Education Background:

2018/10 – present   Assistant Research Fellow         Institute for Interdisciplinary Information Sciences, Tsinghua University

2016/10 – 2018/10  Postdoctoral Researcher           School of Medicine, Tsinghua University    

2015/04 – 2015/09  Visiting scholar                       Stem Cell Center and Department of Genetics, Yale University  

2011/09 – 2016/07   Ph.D.                                     School of Life Science, Peking University

2007/09 –2011/07    B.S.                                      School of Life Science, Lanzhou University

Awards：

2016    The National Postdoctoral Program for Innovative Talents

2015    Special Academic Scholarship, Peking University

2014   Social Work Scholarship, Peking University

2013   “WuSi” Scholarship, Peking University

2010    National Encouragement Scholarship for Under-Graduate Students

2009    National Scholarship for Under-Graduate Students

Publications：

[1] Xingang Peng# , Yipin Lei#, Peiyuan Feng, Lemei Jia, Jianzhu Ma, Dan Zhao*, Jianyang Zeng*. Characterizing the interaction conformation between T cell receptors and epitopes with deep learning. Nature Machine Intelligence. 2023

[2] Chang Liu#, Cuinan Yu#, Yipin Lei#, Kangbo Lyu, Tingzhong Tian, Qianhao Li, Dan Zhao*, Fengfeng Zhou*, Jianyang Zeng*. Improving target-disease association prediction through a graph neural network with credibility information. Pacific Symposium on Biocomputing. 2023.

[3] Xiaolong Feng#, Xiaofan Zhang#, Shuangying Jiang, Yuanwei Tang, Chao Cheng, Parthasarathy Abinand Krishna, Xiaoting Wang, Junbiao Dai, Jianyang Zeng*, Tian Xia*, Dan Zhao*. A DNA-based non-infectious replicon system to study SARS-CoV-2 RNA synthesis. Computational and Structural Biotechnology Journal. 2022

[4] Han Li, Xinyi Zhao, Shuya Li, Fangping Wan, Dan Zhao*, Jianyang Zeng*. Improving molecular property prediction through a task similarity enhanced transfer learning strategy. Iscience. 2022

[5] Han Li, Dan Zhao*, Jianyang Zeng J*. KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction. In Proceedings of the 28th ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD 2022). 2022 

[6] Hantao Shu, Fan Ding, Jingtian Zhou, Yexiang Xue, Dan Zhao, Jianyang Zeng*, Jianzhu Ma*. Boosting single-cell gene regulatory network reconstruction via bulk-cell transcriptomic data. Briefings in Bioinformatics. 2022

[7] Dan Zhao#, Weifan Xu#, Xiaofan Zhang#, Xiaoting Wang, Enming Yuan, Yuanpeng Xiong, Shenyang Wu, Shuya Li, Nian Wu, Tingzhong Tian, Xiaolong Feng, Hantao Shu, Peng Lang, Xiaokun Shen, Haitao Li, Pilong Li,* and Jianyang Zeng*. Understanding the phase separation characteristics of nucleocapsid protein provides a new therapeutic opportunity against SARS-CoV-2. Protein & Cell. 2021

[8] Yiyue Ge#, Tingzhong Tian#, Suling Huang#, Fangping Wan#, Jingxin Li#, Shuya Li, Xiaoting Wang, Hui Yang, Lixiang Hong, Nian Wu, Enming Yuan, Yunan Luo, Lili Cheng, Chengliang Hu, Yipin Lei, Hantao Shu, Xiaolong Feng, Ziyuan Jiang, Yunfu Wu, Ying Chi, Xiling Guo, Lunbiao Cui, Liang Xiao, Zeng Li, Chunhao Yang, Zehong Miao, Ligong Chen, Haitao Li, Hainian Zeng, Dan Zhao*, Fengcai Zhu*, Xiaokun Shen*, and Jianyang Zeng*. An integrative drug repositioning framework discovered a potential therapeutic agent targeting COVID-19. Signal Transduction and Targeted Therapy. 2021

[9] Yipin Lei, Shuya Li, Ziyi Liu, Fangping Wan, Tingzhong Tian, Shao Li, Dan Zhao*, Jianyang Zeng*. A deep-learning framework for multi-level peptide–protein interaction prediction. Nature Communications. 2021

[10] Peiyuan Feng#, An Xiao#, Meng Fang, Fangping Wan, Shuya Li, Peng Lang, Dan Zhao*, and Jianyang Zeng*. A novel machine learning based framework for modeling transcription elongation. Proc Natl Acad Sci USA. 2021

[11] Yuanpeng Xiong#, Xuan He#, Dan Zhao, Tingzhong Tian, Lixiang Hong, Tao Jiang*, and Jianyang Zeng*. Modelling Multi-species RNA Modification through Multi-task Curriculum Learning. Nucleic Acids Research. 2021.

[12] Tingzhong Tian, Shuya Li, Peng Lang, Dan Zhao*, Jianyang Zeng*. Full-length ribosome density prediction by a multi-input and multi-output model. PLoS Computational Biology. 2021.

[13] Hailin Hu#, Xianggen Liu#, An Xiao, YangYang Li, Chengdong Zhang, Tao Jiang, Dan Zhao, Sen Song*, and Jianyang Zeng*. Riboexp: an interpretable reinforcement learning framework for ribosome density modeling. Briefings in Bioinformatics. 2021.

[14] Lixiang Hong, Jinjian Lin, Shuya Li, Fangping Wan, Hui Yang, Tao Jiang, Dan Zhao*, and Jianyang Zeng*. A novel machine learning framework for automated biomedical relation extraction from large-scale literature repositories. Nature Machine Intelligence. 2020.

[15] Shuya Li#, Fangping Wan#, Hantao Shu, Tao Jiang, Dan Zhao*, Jianyang Zeng*. MONN: A Multi-objective Neural Network for Predicting Compound-Protein Interactions and Affinities. Cell Systems. 2020.

[16] Fangping Wan#, Shuya Li#, Tingzhong Tian, Yipin Lei, Dan Zhao*, Jianyang Zeng*. EXP2SL: a Machine Learning Framework for Cell-Line Specific Synthetic Lethality Prediction. Frontiers in Pharmacology. 2020.

[17] Xu Qian, Xinjian Li, Zhumei Shi, Yan Xia, Qingsong Cai, Daqian Xu, Lin Tan, Linyong Du, Yanhua Zheng, Dan Zhao, Chuanbao Zhang, Philip L Lorenzi, Yongping You, Bing-Hua Jiang, Tao Jiang, Haitao Li, Zhimin Lu. PTEN Suppresses Glycolysis by Dephosphorylating and Inhibiting Autophosphorylated PGK1. Molecular Cell. 2019.

[18] Yan Hu, Ziqiang Wang, Hailin Hu, Fangping Wan, Lin Chen, Yuanpeng Xiong , Xiaoxia Wang, Dan Zhao, Weiren Huang, Jianyang Zeng. ACME: pan-specific peptide–MHC class I binding prediction through attention-based deep neural networks. Bioinformatics. 2019.

[19] Chih-Chao Hsu#, Dan Zhao#, Jiejun Shi#, Danni Peng, Haipeng Guan, Yuanyuan Li, Yaling Huang, Hong Wen, Wei Li, Haitao Li *and Xiaobing Shi*. Gas41 links histone acetylation to H2A.Z deposition and maintenance of embryonic stem cell identity. Cell Discovery. 2018.

[20] Chih-Chao Hsu#, Jiejun Shi#, Chao Yuan#, Dan Zhao#, Shiming Jiang, Jie Lyu, Xiaolu Wang, Haitao Li, Hong Wen, Wei Li, and Xiaobing Shi. Recognition of histone acetylation by the GAS41 YEATS domain promotes H2A.Z deposition in non-small cell lung cancer. Genes & Development, 2018.

[21] Wenyi Mi#, Haipeng Guan#, Jie Lyu#, Dan Zhao#, Yuanxin Xi, Shiming Jiang, Forest H. Andrews, Xiaolu Wang, Mihai Gagea, Hong Wen, Laszlo Tora, Sharon Y.R. Dent, Tatiana G. Kutateladze, Wei Li*, Haitao Li*, and Xiaobing Shi*. YEATS2 links histone acetylation to tumorigenesis of non-small cell lung cancer. Nature Communications. 2017.

[22] Dan Zhao, Yuanyuan Li, Xiaozhe Xiong, Zhonglei Chen, Haitao Li. YEATS Domain-A Histone Acylation Reader in Health and Disease. J Mol Biol. 2017.

[23] Zhuang Li, Dan Zhao, Bin Xiang, and Haitao Li. Structural and biochemical characterization of DAXX-ATRX interaction. Protein & Cell. 2017.

[24] Yuanyuan Li, Dan Zhao, Zhonglei Chen, and Haitao Li. YEATS domain: Linking Histone Crotonylation to Gene Regulation. Transcription. 2017

[25] 朱松标 ，张文浩，师晓萌，赵诞，李海涛，邓海腾. 应用氢氘交换质谱研究蛋白相互作用以及翻译后修饰. 第三届全国质谱分析学术报告会. 2017 

[26] Dan Zhao, Haipeng Guan, Shuai Zhao, Wenyi Mi, Hong Wen, Tiemei Li, Yuanyuan Li, Yingming Zhao, C. David Allis, Or Gozani, Xiaobing Shi and Haitao Li. YEATS2 is a selective histone crotonylation reader. Cell Research. 2016.

[27] Dan Zhao, Xiaojie Zhang, Haipeng Guan, Xiaozhe Xiong, Xiaomeng Shi, Haiteng Deng, Haitao Li. The BAH domain of BAHD1 is a histone H3K27me3 reader. Protein & Cell. 2016.

[28] Yuanyuan Li, Benjamin R. Sabari, Tatyana Panchenko, Hong Wen, Dan Zhao, Haipeng Guan, Liling Wan, He Huang, Zhanyun Tang, Yingming Zhao, Robert G. Roeder, Xiaobing Shi, C. David Allis, and Haitao Li. Molecular Coupling of Histone Crotonylation and Active Transcription by AF9 YEATS Domain. Molecular Cell. 2016.

[29] Xiaojie Zhang, Dan Zhao, Xiaozhe Xiong, Zhimin He, and Haitao Li. Multifaceted Histone H3 Methylation and Phosphorylation Readout by the Plant Homeodomain Finger of Human Nuclear Antigen Sp100C. J Biol Chem. 2016.

[30] Kyung-Min Noha#, Ian Mazeb#, Dan Zhao#, Bin Xiang, Wendy Wenderski, Peter W. Lewis, Li Shen, Haitao Li, and C. David Allis. ATRX tolerates activity-dependent histone H3 methyl/phos switching to maintain repetitive element silencing in neurons. Proc Natl Acad Sci USA. 2015