Publications

• Gao, Zhenxiang#, Pingjian Ding#, Cerag Oguztuzun#, and Rong Xu. “Swarm Intelligence in Drug Discovery Applications: Unlocking Deeper Insights on the Identification and Optimization of Potential Drug Candidates.” Drug Design, Development and Therapy (2026): 561251. [Link]

• Cui, Wenchao, Pingjian Ding*, Lingyun Luo, Shunheng Zhou, and Hui Jiang. “A computational framework for predicting drug-target interactions by fusing gene ontology information with cross attention.” Journal of Biomedical Informatics (2026): 104976. [Link]

• Liao, Yaqing, Cong Shen, Lingbin Sun, Pingjian Ding*, Lingyun Luo, and Jiawei Luo. “MRDGNN: A Multi-Relational Reasoning Framework for Predicting Drug Indications via Relational Digraphs.” Computational Biology and Chemistry (2026): 109065. [Link]

• Zhenxiang Gao#, Pingjian Ding#, and Rong Xu*. “IUPHAR review-Data-driven Computational Drug Repurposing Approaches for Opioid Use Disorder.” Pharmacological Research 199 (2024): 106960. [Link]

• Ding, Pingjian, Zhenxiang Gao, Maria P. Gorenflo, and Rong Xu. “GLP-1 Receptor Agonists and Risk of Paralytic Ileus: A drug-target Mendelian Randomization Study.” medRxiv (2024). [Link]

• Pingjian Ding, and Rong Xu*. “Causal association of COVID-19 with brain structure changes: Findings from a non-overlapping 2-sample Mendelian randomization study.” Journal of the Neurological Sciences (2023): 2023-07. [Link]

• Pingjian Ding, Mark Gurney, George Perry, Rong Xu*. “Association of COVID-19 with risk and progression of Alzheimer’s disease: non-overlapping two-sample Mendelian randomization analysis of 2.6 million subjects.” Journal of Alzheimer’s Disease (2023). [Link]

• Pingjian Ding*, Min Zeng*, and Rui Yin*. “Editorial: Computational methods to analyze RNA data for human diseases.” Frontiers in Genetics 14 (2023). [Link]

• Pingjian Ding, Maria P. Gorenflo, Xiaofeng Zhu, and Rong Xu*. “Aspirin Use and Risk of Alzheimer’s Disease: A 2-Sample Mendelian Randomization Study.” Journal of Alzheimer’s Disease (2023): 1-12. [Link]

• Pingjian Ding#, Yiheng Pan#, Quanqiu Wang, and Rong Xu*. “Prediction and evaluation of combination pharmacotherapy using natural language processing, machine learning and patient electronic health records.” Journal of Biomedical Informatics 133 (2022): 104164. [Link]

• Xin Chen, Lingyun Luo, Cong Shen, Pingjian Ding*, and Jiawei Luo. “An in silico method for predicting drug synergy based on multitask learning.” Interdisciplinary Sciences: Computational Life Sciences 13 (2021): 299-311. [Link]

• Pingjian Ding, Cheng Liang, Wenjue Ouyang, Guanghui Li, Qiu Xiao, and Jiawei Luo*. “Inferring synergistic drug combinations based on symmetric meta-path in a novel heterogeneous network.” IEEE/ACM Transactions on Computational Biology and Bioinformatics 18, no. 4 (2019): 1562-1571. [Link]

• Pingjian Ding, Wenjue Ouyang, Jiawei Luo*, and Chee-Keong Kwoh. “Heterogeneous information network and its application to human health and disease.” Briefings in bioinformatics 21, no. 4 (2020): 1327-1346. [Link]

• Pingjian Ding, Cong Shen, Zihan Lai, Cheng Liang, Guanghui Li, and Jiawei Luo*. “Incorporating multisource knowledge to predict drug synergy based on graph co-regularization.” Journal of Chemical Information and Modeling 60, no. 1 (2019): 37-46. [Link]

• Pingjian Ding, Rui Yin, Jiawei Luo*, and Chee-Keong Kwoh. “Ensemble prediction of synergistic drug combinations incorporating biological, chemical, pharmacological, and network knowledge.” IEEE journal of biomedical and health informatics 23, no. 3 (2019): 1336-1345.[Link]

• Pingjian Ding, Jiawei Luo*, Cheng Liang, Qiu Xiao, Buwen Cao, and Guanghui Li. “Discovering synergistic drug combination from a computational perspective.” Current Topics in Medicinal Chemistry 18, no. 12 (2018): 965-974. [Link]

• Pingjian Ding, Jiawei Luo*, Cheng Liang, Qiu Xiao, and Buwen Cao. “Human disease MiRNA inference by combining target information based on heterogeneous manifolds.” Journal of biomedical informatics 80 (2018): 26-36. [Link]

• Pingjian Ding, Jiawei Luo*, Cheng Liang, Jie Cai, Ying Liu, and Xiangtao Chen. “A novel group wise-based method for calculating human miRNA functional similarity.” IEEE Access 5 (2017): 2364-2372. [Link]

• Pingjian Ding, Jiawei Luo*, Qiu Xiao, and Xiangtao Chen. “A path-based measurement for human miRNA functional similarities using miRNA-disease associations.” Scientific Reports 6, no. 1 (2016): 32533. [Link]