🎓 I’m a fourth-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 RNA-Seq gene expression prediction, I build a multi-species fungal language model that integrates genomic sequences, RNA-seq, and ChIP-exo data to decode gene architectures and pinpoint key yeast regulatory motifs. Leveraging self-supervised learning, in silico mutagenesis, attention visualization, and time series perturbations, I reveal how cis-regulatory elements and trans-acting factors drive dynamic changes in motif strength and gene expression (See what my model has learned; Learn more; Talk).
• In splice site predictiong, I built a dilated residual convolutional neural network to decode the complexities of RNA splicing, alternative splicing, and the impact of genetic variants on cryptic splicing (Paper I; Paper II; News; Talk).
• In genome annotation, I used graph-based methods to stitch together fragmented DNA and protein alignments, thereby assembling them into more accurate annotations. (Paper; Talk).
• 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 (Paper; Genome).
• For pangenome indexing, I applied new renaming heuristics and an SMT solver to make the Wheeler graph recognition problem computationally feasible (Paper; News; Talk).

💻 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.