Publications

Cheng-Hung Tsai, Carolina G. Piña Páez, Jason E. Stajich (2026). orthoSynAssign: refine orthogroups using synteny information. bioRxiv.

Cheng-Hung Tsai, Jason E Stajich (2026). Phyling: phylogenetic inference from annotated genomes. G3: Genes, Genomes, Genetics, 16(5).

Xin-Zhan Liu, Cheng-Hung Tsai, Marco A Coelho, Eva Ottum, Cene Gostincar, Benedetta Turchetti, Claudia Coleine, Laura Selbmann, Ian Wheeldon, Nina Gunde-Cimerman, Fengyan Bai, Jason Eric Stajich (2025). Genomic plasticity of the mating-type loci underlies reproductive strategy transitions in extitRhodotorula yeasts. bioRxiv.

Tzu-Chieh Lin, Cheng-Hung Tsai, Cheng-Kai Shiau, Jia-Hsin Huang, Huai-Kuang Tsai (2024). Predicting splicing patterns from the transcription factor binding sites in the promoter with deep learning. BMC Genomics, 25(S3).

Cheng-Hung Tsai, Tzu-Chieh Lin, Yi-Hsien Chang, Huai-Kuang Tsai, Jia-Hsin Huang (2022). Identification and comparative analysis of long non-coding RNAs in the brain of fire ant queens in two different reproductive states. BMC Genomics, 22(S5).

Jia-Hsin Huang, You-Rou Liao, Tzu-Chieh Lin, Cheng-Hung Tsai, Wei-Yun Lai, Yang-Kai Chou, Jun-Yi Leu, Huai-Kuang Tsai, Cheng-Fu Kao (2021). iTARGEX analysis of yeast deletome reveals novel regulators of transcriptional buffering in S phase and protein turnover. Nucleic Acids Research, 49(13), 7318-7329.

Shin Yen Chong, Sam Cutler, Jing-Jer Lin, Cheng-Hung Tsai, Huai-Kuang Tsai, Sue Biggins, Toshio Tsukiyama, Yi-Chen Lo, Cheng-Fu Kao (2020). H3K4 methylation at active genes mitigates transcription-replication conflicts during replication stress. Nature Communications, 11(1).