1. Juntian Qi, Chuan-Yun Li#, Jinzhuao Wang#, Wanqiu Ding#, Interpretable niche-based cell‒cell communication inference using multi-view graph neural networks, Nature Computational Science, 2025
2. Wanqiu Ding, Xiangshang Li, Jie Zhang, Mingjun Ji, Mengling Zhang, Xiaoming Zhong, Yong Cao, Chunqiong Li, Xiaoge Liu, Chunfu Xiao, Ting Li, Qing Yu, Fan Mo,
Boya Zhang, Jianhuan Qi, Jie-Chun Yang, Jiaxin Wang, Juntian Qi, Lu Tian, Xinwei Xu, Qi Peng, Wei-Zhen Zhou,
Zhijin Liu, Aisi Fu, Ni A. An, Xiuqing Zhang, Jian-Jun Zhang, Baoyang Hu, Yujie Sun, Li Zhang# and
Chuan-Yun Li#, Adaptive Structural Variants Encode Human Uniqueness in Brain Developments,
Science Advances, 2024
3. Mingjun Ji, Qing Yu, Xin-Zhuang Yang, Xianhong Yu, Jiaxin Wang, Chunfu Xiao, Ni A. An, Chuanhui Han, Chuan-Yun Li#, Wanqiu Ding#, Long-range alternative splicing contributes to neoantigen specificity in glioblastoma. Briefings in Bioinformatics, 2024
4. Chuanfu Xiao, Fan Mo, Yingfei Lu, Qi Xiao, Chao Yao, Ting Li, Jianhuan Qi, Xiaoge Liu, Jia-Yu Chen, Li Zhang, Tiannan Guo, Baoyang Hu#, Ni A. An# and Chuan-Yun Li#, Reply to: Identification of old coding regions disproves the hominoid de novo status of genes. Nature Ecology & Evolution, 2024
5. Xiaoge Liu, Chunfu Xiao, Xinwei Xu, Jie Zhang, Fan Mo, Jia-Yu Chen, Nicholas Delihas#, Li Zhang#, Ni A. An# and Chuan-Yun Li#, Origin of Functional De Novo Genes in Humans from “Hopeful Monsters”, WIREs RNA, 2024
6. Jie Zhang, Qi Peng, Chengchuan Ma, Chunfu Xiao, Ting Li, Xiaoge Liu, Liankui Zhou, Wei-Zhen Zhou, Wanqiu Ding, Ni A. An, Ying Liu# and Chuan-Yun Li# 6mA-Sniper: Quantifying 6mA Sites in Eukaryotes at Single-Nucleotide Resolution, Science Advances, 2023
7. Xiangshang Li, Chunfu Xiao, Juntian Qi, Weizhen Xue, Xinwei Xu, Zelin Mu, Jie Zhang, Chuan-Yun Li# and Wanqiu Ding#, STellaris: a web server for accurate spatial mapping of single cells based on spatial transcriptomics data Nucleic Acids Research, 2023
8. Chengchuan Ma, Tingling Xue, Qi Peng, Jie Zhang, Jialiang Guan, Wanqiu Ding, Yi Li, Peixue Xia, Liankui Zhou, Tianyu Zhao, Sheng Wang, Li Quan, Chuan-Yun Li#, and Ying Liu#, N6-Deoxyadenine methyltransferase modulates C. elegans immunity via dichotomous mechanisms, Cell Research, 2023 (Featured by Cell Research)
9. Jianhuan Qi, Fan Mo, Ni A. An, Tingwei Mi, Jiaxin Wang, Jun-Tian Qi, Xiangshang Li, Boya Zhang, Longkuo Xia, Yingfei Lu, Gaoying Sun, Xinyue Wang,Chuan-Yun Li#, and Baoyang Hu#, A Human-specific De Novo Protein Promotes Cortical Expansion and Folding,Advanced Science,2023
10. Ni A. An, Jie Zhang, Fan Mo, Xuke Luan, Qing Sunny Shen, Xiangshang Li, Chunqiong Li, Lu Tian, Boya Zhang, Juntian Qi, Mingjun Ji, Jianhuan Qi, Wei-Zhen Zhou, Wanqiu Ding, Li Zhang, Jia-Yu Chen, Shaokun Shu, Baoyang Hu# and Chuan-Yun Li#, Human-specific genes with an lncRNA origin encode unique human brain developmental functionality, Nature Ecology & Evolution, 2023 (Featured by Science and Nature Ecology & Evolution)
11. Yumei Li, Qing Sunny Shen, Qi Peng, Wanqiu Ding, Jie Zhang, Xiaoming Zhong, Ni A. An, Mingjun Ji, Wei-Zhen Zhou, Chuan-Yun Li#; Polyadenylation-related isoform switching in human evolution revealed by full-length transcript structure, Briefings in Bioinformatics, 2021, bbab157
12. Li-Wa Shao, Qi Peng, Mingyue Dong, Kaiyu Gao, Yumei Li, Yi Li, Chuan-Yun Li# and Ying Liu#, Histone deacetylase HDA-1 modulates mitochondrial stress response and longevity, Nature Communications, 2020
13. 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
14. Yumei Li, Shanshan Ai, Xianhong Yu, Chen Li, Xin Li, Yanzhu Yue, Yusheng Wei, Chuan-Yun Li# and Aibin He#, Replication-independent histone turnover underlines the epigenetic homeostasis in adult heart, Circulation Research, 2019 (Featured by Circulation Research)
15. 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
16. 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
17. 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)
18. 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
19. 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 Molecular Biology and Evolution)
20. 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
21. 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 (Featured by Faculty of 1000)
22. 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)
23. 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
24. 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)
25. 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)
26. 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)
27. Chuan-Yun Li, Yong Zhang, Zhanbo Wang, Yan Zhang, Chunmei Cao, Ping-Wu Zhang, Shu-Juan Lu, Xiao-Mo Li, 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
28. 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)
29. 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
30. Chuan-Yun Li, Quan Yu, Zhi-Qiang Ye, 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)
其他合作论文
31. CNCB-NGDC Members and Partners (including Chuan-Yun Li), Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2024, Nucleic Acids Research, 2024
32. Tongtong Zhu, Guangyi Niu, Yuansheng Zhang, Ming Chen, Chuan-Yun Li, Lili Hao, Zhang Zhang, Host-mediated RNA editing in viruses, Biology Direct, 2023
33. CNCB-NGDC Members and Partners (including Chuan-Yun Li), Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023, Nucleic Acids Research, 2023
34. Shuangjin Ding, Jiankun Liu, XiaoRui Han, Wanqiu Ding, Zhirui Liu, Ying Zhu, Wenxing Zhan, Yiqi Wan, Shujie Gai , Junjie Hou, Xiaoxia Wang, Yixia Wu, Andong Wu, Chuan-Yun Li, Zhe Zheng, Xiao-Li Tian, Huiqing Cao, ICAM-1-related noncoding RNA accelerates atherosclerosis by amplifying NF-κB signaling, J Mol Cell Cardiol, 2022
35. CNCB-NGDC Members and Partners (including Chuan-Yun Li), Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022, Nucleic Acids Research, 2022
36. Wei-Zhen Zhou, Wenke Li, Huayan Shen, Ruby W Wang, Wen Chen, Yujing Zhang, Qingyi Zeng, Hao Wang, Meng Yuan, Ziyi Zeng, Jinhui Cui, Chuan-Yun Li, Fred Y Ye, Zhou Zhou, CHDbase: A comprehensive knowledgebase for congenital heart disease-related genes and clinical manifestations, Genomics, Proteomics & Bioinformatics, 2022
37. Fengjiao Wang, Jiahuan He, Siqi Liu, Ai Gao, Liu Yang, Guohuan Sun, Wanqiu Ding, Chuan-Yun Li, Fanglin Gou, Manman He, Fang Wang, Xiaoshuang Wang, Xiangnan Zhao, Ping Zhu, Sha Hao, Yanni Ma, Hui Cheng, Jia Yu, Tao Cheng, A comprehensive RNA editome reveals that edited Azin1 partners with DDX1 to enable hematopoietic stem cell differentiation, Blood, 2021
38. Feng Y, Xu H, Liu J, Xie N, Gao L, He Y, Yao Y, Lv F, Zhang Y, Lu J, Zhang W, Chuan-Yun Li, Hu X, Yang Z, Xiao R. Functional and adaptive significance of promoter mutations that affect divergent myocardial expressions of TRIM72 in primates, Molecular Biology and Evolution, 2021
39. CNCB-NGDC Members and Partners (including Chuan-Yun Li), Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021, Nucleic Acids Research, 2021
40. Yi Li, Wanqiu Ding, Chuan-Yun Li, and Ying Liu#, HLH-11 modulates lipid metabolism in response to nutrient availability, Nature Communications, 2020
41. National Genomics Data Center Members and Partners (including Chuan-Yun Li), Database Resources of the National Genomics Data Center in 2020, Nucleic Acids Research, 2020
42. Dechao Wu, Chongshu Jian, Qi Peng, Tingting Hou, Keling Wu, Bizhi Shang, Minglei Zhao, Yanru Wang, Wen Zheng, Qi Ma, Chuan-Yun Li, Heping Cheng, Xianhua Wang and Ling Zhao#, Prohibitin 2 deficiency impairs cardiac fatty acid oxidation and causes heart failure, Cell Death and Disease, 2020
43. 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
44. 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
45. The BIG Data Center Consortium (including Chuan-Yun Li), Database Resources of the BIG Data Center in 2019, Nucleic Acids Research, 2019
46. 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
47. 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
48. 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
49. 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
50. 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
51. 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
53. 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
54. 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 depression mechanism, Cell Research, 2014
55. 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
56. 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
57. 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
58. 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
59. 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
60. 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
61. 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
62. 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
63. 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
64. 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
专利与软件著作权
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 200610011569.3
