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Items: 1 to 20 of 101

1.

Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome.

Pedersen JS, Valen E, Velazquez AM, Parker BJ, Rasmussen M, Lindgreen S, Lilje B, Tobin DJ, Kelly TK, Vang S, Andersson R, Jones PA, Hoover CA, Tikhonov A, Prokhortchouk E, Rubin EM, Sandelin A, Gilbert MT, Krogh A, Willerslev E, Orlando L.

Genome Res. 2014 Mar;24(3):454-66. doi: 10.1101/gr.163592.113.

2.

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.

3.

Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma.

Nabilsi NH, Deleyrolle LP, Darst RP, Riva A, Reynolds BA, Kladde MP.

Genome Res. 2014 Feb;24(2):329-39. doi: 10.1101/gr.161737.113.

4.

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. Review.

PMID:
21825079
5.

Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX.

Hanghøj K, Seguin-Orlando A, Schubert M, Madsen T, Pedersen JS, Willerslev E, Orlando L.

Mol Biol Evol. 2016 Dec;33(12):3284-3298.

6.

High-resolution analysis of cytosine methylation in ancient DNA.

Llamas B, Holland ML, Chen K, Cropley JE, Cooper A, Suter CM.

PLoS One. 2012;7(1):e30226. doi: 10.1371/journal.pone.0030226.

7.

Genome-wide DNA methylome variation in two genetically distinct chicken lines using MethylC-seq.

Li J, Li R, Wang Y, Hu X, Zhao Y, Li L, Feng C, Gu X, Liang F, Lamont SJ, Hu S, Zhou H, Li N.

BMC Genomics. 2015 Oct 23;16:851. doi: 10.1186/s12864-015-2098-8.

8.

A determining influence for CpG dinucleotides on nucleosome positioning in vitro.

Davey CS, Pennings S, Reilly C, Meehan RR, Allan J.

Nucleic Acids Res. 2004 Aug 13;32(14):4322-31.

9.

Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations.

Portella G, Battistini F, Orozco M.

PLoS Comput Biol. 2013;9(11):e1003354. doi: 10.1371/journal.pcbi.1003354.

10.

Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population.

Schmitz RJ, He Y, Valdés-López O, Khan SM, Joshi T, Urich MA, Nery JR, Diers B, Xu D, Stacey G, Ecker JR.

Genome Res. 2013 Oct;23(10):1663-74. doi: 10.1101/gr.152538.112.

11.

Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression.

Vining KJ, Pomraning KR, Wilhelm LJ, Priest HD, Pellegrini M, Mockler TC, Freitag M, Strauss SH.

BMC Genomics. 2012 Jan 17;13:27. doi: 10.1186/1471-2164-13-27.

12.

Next-generation technologies and data analytical approaches for epigenomics.

Mensaert K, Denil S, Trooskens G, Van Criekinge W, Thas O, De Meyer T.

Environ Mol Mutagen. 2014 Apr;55(3):155-70. doi: 10.1002/em.21841. Review.

PMID:
24327356
13.

[Genome-scale sequence data processing and epigenetic analysis of DNA methylation].

Wang TZ, Shan G, Xu JH, Xue QZ.

Yi Chuan. 2013 Jun;35(6):685-94. Review. Chinese.

PMID:
23774013
14.

Epigenomics: genome-wide study of methylation phenomena.

Novik KL, Nimmrich I, Genc B, Maier S, Piepenbrock C, Olek A, Beck S.

Curr Issues Mol Biol. 2002 Oct;4(4):111-28. Review.

15.

Lsh, chromatin remodeling family member, modulates genome-wide cytosine methylation patterns at nonrepeat sequences.

Tao Y, Xi S, Shan J, Maunakea A, Che A, Briones V, Lee EY, Geiman T, Huang J, Stephens R, Leighty RM, Zhao K, Muegge K.

Proc Natl Acad Sci U S A. 2011 Apr 5;108(14):5626-31. doi: 10.1073/pnas.1017000108. Erratum in: Proc Natl Acad Sci U S A. 2011 Sep 13;108(37):15535.

16.

Contrasting chromatin organization of CpG islands and exons in the human genome.

Choi JK.

Genome Biol. 2010;11(7):R70. doi: 10.1186/gb-2010-11-7-r70.

17.

Roles, and establishment, maintenance and erasing of the epigenetic cytosine methylation marks in plants.

Kumar S, Kumari R, Sharma V, Sharma V.

J Genet. 2013 Dec;92(3):629-66. Review.

18.

Genome-wide analysis of DNA methylation in bovine placentas.

Su J, Wang Y, Xing X, Liu J, Zhang Y.

BMC Genomics. 2014 Jan 8;15:12. doi: 10.1186/1471-2164-15-12.

19.

Pros and cons of methylation-based enrichment methods for ancient DNA.

Seguin-Orlando A, Gamba C, Der Sarkissian C, Ermini L, Louvel G, Boulygina E, Sokolov A, Nedoluzhko A, Lorenzen ED, Lopez P, McDonald HG, Scott E, Tikhonov A, Stafford TW Jr, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Shapiro B, Willerslev E, Prokhortchouk E, Orlando L.

Sci Rep. 2015 Jul 2;5:11826. doi: 10.1038/srep11826.

20.

Nucleosome deposition and DNA methylation at coding region boundaries.

Choi JK, Bae JB, Lyu J, Kim TY, Kim YJ.

Genome Biol. 2009;10(9):R89. doi: 10.1186/gb-2009-10-9-r89.

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