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Items: 1 to 20 of 101

1.

DamMet: ancient methylome mapping accounting for errors, true variants, and post-mortem DNA damage.

Hanghøj K, Renaud G, Albrechtsen A, Orlando L.

Gigascience. 2019 Apr 1;8(4). pii: giz025. doi: 10.1093/gigascience/giz025.

2.

Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX.

Hanghøj K, Seguin-Orlando A, Schubert M, Madsen T, Pedersen JS, Willerslev E, Orlando L.

Mol Biol Evol. 2016 Dec;33(12):3284-3298. Epub 2016 Sep 13.

3.

Detection of Cytosine methylation in ancient DNA from five native american populations using bisulfite sequencing.

Smith RW, Monroe C, Bolnick DA.

PLoS One. 2015 May 27;10(5):e0125344. doi: 10.1371/journal.pone.0125344. eCollection 2015.

4.

DNA methylation: bisulphite modification and analysis.

Patterson K, Molloy L, Qu W, Clark S.

J Vis Exp. 2011 Oct 21;(56). pii: 3170. doi: 10.3791/3170.

5.

Methods for discovering genomic loci exhibiting complex patterns of differential methylation.

Hardcastle TJ.

BMC Bioinformatics. 2017 Sep 18;18(1):416. doi: 10.1186/s12859-017-1836-0.

6.

Resolution of the DNA methylation state of single CpG dyads using in silico strand annealing and WGBS data.

Xu C, Corces VG.

Nat Protoc. 2019 Jan;14(1):202-216. doi: 10.1038/s41596-018-0090-x.

PMID:
30542058
7.

gargammel: a sequence simulator for ancient DNA.

Renaud G, Hanghøj K, Willerslev E, Orlando L.

Bioinformatics. 2017 Feb 15;33(4):577-579. doi: 10.1093/bioinformatics/btw670.

8.

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.

9.

Improving ancient DNA read mapping against modern reference genomes.

Schubert M, Ginolhac A, Lindgreen S, Thompson JF, Al-Rasheid KA, Willerslev E, Krogh A, Orlando L.

BMC Genomics. 2012 May 10;13:178. doi: 10.1186/1471-2164-13-178.

10.

Joint Estimates of Heterozygosity and Runs of Homozygosity for Modern and Ancient Samples.

Renaud G, Hanghøj K, Korneliussen TS, Willerslev E, Orlando L.

Genetics. 2019 Jul;212(3):587-614. doi: 10.1534/genetics.119.302057. Epub 2019 May 14.

PMID:
31088861
11.

Methyl-Analyzer--whole genome DNA methylation profiling.

Xin Y, Ge Y, Haghighi FG.

Bioinformatics. 2011 Aug 15;27(16):2296-7. doi: 10.1093/bioinformatics/btr356. Epub 2011 Jun 17.

12.

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters.

Jónsson H, Ginolhac A, Schubert M, Johnson PL, Orlando L.

Bioinformatics. 2013 Jul 1;29(13):1682-4. doi: 10.1093/bioinformatics/btt193. Epub 2013 Apr 23.

14.

DNA methylome profiling at single-base resolution through bisulfite sequencing of 5mC-immunoprecipitated DNA.

Jia Z, Shi Y, Zhang L, Ren Y, Wang T, Xing L, Zhang B, Gao G, Bu R.

BMC Biotechnol. 2018 Feb 6;18(1):7. doi: 10.1186/s12896-017-0409-7.

15.

MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data.

Xu J, Liu S, Yin P, Bulun S, Dai Y.

BMC Bioinformatics. 2018 Dec 22;19(1):540. doi: 10.1186/s12859-018-2574-7.

16.

A comprehensive evaluation of alignment software for reduced representation bisulfite sequencing data.

Sun X, Han Y, Zhou L, Chen E, Lu B, Liu Y, Pan X, Cowley AW Jr, Liang M, Wu Q, Lu Y, Liu P.

Bioinformatics. 2018 Aug 15;34(16):2715-2723. doi: 10.1093/bioinformatics/bty174.

PMID:
29579198
17.

DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data.

Gaspar JM, Hart RP.

BMC Bioinformatics. 2017 Nov 29;18(1):528. doi: 10.1186/s12859-017-1909-0.

18.

True single-molecule DNA sequencing of a pleistocene horse bone.

Orlando L, Ginolhac A, Raghavan M, Vilstrup J, Rasmussen M, Magnussen K, Steinmann KE, Kapranov P, Thompson JF, Zazula G, Froese D, Moltke I, Shapiro B, Hofreiter M, Al-Rasheid KA, Gilbert MT, Willerslev E.

Genome Res. 2011 Oct;21(10):1705-19. doi: 10.1101/gr.122747.111. Epub 2011 Jul 29.

19.

DREAM: A Simple Method for DNA Methylation Profiling by High-throughput Sequencing.

Jelinek J, Madzo J.

Methods Mol Biol. 2016;1465:111-27. doi: 10.1007/978-1-4939-4011-0_10.

PMID:
27581143
20.

An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping.

Zhou Q, Lim JQ, Sung WK, Li G.

BMC Bioinformatics. 2019 Jan 22;20(1):47. doi: 10.1186/s12859-018-2593-4.

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