🎓 I'm currently a third-year Ph.D. Candidate in Computer Science at the Center for Computational Biology, Johns Hopkins University, working with Steven Salzberg and Mihaela Pertea. . My academic journey started in Electrical Engineering at National Taiwan University (NTU), shifting towards computer science in my final year at the College of Engineering & Computer Science at Australian National University (ANU) 🦘🐨

🧬 My research interest intersects deep learning with genomics and transcriptomics:

• In transcriptional regulatory networks, my work uses sequence models to decode DNA patterns, aiming to uncover insights into how cis-regulatory DNA sequences and trans-regulators interact. I am developing a yeast large language model (LLM) to better understand the mechanisms of yeast gene expression regulation.
• In splice site predictiong, I built a deep dilated residual convolutional neural network to decode the complexities of RNA splicing, alternative splicing, and the impact of genetic variants on cryptic splicing (Learn more).
• In genome assembly, I assembled and annotated the first gapless Southern Chinese Han genome, Han1, using PacBio HiFi and Oxford Nanopore long reads, with T2T-CHM13 as a guide (Learn more).
• In pangenome indexing, I applied new renaming heuristics and an SMT solver to make the Wheeler graph recognition problem computationally feasible (Learn more).
• In genome annotation, I used graph-based methods to stitch together fragmented DNA and protein alignments, thereby assembling them into more accurate annotations. (Learn more).

💻 I am an advocate for open-source software, embracing the philosophy of “build what you need, use what you build”. I invite you to explore my NEWS page for the latest updates on my projects.

💬 Feel free to reach out to me for collaborations, discussions, or just to say hi! Coffee chat! ☕️

🔍 Discover more about my work on my personal website.