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Items: 1 to 20 of 86

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. Epub 2010 Jan 10.

2.

Why do results conflict regarding the prognostic value of the methylation status in colon cancers? The role of the preservation method.

Tournier B, Chapusot C, Courcet E, Martin L, Lepage C, Faivre J, Piard F.

BMC Cancer. 2012 Jan 13;12:12. doi: 10.1186/1471-2407-12-12.

3.

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
4.

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. Epub 2009 Jun 6.

PMID:
19505431
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. Epub 2007 Oct 10. Review.

7.

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. Epub 2011 Mar 18.

PMID:
21412275
8.

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. Epub 2010 Jul 13.

9.

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
10.
11.

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
12.

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. Epub 2011 Jul 5.

13.

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. Epub 2007 May 7.

14.

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.

15.

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.

16.

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. Epub 2009 Mar 29. Erratum in: Nat Biotechnol. 2009 May;27(5):485.

17.

Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3.

Tompa R, McCallum CM, Delrow J, Henikoff JG, van Steensel B, Henikoff S.

Curr Biol. 2002 Jan 8;12(1):65-8.

18.

MethyQESD, a robust and fast method for quantitative methylation analyses in HNPCC diagnostics using formalin-fixed and paraffin-embedded tissue samples.

Bettstetter M, Dechant S, Ruemmele P, Vogel C, Kurz K, Morak M, Keller G, Holinski-Feder E, Hofstaedter F, Dietmaier W.

Lab Invest. 2008 Dec;88(12):1367-75. doi: 10.1038/labinvest.2008.100. Epub 2008 Oct 20.

19.
20.

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.

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