I am a PhD student in Interdisciplinary Bioscience doctoral training program under the supervision of Gerton Lunter and Jim Hughes. My broad interests include complex systems, bioinformatics, and ML applications for genomics. Specifically, my research explores non-coding functional genomics through improved analysis from next-generation sequencing data. This leads to the main projects of my PhD: i) developing EpiCall, a mechanistic, highly sensitive peak calling algorithm for ATAC-seq data; and ii) developing Avocato, a collaboration work for an end-to-end, high-resolution analysis pipeline for scATAC-seq data with functional prioritisation.
Single-cell sequencing has improved the resolution of various kind of sequencing to individual cell level. While the more widely-used scRNA-seq is limited to information within coding regions, scATAC-seq reveals cell-to-cell heterogeneity of DNA accessibility across the entire genome, which provides valuable data with which to study gene regulatory mechanisms at individual cell level. However, the current downstream analysis of scATAC-seq is far from satisfaction. We aim to generate an optimized and comprehensive pipeline for scATAC-seq analysis, extract cell-specific information from transcription profile, and develop machine learning models to predict cell-specific patterns of genome-wide DNA accessibility.
Before coming to Oxford, I completed my undergraduate in Biological Sciences from Nankai University, China in 2018. During the time I gradually formed interest in genomics with the application of mathematical modelling and statistics, which brought me to postgraduate studies in bioinformatics.