1.   [Advanced Science]  scCompass: An integrated cross-species scRNA-seq database for AI-ready. Pengfei Wang, Wenhao Liu, Jiajia Wang, Yana Liu, Pengjiang Li, Ping Xu, Wentao Cui, Ran Zhang, Qingqing Long, Zhilong Hu, Chen Fang, Jingxi Dong, Chunyang Zhang, Yan Chen, Chengrui Wang, Guole Liu, Hanyu Xie, Yiyang Zhang, Meng Xiao, Shubai Chen, X-Compass Consortium, Yiqiang Chen, Ge Yang, Shihua Zhang, Zhen Meng, Xuezhi Wang, Guihai Feng, Xin Li, Yuanchun Zhou. Advanced Science, 2025. 

2.   [ACL] Diversity-Oriented Data Augmentation with Large Language Models. Zaitian Wang, Jinghan Zhang, Xinhao Zhang, Kunpeng Liu, Pengfei Wang*, Yuanchun Zhou. The 63rd Annual Meeting of the Association for Computational Linguistics (ACL 2025)

3.   [IJCAI] scSiameseClu: A Siamese Clustering Framework for Interpreting single-cell RNA Sequencing Data. Ping Xu, Zhiyuan Ning, Pengjiang Li, Wenhao Liu, Pengyang Wang*, Jiaxu Cui, Yuanchun Zhou, Pengfei Wang*. The 34rd International Joint Conference on Artificial Intelligence, 2025. 

4.   [Cell Research (Coevr story)] GeneCompass: Deciphering Universal Gene Regulatory Mechanisms with Knowledge-Informed Cross-Species Foundation Model. Xiaodong Yang, Guole Liu, Guihai Feng, Dechao Bu, Pengfei Wang, Jie Jiang, Shubai Chen, Qinmeng Yang, Yiyang Zhang, Zhenpeng Man, Zhongming Liang, Zichen Wang, Yaning Li, Zheng Li, Yana Liu, Yao Tian, Ao Li, Jingxi Dong, Zhilong Hu, Chen Fang, Hefan Miao, Lina Cui, Zixu Deng, Haiping Jiang, Wentao Cui, Jiahao Zhang, Zhaohui Yang, Handong Li, Xingjian He, Liqun Zhong, Jiaheng Zhou, Zijian Wang, Qingqing Long, Ping Xu, Hongmei Wang, Zhen Meng, Xuezhi Wang, Yangang Wang, Yong Wang, Shihua Zhang, Jingtao Guo, Yi Zhao, Yuanchun Zhou, Fei Li, Jing Liu, Yiqiang Chen, Ge Yang, Xin Li. Cell Research, 2024, 34(12): 830-845.

5.   [AAAI] Motif-Oriented Representation Learning with Topology Refinement for Drug-Drug Interaction Prediction. Ran Zhang, Xuezhi Wang, Guannan Liu, Pengyang Wang, Yuanchun Zhou, Pengfei Wang*.  Proceedings of the AAAI Conference on Artificial Intelligence. 2025. 

6.   [IJCAI] TFWT: Tabular Feature Weighting with Transformer. Xinhao Zhang, Zaitian Wang, Lu Jiang, Wanfu Gao, Pengfei Wang*, Kunpeng Liu*. The 33rd International Joint Conference on Artificial Intelligence, 2024. 

7.   [AIJ] Temporal Inductive Path Neural Network for Temporal Knowledge Graph Reasoning. Hao Dong, Pengyang Wang*, Meng Xiao, Zhiyuan Ning, Pengfei Wang*, Yuanchun Zhou. Artificial Intelligence, 2024. 

8.   [IJCAI] Adaptive Path-Memory Network for Temporal Knowledge Graph Reasoning. Hao Dong, Zhiyuan Ning, Pengyang Wang, Ziyue Qiao, Pengfei Wang*, Yuanchun Zhou, Yanjie Fu. The 32rd International Joint Conference on Artificial Intelligence, 2023. 

9.   [Briefings in Bioinformatics] HTCL-DDI: a hierarchical triple-view contrastive learning framework for drug–drug interaction prediction. Ran Zhang, Xuezhi Wang, Pengfei Wang*, Zhen Meng, Wenjuan Cui, Yuanchun Zhou. Briefings in Bioinformatics.

10. [KDD] Human Mobility Synchronization and Trip Purpose Detection with Mixture of Hawkes Processes. Pengfei Wang, Y Fu, G Liu, W Hu, C AggarwalProceedings of the 23rd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining.