Whole genome bisulfite sequencing: Analytical methods and biological insights

Whole genome bisulfite sequencing is a powerful technique for profiling methylation patterns, which provides measurement of methylation levels of individual cytosine sites across the genome. This dissertation presents the computational methods to analyze whole genome bisulfite sequencing data. Besides mapping bisulfite converted reads and estimating methylation levels of individual cytosines, this dissertation particularly studies epigenomic domains marked by characteristics methylation status. The biological insights from the application of the computational methods to the analysis of mammalian methylomes and plant methylomes are also reported.