| 2025 | CIBCB | Self-Attention Enhanced Deep Learning Models for Immune Cell Deconvolution from Bulk RNA-Seq. | Chia-Ru Chung, Yen-Lin Chen, Yun Tang, Justin Bo-Kai Hsu, Li-Ching Wu, Tzong-Yi Lee, Jorng-Tzong Horng |
| 2025 | CIBCB | Explainable AI-Enhanced Kinase Activity Profiling Through Phosphoproteomics. | Chia-Ru Chung, Ming-Feng Ho, Yun Tang, Li-Ching Wu, Justin Bo-Kai Hsu, Tzong-Yi Lee, Jorng-Tzong Horng |
| 2025 | CIBCB | miSAM: Robust MicroRNA Expression Estimation Using Bi-Objective Evolutionary Learning Algorithm in Cancer Transcriptomics. | Yann-Lin Ho, Yann-Jen Ho, Shinn-Ying Ho, Tzong-Yi Lee |
| 2025 | CIBCB | EL-DRP: An Evolutionary Learning-Based Multi-Omics Framework for Drug Response Prediction with Interpretable Biomarker Selection. | Yann-Jen Ho, Paik You Sheng, Yu-Ruo Chen, Yun Tang, Shinn-Ying Ho, Tzong-Yi Lee |
| 2025 | CIBCB | Integrative Multi-Omics Prognostic Modeling of Glioma Recurrence Using Variational Autoencoder and Similarity Network Fusion. | Phuong Lam Tran, Yun Tang, Justin Bo-Kai Hsu, Tzong-Yi Lee |
| 2025 | CIBCB | Towards Accurate Identification of Anti-Hepatitis C Peptides Using Stack-AHCP. | Lantian Yao, Chang Liu, Yen-Peng Chiu, Jiahui Guan, Peilin Xie, Zhihao Zhao, Xingchen Liu, Yilin Guo, Yulan Liu, Yunlu Peng, Ying-Chih Chiang, Tzong-Yi Lee |