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Principles and challenges of genomewide DNA methylation analysis.

Laird PW.

Nat Rev Genet. 2010 Mar;11(3):191-203. doi: 10.1038/nrg2732. Review.


Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk.

Brinkman AB, Gu H, Bartels SJ, Zhang Y, Matarese F, Simmer F, Marks H, Bock C, Gnirke A, Meissner A, Stunnenberg HG.

Genome Res. 2012 Jun;22(6):1128-38. doi: 10.1101/gr.133728.111. Epub 2012 Mar 30.


Global DNA methylation profiling technologies and the ovarian cancer methylome.

Tang J, Fang F, Miller DF, Pilrose JM, Matei D, Huang TH, Nephew KP.

Methods Mol Biol. 2015;1238:653-75. doi: 10.1007/978-1-4939-1804-1_34. Review.


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.


Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements.

Zhang W, Spector TD, Deloukas P, Bell JT, Engelhardt BE.

Genome Biol. 2015 Jan 24;16:14. doi: 10.1186/s13059-015-0581-9.


Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion.

Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J.

Genome Res. 2008 Mar;18(3):469-76. doi: 10.1101/gr.7073008. Epub 2008 Jan 24.


Genomics of CpG methylation in developing and developed zebrafish.

McGaughey DM, Abaan HO, Miller RM, Kropp PA, Brody LC.

G3 (Bethesda). 2014 Mar 21;4(5):861-9. doi: 10.1534/g3.113.009514.


Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF.

Nat Biotechnol. 2010 Oct;28(10):1097-105. doi: 10.1038/nbt.1682. Epub 2010 Sep 19.


Analysis of DNA methylation profiles in preimplantation embryos using bisulfite mutagenesis.

Han YM, Kim SH, Kang YK.

Methods Mol Biol. 2006;325:251-60.


Methylation analysis by DNA immunoprecipitation.

Thu KL, Pikor LA, Kennett JY, Alvarez CE, Lam WL.

J Cell Physiol. 2010 Mar;222(3):522-31. doi: 10.1002/jcp.22009. Review.


Double restriction-enzyme digestion improves the coverage and accuracy of genome-wide CpG methylation profiling by reduced representation bisulfite sequencing.

Wang J, Xia Y, Li L, Gong D, Yao Y, Luo H, Lu H, Yi N, Wu H, Zhang X, Tao Q, Gao F.

BMC Genomics. 2013 Jan 16;14:11. doi: 10.1186/1471-2164-14-11.


Methylation profiling using methylated DNA immunoprecipitation and tiling array hybridization.

Cheung HH, Lee TL, Rennert OM, Chan WY.

Methods Mol Biol. 2012;825:115-26. doi: 10.1007/978-1-61779-436-0_10.


Techniques used in studies of age-related DNA methylation changes.

Wojdacz TK, Hansen LL.

Ann N Y Acad Sci. 2006 May;1067:479-87. Review.


Strategies for discovery and validation of methylated and hydroxymethylated DNA biomarkers.

Olkhov-Mitsel E, Bapat B.

Cancer Med. 2012 Oct;1(2):237-60. doi: 10.1002/cam4.22. Epub 2012 Sep 14. Review.


Hairpin-bisulfite PCR: assessing epigenetic methylation patterns on complementary strands of individual DNA molecules.

Laird CD, Pleasant ND, Clark AD, Sneeden JL, Hassan KM, Manley NC, Vary JC Jr, Morgan T, Hansen RS, Stöger R.

Proc Natl Acad Sci U S A. 2004 Jan 6;101(1):204-9. Epub 2003 Dec 12.


Genome-wide methylation analysis.

Unterberger A, Dubuc AM, Taylor MD.

Methods Mol Biol. 2012;863:303-17. doi: 10.1007/978-1-61779-612-8_19.


Microarray-based DNA methylation profiling: technology and applications.

Schumacher A, Kapranov P, Kaminsky Z, Flanagan J, Assadzadeh A, Yau P, Virtanen C, Winegarden N, Cheng J, Gingeras T, Petronis A.

Nucleic Acids Res. 2006 Jan 20;34(2):528-42. Print 2006.


Single Base-Resolution Methylome of the Dizygotic Sheep.

Wang Y, Wu J, Ma X, Liu B, Su R, Jiang Y, Wang W, Dong Y.

PLoS One. 2015 Nov 4;10(11):e0142034. doi: 10.1371/journal.pone.0142034. eCollection 2015.


Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods.

Stevens M, Cheng JB, Li D, Xie M, Hong C, Maire CL, Ligon KL, Hirst M, Marra MA, Costello JF, Wang T.

Genome Res. 2013 Sep;23(9):1541-53. doi: 10.1101/gr.152231.112. Epub 2013 Jun 26.

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