Computational Tool Development and Protocol Improvement

Epigenetic modifications such as carbon 5 methylation of cytosine base in a CpG dinucleotide context are involved in the onset and progression of human diseases. A comprehensive understanding of the role of genome wide DNA methylation patterns, the methylome, requires quantitative determination of the methylation states of all CpG sites in a genome. Analyses of the complete methylome by whole-genome bisulfite sequencing (WGBS) are rare because of the required large DNA quantities, substantial bioinformatics resources and high sequencing costs.

We improved the WGBS protocol, which allows investigating the methylome at single base resolution by using 5 ng of input DNA compared to 3-5 ug required for traditional WGBS. Hence, the improved protocol allows the comprehensive methylome analysis of limited amounts of DNA isolated from precious biological specimens. (Nature Protocols, 2013)

Circular layout is an efficient way for the visualization of huge amounts of genomic information. We developed a computational package named “circlize”, which provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of this package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, circlize gives users more convenience and freedom to design figures for better understanding genomic patterns behind multi-dimensional data. (Bioinformatics, 2014)

We also develop novel computational approach for better diagnosis in eye disease and characterization of the hypusine sites which is a unique modification on lysine residues in eukaryotic translation initiation factor 5A (Eif5a). (Scientific Reports, 2021; Current Proteomics, 2018)