CirPred, the first structure modeling and linker design system for circularly permuted proteins. - Teng-Ruei Chen; Yen-Cheng Lin; Yu-Wei Huang; Chih-Chieh Chen; Wei-Cheng Lo (BMC Bioinform., 2021)

Plan2Align: Predictive Planning Based Test-Time Preference Alignment in Paragraph-Level Machine Translation. - Kuang-Da Wang; Teng-Ruei Chen; Yu-Heng Hung; Shuoyang Ding; Yueh-Hua Wu; Yu-Chiang Frank Wang; Chao-Han Huck Yang; Wen-Chih Peng; Ping-Chun Hsieh (CoRR, 2025)

Dual Engines of Thoughts: A Depth-Breadth Integration Framework for Open-Ended Analysis. - Fei-Hsuan Yu; Yun-Cheng Chou; Teng-Ruei Chen (CoRR, 2025)