The short version
Genomes accumulate duplicate genes. Most copies decay, some are kept, and a few take on new roles — but which ones, and why, is hard to answer at genome scale without a lot of careful pipeline work. My dissertation looks at that question in Populus (poplar trees), using expert-annotated and published case studies as a ground-truth reference set to check whether automated analysis pipelines are finding real biology or artifacts.
Below is the detail. If you want the compressed version, it is on my resume.
PhD dissertation research
Tsai Lab, Institute of Bioinformatics, University of Georgia — 2020–present
- Dissertation on lineage-specific genes and the gene-duplication landscape in Populus, using expert-annotated and published case studies as a ground-truth reference set to improve automated analysis pipelines.
- Reprocessed large-scale community RNA-seq data (raw FASTQ through differential expression) on reproducible, HPC-scalable pipelines, and built genome-wide protein structure annotation workflows.
- Modeled ohnolog expression divergence with XGBoost and SHAP under leakage-aware validation — chromosome-held-out cross-validation and permuted-label controls, so the reported performance is not an artifact of related sequences leaking between folds.
- Evaluated seven DNA foundation models (Nucleotide Transformer, PlantCAD2, DNABERT2, AgroNT, HyenaDNA, Grover) on Populus promoter sequences, diagnosing embedding quality and establishing architecture-specific pooling. This is what pulled me toward the foundation-model robustness work.
- Contributed to Populus VariantDB v3.2, a CRISPR gRNA verification tool, and to a coexpression analysis of a perennial-specific sulfate transporter subgroup associated with lignification. Both published in Tree Physiology (2025).
Tools: Python, R, Snakemake, SLURM/HPC, STAR, HISAT2, DESeq2, edgeR.
MSc research
Plant Biotechnology and Molecular Biology Lab, Department of Horticulture, National Taiwan University — 2017–2019
- Comparative transcriptome analysis of mycorrhiza-enhanced salt tolerance in rice, published in Frontiers in Plant Science (2022) as co-first author.
- Automated high-resolution melting (HRM) analysis output processing with custom scripts, which streamlined genotyping for a peach (Prunus persica) chilling requirement study (IJMS, 2020).
- Designed RNA-seq experiments and identified the genome-wide MADS-box gene family to study gibberellin-induced sex determination in bitter gourd. Presented at the International Horticultural Congress in Istanbul (2018); first prize at the NTU graduate student research poster competition (2019).
Full citations are on the publications page. Talks and posters are listed there too.