Qiangfeng Cliff ZHANG Ph.D.
Associate Professor TsienTang Associate Professor
1996-2000 University of Science and Technology of China, B.S. in Computer Science and Technology
2000-2006 University of Science and Technology of China, Ph.D. in Computer Science
2006-2011 Columbia University, Ph.D. in Biochemistry and Molecular Biophysics
2011-2012 Columbia University, Center of Computational Biology and Bioinformatics, Postdoctoral scholar
2012-2015 Columbia University, School of Medicine, Postdoctoral scholar
2015-2018 Tsinghua University, School of Life Sciences, Assistant Professor
2018-present Tsinghua University, School of Life Sciences, Associate Professor
Research interest
Our laboratory is dedicated to interdisciplinary research at the intersection of artificial intelligence and life sciences. By integrating artificial intelligence and big data analysis, we focus on the development of technologies and the investigation of scientific questions in structural biology, genomics, RNA biology, and other related fields. Our research interests include, but are not limited to, RNA structure determination techniques and algorithms, single-cell genomic sequencing technologies and algorithms, and protein structure modeling based on cryo-electron microscopy.
We are particularly interested in the development of artificial intelligence algorithms, specifically exploring the current capabilities of AI methods in addressing biological questions, the unique aspects of AI approaches in biomedical data analysis that differentiate them from other AI domains, and even the potential of artificial intelligence in introducing new research paradigms for life science research.
Selected publications
1. Lei Tang*, Kang Tian*#, Xiaolei Fu*, Yingjia Xu*, Jincheng Wu, Jinsong Zhang, Xi-Wen Wang, Chunxiang Ye, Qiong Wu, Wei Wu#, Changjiang Feng#, Qiangfeng Cliff Zhang#. (2026) Resolving cell-cell interaction networks and their molecular logic in complex tissues, Nature Methods, 23(10):2042-2053. doi: 10.1038/s41592-026-03237-0
2. Yuhan Fei*, Pengfei Wang*, Jiasheng Zhang*, Xinyue Shan, Zilin Cai, Jianbo Ma, Yangming Wang#, Qiangfeng Cliff Zhang#.(2026) Predicting small molecule–RNA interactions without RNA tertiary structures, Nature Biotechnology, doi:10.1038/s41587-025-02942-z
3. Yuzhe Li*, Jinsong Zhang*, Xin Gao#, Qiangfeng Cliff Zhang#. (2024) Tissue module discovery in single-cell-resolution spatial transcriptomics data via cell-cell interaction-aware cell embedding, Cell Systems ,15(6):578-592.E7
4. Wenze Huang*, Tuanlin Xiong*, Yuting Zhao*, Jian Heng, Ge Han, Pengfei Wang, Zhihua Zhao, Ming Shi, Juan Li, Jiazhen Wang, Yixia Wu, Feng Liu, Jianzhong Jeff Xi#, Yangming Wang#, Qiangfeng Cliff Zhang# (2024) Computational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human, Nature Genetics. 56(1): 124-135
5. 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.
6. 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.
7. 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.
8. 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.
9. 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.
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. 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
Contact information
Email: qczhang@tsinghua.edu.cn
Phone: 010-6279-6439 (Office), 010-6279-5823 (Lab)
Homepage: http://zhanglab.net
