References
- Luo C, Hajkova P, Ecker JR. Dynamic DNA methylation: in the right place at the right time. Science. 2018;361(6409):1336–1340.
- Greenberg MVC, Bourc’his D. The diverse roles of DNA methylation in mammalian development and disease. Nat Rev Mol Cell Biol. 2019;20(10):590–607.
- Zhang Q, Cao X. Epigenetic regulation of the innate immune response to infection. Nat Rev Immunol. 2019;19(7):417–432.
- Grunau C, Clark SJ, Rosenthal A. Bisulfite genomic sequencing: systematic investigation of critical experimental parameters. Nucleic Acids Res. 2001;29(13):E65.
- Smallwood SA, Lee HJ, Angermueller C, et al. Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity. Nat Methods. 2014;11(8):817–820.
- Vaisvila R, Ponnaluri VKC, Sun Z, et al. Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA. Genome Res. 2021;31(7):1280–1289.
- Sun Z, Vaisvila R, Hussong LM, et al. Nondestructive enzymatic deamination enables single-molecule long-read amplicon sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Genome Res. 2021;31(2):291–300.
- Di Tommaso P, Chatzou M, Floden EW, et al. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017;35(4):316–319.
- Ewels PA, Peltzer A, Fillinger S, et al. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020;38(3):276–278.
- Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. 2011;27(11):1571–1572.
- Garcia-Alcalde F, Okonechnikov K, Carbonell J, et al. Qualimap: evaluating next-generation sequencing alignment data. Bioinformatics. 2012;28(20):2678–2679.
- Ewels P, Magnusson M, Lundin S, et al. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32(19):3047–3048.
- Yates AD, Achuthan P, Akanni W, et al. Ensembl 2020. Nucleic Acids Res. 2020;48:D682–D688.
- Wei T, Nie J, Larson NB, Ye Z, Eckel Passow JE, Robertson KD, Kocher JA, Wang L. CpGtools: a python package for DNA methylation analysis. Bioinformatics. 2019;37(11):1598–1599
- Crary-Dooley FK, Tam ME, Dunaway KW, et al. A comparison of existing global DNA methylation assays to low-coverage whole-genome bisulfite sequencing for epidemiological studies. Epigenetics. 2017;12(3):206–214.
- Olova N, Krueger F, Andrews S, et al. Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data. Genome Biol. 2018;19(1):33.
- Freedman AH, Gaspar JM, Sackton TB. Short paired-end reads trump long single-end reads for expression analysis. BMC Bioinformatics. 2020;21(1):149.
- Zhao LY, Song J, Liu Y, et al. Mapping the epigenetic modifications of DNA and RNA. Protein Cell. 2020;11(11):792–808.
- Gretarsson KH, Hackett JA. Dppa2 and Dppa4 counteract de novo methylation to establish a permissive epigenome for development. Nat Struct Mol Biol. 2020;27:(8):706–716.
- Ross SE, Angeloni A, Geng FS, et al. Developmental remodelling of non-CG methylation at satellite DNA repeats. Nucleic Acids Res. 2020;48(22):12675–12688.
- Feng S, Zhong Z, Wang M, et al. Efficient and accurate determination of genome-wide DNA methylation patterns in Arabidopsis thaliana with enzymatic methyl sequencing. Epigenetics Chromatin. 2020;13(1):42.