Peer-reviewed publications
Surber, S. M., Hsieh, C., Na, L., Harding, S. A., & Tsai, C.-J. (2025). An updated sulfate transporter phylogeny uncovers a perennial-specific subgroup associated with lignification. Tree Physiology. doi:10.1093/treephys/tpaf080
An updated phylogeny of plant sulfate transporters that finds a subgroup present only in perennials, with expression tracking lignification. My contribution: comparative transcriptomics and the coexpression analysis behind the lignification link.
Zhou, R., Seth, S. R., Reeves, J., Burns, A. H., Hsieh, C., Horn, T. W., Xue, L.-J., & Tsai, C.-J. (2025). Populus VariantDB v3.2 facilitates CRISPR and functional genomics research. Tree Physiology. doi:10.1093/treephys/tpaf081
A community database release that lets researchers check CRISPR guide RNAs against natural sequence variation in Populus before ordering them, so guides are not silently broken by a SNP. My contribution: gRNA verification tooling.
Tuma, T. T., Nyamdari, B., Hsieh, C., Chen, Y.-H., Harding, S. A., & Tsai, C.-J. (2024). Perturbation of tonoplast sucrose transport alters carbohydrate utilization for seasonal growth and defense metabolism in coppiced poplar. Tree Physiology, 44(7), tpae061. doi:10.1093/treephys/tpae061
Disrupting sugar transport across the vacuole membrane changes how coppiced poplar splits carbohydrate between regrowth and defense chemistry over a season.
Hsieh, C., Chen, Y.-H., Chang, K.-C., & Yang, S.-Y. (2022). Transcriptome analysis reveals the mechanisms for mycorrhiza-enhanced salt tolerance in rice. Frontiers in Plant Science, 13, 1072171. (co-first author) doi:10.3389/fpls.2022.1072171
Rice colonized by mycorrhizal fungi handles salt stress better; this compares transcriptomes to work out which pathways carry that effect. My contribution: co-first author — designed and ran the comparative transcriptome analysis.
Chou, L., Huang, S.-J., Hsieh, C., Lu, M.-T., Song, C.-W., & Hsu, F.-C. (2020). A high-resolution melting analysis-based genotyping toolkit for the peach (Prunus persica) chilling requirement. International Journal of Molecular Sciences, 21(4), 1543. doi:10.3390/ijms21041543
A genotyping toolkit for predicting how much winter chilling a peach cultivar needs before it will flower. My contribution: automated the high-resolution melting output processing, which removed the manual step from genotyping.
See also my Google Scholar profile. If you hit a paywall on any of these, email me and I will send the accepted manuscript.
In preparation
Adversarial robustness of genomic foundation models. Submitted to a workshop, August 2026. Under review, not yet peer-reviewed. Method and current results are on the genomic AI page.
Talks
Investigating de novo gene birth in Populus. SMBE Satellite Meeting on De Novo Gene Birth, Texas A&M University (2023).
Posters
Characterization of stress-responsive lineage-specific genes in Populus. IUFRO Tree Biotechnology Conference (2024).
Searching for orphan genes in Populus. ASPB Worldwide Summit (2021).
Comparative transcriptome analysis of gibberellin-induced sex determination in bitter gourd. XXX International Horticultural Congress, Istanbul (2018). First prize, NTU graduate student research poster competition (2019).
Background on the projects behind these papers is on the research page.