Chuan-Yun Li, Ph.D.
Principal Investigator, Director
Peking University
Institute of Molecular Medicine
Tel: +86(10)**;
Email: chuanyunli@pku.edu.cn
Lab URL: rhesusbase.cbi.pku.edu.cn/lab/
Dr. Chuan-Yun Li graduated from Peking University in 2009 and received Ph.D. degree in Bioinformatics. He worked in the Molecular Neurobiology Branch in NIH Intramural Research Program as a visiting scholar. In November 2010, he joined IMM as a full-time investigator to develop the Laboratory of Bioinformatics and Genomic Medicine. Combining the next-generation sequencing technology (NGS) and the non-human primate resource, Dr. Li developed a new direction for functional interrogation of human biology in the genomic context of rhesus macaque, by elucidating human regulations in a pertinent genomic reference of rhesus macaque (Monkey Genomics), as well as by identifying genetic susceptible factors in macaque families with extreme metabolic phenotype (Monkey Genetics). His research focus on i) systems biology analyses to study the molecular mechanisms underlying complex human disease in the framework of development, regulation and evolution; ii) refinements of genome annotations through meta-analyses and functional genomics analyses, facilitating better understanding of gene functions in well-established knowledge contexts; and iii) combing population genetics analyses (within-species) and comparative genomics analyses (between-species), performing molecular evolution studies to understand the primate-specific gene-behavior relationships. Dr. Li's group has published multiple peer-reviewed articles to report new translational and evolutionary discoveries, bringing novel insights into understanding of human gene regulations and associated diseases from the perspective of monkey genomics and genetics.
Representative Publication
(#correspondence, *co-first author)
1. Yumei Li*, Shanshan Ai*, Xianhong Yu*, Chen Li, Xin Li, Yanzhu Yue, Cheng Li, Chuan-Yun Li# and Aibin He#. Replication-independent histone turnover underlines the epigenetic homeostasis in adult heart, Circulation Research, 2019
2. Ni A. An*, Wanqiu Ding*, Xin-Zhuang Yang*, Jiguang Peng, Bin Z. He, Qing Sunny Shen, Fujian Lu, Aibin He, Yong E. Zhang, Bertrand Chin-Ming Tan, Jia-Yu Chen# and Chuan-Yun Li#, Evolutionarily Significant A-to-I RNA Editing Events Originated through G-to-A Mutations in Primates, Genome Biology, 2019
3. Yumei Li*, Chen Li*, Shuxian Li, Qi Peng, Ni A. An, Aibin He# and Chuan-Yun Li#, Human Exonization through Differential Nucleosome Occupancy, PNAS, 2018
4. Yao Xiao, Can Wang, Jia-Yu Chen, Fujian Lu, Jue Wang, Ning Hou, Xiaomin Hu, Fanxin Zeng, Dongwei Ma, Xueting Sun, Yi Ding, Yan Zhang, Wen Zheng, Yuli Liu, Haibao Shang, Wenzhen Zhu, Chensheng Han, Yulin Zhang, Kunfu Ouyang, Liangyi Chen, Ju Chen, Rui-Ping Xiao, Chuan-Yun Li# and Xiuqin Zhang#, Deficiency of PRKD2 Triggers Hyperinsulinemia and Metabolic Disorders, Nature Communications, 2018
5. Shi-Jian Zhang*, Chenqu Wang*, Shouyu Yan, Aisi Fu, Xuke Luan, Yumei Li, Qing Sunny Shen, Xiaoming Zhong, Jia-Yu Chen, Xiangfeng Wang, Bertrand Chin-Ming Tan, Aibin He and Chuan-Yun Li#, Isoform Evolution in Primates Through Independent Combination of Alternative RNA Processing Events, Molecular Biology and Evolution, 2017 (Cover Story, Fast Track Story)
6. Lei Lei*, Shou-Yu Yan*, Ran Yang, Jia-Yu Chen, Yumei Li, Ye Bu, Nannan Chang, Qinchao Zhou, Xiaojun Zhu, Chuan-Yun Li#, Jing-Wei Xiong#, Spliceosomal protein eftud2 mutation leads to p53-dependent apoptosis in zebrafish neural progenitors, Nucleic Acids Research, 2016
7. Xiaoming Zhong*, Jiguang Peng*, Qing Sunny Shen*, Jia-Yu Chen, Han Gao, Xuke Luan, Shouyu Yan, Xin Huang, Shi-Jian Zhang, Luying Xu, Xiuqin Zhang, Bertrand Tan and Chuan-Yun Li#, RhesusBase PopGateway: Genome-wide Population Genetics Atlas in Rhesus Macaque, Molecular Biology and Evolution, 2016 (Featured by MBE)
8. Xin-Zhuang Yang*, Jia-Yu Chen*, Chu-Jun Liu, Jiguang Peng, Yin Rei Wee, Xiaorui Han, Chenqu Wang, Xiaoming Zhong, Qing Sunny Shen, Hsuan Liu, Huiqing Cao, Xiaowei Chen, Bertrand Chin-Ming Tan# and Chuan-Yun Li#, Selectively Constrained RNA Editing Regulation Crosstalks with piRNA Biogenesis in Primates, Molecular Biology and Evolution, 2015
9. Jia-Yu Chen*, Qing Sunny Shen*, Wei-Zhen Zhou*, Jiguang Peng, Bin Z He, Yumei Li, Chu-Jun Liu, Xuke Luan, Wanqiu Ding, Shuxian Li, Chunyan Chen, Bertrand Chin-Ming Tan, Yong E Zhang, Aibin He# and Chuan-Yun Li#, Emergence, Retention and Selection: a Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates, PLoS Genetics, 2015
10. Shi-Jian Zhang*, Chu-Jun Liu*, Peng Yu*, Xiaoming Zhong, Jia-Yu Chen, Xin-Zhuang Yang, Jiguang Peng, Shouyu Yan, Chenqu Wang, Xiaotong Zhu, Jingwei Xiong, Yong E. Zhang, Bertrand Chin-Ming Tan and Chuan-Yun Li#, Evolutionary Interrogation of Human Biology in Well-annotated Genomic Framework of Rhesus Macaque, Molecular Biology and Evolution, 2014 (Cover Story, MBE Most Read)
11. Jia-Yu Chen*, Zhiyu Peng*, Rongli Zhang*, Xin-Zhuang Yang, Bertrand Chin-Ming Tan, Huaying Fang, Chu-Jun Liu, Yong E. Zhang, Mingming Shi, Zhi-Qiang Ye, Minghua Deng, Xiuqin Zhang# and Chuan-Yun Li#, RNA Editome in Rhesus Macaque Shaped by Purifying Selection, PLoS Genetics, 2014
12. Shi-Jian Zhang*, Chu-Jun Liu*, M Shi*, Lei Kong, Jia-Yu Chen, Wei-Zhen Zhou, Xiaotong Zhu, Peng Yu, Jue Wang, Xinzhuan Yang, Ning Hou, Zhiqiang Ye, Rongli Zhang, Ruiping Xiao, Xiuqin Zhang# and Chuan-Yun Li#, RhesusBase: a Knowledgebase for the Monkey Research Community. Nucleic Acids Research, 2013 (Featured by Nucleic Acids Research and Biomart)
13. Chen Xie*, Yong E. Zhang*, Jia-Yu Chen*, Chu-Jun Liu, Wei-Zhen Zhou, Ying Li, Mao Zhang, Rongli Zhang, Liping Wei# and Chuan-Yun Li#, Hominoid-specific De Novo Protein-coding Genes Originating from Long Non-coding RNAs, PLoS Genetics, 2012 (Featured by Faculty of 1000)
14. Chuan-Yun Li#, Wei-Zhen Zhou, Ping-Wu Zhang, Catherine Johnson, Liping Wei, George R Uhl#, Meta-analysis and genome-wide interpretation of genetic susceptibility to drug addiction, BMC Genomics, 2011 (Highly accessed article)
15. Chuan-Yun Li, Yong Zhang, Zhanbo Wang, Yan Zhang, Chunmei Cao, Xiao-Mo Li, Ping-Wu Zhang, Shu-Juan Lu, Quan Yu, Xiaofeng Zheng, Quan Du, Qing-Rong Liu* and Liping Wei*, A Human-Specific De Novo Protein-Coding Gene Associated with Human Brain Functions, PLoS Computational Biology, 2010
16. Chuan-Yun Li, Xizeng Mao & Liping Wei, Genes and (Common) Pathways Underlying Drug Addiction, PLoS Computational Biology, 2008 (Featured by Science Signaling “Editor’s Choice”; Nature China “Research Highlights”; the Economist, Scientific America, Reuters and China Daily; Top 10 Papers downloaded from PLoS Computational Biology)
17. Chuan-Yun Li, Qingrong Liu, Ping-Wu Zhang, Xiao-Mo Li, Liping Wei, George R Uhl, OKCAM: An Ontology-based, Human-centered Knowledgebase for Cell Adhesion Molecules, Nucleic Acids Research, 2008
18. Chuan-Yun Li*, Zhi-Qiang Ye*, Quan Yu*, Ying Sun, Quanyuan He, Xiao-Mo Li, Wuxue Zhang, Jingchu Luo, Xiaocheng Gu, Xiaofeng Zheng & Liping Wei, A nonsynonymous SNP in human cytosolic sialidase in a small Asian population results in reduced enzyme activity: potential link with severe adverse reactions to oseltamivir, Cell Research, 2007 (Cover story and featured by a Research Highlight; Cited by US FDA annual Pediatric Safety Update for Tamiflu; Interviewed by NHK and CCTV)
Collaborative Publication
1. Mao Zhang ,Hua Gao, Dairu Liu, Xiaoming Zhong, Xiaolu Shi, Peng Yu, Li Jin, Yun Liu, Yajie Tang, Yunhu Song, Jinghao Liu, Xinli Hu, Chuan-Yun Li, Lei Song, Jun Qin, Fujian Wu, Feng Lan, Rui-Ping Xiao, Yan Zhang, Cardiomyocyte Fate Regulation by CaMKII-δ9-UBE2T-DNA Damage Signaling, Nature Cell Biology, 2019
2. Chung-Pei Ma, Hsuan Liu, Ian Yi‐Feng Chang, Wan-Cheng Wang, Yi-Tung Chen, Shao-Min Wu, Hui-Wen Chen, Yu-Ping Kuo, Chieh-Tien Shih, Chuan-Yun Li, Bertrand Chin-Ming Tan, ADAR1 promotes robust hypoxia signaling via distinct regulation of multiple HIF-1-inhibiting factors, EMBO reports, 2019
3. Chengchuan Ma, Rong Niu, Tianxiao Huang, Li-Wa Shao, Yong Peng, Wanqiu Ding, Ye Wang, Guifang Jia, Chuan He, Chuan-Yun Li, Aibin He, and Ying Liu, N6-methyldeoxyadenine is a transgenerational epigenetic signal for mitochondrial stress adaptation, Nature Cell Biology, 2018
4. Fanxin Zeng, Wei Wen, Weiyi Cui, Wen Zheng, Yuli Liu, Xueting Sun, Ning Hou, Dongwei Ma, Ye Yuan, Huiping Shi, Zhimin Wang, Zezhong Li, Yao Xiao, Can Wang, Yumei Li, Haibao Shang, Chuan-Yun Li, Jue Wang, Yan Zhang, Rui-ping Xiao and Xiuqin Zhang, Central role of RIPK1-VDAC1 pathway on cardiac impairment in a non-human primate model of rheumatoid arthritis, Journal of Molecular and Cellular Cardiology, 2018
5. The BIG Data Center Consortium (including Chuan-Yun Li), Database Resources of the BIG Data Center in 2019, Nucleic Acids Research, 2018
6. Shanshan Ai*, Xianhong Yu*, Yumei Li*, Yong Peng, Chen Li, Yanzhu Yue, Ge Tao, Chuan-Yun Li, William T Pu, Aibin He#, Divergent Requirements for EZH1 in Heart Development Versus Regeneration, Circulation Research, 2017
7. Xiaoming Zhong, Jana Drgonova, Chuan-Yun Li, and George R. Uhl, Human cell adhesion molecules: annotated functional subtypes and overrepresentation of addiction-associated genes, ANNALS OF THE NEW YORK ACADEMY OF SCIENCES, 2015
8. Fenghua Liu, Ruisheng Song, Yuanqing Feng, Jiaojiao Guo, Yanmin Chen, Yong Zhang, Tao Chen, Yanru Wang, Yanyi Huang, Chuan-Yun Li, Chunmei Cao, Yan Zhang, Xinli Hu, Rui-ping Xiao, Upregulation of MG53 Induces Diabetic Cardiomyopathy via Transcriptional Activation of PPAR-α, Circulation, 2015
9. Ran Yang, Shouyu Yan, Xiaojun Zhu, Chuan-Yun Li, Zhenming Liu, Jing-Wei Xiong, Anti-malarial Drug Artemisinin Depletes Erythrocytes by Activating Apoptotic Pathways in Zebrafish, Experimental Hematology, 2015
10. The BioMart Consortium (including Chuan-Yun Li), The BioMart community portal: an innovative alternative to large, centralized data repositories, Nucleic acids research, 2015
11. Hai-Ying Zhang, Guo-Hua Bi, Xia Li, Jie Li, Hong Qu, Shi-Jian Zhang, Chuan-Yun Li, Emmanuel Onaivi, Eliot Gardner, Zheng-Xiong Xi, and Qing-Rong Liu, Species differences in cannabinoid receptor 2 and receptor responses to cocaine self-administration in mice and rats, NEUROPSYCHOPHARMACOLOGY, 2014
12. Peidong Han, Xiao-Hai Zhou, Nannan Chang, Cheng-Lu Xiao, Shouyu Yan, He Ren, Xin-Zhuang Yang, Mei-Ling Zhang, Qing Wu, Boyang Tang, Ju-Peng Diao, Xiaojun Zhu, Chuanmao Zhang, Chuan-Yun Li, Heping Cheng and Jing-Wei Xiong, Hydrogen peroxide primes heart regeneration with a derepression mechanism, Cell Research, 2014
13. Yongxin Ye, Min Zhao, Qing-Rong Liu, Chuan-Yun Li, Hong Qu. Human Transporter Database: comprehensive knowledge and discovery tools in the human transporter genes. PLoS One, 2014
14. Y Huang, C Xie, Adam Y. Ye, Chuan-Yun Li, G Gao, L Wei. Recent Adaptive Events in Human Brain Revealed by Meta-Analysis of Positively Selected Genes. PLoS One, 2013
15. Chen Xie, Xizeng Mao, Jiaju Huang, Yang Ding, Jianmin Wu, Shan Dong, Lei Kong, Ge Gao, Chuan-Yun Li, Liping Wei. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases, Nucleic Acids Research, 2011
16. Xiuqin Zhang, Rongli Zhang, Susanne Raab, Wen Zheng, Jue Wang, Na Liu, Tiangang Zhu, Lifang Xue, Zhentao Song, Jiaming Mao, Kaitao Li, Huiliang Zhang, Yan Zhang, Chao Han, Yi Ding, Hui Wang, Ning Hou, Yuli Liu, Shujiang Shang, Chuan-Yun Li, Elena Sebokova, Heping Cheng and Paul L. Huang. Rhesus macaques develop metabolic syndrome with reversible vascular dysfunction responsive to pioglitazone. Circulation, 2011
17. Liu QR, Pan CH, Hishimoto A, Chuan-Yun Li, Xi ZX, Llorente-Berzal A, Viveros MP, Ishiguro H, Arinami T, Onaivi ES, Uhl GR. Species differences in cannabinoid receptor 2 (CNR2 gene): identification of novel human and rodent CB2 isoforms, differential tissue expression and regulation by cannabinoid receptor ligands. Genes Brain Behav. 2009
18. Uhl GR, Drgon T, Chuan-Yun Li, Johnson C, Liu QR. Smoking and smoking cessation in disadvantaged women: Assessing genetic contributions. Drug Alcohol Depend. 2009
19. Saccone SF, Bierut LJ, Chesler EJ, Kalivas PW, Lerman C, Saccone NL, Uhl GR, Chuan-Yun Li, Philip VM, Edenberg HJ, Sherry ST, Feolo M, Moyzis RK, Rutter JL. Supplementing high-density SNP microarrays for additional coverage of disease-related genes: addiction as a paradigm. PLoS One. 2009
20. George R Uhl, Tomas Drgon, Catherine Johnson, Chuan-Yun Li, Judith Hess, Daniel Naimen, Qing-Rong Liu. Molecular genetics of addiction and related heritable phenotypes: genome wide association approaches identify “connectivity constellation” and drug target genes with pleiotropic effects. Ann N Y Acad Sci, 2008
21. Catherine Johnson, Tomas Drgon, Qing-Rong Liu, Ping-Wu Zhang, Donna Walther, Chuan-Yun Li, James Anthony, Yulan Ding, William Eaton and George R Uhl. Genome wide association for substance dependence: convergent results from epidemiologic and research volunteer samples. BMC Medical Genetics, 2008
22. George R Uhl, Tomas Drgon, Catherine Johnson, Oluwatosin O. Fatusin, Qing-Rong Liu, Chuan-Yun Li, Kari Buck, John Crabbe. "Higher order" addiction molecular genetics: convergent data from genome-wide association in humans and mice. Biochemical Pharmacology, 2007
Patents
1. Chuan-Yun Li, SJ Zhang, CJ Liu, et al. RhesusBase: A KnowledgeBase for the Monkey Research Community. Computer Software Copyright Registration Certificate. 2013SR055211
2. L Wei, Chuan-Yun Li, ZQ Ye, QY He, Q Yu, W Zhang, Y Sun, J Luo, X Gu, X Zheng. METHOD OF PREDICTING ADMINISTRATING SAFETY OF OSELTAMIVIR PHOSPHATE MEDICINE. PCT Patent number：WO/2007/11546，Chinese Patent ID：ZL 9.3