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Items: 1 to 20 of 105

1.

gemBS: high throughput processing for DNA methylation data from bisulfite sequencing.

Merkel A, Fernández-Callejo M, Casals E, Marco-Sola S, Schuyler R, Gut IG, Heath SC.

Bioinformatics. 2019 Mar 1;35(5):737-742. doi: 10.1093/bioinformatics/bty690.

PMID:
30137223
2.

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.

3.

B-SOLANA: an approach for the analysis of two-base encoding bisulfite sequencing data.

Kreck B, Marnellos G, Richter J, Krueger F, Siebert R, Franke A.

Bioinformatics. 2012 Feb 1;28(3):428-9. doi: 10.1093/bioinformatics/btr660. Epub 2011 Dec 6.

4.

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.

5.

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.

6.

BS-Seeker3: ultrafast pipeline for bisulfite sequencing.

Huang KYY, Huang YJ, Chen PY.

BMC Bioinformatics. 2018 Apr 3;19(1):111. doi: 10.1186/s12859-018-2120-7.

7.

pWGBSSimla: a profile-based whole-genome bisulfite sequencing data simulator incorporating methylation QTLs, allele-specific methylations and differentially methylated regions.

Chung RH, Kang CY.

Bioinformatics. 2019 Aug 9. pii: btz635. doi: 10.1093/bioinformatics/btz635. [Epub ahead of print]

PMID:
31397839
8.

Software updates in the Illumina HiSeq platform affect whole-genome bisulfite sequencing.

Toh H, Shirane K, Miura F, Kubo N, Ichiyanagi K, Hayashi K, Saitou M, Suyama M, Ito T, Sasaki H.

BMC Genomics. 2017 Jan 5;18(1):31. doi: 10.1186/s12864-016-3392-9.

9.

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.

10.

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.

11.

ViewBS: a powerful toolkit for visualization of high-throughput bisulfite sequencing data.

Huang X, Zhang S, Li K, Thimmapuram J, Xie S, Wren J.

Bioinformatics. 2018 Feb 15;34(4):708-709. doi: 10.1093/bioinformatics/btx633.

12.

Using local alignment to enhance single-cell bisulfite sequencing data efficiency.

Wu P, Gao Y, Guo W, Zhu P.

Bioinformatics. 2019 Sep 15;35(18):3273-3278. doi: 10.1093/bioinformatics/btz125.

PMID:
30859188
13.

HBS-Tools for Hairpin Bisulfite Sequencing Data Processing and Analysis.

Sun MA, Velmurugan KR, Keimig D, Xie H.

Adv Bioinformatics. 2015;2015:760423. doi: 10.1155/2015/760423. Epub 2015 Dec 20.

14.

Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data.

Akman K, Haaf T, Gravina S, Vijg J, Tresch A.

Bioinformatics. 2014 Jul 1;30(13):1933-4. doi: 10.1093/bioinformatics/btu142. Epub 2014 Mar 10.

15.

Bisulfite Sequencing Using Small DNA Amounts.

Edelmann S, Scholten S.

Methods Mol Biol. 2018;1675:45-60. doi: 10.1007/978-1-4939-7318-7_3. Erratum in: Methods Mol Biol. 2018;1675:E1.

PMID:
29052184
16.

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.

17.

Comprehensive Whole DNA Methylome Analysis by Integrating MeDIP-seq and MRE-seq.

Xing X, Zhang B, Li D, Wang T.

Methods Mol Biol. 2018;1708:209-246. doi: 10.1007/978-1-4939-7481-8_12.

18.

Whole-Genome Bisulfite Sequencing for the Analysis of Genome-Wide DNA Methylation and Hydroxymethylation Patterns at Single-Nucleotide Resolution.

Kernaleguen M, Daviaud C, Shen Y, Bonnet E, Renault V, Deleuze JF, Mauger F, Tost J.

Methods Mol Biol. 2018;1767:311-349. doi: 10.1007/978-1-4939-7774-1_18.

PMID:
29524144
19.

meRanTK: methylated RNA analysis ToolKit.

Rieder D, Amort T, Kugler E, Lusser A, Trajanoski Z.

Bioinformatics. 2016 Mar 1;32(5):782-5. doi: 10.1093/bioinformatics/btv647. Epub 2015 Nov 4.

PMID:
26543174
20.

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.

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