Publications

1. Tianqi Ma, Yating Qu, Chenxian Guan, Hang Yin, Wenmian Yang, Shing Fung Chow, Henry Hoi Yee Tong, Defang Ouyang*, Zhuyifan Ye*. Advances and Challenges in Machine Learning-based Image Analysis for Monitoring and Predicting Organic Crystal Formation, Aggregate, 2026. (JCR Q1, IF=14.5)

2. Jiayin Deng, Qiong Huang, Jiayi Lv, Yiqi Yang, Zhuyifan Ye, Yanyi Chu, Yiyang Wu, Qi Zhao*, Wei-Jie Fang*, Defang Ouyang*. Multimodal framework for early developability assessment to accelerate protein and antibody development, International Journal of Pharmaceutics, 2026. (JCR Q1, IF=6.0)

3. Bingwei Ni, Wanxiang Shen, Zhuyifan Ye*. TradePool: A Novel Interpretable Framework for Quantifying Atomic Attribution Values in Molecular Property Prediction, Journal of Chemical Information and Modeling, 2026. (JCR Q1, IF=6.4)

4. Wei Wang, Nannan Wang, Yiyang Wu, Zhuyifan Ye, Liang Zhao, Xianfeng Chen, Defang Ouyang*. An Integrated AI-PBPK Platform for Predicting Drug In Vivo Fate and Tissue Distribution in Human and Inter-Species Extrapolation, Clinical Pharmacology and Therapeutics, 2025. (JCR Q1, IF=5.5)

5. Shiwei Deng, Yiyang Wu, Zhuyifan Ye, Defang Ouyang*. In silico prediction of metabolic stability for ester-containing molecules: Machine learning and quantum mechanical methods, Chemometrics and Intelligent Laboratory Systems, 2025. (JCR Q2, IF=3.7)

6. Zheng Wu, Nannan Wang, Zhuyifan Ye, Huanle Xu, Ging Chan, Ouyang, Defang*. FormulationBCS: A Machine Learning Platform Based on Diverse Molecular Representations for Biopharmaceutical Classification System (BCS) Class Prediction, Molecular Pharmaceutics, 2024. (JCR Q1, IF=4.5)

7. Zhuyifan Ye, Nannan Wang, Jiantao Zhou, Defang Ouyang*. Organic crystal structure prediction via coupled generative adversarial networks and graph convolutional networks, The Innovation, 2024, 100562. (JCR Q1, IF=33.2)

8. Run Han, Zhuyifan Ye, Yunsen Zhang, Yaxin Cheng, Ying Zheng*, Defang Ouyang*. Predicting liposome formulations by the integrated machine learning and molecular modeling approaches, Asian Journal of Pharmaceutical Sciences, 2023, 18(3), 100811. (Co-first author, JCR Q1, IF=10.2)

9. Nannan Wang, Yunsen Zhang, Wei Wang, Zhuyifan Ye, Hongyu Chen, Guanghui Hu, Defang Ouyang*. How can machine learning and multiscale modeling benefit ocular drug development?, Advanced Drug Delivery Reviews, 2023, 196, 114772. (JCR Q1, IF=16.1)

10. Jiayin Deng, Zhuyifan Ye, Wenwen Zheng, Jian Chen, Haoshi Gao, Zheng Wu, Ging Chan, Yongjun Wang, Dongsheng Cao, Yanqing Wang*, Simon Ming-Yuen Lee*, Defang Ouyang*. Machine learning in accelerating microsphere formulation development, Drug Delivery and Translational Research, 2023, 13(4), pp. 966-982. (Co-first author, JCR Q1, IF=5.4)

11. Wenwen Zheng, Junjun Li, Yu Wang, Zhuyifan Ye, Hao Zhong, Hung Wan Kot, Defang Ouyang*, Ging Chan*. Quantitative Analysis for Chinese and US-listed Pharmaceutical Companies by the LightGBM Algorithm, Current computer-aided drug design, 2023, 13(4), pp. 966-982. (JCR Q4, IF=1.7)

12. Haoshi Gao, Stanislav Kan, Zhuyifan Ye, Yuchen Feng, Lei Jin, Xudong Zhang, Jiayin Deng, Ging Chan, Yuanjia Hu, Yongjun Wang, Dongsheng Cao, Yuanhui Ji, Mingtao Liang*, Haifeng Li*, Defang Ouyang*. Development of in silico methodology for siRNA lipid nanoparticle formulations, Chemical Engineering Journal, 2022, 442, 136310. (Co-first author, JCR Q1, IF=15.1)

13. Wei Wang, Shuo Feng, Zhuyifan Ye, Hanlu Gao, Jinzhong Lin*, Defang Ouyang*. Prediction of lipid nanoparticles for mRNA vaccines by the machine learning algorithm, Acta Pharmaceutica Sinica B, 2022, 12(6), pp. 2950-2962. (Co-first author, JCR Q1, IF=14.5)

14. Junjun Li, Hanlu Gao, Zhuyifan Ye, Jiayin Deng, Defang Ouyang*. In silico formulation prediction of drug/cyclodextrin/polymer ternary complexes by machine learning and molecular modeling techniques, Carbohydrate Polymers, 2022, 275, 118712. (JCR Q1, IF=11.2)

15. Zhuyifan Ye, Defang Ouyang*. Prediction of small-molecule compound solubility in organic solvents by machine learning algorithms, Journal of Cheminformatics, 2021, 13(1), 98. (JCR Q1, IF=8.6)

16. Zhuyifan Ye, Wenmian Yang, Yilong Yang, Defang Ouyang*. Interpretable machine learning methods for in vitro pharmaceutical formulation development, Food Frontiers, 2021, 2, pp. 195-207. (JCR Q1, IF=9.9)

17. Wei Wang, Zhuyifan Ye, Hanlu Gao, Defang Ouyang*. Computational pharmaceutics-A new paradigm of drug delivery, Journal of Controlled Release, 2021, 338, pp. 119-136. (Co-first author, JCR Q1, IF=10.8)

18. Hanlu Gao, Wei Wang, Jie Dong, Zhuyifan Ye, Defang Ouyang*. An integrated computational methodology with data-driven machine learning, molecular modeling and PBPK modeling to accelerate solid dispersion formulation design, European Journal of Pharmaceutics and Biopharmaceutics, 2021, 158, pp. 336-346. (JCR Q1, IF=4.9)

19. Yuan He, Zhuyifan Ye, Xinyang Liu, Zhengjie Wei, Fen Qiu, Haifeng Li, Ying Zheng*, Defang Ouyang*. Can machine learning predict drug nanocrystals?, Journal of Controlled Release, 2020, 322, pp. 274–285. (Co-first author, JCR Q1, IF=10.8, Cover)

20. Haoshi Gao, Zhuyifan Ye, Jie Dong, Hanlu Gao, Hua Yu, Haifeng Li, Defang Ouyang*. Predicting drug/phospholipid complexation by the lightGBM method, Chemical Physics Letters, 2020, 747, 137354. (JCR Q3, IF=2.8)

21. Qianqian Zhao, Zhuyifan Ye, Yan Su, Defang Ouyang*. Predicting complexation performance between cyclodextrins and guest molecules by integrated machine learning and molecular modeling techniques, Acta Pharmaceutica Sinica B, 2019, 9(6), pp. 1241-1252. (JCR Q1, IF=14.5)

22. Run Han, Hui Xiong, Zhuyifan Ye, Yilong Yang, Tianhe Huang, Qiufang Jing, Jiahong Lu, Hao Pan, Fuzheng Ren*, Defang Ouyang*. Predicting physical stability of solid dispersions by machine learning techniques, Journal of Controlled Release, 2019, 311-312, pp. 16-25. (Co-first author, JCR Q1, IF=10.8, Cover)

23. Zhuyifan Ye, Yilong Yang, Xiaoshan Li, Dongsheng Cao, Defang Ouyang*. An integrated transfer learning and multitask learning approach for pharmacokinetic parameter prediction, Molecular Pharmaceutics, 2019, 16(2), pp. 533-541. (JCR Q1, IF=4.9)

24. Yilong Yang, Zhuyifan Ye, Yan Su, Qianqian Zhao, Xiaoshan Li, Defang Ouyang*. Deep learning for in vitro prediction of pharmaceutical formulations, Acta Pharmaceutica Sinica B, 2019, 9(1), pp. 177-185. (Co-first author, JCR Q1, IF=14.5)