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Items: 1 to 20 of 202

1.

Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm.

Zhang B, Zhou Y, Lin N, Lowdon RF, Hong C, Nagarajan RP, Cheng JB, Li D, Stevens M, Lee HJ, Xing X, Zhou J, Sundaram V, Elliott G, Gu J, Shi T, Gascard P, Sigaroudinia M, Tlsty TD, Kadlecek T, Weiss A, O'Geen H, Farnham PJ, Maire CL, Ligon KL, Madden PA, Tam A, Moore R, Hirst M, Marra MA, Zhang B, Costello JF, Wang T.

Genome Res. 2013 Sep;23(9):1522-40. doi: 10.1101/gr.156539.113. Epub 2013 Jun 26.

2.

Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation.

Li D, Zhang B, Xing X, Wang T.

Methods. 2015 Jan 15;72:29-40. doi: 10.1016/j.ymeth.2014.10.032. Epub 2014 Nov 6.

3.

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.

4.

Analyzing the cancer methylome through targeted bisulfite sequencing.

Lee EJ, Luo J, Wilson JM, Shi H.

Cancer Lett. 2013 Nov 1;340(2):171-8. doi: 10.1016/j.canlet.2012.10.040. Epub 2012 Nov 28. Review.

5.

A comparison of the whole genome approach of MeDIP-seq to the targeted approach of the Infinium HumanMethylation450 BeadChip(®) for methylome profiling.

Clark C, Palta P, Joyce CJ, Scott C, Grundberg E, Deloukas P, Palotie A, Coffey AJ.

PLoS One. 2012;7(11):e50233. doi: 10.1371/journal.pone.0050233. Epub 2012 Nov 29.

6.

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.

7.

Whole genome DNA methylation analysis based on high throughput sequencing technology.

Li N, Ye M, Li Y, Yan Z, Butcher LM, Sun J, Han X, Chen Q, Zhang X, Wang J.

Methods. 2010 Nov;52(3):203-12. doi: 10.1016/j.ymeth.2010.04.009. Epub 2010 Apr 27.

PMID:
20430099
8.

Methylated DNA immunoprecipitation and high-throughput sequencing (MeDIP-seq) using low amounts of genomic DNA.

Zhao MT, Whyte JJ, Hopkins GM, Kirk MD, Prather RS.

Cell Reprogram. 2014 Jun;16(3):175-84. doi: 10.1089/cell.2014.0002. Epub 2014 Apr 28.

PMID:
24773292
9.

An integrative approach for efficient analysis of whole genome bisulfite sequencing data.

Lee JH, Park SJ, Kenta N.

BMC Genomics. 2015;16 Suppl 12:S14. doi: 10.1186/1471-2164-16-S12-S14. Epub 2015 Dec 9.

10.

MethGo: a comprehensive tool for analyzing whole-genome bisulfite sequencing data.

Liao WW, Yen MR, Ju E, Hsu FM, Lam L, Chen PY.

BMC Genomics. 2015;16 Suppl 12:S11. doi: 10.1186/1471-2164-16-S12-S11. Epub 2015 Dec 9.

11.

Genome wide analysis of acute myeloid leukemia reveal leukemia specific methylome and subtype specific hypomethylation of repeats.

Saied MH, Marzec J, Khalid S, Smith P, Down TA, Rakyan VK, Molloy G, Raghavan M, Debernardi S, Young BD.

PLoS One. 2012;7(3):e33213. doi: 10.1371/journal.pone.0033213. Epub 2012 Mar 29.

12.

Genome-wide high-resolution mapping of DNA methylation identifies epigenetic variation across embryo and endosperm in Maize (Zea may).

Wang P, Xia H, Zhang Y, Zhao S, Zhao C, Hou L, Li C, Li A, Ma C, Wang X.

BMC Genomics. 2015 Jan 23;16:21. doi: 10.1186/s12864-014-1204-7.

13.

Analyses of Methylomes Derived from Meso-American Common Bean (Phaseolus vulgaris L.) Using MeDIP-Seq and Whole Genome Sodium Bisulfite-Sequencing.

Crampton M, Sripathi VR, Hossain K, Kalavacharla V.

Front Plant Sci. 2016 Apr 26;7:447. doi: 10.3389/fpls.2016.00447. eCollection 2016.

14.

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.

Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavaré S, Beck S.

Nat Biotechnol. 2008 Jul;26(7):779-85. doi: 10.1038/nbt1414.

15.

Evaluation of MeDIP-chip in the context of whole-genome bisulfite sequencing (WGBS-seq) in Arabidopsis.

Wardenaar R, Liu H, Colot V, Colomé-Tatché M, Johannes F.

Methods Mol Biol. 2013;1067:203-24. doi: 10.1007/978-1-62703-607-8_13.

PMID:
23975794
16.

Whole-genome DNA methylation in skin lesions from patients with psoriasis vulgaris.

Zhang P, Zhao M, Liang G, Yin G, Huang D, Su F, Zhai H, Wang L, Su Y, Lu Q.

J Autoimmun. 2013 Mar;41:17-24. doi: 10.1016/j.jaut.2013.01.001. Epub 2013 Jan 29.

PMID:
23369618
17.

Semiconductor-based sequencing of genome-wide DNA methylation states.

Corley MJ, Zhang W, Zheng X, Lum-Jones A, Maunakea AK.

Epigenetics. 2015;10(2):153-66. doi: 10.1080/15592294.2014.1003747.

18.

Whole-genome fetal and maternal DNA methylation analysis using MeDIP-NGS for the identification of differentially methylated regions.

Keravnou A, Ioannides M, Tsangaras K, Loizides C, Hadjidaniel MD, Papageorgiou EA, Kyriakou S, Antoniou P, Mina P, Achilleos A, Neofytou M, Kypri E, Sismani C, Koumbaris G, Patsalis PC.

Genet Res (Camb). 2016 Nov 11;98:e15.

PMID:
27834155
19.

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.

20.

AutoMeDIP-seq: a high-throughput, whole genome, DNA methylation assay.

Butcher LM, Beck S.

Methods. 2010 Nov;52(3):223-31. doi: 10.1016/j.ymeth.2010.04.003. Epub 2010 Apr 10.

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