CFA: An explainable deep learning model for annotating the transcriptional roles of cis-regulatory modules based on epigenetic codes. - Tzu-Hsien Yang; Yu-Huai Yu; Sheng-Hang Wu; Fang-Yuan Zhang (Comput. Biol. Medicine, 2023)

RDDL: A systematic ensemble pipeline tool that streamlines balancing training schemes to reduce the effects of data imbalance in rare-disease-related deep-learning applications. - Tzu-Hsien Yang; Zhan-Yi Liao; Yu-Huai Yu; Min Hsia (Comput. Biol. Chem., 2023)

DMLS: an automated pipeline to extract the Drosophila modular transcription regulators and targets from massive literature articles. - Tzu-Hsien Yang; Yu-Huai Yu; Sheng-Hang Wu; Fang-Yuan Chang; Hsiu-Chun Tsai; Ya-Chiao Yang (Database J. Biol. Databases Curation, 2024)