Dongyu Zhao, Ph.D.

Principal Investigator, Doctoral Supervisor

Email: zhaodongyu|at|bjmu.edu.cn

Research Interests

1. Developing precise methods for disease gene identification and related bioinformatics analysis tools;

2. Investigating disease (primarily cancer and cardiovascular) genomic variations and transcriptional regulation using multi-omics data;

3. Developing analysis software based on third-generation nanopore sequencing data.

Biography

Dongyu Zhao is the Chair of Department of Biomedical Informatics at the Peking University Health Science Center (PKUHSC). He is a recipient of the National High-Level Young Talent Program, a Boya Young Scholar of Peking University, and a Principal Investigator at the State Key Laboratory of Vascular Homeostasis and Remodeling. He obtained his Ph.D. in 2013 from the Beijing Institute of Genomics, Chinese Academy of Sciences. He subsequently conducted postdoctoral research at the Houston Methodist Research Institute, Cornell University, and Harvard Medical School. He returned to China in 2021 and joined the School of Basic Medical Sciences at PKUHSC. His primary research focuses on bioinformatics, disease gene discovery and mechanistic exploration. He has published over 60 academic papers, including nearly 30 as first or corresponding author (including co-author) in high-impact international journals such as  European Heart Journal ,  Nucleic Acids Research ,  Military Medical Research , and  Nature Communications . He holds 6 software copyrights. He has presided over projects funded by the National Natural Science Foundation of China and the Beijing Natural Science Foundation. He has received awards including the PKUHSC Teaching Excellence Award, the Young Faculty Award from the School of Basic Medical Sciences, and the School of Basic Medical Sciences Outstanding Teaching Award. He currently serves as a Council Member of the Computational Systems Biology Branch of the China Operational Research Society, and as a Committee Member of the Epigenetic Informatics and Systems Biology Professional Committees of the China Society of Bioinformatics.

Representative Publications (^ Corresponding Author)

1．Wenqiang Li, Yunxi Liao, Zhujiang Liu, Longjian Niu, Jiaqi Huang, Yiting Jia, Ran Xu, Sudun Guan, Zhenhui Liang, Yiran Li, Hao Wu, Shirong Zhu, Liao Tan, Fang Yu, Zhihua Wang, Luyang Sun, Dongyu Zhao^, Wei Kong^, Yi Fu^. The inner nuclear membrane protein LEMD3 organizes the 3D chromatin architecture to maintain vascular smooth muscle cell identity.  Nature Communications . (In press)

2．Shaodong Huang, Yulong Han, Yiran Liu, Lina Bu, Chenyang Wu, Ziyan Rao, Chuan Ye, Hansen Cheng, Yunxi Liao, Yunan Sun, Yushu Zou, Zixu Wang, Bryan-Yu Sun, Shu Meng^, Dongyu Zhao^. Super-enhancer-mediated circRNAs exhibit high splicing circularization diversity and transcriptional activity.  Nucleic Acids Research , 2025, 53(11): gkaf505.

3．Yitong Xu, Jingxuan Chen, Yiran Liu, Ge Zhang, Guolin Miao, Jingdong Wu, Kaikai Lu, Yinqi Zhao, Wenxi Zhang, Liwen Zheng, Lianxin Zhang, Jinxuan Chen, Zihao Zhou, Yufei Han, Pingping Lai, Jiabao Guo, Donghui Wu, Si Mei, Ling Zhang, Yang Zhao, Wei Huang, Yuhui Wang, Junnan Tang^, Dongyu Zhao^, Xunde Xian^. The macrophage-derived motor protein KIF13B enhances MERTK-mediated efferocytosis and prevents atherosclerosis in mice.  European Heart Journal , 2025. doi: 10.1093/eurheartj/ehaf523.

4．Ziyan Rao, Chenyang Wu, Yunxi Liao, Chuan Ye, Shaodong Huang, Dongyu Zhao^. POCALI: Prediction and Insight on CAncer LncRNAs by Integrating Multi-Omics Data with Machine Learning.  Small Methods , 2025, 23: e2401987.

5．Ziyan Rao, Min Zhang^, Shaodong Huang, Chenyang Wu, Yuheng Zhou, Weijie Zhang, Xia Lin, Dongyu Zhao^. Cancer Driver Topologically Associated Domains identify oncogenic and tumor suppressive lncRNAs.  Genome Research , 2025, doi: 10.1101/gr.280235.124.

6． Guolin Miao, Wenxi Zhang, Yitong Xu, Yiran Liu, Pingping Lai, Jiabao Guo, Gonglie Chen, Jingxuan Chen, Zihao Zhou, Yanwei Li, Chong Zhang, Yang Ding, Lianxin Zhang, Yufei Han, Jinxuan Chen, Jingdong Wu, Yinqi Zhao, Si Mei, Yang Zhao, Yuanwu Ma, Ling Zhang, Wei Huang, Dongyu Zhao^, Erdan Dong^, Yuhui Wang^, Xunde Xian^. Motor protein KIF13B orchestrates hepatic metabolism to prevent metabolic dysfunction-associated fatty liver disease.  Military Medical Research , 2025, 12(1):11.

7．Xuyang Wang, Ruoqi Cheng, Chenyang Wu, Haiyin Liu, Zining Li, Yunfei Huo, Bo Li, Dongyu Zhao^, Cheng Li^, Hongkui Deng^, Jun Xu^. Trophectoderm-like cells from EPS cells enable generating EPS cell-derived post-implantation embryoids that complete gastrulation.  Protein&Cell , 2025. doi: 10.1093/procel/pwaf059.

8．Chuan Ye, Xuemei Wang, Jun Lin, Chenyang Wu, Yuhua Gao, Chenghao Guo, Yunxi Liao, Ziyan Rao, Shaodong Huang, Weixuan Chen, Ying Huang, Jinpeng Sun, Dongyu Zhao^, Changtao Jiang^. Systematical identification of regulatory GPCRs by single-cell trajectory inference reveals the role of ADGRD1 and GPR39 in adipogenesis.  Science China Life Sciences , 2024. 68(4): 1057-1072.

9．Xuyuan Liu, Siqi Wang, Yunan Sun, Yunxi Liao, Guangzhen Jiang, Bryan-Yu Sun, Jingyou Yu^, Dongyu Zhao^. Unlocking the potential of circular RNA vaccines: a bioinformatics and computational biology perspective.  EBioMedicine  (Review), 2025, 114:105638.

10．Guangzhen Jiang, Yushu Zou, Dongyu Zhao^, Jingyou Yu^. Optimising vaccine immunogenicity in ageing populations: key strategies.  The Lancet Infectious Diseases  (Review), 2024, 25(1):e23-e33.