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Items: 1 to 20 of 112

1.

BisQC: an operational pipeline for multiplexed bisulfite sequencing.

Chen GG, Diallo AB, Poujol R, Nagy C, Staffa A, Vaillancourt K, Lutz PE, Ota VK, Mash DC, Turecki G, Ernst C.

BMC Genomics. 2014 Apr 16;15:290. doi: 10.1186/1471-2164-15-290.

2.

Technical considerations for reduced representation bisulfite sequencing with multiplexed libraries.

Chatterjee A, Rodger EJ, Stockwell PA, Weeks RJ, Morison IM.

J Biomed Biotechnol. 2012;2012:741542. doi: 10.1155/2012/741542. Epub 2012 Oct 10.

4.

Library-free methylation sequencing with bisulfite padlock probes.

Diep D, Plongthongkum N, Gore A, Fung HL, Shoemaker R, Zhang K.

Nat Methods. 2012 Feb 5;9(3):270-2. doi: 10.1038/nmeth.1871.

5.

MethyQA: a pipeline for bisulfite-treated methylation sequencing quality assessment.

Sun S, Noviski A, Yu X.

BMC Bioinformatics. 2013 Aug 23;14:259. doi: 10.1186/1471-2105-14-259.

6.

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.

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.

Determining DNA methylation profiles using sequencing.

Feng S, Rubbi L, Jacobsen SE, Pellegrini M.

Methods Mol Biol. 2011;733:223-38. doi: 10.1007/978-1-61779-089-8_16.

PMID:
21431774
9.

BS Seeker: precise mapping for bisulfite sequencing.

Chen PY, Cokus SJ, Pellegrini M.

BMC Bioinformatics. 2010 Apr 23;11:203. doi: 10.1186/1471-2105-11-203.

10.

Whole methylome analysis by ultra-deep sequencing using two-base encoding.

Bormann Chung CA, Boyd VL, McKernan KJ, Fu Y, Monighetti C, Peckham HE, Barker M.

PLoS One. 2010 Feb 22;5(2):e9320. doi: 10.1371/journal.pone.0009320.

11.

Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing.

Adey A, Shendure J.

Genome Res. 2012 Jun;22(6):1139-43. doi: 10.1101/gr.136242.111. Epub 2012 Mar 30.

12.

Single nucleotide analysis of cytosine methylation by whole-genome shotgun bisulfite sequencing.

Johnson MD, Mueller M, Game L, Aitman TJ.

Curr Protoc Mol Biol. 2012 Jul;Chapter 21:Unit21.23. doi: 10.1002/0471142727.mb2123s99.

PMID:
22870857
13.

In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes.

Ivanov M, Kals M, Kacevska M, Metspalu A, Ingelman-Sundberg M, Milani L.

Nucleic Acids Res. 2013 Apr 1;41(6):e72. doi: 10.1093/nar/gks1467. Epub 2013 Jan 15.

14.

DNA methylation analysis by bisulfite conversion, cloning, and sequencing of individual clones.

Zhang Y, Rohde C, Tierling S, Stamerjohanns H, Reinhardt R, Walter J, Jeltsch A.

Methods Mol Biol. 2009;507:177-87. doi: 10.1007/978-1-59745-522-0_14.

PMID:
18987815
15.

Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data.

Hong C, Clement NL, Clement S, Hammoud SS, Carrell DT, Cairns BR, Snell Q, Clement MJ, Johnson WE.

BMC Bioinformatics. 2013 Nov 21;14:337. doi: 10.1186/1471-2105-14-337.

16.

BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data.

Guo W, Fiziev P, Yan W, Cokus S, Sun X, Zhang MQ, Chen PY, Pellegrini M.

BMC Genomics. 2013 Nov 10;14:774. doi: 10.1186/1471-2164-14-774.

17.

Single-molecule polymerase chain reaction reduces bias: application to DNA methylation analysis by bisulfite sequencing.

Chhibber A, Schroeder BG.

Anal Biochem. 2008 Jun 1;377(1):46-54. doi: 10.1016/j.ab.2008.02.026. Epub 2008 Mar 4.

PMID:
18358818
18.

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
19.

Investigation of genomic methylation status using methylation-specific and bisulfite sequencing polymerase chain reaction.

Carless M.

Methods Mol Biol. 2009;523:217-34. doi: 10.1007/978-1-59745-190-1_15.

PMID:
19381936
20.

BSMAP: whole genome bisulfite sequence MAPping program.

Xi Y, Li W.

BMC Bioinformatics. 2009 Jul 27;10:232. doi: 10.1186/1471-2105-10-232.

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