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Results: 1 to 20 of 96

1.

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions.

Hansen KD, Langmead B, Irizarry RA.

Genome Biol. 2012 Oct 3;13(10):R83. doi: 10.1186/gb-2012-13-10-r83.

PMID:
23034175
[PubMed - in process]
Free PMC Article
2.

Methy-Pipe: an integrated bioinformatics pipeline for whole genome bisulfite sequencing data analysis.

Jiang P, Sun K, Lun FM, Guo AM, Wang H, Chan KC, Chiu RW, Lo YM, Sun H.

PLoS One. 2014 Jun 19;9(6):e100360. doi: 10.1371/journal.pone.0100360. eCollection 2014.

PMID:
24945300
[PubMed - in process]
Free PMC Article
3.

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.

PMID:
24206606
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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.

PMID:
23968174
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

GBSA: a comprehensive software for analysing whole genome bisulfite sequencing data.

Benoukraf T, Wongphayak S, Hadi LH, Wu M, Soong R.

Nucleic Acids Res. 2013 Feb 1;41(4):e55. doi: 10.1093/nar/gks1281. Epub 2012 Dec 24.

PMID:
23268441
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
24261665
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
23804401
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Methodological aspects of whole-genome bisulfite sequencing analysis.

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

Brief Bioinform. 2014 May 27. pii: bbu016. [Epub ahead of print]

PMID:
24867940
[PubMed - as supplied by publisher]
9.

RRBS-analyser: a comprehensive web server for reduced representation bisulfite sequencing data analysis.

Wang T, Liu Q, Li X, Wang X, Li J, Zhu X, Sun ZS, Wu J.

Hum Mutat. 2013 Dec;34(12):1606-10. doi: 10.1002/humu.22444. Epub 2013 Oct 10.

PMID:
24106010
[PubMed - indexed for MEDLINE]
10.

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.

PMID:
22941633
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data.

Barturen G, Rueda A, Oliver JL, Hackenberg M.

Version 2. F1000Res. 2013 Oct 15 [revised 2014 Feb 21];2:217. doi: 10.12688/f1000research.2-217.v2. eCollection 2013.

PMID:
24627790
[PubMed]
Free PMC Article
12.

Detection of significantly differentially methylated regions in targeted bisulfite sequencing data.

Hebestreit K, Dugas M, Klein HU.

Bioinformatics. 2013 Jul 1;29(13):1647-53. doi: 10.1093/bioinformatics/btt263. Epub 2013 May 8.

PMID:
23658421
[PubMed - indexed for MEDLINE]
Free Article
13.

SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing.

Sun Z, Baheti S, Middha S, Kanwar R, Zhang Y, Li X, Beutler AS, Klee E, Asmann YW, Thompson EA, Kocher JP.

Bioinformatics. 2012 Aug 15;28(16):2180-1. doi: 10.1093/bioinformatics/bts337. Epub 2012 Jun 10.

PMID:
22689387
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
19635165
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
20416082
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome.

Serre D, Lee BH, Ting AH.

Nucleic Acids Res. 2010 Jan;38(2):391-9. doi: 10.1093/nar/gkp992. Epub 2009 Nov 11.

PMID:
19906696
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples.

Lee YK, Jin S, Duan S, Lim YC, Ng DP, Lin XM, Yeo GSh, Ding C.

Biol Proced Online. 2014 Jan 9;16(1):1. doi: 10.1186/1480-9222-16-1.

PMID:
24406024
[PubMed]
Free PMC Article
18.

MOABS: model based analysis of bisulfite sequencing data.

Sun D, Xi Y, Rodriguez B, Park HJ, Tong P, Meong M, Goodell MA, Li W.

Genome Biol. 2014 Feb 24;15(2):R38. doi: 10.1186/gb-2014-15-2-r38.

PMID:
24565500
[PubMed - in process]
Free PMC Article
19.

A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data.

Feng H, Conneely KN, Wu H.

Nucleic Acids Res. 2014 Apr;42(8):e69. doi: 10.1093/nar/gku154. Epub 2014 Feb 22.

PMID:
24561809
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

WBSA: web service for bisulfite sequencing data analysis.

Liang F, Tang B, Wang Y, Wang J, Yu C, Chen X, Zhu J, Yan J, Zhao W, Li R.

PLoS One. 2014 Jan 30;9(1):e86707. doi: 10.1371/journal.pone.0086707. eCollection 2014.

PMID:
24497972
[PubMed - in process]
Free PMC Article

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