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Items: 1 to 20 of 95

1.

Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution.

Gu H, Bock C, Mikkelsen TS, Jäger N, Smith ZD, Tomazou E, Gnirke A, Lander ES, Meissner A.

Nat Methods. 2010 Feb;7(2):133-6. doi: 10.1038/nmeth.1414.

2.

AKSmooth: enhancing low-coverage bisulfite sequencing data via kernel-based smoothing.

Chen J, Lutsik P, Akulenko R, Walter J, Helms V.

J Bioinform Comput Biol. 2014 Dec;12(6):1442005. doi: 10.1142/S0219720014420050.

PMID:
25553811
3.

Formamide as a denaturant for bisulfite conversion of genomic DNA: Bisulfite sequencing of the GSTPi and RARbeta2 genes of 43 formalin-fixed paraffin-embedded prostate cancer specimens.

Zon G, Barker MA, Kaur P, Groshen S, Jones LW, Imam SA, Boyd VL.

Anal Biochem. 2009 Sep 15;392(2):117-25. doi: 10.1016/j.ab.2009.06.001.

PMID:
19505431
4.

Methodological aspects of whole-genome bisulfite sequencing analysis.

Adusumalli S, Mohd Omar MF, Soong R, Benoukraf T.

Brief Bioinform. 2015 May;16(3):369-79. doi: 10.1093/bib/bbu016. Review.

PMID:
24867940
5.

Direct bisulfite sequencing for examination of DNA methylation with gene and nucleotide resolution from brain tissues.

Parrish RR, Day JJ, Lubin FD.

Curr Protoc Neurosci. 2012 Jul;Chapter 7:Unit 7.24. doi: 10.1002/0471142301.ns0724s60.

6.

Genome-wide analysis of DNA methylation patterns.

Zilberman D, Henikoff S.

Development. 2007 Nov;134(22):3959-65. Review.

7.

Methylation assay by nucleotide incorporation: a quantitative assay for regional CpG methylation density.

Yamamoto T, Nagasaka T, Notohara K, Sasamoto H, Murakami J, Tanaka N, Matsubara N.

Biotechniques. 2004 May;36(5):846-50, 852, 854.

PMID:
15152605
8.

Bisulfite conversion-specific and methylation-specific PCR: a sensitive technique for accurate evaluation of CpG methylation.

Sasaki M, Anast J, Bassett W, Kawakami T, Sakuragi N, Dahiya R.

Biochem Biophys Res Commun. 2003 Sep 19;309(2):305-9.

PMID:
12951050
9.
10.

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling.

Gu H, Smith ZD, Bock C, Boyle P, Gnirke A, Meissner A.

Nat Protoc. 2011 Apr;6(4):468-81. doi: 10.1038/nprot.2010.190.

PMID:
21412275
11.

Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples.

Varley KE, Mitra RD.

Genome Res. 2010 Sep;20(9):1279-87. doi: 10.1101/gr.101212.109.

12.

AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes.

Dicks E, Teague JW, Stephens P, Raine K, Yates A, Mattocks C, Tarpey P, Butler A, Menzies A, Richardson D, Jenkinson A, Davies H, Edkins S, Forbes S, Gray K, Greenman C, Shepherd R, Stratton MR, Futreal PA, Wooster R.

Bioinformatics. 2007 Jul 1;23(13):1689-91.

13.

Investigating bisulfite short-read mapping failure with hairpin bisulfite sequencing data.

Porter J, Sun MA, Xie H, Zhang L.

BMC Genomics. 2015;16 Suppl 11:S2. doi: 10.1186/1471-2164-16-S11-S2.

14.

Tools for translational epigenetic studies involving formalin-fixed paraffin-embedded human tissue: applying the Infinium HumanMethyation450 Beadchip assay to large population-based studies.

Wong EM, Joo JE, McLean CA, Baglietto L, English DR, Severi G, Hopper JL, Milne RL, FitzGerald LM, Giles GG, Southey MC.

BMC Res Notes. 2015 Oct 6;8:543. doi: 10.1186/s13104-015-1487-z.

15.

Enhanced reduced representation bisulfite sequencing for assessment of DNA methylation at base pair resolution.

Garrett-Bakelman FE, Sheridan CK, Kacmarczyk TJ, Ishii J, Betel D, Alonso A, Mason CE, Figueroa ME, Melnick AM.

J Vis Exp. 2015 Feb 24;(96):e52246. doi: 10.3791/52246.

16.

Bisulfite-Based DNA Methylation Analysis from Recent and Archived Formalin-Fixed, Paraffin Embedded Colorectal Tissue Samples.

Kalmár A, Péterfia B, Hollósi P, Wichmann B, Bodor A, Patai ÁV, Schöller A, Krenács T, Tulassay Z, Molnár B.

Pathol Oncol Res. 2015 Sep;21(4):1149-56. doi: 10.1007/s12253-015-9945-4.

PMID:
25991403
17.

Pipeline for large-scale microdroplet bisulfite PCR-based sequencing allows the tracking of hepitype evolution in tumors.

Herrmann A, Haake A, Ammerpohl O, Martin-Guerrero I, Szafranski K, Stemshorn K, Nothnagel M, Kotsopoulos SK, Richter J, Warner J, Olson J, Link DR, Schreiber S, Krawczak M, Platzer M, Nürnberg P, Siebert R, Hampe J.

PLoS One. 2011;6(7):e21332. doi: 10.1371/journal.pone.0021332.

18.

Mapping recently identified nucleotide variants in the genome and transcriptome.

Song CX, Yi C, He C.

Nat Biotechnol. 2012 Nov;30(11):1107-16. Review.

19.

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.

20.

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells.

Ball MP, Li JB, Gao Y, Lee JH, LeProust EM, Park IH, Xie B, Daley GQ, Church GM.

Nat Biotechnol. 2009 Apr;27(4):361-8. doi: 10.1038/nbt.1533. Erratum in: Nat Biotechnol. 2009 May;27(5):485.

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