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Chuan-Yun Li

发布时间:2011-01-04   阅读次数:10497  
Chuan-Yun Li, Ph.D.
Principal Investigator, Director
Laboratory of Bioinformatics and Genomic Medicine

Peking University, Beijing, China 100871
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.

Selected Publications (#correspondence):
28. 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 Chin-Ming Tan and Chuan-Yun Li#, RhesusBase PopGateway: Genome-wide Population Genetics Atlas in Rhesus Macaque, Molecular Biology and Evolution, 2016
27. 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
26. 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
25. 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)
24. 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
23. 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)
22. 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) Access the recommendation on F1000
21. 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)
20. 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
19. 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)
18. 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
17. 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)
16. 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
15. 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
14. 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
13. 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
11. 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
10. 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
9. 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
8. 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
7. 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
6. 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
5. 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
4. 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
3. 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
2. HUANG Mo-Li, SUN Dao-Chun, Lou Ya-Xin, YIN Yan-Bin, Chuan-Yun Li, ZHANG Yong, GAO Ge, WANG Sheng-Qi, BO Xiao-Chen, WEI Li-Ping, LI Song-Gang. Analysis and Preparation of Oligonucletide Microarray of Apoptosis-related Genes. PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS. 2008
1. 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
1. 魏丽萍,李川昀,叶志强等;一种预测达菲类药物用药安全性的方法;授权日期:2008年3月26日;授权国家:中国;专利号:ZL 200610011569.3;PCT Patent number:WO/2007/115467
2. 中华人民共和国计算机软件著作权; 恒河猴功能基因组学信息注释系统RhesusBase; 授权国家:中国;著作权登记号2013SR055211