Research interest/work responsibility
My main role at the Penn Epigenetics Institute is to provide bioinformatic services to the Institute’s core members. I am interested in analyzing next-generation sequencing data to gain biological insights. In addition, I am interested in training and applying machine learning models to tackle biological questions.
Skills
- Whole genome bisulfite sequencing, DNA methylation ChIP array
- Bulk/single-cell RNA-seq, small RNA-seq (piRNA)
- ChIP-seq, CUT&RUN, ATAC-seq
- HiC
Background
I have ten years of hands-on experience in analyzing a variety of next-generation sequencing data. During my PhD research in genomics, I developed a novel computational pipeline to annotate transposable elements (DNA parasites accounting for ~45% of the human genome) from a terabyte-scale whole genome re-sequencing D. melanogaster strains. During my first postdoctoral training, I developed computational pipelines that used HiC data to identify three-dimensional chromatin changes, including split/merge of topologically associated domains (TADs) and changes in chromatin stripes. During my postdoctoral training under the mentorship of Dr. Elizabeth A Heller, I expanded my expertise towards computational analysis of neuronal epigenetic regulation. This training involved analysis and mining of CUT&RUN, ChIP-seq and RNA-seq data. I have also expanded my expertise into machine learning models, such as PLIER, to interrogate cocaine-regulated gene expression in preclinical models of addiction.