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Items: 1 to 20 of 276

1.

Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing.

Kunde-Ramamoorthy G, Coarfa C, Laritsky E, Kessler NJ, Harris RA, Xu M, Chen R, Shen L, Milosavljevic A, Waterland RA.

Nucleic Acids Res. 2014 Apr;42(6):e43. doi: 10.1093/nar/gkt1325. Epub 2014 Jan 3.

2.

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.

3.

BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation.

Lim JQ, Tennakoon C, Li G, Wong E, Ruan Y, Wei CL, Sung WK.

Genome Biol. 2012 Oct 3;13(10):R82. doi: 10.1186/gb-2012-13-10-r82.

4.

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.

5.

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.

6.

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. Epub 2014 May 27. Review.

PMID:
24867940
7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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. Epub 2015 Nov 10.

13.

Fast, accurate, and lightweight analysis of BS-treated reads with ERNE 2.

Prezza N, Vezzi F, Käller M, Policriti A.

BMC Bioinformatics. 2016 Mar 2;17 Suppl 4:69. doi: 10.1186/s12859-016-0910-3.

14.

BSPAT: a fast online tool for DNA methylation co-occurrence pattern analysis based on high-throughput bisulfite sequencing data.

Hu K, Ting AH, Li J.

BMC Bioinformatics. 2015 Jul 11;16:220. doi: 10.1186/s12859-015-0649-2.

15.
16.

A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing.

Wang X, Yu X, Zhu W, McCombie WR, Antoniou E, Powers RS, Davidson NO, Li E, Williams J.

Bioinformatics. 2015 Jun 15;31(12):2040-2. doi: 10.1093/bioinformatics/btv089. Epub 2015 Feb 13.

17.

Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing.

Coarfa C, Yu F, Miller CA, Chen Z, Harris RA, Milosavljevic A.

BMC Bioinformatics. 2010 Nov 23;11:572. doi: 10.1186/1471-2105-11-572.

18.

PrEMeR-CG: inferring nucleotide level DNA methylation values from MethylCap-seq data.

Frankhouser DE, Murphy M, Blachly JS, Park J, Zoller MW, Ganbat JO, Curfman J, Byrd JC, Lin S, Marcucci G, Yan P, Bundschuh R.

Bioinformatics. 2014 Dec 15;30(24):3567-74. doi: 10.1093/bioinformatics/btu583. Epub 2014 Aug 31.

19.

CpG_MPs: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data.

Su J, Yan H, Wei Y, Liu H, Liu H, Wang F, Lv J, Wu Q, Zhang Y.

Nucleic Acids Res. 2013 Jan 7;41(1):e4. doi: 10.1093/nar/gks829. Epub 2012 Aug 31.

20.

Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS).

Yang Y, Sebra R, Pullman BS, Qiao W, Peter I, Desnick RJ, Geyer CR, DeCoteau JF, Scott SA.

BMC Genomics. 2015 May 6;16:350. doi: 10.1186/s12864-015-1572-7.

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