| 2025 | ICLR | Group Ligands Docking to Protein Pockets. | Jiaqi Guan, Jiahan Li, Xiangxin Zhou, Xingang Peng, Sheng Wang, Yunan Luo, Jian Peng, Jianzhu Ma |
| 2025 | RECOMB | Rewiring Protein Sequence and Structure Generative Models to Enhance Protein Stability Prediction. | Ziang Li, Yunan Luo |
| 2025 | RECOMB | Learning Maximally Spanning Representations Improves Protein Function Annotation. | Jiaqi Luo, Yunan Luo |
| 2024 | ICML | FAFE: Immune Complex Modeling with Geodesic Distance Loss on Noisy Group Frames. | Ruidong Wu, Ruihan Guo, Rui Wang, Shitong Luo, Yue Xu, Jiahan Li, Jianzhu Ma, Qiang Liu, Yunan Luo, Jian Peng |
| 2024 | RECOMB | Contrastive Fitness Learning: Reprogramming Protein Language Models for Low-N Learning of Protein Fitness Landscape. | Junming Zhao, Chao Zhang, Yunan Luo |
| 2023 | ICLR | Interpretable Geometric Deep Learning via Learnable Randomness Injection. | Siqi Miao, Yunan Luo, Mia Liu, Pan Li |
| 2020 | RECOMB | Evolutionary Context-Integrated Deep Sequence Modeling for Protein Engineering. | Yunan Luo, Lam Vo, Hantian Ding, Yufeng Su, Yang Liu, Wesley Wei Qian, Huimin Zhao, Jian Peng |
| 2019 | RECOMB | Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning. | Yunan Luo, Jianzhu Ma, Xiaoming Zhao, Yufeng Su, Yang Liu, Trey Ideker, Jian Peng |
| 2018 | PSB | Large-scale integration of heterogeneous pharmacogenomic data for identifying drug mechanism of action. | Yunan Luo, Sheng Wang, Jinfeng Xiao, Jian Peng |
| 2018 | RECOMB | Deciphering Signaling Specificity with Deep Neural Networks. | Yunan Luo, Jianzhu Ma, Yang Liu, Qing Ye, Trey Ideker, Jian Peng |
| 2017 | RECOMB | A Network Integration Approach for Drug-Target Interaction Prediction and Computational Drug Repositioning from Heterogeneous Information. | Yunan Luo, Xinbin Zhao, Jingtian Zhou, Jinling Yang, Yanqing Zhang, Wenhua Kuang, Jian Peng, Ligong Chen, Jianyang Zeng |
| 2016 | RECOMB | Low-Density Locality-Sensitive Hashing Boosts Metagenomic Binning. | Yunan Luo, Jianyang Zeng, Bonnie Berger, Jian Peng |