Qiangfeng Zhang
Email：qczhang@tsinghua.edu.cn
Discipline direction:
Zhang’s lab works at the nexus of structural biology, genomics, and AI-informed big data analysis.
Research Area:
The lab is dedicated to pushing the frontier of technology development for RNA structural studies (Weng et al. Nature Chem Bio 2020, Luo et al. Nature Comm 2021, Sun et al. Cell Res 2021, Gong et al. Nature Machi Intelli 2022). The group revealed the role of RNA structure in connecting transcription, translation, and RNA degradation (Sun et al. Nat Struct Mol Bio 2019), the RNA genome structure of ZIKV and SARS-CoV-2 in infected cells, and discovered how conserved RNA structural elements interact with host proteins and affect viral infection (Li et al. Cell Host & Microbe 2018, Sun et al. Cell 2021, Zhang et al. Cell Res 2022). These structural data were then harnessed using a deep learning tool to predict viral RNA-binding host proteins, which can then inform repurposing of FDA-approved drugs to inhibit SARS-CoV-2 infection (Sun et al. Cell 2021, Zhang et al. Cell Res 2022).
Lab website：
http://zhanglab.net
代表性科研论文:
1. Lei Xiong*, Kang Tian*, Yuzhe Li, Weixi Ning, Xin Gao, Qiangfeng Cliff Zhang#. (2022) Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space. Nature Communications. 13(1):6118.
2. Meiling Piao*, Pan Li, Xiaomin Zeng*, Xi-Wen Wang*, Lan Kang, Jinsong Zhang, Yifan Wei, Shaojun Zhang, Lei Tang, Jianghui Zhu, Chun Kit Kwok, Xiaoyu Hu#, Qiangfeng Cliff Zhang#. (2022) An ultra low-input method for global RNA structure probing uncovers Regnase-1-mediated regulation in macrophages. Fundamental Research, 2(1):2-13.
3. Shaojun Zhang*, Wenze Huang*, Lili Ren*, Xiaohui Ju*, Mingli Gong*, Jian Rao*, Lei Sun, Pan Li, Qiang Ding#, Jianwei Wang#, Qiangfeng Cliff Zhang#. (2021) Comparison of viral RNA-host protein interactomes across pathogenic RNA viruses informs rapid antiviral drug discovery for SARS-CoV-2. Cell Research, 32 (1):9-23.
4. Jing Gong*, Kui Xu*, Ziyuan Ma, Zhi John Lu, Qiangfeng Cliff Zhang#. (2021) A deep learning method for recovering missing signals in transcriptome-wide RNA structure profiles from probing experiments. Nature Machine Intelligence, 3(11):995-1006.
5. Qing-Jun Luo*, Jinsong Zhang*, Pan Li*, Qing Wang, Yue Zhang, Biswajoy Roy-Chaudhuri, Jianpeng Xu, Mark A. Kay#, Qiangfeng Cliff Zhang#. (2021) RNA structure probing reveals the structural basis of Dicer binding and cleavage. Nature Communications, 12 (1):1-12
6. Lei Sun*, Pan Li*, Xiaohui Ju*, Jian Rao*, Wenze Huang*, Lili Ren, Shaojun Zhang, Tuanlin Xiong, Kui Xu, Xiaolin Zhou, Mingli Gong, Eric Miska, Qiang Ding#, Jianwei Wang#, Qiangfeng Cliff Zhang#. (2021) In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs. Cell. 184(7):1865-1883.e20.
7. Lei Sun*, Kui Xu*, Wenze Huang*, Yucheng T.Yang*, Pan Li, Lei Tang, Tuanlin Xiong, Qiangfeng Cliff Zhang#. (2021) Predicting dynamic cellular protein-RNA interactions by deep learning using in vivo RNA structures. Cell Research. 31(5):495-516.
8. Boyang Shi*, Jinsong Zhang*, Jian Heng*, Jing Gong*, Ting Zhang, Pan Li, Bao-Fa Sun, Ying Yang, Ning Zhang, Yong-Liang Zhao, Hai-Lin Wang, Feng Liu#, Qiangfeng Cliff Zhang#, Yun-Gui Yang#. (2020) RNA structural dynamics regulates early embryogenesis through controlling transcriptome fate and function. Genome Biology, 21(1):1-27.
9. Xiaocheng Weng*, Jing Gong*, Yi Chen*, Tong Wu*, Fang Wang, Shixi Yang, Yushu Yuan, Guanzheng Luo, Kai Chen, Lulu Hu, Honghui Ma, Pingluan Wang, Qiangfeng Cliff Zhang#, Xiang Zhou#, Chuan He#. (2020) Keth-seq for transcriptome-wide RNA structure mapping. Nature Chemical Biology, 16(5):489-492.
10. Lei Xiong, Kui Xu, Kang Tian, Yanqiu Shao, Lei Tang, Ge Gao, Michael Zhang, Tao Jiang, Qiangfeng Cliff Zhang#. (2019) SCALE method for single-cell ATAC-seq analysis via latent feature extraction. Nature Communications, 10(1):4576
11. Lei Sun*, Furqan M Fazal*, Pan Li*, James P Broughton, Byron Lee, Lei Tang, Wenze Huang, Eric T Kool, Howard Y Chang#, Qiangfeng Cliff Zhang#. (2019) RNA structure maps across mammalian cellular compartments. Nature structural & molecular biology. 26(4):322-330.
12. Kui Xu, Zhe Wang, Jianping Shi, Hongsheng Li, Qiangfeng Cliff Zhang#. (2019) A2-Net: Molecular Structure Estimation from Cryo-EM Density Volumes. In the Proceedings of the Thirty-Fourth AAAI Conference on Artificial Intelligence (AAAI 2019):1230-1237. Jan. 27 – Feb.1, Hawaii, USA
13. Pan Li*, Yifan Wei*, Miao Mei*, Lei Tang*, Lei Sun, Wenze Huang, Jianyu Zhou, Chunlin Zou, Shaojun Zhang, Cheng-feng Qin, Tao Jiang, Jianfeng Dai, Xu Tan#, Qiangfeng Cliff Zhang#. (2018) Integrative Analysis of Zika Virus Genome RNA Structure Reveals Critical Determinants of Viral Infectivity. Cell Host & Microbe. 24(6):875-886