin Microbiol. 2015 Jun;25:9-16. doi: 10.1016/j.mib.2015.03.004. Epub 2015 Mar 26. Review.

PMID:
25818841
12.

The Epigenomic Landscape of Prokaryotes.

Blow MJ, Clark TA, Daum CG, Deutschbauer AM, Fomenkov A, Fries R, Froula J, Kang DD, Malmstrom RR, Morgan RD, Posfai J, Singh K, Visel A, Wetmore K, Zhao Z, Rubin EM, Korlach J, Pennacchio LA, Roberts RJ.

PLoS Genet. 2016 Feb 12;12(2):e1005854. doi: 10.1371/journal.pgen.1005854. eCollection 2016 Feb. Erratum in: PLoS Genet. 2016 May;12(5):e1006064.

13.

Analysis of gene-specific and genome-wide sperm DNA methylation.

Hammoud SS, Cairns BR, Carrell DT.

Methods Mol Biol. 2013;927:451-8. Review.

PMID:
22992936
14.

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules.

Kelly TK, Liu Y, Lay FD, Liang G, Berman BP, Jones PA.

Genome Res. 2012 Dec;22(12):2497-506. doi: 10.1101/gr.143008.112. Epub 2012 Sep 7.

15.

Bisulphite sequencing of plant genomic DNA.

Aichinger E, Köhler C.

Methods Mol Biol. 2010;655:433-43. doi: 10.1007/978-1-60761-765-5_29.

PMID:
20734278
16.

Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes.

Beaulaurier J, Zhang XS, Zhu S, Sebra R, Rosenbluh C, Deikus G, Shen N, Munera D, Waldor MK, Chess A, Blaser MJ, Schadt EE, Fang G.

Nat Commun. 2015 Jun 15;6:7438. doi: 10.1038/ncomms8438.

17.

Methylome analysis using MeDIP-seq with low DNA concentrations.

Taiwo O, Wilson GA, Morris T, Seisenberger S, Reik W, Pearce D, Beck S, Butcher LM.

Nat Protoc. 2012 Mar 8;7(4):617-36. doi: 10.1038/nprot.2012.012.

PMID:
22402632
18.

Studying the epigenome using next generation sequencing.

Ku CS, Naidoo N, Wu M, Soong R.

J Med Genet. 2011 Nov;48(11):721-30. doi: 10.1136/jmedgenet-2011-100242. Epub 2011 Aug 8. Review.

PMID:
21825079
19.

DNA methylation analysis of germ cells by using bisulfite-based sequencing methods.

Kobayashi H, Kono T.

Methods Mol Biol. 2012;825:223-35. doi: 10.1007/978-1-61779-436-0_17.

PMID:
22144248
20.

The methylomes of six bacteria.

Murray IA, Clark TA, Morgan RD, Boitano M, Anton BP, Luong K, Fomenkov A, Turner SW, Korlach J, Roberts RJ.

Nucleic Acids Res. 2012 Dec;40(22):11450-62. doi: 10.1093/nar/gks891. Epub 2012 Oct 2. Erratum in: Nucleic Acids Res. 2014 Apr;42(6):4140.

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