Kun QU,Ph.D.

Professor, Division of Life Sciences and Medicine

University of Science and Technology of China (USTC)

373 Huangshang Road, Hefei City, Anhui, 230027, P. R. China

Email: qukun@ustc.tsg211.com

Homepage: qulab.ustc.tsg211.com

Education: 

2004-2010:Ph.D., Physical Chemistry, Indiana University, USA

1999-2004:B.S., Chemical Physics, USTC, China

Research Experience: 

2018-Pre:    Professor, The First Affiliated Hospital of USTC, USTC, China

2018-Pre:    Professor, School of Data Science, USTC, China

2016-Pre:    Professor, Division of Life Sciences and Medicine, USTC, China

2014-2016:Director of Bioinformatics, School of Medicine, Stanford University

2012-2014:Sr. Bioinformatics Scientist, School of Medicine, Stanford University

2010-2011:Bioinformatician, School of Medicine, Stanford University, USA

2009-2010:Bioinformatics Specialist, City of Hope Cancer Center, USA

Administrative Experience: 

2021-Pre:    Director, Office of Hong Kong, Macao and Taiwan Affairs, USTC, China

2020-Pre:    Director, Office of International Cooperation, USTC, China

2019-2020:Deputy Director, Office of International Cooperation, USTC, China

Honors and Awards: 

Research Fields of Interests: 

1.   Method development: innovatively develop new technologies such as ultra-high-throughput single-cell multi-omics, spatial single-cell transcriptomics, super-resolution and functional imaging; develop new technologies that integrate single-cell multi-omics and spatial transcriptomics data analysis algorithms, software, and databases and provide new tools for systematic research on the pathogenic mechanism and evolution of cancer and autoimmune diseases.

2.   Applied research: use these tools to construct a single-cell spatiotemporal transcriptional and epigenetic landscape of the tumor microenvironment to reveal the heterogeneity of multiple cells in the microenvironment and their evolutionary spatiotemporal organization laws, and discover the regulation of tumorigenesis and development new targets, new mechanisms, and explore new and effective clinical treatment options.

Selected Publications 

1.   Nianping Liu*, Chen Jiang*, Pengfei Cai*, Zhuoqiao Shen, Wujianan Sun, Hao Xu, Minghao Fang, Xinfeng Yao, Lin Zhu, Xuyuan Gao, Jingwen Fang, Jun Lin, Chuang Guo^#, Kun Qu^# “Single-cell analysis of COVID-19, sepsis, and HIV infection reveals hyperinflammatory and immunosuppressive signatures in monocytes”, Cell Reports, 2021.

2.   Xianwen Ren*, Wen Wen*, Xiaoying Fan*, Wenhong Hou*, Bin Su*, Pengfei Cai*, Jiesheng Li*, Yang Liu*, Fei Tang*, Fan Zhang*, Yu Yang*, Jiangping He*, Wenji Ma*, Jingjing He*, Pingping Wang*, et al, Penghui Zhou^#, Qinghua Jiang^#, Zhiwei Huang^#, Jin-Xin Bei^#, Lai Wei^#, Xiu-Wu Bian^#, Xindong Liu^#, Tao Cheng^#, Xiangpan Li^#, Pingsen Zhao^#, Fu-Sheng Wang^#, Hongyang Wang^#, Bing Su^#, Zheng Zhang^#, Kun Qu^#, Xiaoqun Wang^#, Jiekai Chen^#, Ronghua Jin^#, Zemin Zhang^# “COVID-19 immune features revealed by a large-scale single cell transcriptome atlas ”, Cell , 2021.

3.  Dandan Zong*, Beibei Huang*, Young Li^#, Yichen Lu, Nan Xiang, Chuang Guo, Qian Liu, Qing Sha, Pengcheng Du, Qiaoni Yu, Wen Zhang, Pengfei Cai, Yanping Sun, Jinhui Tao, Xiaomei Li^#, Shanbao Cai^#, Kun Qu^# “Chromatin accessibility landscapes of immune cells in rheumatoid arthritis nominate monocytes in disease pathogenesis”, BMC Biology, 2021.

4.   Yinlei Hu*, Bin Li*, Wen Zhang, Nianping Liu, Pengfei Cai, Falai Chen^#, Kun Qu^# “WEDGE: imputation of gene expression values from single-cell RNA-seq datasets using biased matrix decomposition”, Briefings in Bioinformatics, 2021.

5.   Young Li*, Kun Li*, Lianbang Zhu, Bin Li, Dandan Zong, Pengfei Cai, Chen Jiang, Pengcheng Du, Jun Lin, Kun Qu^# “Development of double-positive thymocytes at single-cell resolution”, Genome Medicine, 2021.

6.   Chuang Guo*, Pengfei Cai*, Liying Jin*, Qing Sha, Qiaoni Yu, Wen Zhang, Chen Jiang, Qian Liu, Dandan Zong, Kun Li, Jingwen Fang, Fangting Lu, Yanshi Wang, Daojing Li, Jun Lin, Lu Li, Zhutian Zeng, Xianhong Tong, Haiming Wei, Kun Qu^# “Single-cell profiling of the human decidual immune microenvironment in patients with recurrent pregnancy loss”, Cell Discovery, 2021.

7.  Qian Liu*, Lisa C. Zaba*, Ansuman T. Satpathy, Michelle Longmire, Wen Zhang, Kun Li, Jeffrey Granja, Chuang Guo, Jun Lin, Rui Li, Karen Tolentino, Gabriela Kania, Oliver Distler, David Fiorentino, Lorinda Chung, Kun Qu^# & Howard Y. Chang^# “Chromatin accessibility landscapes of skin cells in systemic sclerosis nominate dendritic cells in disease pathogenesis”, Nature Communications, 2020.

8.  Chuang Guo*, Bin Li*, Huan Ma, Xiaofang Wang, Pengfei Cai, Qiaoni Yu, Lin Zhu, Liying Jin, Chen Jiang, Jingwen Fang, Qian Liu, Dandan Zong, Wen Zhang, Yichen Lu, Kun Li, Xuyuan Gao, Binqing Fu, Lianxin Liu, Xiaoling Ma, Jianping Weng, Haiming Wei, Tengchuan Jin^#, Jun Lin^# & Kun Qu^# “Single-cell analysis of two severe COVID-19 patients reveals a monocyte-associated and tocilizumab-responding cytokine storm”, Nature Communications, 2020.

9.   Bin Li*, Young Li*, Kun Li, Lianbang Zhu, Qiaoni Yu, Pengfei Cai, Jingwen Fang, Wen Zhang, Pengcheng Du, Chen Jiang, Jun Lin & Kun Qu^# “APEC: an accesson-based method for single-cell chromatin accessibility analysis”, Genome Biology, 2020.

10.  Haohuan Xie*, Wen Zhang*, Mei Zhang*^#, Tasneem Akhtar, Young Li, Wenyang Yi, Xiao Sun, Zuqi Zuo, Min Wei, Xin Fang, Ziqin Yao, Kai Dong, Suijuan Zhong, Qiang Liu, Yong Shen, Qian Wu, Xiaoqun Wang, Huan Zhao, Jin Bao, Kun Qu^# & Tian Xue^# “Chromatin accessibility analysis reveals regulatory dynamics of developing human retina and hiPSC-derived retinal organoids”, Science Advances, 2020.

11.  Pengfei Cai*, Auke B.C. Otten*, Binbin Cheng, Mitsuhiro A. Ishii, Wen Zhang, Beibei Huang, Kun Qu^#, Bryan K. Sun^# “A genome-wide long noncoding RNA CRISPRi screen identifies PRANCR as a novel regulator of epidermal homeostasis”, Genome Research, 2020.

12.  Jingwen Fang*, Qing Ma*, Ci Chu, Beibei Huang, Lingjie Li, Pengfei Cai, Pedro J. Batista, Karen Erisse Martin Tolentino, Jin Xu, Rui Li, Pengcheng Du, Kun Qu^#, Howard Y. Chang^# “Functional classification of noncoding RNAs associated with distinct histone modifications by PIRCh-seq”, Genome Biology, 2019.

13.  Kun Qu*, Lisa C. Zaba*, Ansuman T. Satpathy, Paul G. Giresi, Rui Li, Yonghao Jin, Randall Armstrong, Chen Jin, Nathalie Schmitt, Ziba Rahbar, Hideki Ueno, William J. Greenleaf, Youn H. Kim#, Howard Y. Chang# “Chromatin accessibility landscape of cutaneous T cell lymphoma and dynamic response to HDAC inhibitors”, Cancer Cell, 2017.

14.  Kun Qu*, Sara Garamszegi*, Felix Wu*, Helga Thorvaldsdottir, Ted Liefeld, Marco Ocana, Diego Borges-Rivera, Nathalie Pochet, James T Robinson, Barry Demchak, Tim Hull, Gil Ben-Artzi, Daniel Blankenberg, Galt P Barber, Brian T Lee, Robert M Kuhn, Anton Nekrutenko, Eran Segal, Trey Ideker, Michael Reich, Aviv Regev, Howard Y. Chang, Jill P Mesirov# “Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace”, Nature Methods, 2016.

15.  Kun Qu*, Lisa C. Zaba*, Paul G. Giresi, Rui Li, Michelle Longmire, Youn H. Kim, William J. Greenleaf, Howard Y. Chang# “Individuality and variation of personal regulomes in primary human T cells”, Cell Systems, 2015.

16.  Yue Wan*^#, Kun Qu*, Qiangfeng Cliff Zhang, Ryan A. Flynn1, Ohad Manor, Zhengqing Ouyang, Jiajing Zhang ,Robert C. Spitale, Michael P. Snyder, Eran Segal, Howard Y. Chang# “Landscape and variation of RNA secondary structure across the human transcriptome”, Nature, 2014.

Google Scholar: http://scholar.google.com/citations?hl=en&user=2CdOi4EAAAAJ

Job Opportunities:

We are seeking highly motivated undergraduates, graduate students, and post-doctoral fellows to join our research team. Applicants with expertise in bioinformatics, computer science, immunology, and molecular and cellular biology are particularly welcome. Please contact Dr. QU Kun directly with your CV and a description of your previous research experience.