🧑🏻💻 About me
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 area of interest lies in the creation of innovative algorithms that can be applied to computational genomics, with a particular emphasis on transcriptome (RNA sequencing) and genome assembly. I have a particular passion for developing highly efficient algorithms and ultra-fast tools that improve gene annotation precision and the quality of genome. I am also a big fan of open source software. Two of my R packages on Bioconductor are sangeranalyseR and RNASeqR. Visit my research page 🔬 for more information.
Salzberg & Pertea Lab, Center for Computational Biology, JHU
Ph.D. student
- 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.)
Langmead Lab, Department of Computer Science, JHU
collab with
Seshia Lab, Department of Electrical Engineering and Computer Sciences, UC Berkeley
Research student
- 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
Research assistant
Lanfear Lab, Division of Ecology and Evolution, Research School of Biology, ANU
Research assistant
- 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
Research assistant
- 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.
