FEI-MAN HSUGohain, MoloyaMoloyaGohainChang, PearlPearlChangLu, Jui-HsienJui-HsienLuChen, Pao-YangPao-YangChen2026-03-062026-03-06201897801281221509780128123294https://www.scopus.com/pages/publications/85088909864?origin=resultslisthttps://scholars.lib.ntu.edu.tw/handle/123456789/736099With the advances in next-generation sequencing (NGS), epigenetic modifications can be profiled on a genome-wide scale. Chromatin immunoprecipitation sequencing (ChIP-seq) can identify the distribution of histone marks. DNaseI-seq, MNase-seq and ATAC-seq use different enzyme characteristics to reveal histone occupancy and chromatin accessibility. BS-seq profiles DNA methylation with single-base resolution. Small ribonucleic acid (sRNA) sequencing can identify the source and target of sRNA. Hi-C reveals the all-to-all chromosomal interactions in three dimensions. These high-throughput sequencing-based techniques yield large-scale sequencing data that requires advanced computational ability to analyze. In this chapter, we describe the specialty of each NGS technique and explain the analysis the sequencing data with popular bioinformatics tools. We also provide case studies as practical applications. Lastly, we described prediction methods of transcription factor binding sites using integrative epigenome data.falseATAC-seqBioinformaticsBS-seqChIP-seqEpigenomicHi-CNGSSmall ribonucleic acidbook part10.1016/b978-0-12-812215-0.00004-22-s2.0-85088909864