性别: 男
职称: 教授
电子邮件: [email protected]
导师类型: 博士生导师
学科方向:
071010-生物化学与分子生物学
0710Z1-生物信息学
0860-生物与医药
研究方向
最新消息
本实验招收2025年生化方向学硕1名,生物与医药专硕1名,欢迎感兴趣的学生联系报考!
研究方向:RNA编辑、修饰和RNA治疗
基因编辑作为近年来生命科学中最重要的技术之一,在疾病治疗,尤其遗传疾病、各类慢性病和肿瘤治疗中有无限的潜能和优势。可以预见未来的5-10年,传统的遗传疾病和罕见病治疗,以及一些威胁人类健康的慢性病、老年病和肿瘤的治疗理念将被彻底颠覆,基于基因编辑的医疗在不远的将来会帮助到无数病患者。基因编辑根据靶标不同可以分为DNA编辑和RNA编辑。目前最流行的基于CRISPR-Cas9的DNA编辑技术带来的是永久水平的遗传物质的改变,在DNA和RNA水平都有一定的脱靶效应,并且Cas9蛋白本身会刺激人体细胞免疫反应,因此在临床应用和药物开发方面针对不同类型的疾病还需要不断的优化和摸索。相对于DNA编辑,RNA编辑在RNA水平修复突变,不改变基因组序列,可逆可控,具有更安全的特性,在某些疾病场景下有巨大的优势。
我们实验室致力于开发RNA层面的各种RNA靶向编辑工具,用于致病突变修复,以及在RNA的各个层面调控致病基因。这些系统在RNA水平修复致病基因,具有可控和可逆性,不影响基因组稳定性,在临床上比其他系统比如DNA编辑系统具有一系列优势性。此外,我们通过建立各种新颖的生信算法(比如机器学习和深度学习)用于分析多组学数据、三代测序数据、高通量筛选数据,以建立RNA调控和编辑的新型模型和拓展其应用。
此外,我们也对内源的RNA编辑现象,特别是A-to-I RNA编辑的调控和功能感兴趣。 我们实验室通过分子细胞表型等实验生物学方法和大规模多组学数据分析和建模,揭示A-to-I RNA编辑在自身免疫和免疫相关疾病和肿瘤免疫中的作用和潜在关键靶标。
研究生招生
实验室欢迎热爱相关研究的优秀学生来了解其硕士和博士研究生招生计划。
实验室的宗旨是:“Enjoy Science”。实验室的研究生培养目标是:瞄准有开拓性的研究课题,系统严密的训练科研能力(比如critical thinking,writing和presentation)。实验室会提供先进的科研实验条件,资助研究生参加国内外学术会议以开阔视野,跟国内外其他实验室相互合作,以使每一位研究生有机会作出第一流的研究工作,为他(她)们将来成为优秀科学家或者企业人才奠定基础、提供通道。
实验室坚持宁缺勿滥的原则,鼓励和甄选最优秀的学生跟导师共同工作。实验室希望招收的学生要独立自主,热爱科学,对相关方向有强烈兴趣,对自己有较高的期望值。希望每一位有兴趣报考的同学能尽早与实验室联系,同时提交一份详细的简历和大学成绩单。
欢迎感兴趣报考的学生直接联系张锐教授([email protected]),实验室地址:新港西路中山大学新生物楼A栋2楼240室。
实验室人员
客座教授:黄涛
博士后:赵成成
科研助理:诸葛福艳
博士研究生:吴英尹(华东师范大学)、孙傲龙(湖南大学)、马孟丹(汕头大学医学院)
硕博连读生:罗慧 (吉林大学)、张钰森(中山大学)、曹勇(天津大学)、孙远帆(兰州大学)、姚静(电子科技大学)、高宙峰(苏州大学)
硕士研究生:何梓华(华南理工大学)、侯文豪(合肥工业大学)、王燚莹(湖南大学)、高嘉熙(澳门大学)、李鑫(中南大学)、黄敬潼(中山大学)
已毕业学生
李丽诗、赵雪泥、黄子超、杨文兵、章辉、史欣蕊、李文卿、何修驹、刘建恒、付强、陈婉颖、丘莹、赵天璇
已离职博后/专职科研人员
宋玉龙(现任广州医科大学赌博app 教授)
研究生获奖情况
陈婉颖:研究生国家奖学金,有害生物控制与资源利用国家重点实验室“杰出研究生”二等奖
李丽诗:有害生物控制与资源利用国家重点实验室“杰出研究生”一等奖
刘健恒:研究生国家奖学金、中山大学优秀博士论文
杨文兵:中国博士后科学基金会特别资助(站前)
实验室activity见:
个人经历
2003年毕业于四川大学生科院, 获学士学位。2009年于中科院昆明动物所获得博士学位,在宿兵研究员指导下研究小RNA的进化和功能。2009年-2011年期间分别在伦敦皇家学会会员Stephen Cohen教授和台湾中研院院士Chung-I Wu教授实验室从事小RNA进化领域研究工作。2011年-2015年在美国斯坦福大学医学院遗传系Jin Billy Li教授实验室从事博士后研究,通过发展微流控技术、高通量测序相关高新生物技术研究RNA编辑的进化、调控和功能。
讲授课程
生化细胞讨论课,强基班/拔尖班,生科院
细胞生物学,本科生,生科院
现代生命科学进展,本科生,生科院
进化基因组学,研究生,生科院
学术成就
赌博app-网络赌博软件 教授,博士生导师。入选中山大学2015“百人计划”引进人才,2015国家海外高层次人才,2017年广东省“珠江人才计划”创新创业团队人才。担任广东省生物信息学会委员会委员。近五年作为通讯作者在国际知名学术杂志发表多篇论文,包括:Nature Structural & Molecular Biology,National Science Review, Blood, Nature Communications, Genome Research, Genome Biology, Nucleic Acids Research,授权发明权利4项。研究成果被Science, Nature Structural & Molecular Biology等专题报道。现担任Nature Biotechnology, Nature Chemical Biology, Genome Research, Nature Communications, Trends in Genetics, PLOS Genetics, Molecular Biology and Evolution, Nucleic Acids Research等学术期刊审稿人。迄今为止,根据 Google Scholar 数据库统计,所发表文章被引用 4238 次(2023-01), H-index 为 27。
在RNA编辑和RNA m5C领域的工作受到RNA领域同行的广泛认可,受邀参与编写复旦大学牵头的《表观遗传学》教科书编写,负责“RNA编辑”这一章节;受邀RNA领域重要国际国内学术会议特邀报告,比如RNA Editing Gordon Research Conference、全国核糖核酸(RNA)学术讨论会等会议。评审国自然项目、美国以色列联合科学基金(United States-Israel Binational Science Foundation)、奥地利科学基金(Austrian Science Fund)等国际基金项目。
承担课题
中山大学百人计划(2015-2017)
国家级人才项目(2015-2018)
国家自然基金面上项目(2016-2019)
国家自然基金重大计划培育项目(2017-2019)
珠江人才计划创新创业团队[子课题] (2017-2022)
广东省重大科技专项(前沿与关键技术创新方向)(2017-2019)
国家重点研发计划生殖健康及重大出生缺陷防控研究子课题 (2018-2020)
国家重点研发计划蛋白质机器与生命过程调控研究子课题 (2020-2025)
论文专著
15. Jianheng Liu, Tao Huang, Jing Yao, Tianxuan Zhao, Yusen Zhang, Rui Zhang (2023) Epitranscriptomic subtyping, visualization, and denoising by global motif visualization. Nature Communications, 14, 5944.
14. Yanli Ji*; Yalin Luo*; Jizhi Wen*; Yuanfan Sun; Shuangshuang Jia; Chunquan Ou, Wenbing Yang; Jingwang Chen; Hanshen Ye; Xiangfu Liu; Yongneng Liang; Zhigang Lu; Ying Feng; Xinzhong Wu; Muzhou Xiao; Jiankun Mo; Zhenhai Zhou; Zhen Wang; Zhijian Liao; Junhu Chen; Ling Wei; Guangping Luo; Sentot Santoso, Yann Fichou, Willy Albert Flegel, Chaopeng Shao; Chengyao Li#; Rui Zhang#; Yongshui Fu# (2023) Patients with Asian-type DEL can safely be transfused using RhD-positive blood. Blood.
13. Jianheng Liu*, Tao Huang*, Wanying Chen*, Chenhui Ding*, Tianxuan Zhao*, Xueni Zhao*, Bing Cai*, Yusen Zhang*, Song Li, Ling Zhang, Maoguang Xue, Xiuju He, Wanzhong Ge#, Canquan Zhou#, Yanwen Xu#, Rui Zhang# (2022) Developmental mRNA m5C landscape and regulatory innovations of massive m5C modification of maternal mRNAs in animals. Nature Communications. 13, Article number: 2484.
12. Yulong Song*, #, Xiuju He*, Wenbing Yang*, Yaoxing Wu, Jun Cui, Tian Tang, Rui Zhang# (2022) Virus-specific editing identification approach reveals the landscape of A-to-I editing and its impacts on SARS-CoV-2 characteristics and evolution. Nucleic Acids Research, gkac120
11. Jianheng Liu*, Tao Huang*,#, Yusen Zhang*, Tianxuan Zhao*, Xueni Zhao, Wanying Chen, Rui Zhang# (2021) Sequence- and structure-selective mRNA m5C methylation by NSUN6 in animals. National Science Review. 8, 1-12
10. Hui Zhang*, Qiang Fu*, Xinrui Shi*, Ziqing Pan, Wenbing Yang, Zichao Huang, Tian Tang, Xionglei He, Rui Zhang (2020) Human A-to-I RNA editing SNP loci are enriched in GWAS signals for autoimmune diseases and under balancing selection. Genome Biology. 21:288, 1-16
9. Yulong Song*, Wenbing Yang*, Qiang Fu, Liang Wu, Xueni Zhao, Yusen Zhang, Rui Zhang (2020) irCLASH reveals RNA substrates recognized by human ADARs. Nature Structural & Molecular Biology, 27,4,351–362. (同期评论文章:It takes two (and some distance) to tango: how ADARs join to edit RNA. Nature Structural & Molecular Biology, //www.nature.com/articles/s41594-020-0411-y)
8. Yulong Song*, Lishi Li*, Wenbing Yang, Qiang Fu, Wanying Chen, Zeng Fang, Wen Li#, Nannan Gu#, Rui Zhang#. (2020) Sense-antisense miRNA pairs constitute an elaborate reciprocal regulatory circuit. Genome Research, 30, 5, 661-672.
7. Hui Zhang*, Xinrui Shi*, Tao Huang*,#, Wanying, Chen, Nannan Gu, Rui Zhang#. (2020) Dynamic landscape and evolution of m6A methylation in human, Nucleic Acids Research. 48, 11, 6251–6264.
6. Kun Liao, Shuye Deng, Liyan Xu, Wenfeng Pan, Shiyu Yang, Fufu Zheng, Xingui Wu, Hongrong Hu, Zhijun Liu, Junhang Luo, Rui Zhang, Dong-Ming Kuang, Jiajun Dong, Yi Wu, Hui Zhang, Penghui Zhou, Jin-Xin Bei, Yang Xu, Yin Ji, Peng Wang, Huai-Qiang Ju, Rui-Hua Xu, Bo Li (2020) A Feedback Circuitry between Polycomb Signaling and Fructose-1, 6-Bisphosphatase Enables Hepatic and Renal Tumorigenesis, Cancer Research. 10.1158/0008-5472.CAN-19-2060.
5. Tao Huang*, Wanying Chen*, Jianheng Liu*, Nannan Gu, Rui Zhang (2019) Genome-wide identification of mRNA 5-methylcytosine in mammals. Nature Structural & Molecular Biology, 26, 380-388 (同期评论文章:Getting a hold on cytosine methylation in mRNA. Nature Structural & Molecular Biology 26, 339–340)
4. Lishi Li *, Yulong Song *, Xinrui Shi, Jianheng Liu, Shaolei Xiong, Wanying Chen, Qiang Fu, Zichao Huang, Nannan Gu#, Rui Zhang# (2018) The landscape of miRNA editing in animals and its impact on miRNA biogenesis and targeting. Genome Research. 28: 132-143
3. Rui Zhang*,#, Patricia Deng*, Dionna Jacobson, Jin Billy Li# (2017) Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing. PLOS Genetics 13(2): e1006563:1-24. (Highlighted by Science: The evolution of edited RNA transcripts //science.sciencemag.org/content/355/6331/1278.4 )
2. Meng How Tan*, Qin Li*, et al. (2017) Dynamic landscape and regulation of RNA editing in mammals. Nature 550, 249–254
1. eGTEx Project (2017) Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease. Nature Genetics 49(12):1664-1670
2015 and before:
19. Gokul Ramaswami *, Patricia Deng *, Rui Zhang, Mary Anne Carbone, Trudy F.C. Mackay, Li Jin Billy (2015) Genetic mapping uncovers cis-regulatory landscape of RNA editing. Nature Communications. 6:8194. doi: 10.1038/ncomms9194
18. Leng Han*, Lixia Diao*, Shuangxing Yu*, Xiaoyan Xu*, et al (2015) The Genomic Landscape and Clinical Relevance of A-to-I RNA Editing in Human Cancers. Cancer Cell 28 (4), 515–528
17. Manuel A Rivas et al (2015) Effect of predicted protein-truncating genetic variants on the human transcriptome. Science 348 (6235), 666-669
16. Yael Baran et al. (2015) The landscape of genomic imprinting across diverse adult human tissues. Genome Research, gr. 192278.115
15. Tomas Babak, Brian DeVeale, Emily K Tsang, Yiqi Zhou, Xin Li, Kevin S Smith, Kim R Kukurba, Rui Zhang, Jin Billy Li, Derek van der Kooy, Stephen B Montgomery and Hunter B Fraser (2015) Genetic conflict reflected in tissue-specific maps of genomic imprinting. Nature Genetics 47 (5), 544-549
14. Anne L. Sapiro, Patricia Deng, Rui Zhang, Jin Billy Li (2015) Cis regulatory effects on A-to-I RNA editing in related Drosophila species. Cell Reports, 11:697-703
13. Guojing Liu*, Rui Zhang*, Jin Xu, Chung-I Wu and Xuemei Lu (2014) Functional conservation of both CDS- and 3’-UTR-located microRNA binding sites between species. Mol Biol Evol doi: 10.1093/molbev/msu323
12. Kimberly R. Kukurba, Rui Zhang, Xin Li, Kevin S. Smith, David A. Knowles, Meng How Tan, Robert Piskol, Monkol Lek, Michael Snyder, Daniel G. MacArthur, Jin Billy Li and Stephen B. Montgomery (2014) Allelic expression of deleterious protein-coding variants across human tissues. PLOS Genetics 10(5):e1004304.doi:10.1371/journal.pgen.1004304
11. Rui Zhang, Xin Li, Gokul Ramaswami, Kevin S Smith, Gustavo Turecki, Stephen B Montgomery and Jin Billy Li (2014) Quantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing. Nature Methods 11:51–54
10. Xin Hong, Hung Thanh Nguyen, Qingfeng Chen, Rui Zhang, Zandra Hagman, P Mathijs and Stephen Cohen (2014) Opposing activities of the Ras and Hippo pathways converge on regulation of YAP protein turnover. EMBO Journal, DOI: 10.15252/embj.201489385
9. Lily Bazak, Ami Haviv, Michal Barak, Jasmine Jacob-Hirsch, Patricia Deng, Rui Zhang, Farren J Isaacs, Gideon Rechavi, Jin Billy Li, Eli Eisenberg and Erez Y Levanon (2013) A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes. Genome Res 24(3):365-376
8. Jin Xu*, Rui Zhang*, Yang Shen, Guojing Liu, Xuemei Lu and Chung-I Wu (2013) The evolution of evolvability in microRNA target sites in vertebrates. Genome Res 23:1810-1816
7. Gokul Ramaswami*, Rui Zhang*, Robert Piskol, Liam P Keegan, Patricia Deng, Mary A O'Connell and Jin Billy Li (2013) Identifying RNA editing sites using RNA sequencing data alone. Nature Methods 10:128–132
6. Yang Shen, Yang Lv, Lei Huang, Wensheng Liu, Ming Wen, Tian Tang, Rui Zhang, Eric Hungate, Suhua Shi and Chung-I Wu (2011) Testing hypotheses on the rate of molecular evolution in relation to gene expression using microRNAs. PNAS 108:15942-15947
5. Wanzhong Ge, Yawen Chen, Ruifen Weng, Singfee Lim, Marita Buescher, Rui Zhang and Stephen M. Cohen (2011) Overlapping functions of microRNAs in control of apoptosis during Drosophila embryogenesis. Cell Death Differ 19:839-846
4. Xiaodong Fang*, Yanfeng Zhang*, Rui Zhang*, Lixin Yang, Ming Li, Kaixiong Ye, Xiaosen Guo, Jun Wang and Bing Su (2011) Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque. Genome Biol 12:R63
3. Rui Zhang, and Bing Su (2008) MicroRNA regulation and the variability of human cortical gene expression. Nucleic Acids Res 36:4621-4628
2. Rui Zhang, Yinqiu Wang and Bing Su (2008) Molecular evolution of a primate-specific microRNA family. Mol Biol Evol 25:1493-1502
1. Rui Zhang, Yi Peng, Wen Wang and Bing Su (2007) Rapid evolution of an X-linked microRNA cluster in primates. Genome Res 17:612-617
*Co-first authors
#Co-corresponding authors