I am a second-year computer science Ph.D. student supervised by Dr. Steven Salzberg and Dr. Mihaela Pertea at Center for Computational Biology, Johns Hopkins University. I received my Bachelor of Science in Electrical Engineering from National Taiwan University (NTU). In my senior year of college, I went on exchange to study at the College of Engineering & Computer Science, Australian National University (ANU).
My research interests are genome assembly and transcriptome (RNA sequencing). I am also passionate about developing open source bioinformatics tools and designing algorithms. I have developed two Bioconductor R packages which are RNASeqR and sangeranalyseR. Fore more information, please visit my research page 🔬.
- Building a multi-sample assembler upon StringTie aming to construct a more precise gene catalog. C++ |
- Improving Liftoff to achieve higher cross-species lift-over accuracy.
- Assembled Han1, the first gapless Southern Han Chinese individual genome | Han1
- Conducted the first-ever gene content comparison between two fully annotated individuals, Han1 and T2T-CHM13. Han1 paper (Chao et.al.)
- Developing algorithms to improve the graph-based sequence indexing aiming to apply them to the pan-genome graph.
- Developed the first Wheeler graph toolkit, WGT, to generate, recognize, and visualize Wheeler graph. C++
- Proposed a fast algorithm, Wheelie , making the NP-complete Wheeler Graph recognition problem solvable in practice. WGT paper (Chao et.al.)
HK Tsai Lab, Institute of Information Science, Academia Sinica
Lanfear Lab, Division of Ecology and Evolution, Research School of Biology, ANU
- Developed a bioconductor R package, sangeranalyseR, to democratize sanger sequencing data analysis in R.
- Implemented Bandelt tree encoding/decoding algorithm published in 1985. sangeranalyseR paper (Chao et.al.)
Bioinformatics Core Lab, Centers of Genomic and Precision Medicine, NTU
- Conducted differential gene expression analysis and pathway enrichment analysis using RNA-Seq data.
- Developed a bioconductor R package to provide a robust pipeline to automate the standard two-group RNA-Seq analysis in R. RNASeqR paper (Chao et.al.)
Information Security Research Institute, Institute for Information Industry
Software engineer intern
- Processed and visualized PC login and logoff history to help the team build a system to find insiders in the company.