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Results: 1 to 20 of 100

1.

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
2.

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
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.

BSeQC: quality control of bisulfite sequencing experiments.

Lin X, Sun D, Rodriguez B, Zhao Q, Sun H, Zhang Y, Li W.

Bioinformatics. 2013 Dec 15;29(24):3227-9. doi: 10.1093/bioinformatics/btt548. Epub 2013 Sep 23.

PMID:
24064417
[PubMed - indexed for MEDLINE]
5.

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
6.

Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine.

Booth MJ, Ost TW, Beraldi D, Bell NM, Branco MR, Reik W, Balasubramanian S.

Nat Protoc. 2013 Oct;8(10):1841-51. doi: 10.1038/nprot.2013.115. Epub 2013 Sep 5.

PMID:
24008380
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
24391148
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Whole genome DNA methylation analysis based on high throughput sequencing technology.

Li N, Ye M, Li Y, Yan Z, Butcher LM, Sun J, Han X, Chen Q, Zhang X, Wang J.

Methods. 2010 Nov;52(3):203-12. doi: 10.1016/j.ymeth.2010.04.009. Epub 2010 Apr 27.

PMID:
20430099
[PubMed - indexed for MEDLINE]
9.

Double restriction-enzyme digestion improves the coverage and accuracy of genome-wide CpG methylation profiling by reduced representation bisulfite sequencing.

Wang J, Xia Y, Li L, Gong D, Yao Y, Luo H, Lu H, Yi N, Wu H, Zhang X, Tao Q, Gao F.

BMC Genomics. 2013 Jan 16;14:11. doi: 10.1186/1471-2164-14-11.

PMID:
23324053
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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
11.

MethylSig: a whole genome DNA methylation analysis pipeline.

Park Y, Figueroa ME, Rozek LS, Sartor MA.

Bioinformatics. 2014 Sep 1;30(17):2414-22. doi: 10.1093/bioinformatics/btu339. Epub 2014 May 16.

PMID:
24836530
[PubMed - in process]
12.

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
13.

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
14.

A classification approach for DNA methylation profiling with bisulfite next-generation sequencing data.

Cheng L, Zhu Y.

Bioinformatics. 2014 Jan 15;30(2):172-9. doi: 10.1093/bioinformatics/btt674. Epub 2013 Nov 21.

PMID:
24273245
[PubMed - indexed for MEDLINE]
15.

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
16.

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF.

Nat Biotechnol. 2010 Oct;28(10):1097-105. doi: 10.1038/nbt.1682. Epub 2010 Sep 19.

PMID:
20852635
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

BRAT-BW: efficient and accurate mapping of bisulfite-treated reads.

Harris EY, Ponts N, Le Roch KG, Lonardi S.

Bioinformatics. 2012 Jul 1;28(13):1795-6. doi: 10.1093/bioinformatics/bts264. Epub 2012 May 3.

PMID:
22563065
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications.

Krueger F, Andrews SR.

Bioinformatics. 2011 Jun 1;27(11):1571-2. doi: 10.1093/bioinformatics/btr167. Epub 2011 Apr 14.

PMID:
21493656
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq).

Kofler R, Pandey RV, Schlötterer C.

Bioinformatics. 2011 Dec 15;27(24):3435-6. doi: 10.1093/bioinformatics/btr589. Epub 2011 Oct 23.

PMID:
22025480
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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.

PMID:
23200671
[PubMed - indexed for MEDLINE]

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