| 2024 | RECOMB | PRS-Net: Interpretable Polygenic Risk Scores via Geometric Learning. | Han Li, Jianyang Zeng, Michael P. Snyder, Sai Zhang |
| 2022 | KDD | KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction. | Han Li, Dan Zhao, Jianyang Zeng |
| 2020 | RECOMB | MONN: A Multi-objective Neural Network for Predicting Pairwise Non-covalent Interactions and Binding Affinities Between Compounds and Proteins. | Shuya Li, Fangping Wan, Hantao Shu, Tao Jiang, Dan Zhao, Jianyang Zeng |
| 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 |
| 2017 | RECOMB | ROSE: A Deep Learning Based Framework for Predicting Ribosome Stalling. | Sai Zhang, Hailin Hu, Jingtian Zhou, Xuan He, Tao Jiang, Jianyang Zeng |
| 2016 | RECOMB | Low-Density Locality-Sensitive Hashing Boosts Metagenomic Binning. | Yunan Luo, Jianyang Zeng, Bonnie Berger, Jian Peng |
| 2015 | AAAI | Massively Parallel A* Search on a GPU. | Yichao Zhou, Jianyang Zeng |
| 2015 | RECOMB | Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data. | Huichao Gong, Sai Zhang, Jiangdian Wang, Haipeng Gong, Jianyang Zeng |
| 2015 | RECOMB | Computational Protein Design Using AND/OR Branch-and-Bound Search. | Yichao Zhou, Yuexin Wu, Jianyang Zeng |
| 2011 | RECOMB | Protein Loop Closure Using Orientational Restraints from NMR Data. | Chittaranjan Tripathy, Jianyang Zeng, Pei Zhou, Bruce Randall Donald |
| 2011 | RECOMB | A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data. | Jianyang Zeng, Kyle E. Roberts, Pei Zhou, Bruce Randall Donald |
| 2010 | RECOMB | A Markov Random Field Framework for Protein Side-Chain Resonance Assignment. | Jianyang Zeng, Pei Zhou, Bruce Randall Donald |
| 2005 | COCOON | Construction of Scale-Free Networks with Partial Information. | Jianyang Zeng, Wen-Jing Hsu, Suiping Zhou |
| 2005 | ISPA | Near Optimal Routing in a Small-World Network with Augmented Local Awareness. | Jianyang Zeng, Wen-Jing Hsu, Jiangdian Wang |
| 2005 | PDCAT | ReCord: A Distributed Hash Table with Recursive Structure. | Jianyang Zeng, Wen-Jing Hsu |
| 2005 | PDCAT | Optimal Routing in a Small-World Network. | Jianyang Zeng, Wen-Jing Hsu |
| 2003 | ICRA | Conflict-free routing of AGVs on the mesh topology based on a discrete-time model. | Jianyang Zeng, Wen-Jing Hsu |