CiNet: Redesigning Deep Neural Networks for Efficient Mobile-Cloud Collaborative Inference. - Xin Dai; Xiangnan Kong; Tian Guo 001; Yixian Huang (SDM, 2021)

MethHC 2.0: information repository of DNA methylation and gene expression in human cancer. - Hsi-Yuan Huang; Jing Li; Yun Tang; Yixian Huang; Yigang Chen 001; Yue-Yang Xie; Zhe-Yuan Zhou; Xin-Yi Chen; Si-Yuan Ding; Meng-Fan Luo; Chen-Nan Jin; Le-Shan Zhao; et al. (Nucleic Acids Res., 2021)

miRTarBase update 2022: an informative resource for experimentally validated miRNA-target interactions. - Hsi-Yuan Huang; Yang-Chi-Dung Lin; Shi-Dong Cui; Yixian Huang; Yun Tang; Jia-Tong Xu; Jiayang Bao; Yulin Li; Jia Wen; Hua-Li Zuo; Weijuan Wang; Jing Li; et al. (Nucleic Acids Res., 2022)

DeepDrugmiR: a two-stage deep learning method for inferring small molecules' regulatory effects on microRNA expression. - Yixian Huang; Huacong Wu; Ying Cai; Danhong Dong; Sicong Yu; Yigang Chen 001; Zihao Zhu; Yang-Chi-Dung Lin; Hsien-Da Huang; Hsi-Yuan Huang (BCB, 2024)

A two-stage computational framework for identifying antiviral peptides and their functional types based on contrastive learning and multi-feature fusion strategy. - Jiahui Guan; Lantian Yao; Peilin Xie; Chia-Ru Chung; Yixian Huang; Ying-Chih Chiang; Tzong-Yi Lee (Briefings Bioinform., 2024)

ACP-CapsPred: an explainable computational framework for identification and functional prediction of anticancer peptides based on capsule network. - Lantian Yao; Peilin Xie; Jiahui Guan; Chia-Ru Chung; Wenyang Zhang; Junyang Deng; Yixian Huang; Ying-Chih Chiang; Tzong-Yi Lee (Briefings Bioinform., 2024)

CapsEnhancer: An Effective Computational Framework for Identifying Enhancers Based on Chaos Game Representation and Capsule Network. - Lantian Yao; Peilin Xie; Jiahui Guan; Chia-Ru Chung; Yixian Huang; Yuxuan Pang; Huacong Wu; Ying-Chih Chiang; Tzong-Yi Lee (J. Chem. Inf. Model., 2024)

DrugRepoBank: a comprehensive database and discovery platform for accelerating drug repositioning. - Yixian Huang; Danhong Dong; Wenyang Zhang; Ruiting Wang; Yang-Chi-Dung Lin; Hua-Li Zuo; Hsi-Yuan Huang; Hsien-Da Huang (Database J. Biol. Databases Curation, 2024)

EditBoard: Towards a Comprehensive Evaluation Benchmark for Text-Based Video Editing Models. - Yupeng Chen; Penglin Chen; Xiaoyu Zhang; Yixian Huang; Qian Xie (AAAI, 2025)

Beyond English: Unveiling Multilingual Bias in LLM Copyright Compliance. - Yupeng Chen; Xiaoyu Zhang; Yixian Huang; Qian Xie (CoRR, 2025)

SCOPE-DTI: Semi-Inductive Dataset Construction and Framework Optimization for Practical Usability Enhancement in Deep Learning-Based Drug Target Interaction Prediction. - Yigang Chen 001; Xiang Ji; Ziyue Zhang; Yuming Zhou; Yang-Chi-Dung Lin; Hsi-Yuan Huang; Tao Zhang; Yi Lai; Ke Chen; Chang Su; Xingqiao Lin; Zihao Zhu; et al. (CoRR, 2025)