性别: 男
工作电话: 84112517
职称: 教授
学历: 博士研究生
个人主页: 实验室的网站
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
研究方向
招生方向
本实验室长期招聘RNA组学、RNA生物学、RNA医学和RNA信息学方向博士后多名，欢迎感兴趣的博士生联系！
研究方向
1、开发新的高通量测序技术发现新类型RNA及功能机制
2、开发新的实验和生物信息学方法鉴定非编码RNA及RNA修饰
3、解析非编码RNA和RNA修饰及其互作蛋白的作用机制及在疾病发生发展中的作用
个人经历
1998/9-2002/7 西南农业大学（现西南大学）， 农学， 学士
2003/9-2008/7 中山大学，生物化学与分子生物学， 博士，导师：屈良鹄
2008/7-2010/12 中山大学，赌博app ，讲师（师资博士后）
2011/1-2015/12 中山大学，赌博app ，副教授
2016/1-至今 中山大学，赌博app ，教授
2022年 获得国家杰出青年科学基金项目资助
讲授课程
本科生
《计算机程序设计语言》
《科技论文写作》
研究生
《RNA分子生物学》
本科生竞赛
1、带领的中大SYSU-Software队在国际遗传工程机器设计大赛（iGEM）上
获得4次软件组冠军（Best Software Project）和9次获得金牌
2、带领的中大iGEM队获得首届大学生“小平科技创新团队”奖
3、指导本科生获得挑战杯“全国二等奖”和“广东省特等奖”
学术成就
赌博app-网络赌博软件 教授，国家杰出青年科学基金获得者；长期致力于开发新的RNA组学技术研究非编码RNA基因和RNA修饰及其互作RNA结合蛋白的结构、功能和作用机制。
以通讯作者或共同通讯作者身份在Nature、Nature Biotechnology、Nature Cell Biology、Accounts of Chemical Research、Genome Research、Nucleic Acids Res.、Science Advances、European Urology、Cell Reports、Human Molecular Genetics、EMBO Reports等杂志发表20多篇研究论文，以合作者身份在Nature Methods(2篇)、Cell Stem Cell等杂志发表10多篇研究论文。发表的研究论文的9篇论文被选为ESI高引用论文，1篇被Nature Reviews Genetics、Nature Chemical Biology和Cancer Research杂志亮点评述，1篇被Nature Cell Biology杂志亮点评述，1篇被选为Cell Research杂志的封面和亮点评述,1篇被European Urology杂志亮点评述,1篇被EMBO Reports杂志亮点评述,1篇论文入选“中国百篇最具影响国际学术论文”。开发的一系列RNA组学软件和平台被Nature、Cell等杂志引用超过15000次（Google Scholar），受邀在Accounts of Chemical Research和WIREs RNA杂志撰写RNA修饰及RNA-protein互作的综述论文，受邀在Springer出版社出版了4篇关于非编码RNA研究方法的论著章节。受邀为期刊Advanced Biotechnology的执行副主编、其他期刊Genomics, Proteomics & Bioinformatics、Front. Cell Dev. Biol.、Frontiers in Genetics、Non-coding RNA journal的编委。是海外French National Alliance (AVIESAN) and French National Cancer Institute (INCa)、Netherlands Organisation for Scientific Research (NWO)等基金评审专家。
率先利用CLIP-seq、Epitranscriptome与RNA Interactome数据及概率基因模型、机器学习算法及人工智能算法等开发新的软件和平台，包括starBase、kturnSeeker、snoSeeker、 StarScan、 circScan、circAnno、endSeeker、clipSearch、RMBase、tRF2cancer、ChIPBase、deepBase等。多个软件和平台已成为国际同行最广泛使用的非编码RNA功能机制解析工具之一(如：starBase工具在Google Scholar总引用超过18000次)。
承担课题
主持项目
2023-2027, 国家杰出青年科学基金项目
2019-2024，国家重点研发项目课题
2020-2023，国家自然科学面上项目
2020-2023，广东省科技创新青年拔尖人才项目
2018-2021，国家自然科学面上项目
2015-2017，国家自然科学基金重大研究计划培育项目
2014-2017，国家自然科学面上项目
2010-2012，国家自然科学青年项目
2013-2015， 珠江科技新星项目
课题骨干
2023-2027， 国家重点研发项目
2017-2021， 国家重点研发项目
2019-2022，国家自然科学基金重大研究计划集成项目
论文专著
研究论文
最新的部分代表性论文
Li B+, Liu S+, Zheng W+, Liu A+, Yu P+, Wu D, Zhou J, Zhang P, Liu C, Lin Q, Ye J, He S, Huang Q, Zhou H, Chen J, Qu L*, Yang J*. (2023). RIP-PEN-seq identifies a class of kink-turn RNAs as splicing regulators. Nature Biotechnology. 2023, //www.nature.com/articles/s41587-023-01749-0 (* Correspondence Author, +Co-first author)
Li B, Qu L*, Yang J*. RNA-Guided RNA Modifications: Biogenesis, Functions, and Applications. Accounts of Chemical Research, 2023 Nov 6. doi: 10.1021/acs.accounts.3c00474. (* Correspondence Author, 受邀撰写的综述论文)
Xu W+, Liu C+, Deng B+, Lin P+, Sun Z, Liu A, Xuan J, Li Y, Zhou K, Zhang X, Huang Q, Zhou H, He Q, Li B*, Qu L*, Yang J*. TP53-inducible putative long noncoding RNAs encode functional polypeptides that suppress cell proliferation. Genome Res. 2022 Jun;32(6):1026-1041. (* Correspondence Author, +Co-first author)
Zhang P+, Huang J+, Zheng W, Chen L, Liu S, Liu A, Ye J, Zhou J, Chen Z, Huang Q, Liu S, Zhou K, Qu L*, Li B*, Yang J*. Single-base resolution mapping of 2'-O-methylation sites by an exoribonuclease-enriched chemical method. Sci China Life Sci. 2023 Apr;66(4):800-818. (* Correspondence Author, +Co-first author)
Xuan J*, Chen L, Chen Z, Pang J, Huang J, Lin J, Zheng L, Li B*, Qu L*, Yang J*. RMBase v3.0: decode the landscape, mechanisms and functions of RNA modifications. Nucleic Acids Res. 2023. doi: 10.1093/nar/gkad1070. (* Correspondence Author)
Liu S, Li B, Liang Q, Liu A, Qu L*, Yang J*. Classification and function of RNA-protein interactions. Wiley Interdiscip Rev RNA. 2020 Nov;11(6):e1601. doi: 10.1002/wrna.1601.(* Correspondence Author, 受邀撰写的综述论文)
2019年
Huang H+, Weng H+, Zhou K+, Wu T+, Zhao B. S+, Sun M, Chen Z, Deng X, Xiao G, Auer F, Klemm L, Wu H, Zuo Z, Qin X, Dong Y, Zhou Y, Qin H, Tao S, Du J, Liu J, Lu Z, Yin H, Mesquita A, Yuan C. L, Hu Y.-C, Sun W, Su R, Dong L, Shen C, Li C, Qing Y, Jiang X, Wu X, Sun M, Guan J.-L, Qu L, Wei M, Müschen M, Huang G*, He C*, Yang J*, Chen J*. Histone H3 trimethylation at lysine 36 guides m6A RNA modification co-transcriptionally. Nature. 2019 Mar;567(7748):414-419. (* Correspondence Author, +Co-first author) Highlight in Nature Reviews Genetics & Highlight in Nature Chemical Biology.
Deng B+, Xu W+, Wang Z, Liu C, Lin P, Li B, Huang Q, Yang J*, Zhou H*, Qu L*. An LTR retrotransposon-derived lncRNA interacts with RNF169 to promote homologous recombination. EMBO Rep. 2019 Sep 5:e47650. (* Correspondence Author, +Co-first author) Highlight in EMBO Reports.
2018年
Huang H+, Weng H+, Sun W+, Qin X+, Shi H+, Wu H, Zhao BS, Mesquita A, Liu C, Yuan CL, Hu YC, Hüttelmaier S, Skibbe JR, Su R, Deng X, Dong L, Sun M, Li C, Nachtergaele S, Wang Y, Hu C, Ferchen K, Greis KD, Jiang X, Wei M, Qu L, Guan JL, He C*, Yang J*, Chen J*. Recognition of RNA N(6)-methyladenosine by IGF2BP proteins enhances mRNA stability and translation. Nature Cell Biology. 2018 Mar;20(3):285-295. (* Correspondence Author, +Co-first author) ESI Highly Cited Paper, News & Views in Nature Cell Biology.
Qu L+, Wang ZL+, Chen Q+, Li YM+, He HW, Hsieh JJ, Xue S, Wu ZJ, Liu B, Tang H, Xu XF, Xu F, Wang J, Bao Y, Wang AB, Wang D, Yi XM, Zhou ZK, Shi CJ, Zhong K, Sheng ZC, Zhou YL, Jiang J, Chu XY, He J, Ge JP, Zhang ZY, Zhou WQ*, Chen C*, Yang JH*, Sun YH*, Wang LH*. Prognostic Value of a Long Non-coding RNA Signature in Localized Clear Cell Renal Cell Carcinoma. European Urology 2018 Dec;74(6):756-763. (* Correspondence Author, +Co-first author) Highlight in European Urology
Bao X, Guo X, Yin M, Tariq M, Lai Y, Kanwal S, Zhou J, Li N, Lv Y, Pulido-Quetglas C, Wang X, Ji L, Khan MJ, Zhu X, Luo Z, Shao C, Lim DH, Liu X, Li N, Wang W, He M, Liu YL, Ward C, Wang T, Zhang G, Wang D, Yang J, Chen Y, Zhang C, Jauch R, Yang YG, Wang Y, Qin B, Anko ML, Hutchins AP, Sun H, Wang H, Fu XD, Zhang B, Esteban MA. Capturing the interactome of newly transcribed RNA. Nat Methods. 2018 Mar;15(3):213-220.
Weng H, Huang H, Wu H, Qin X, Zhao BS, Dong L, Shi H, Skibbe J, Shen C, Hu C, Sheng Y, Wang Y, Wunderlich M, Zhang B, Dore LC, Su R, Deng X, Ferchen K, Li C, Sun M, Lu Z, Jiang X, Marcucci G, Mulloy JC, Yang J, Qian Z, Wei M, He C, Chen J. METTL14 Inhibits Hematopoietic Stem/Progenitor Differentiation and Promotes Leukemogenesis via mRNA m(6)A Modification. Cell Stem Cell.2018 Feb 1;22(2):191-205.ESI Highly Cited Paper, Highlight in Cell Stem Cell, Top 10 Papers of 2018 Cell Stem Cell.
Wang ZL+, Li B+, Luo YX, Lin Q, Liu SR, Zhang XQ, Zhou H, Yang JH*#, Qu LH*. Comprehensive Genomic Characterization of RNA-Binding Proteins across Human Cancers. Cell Reports. 2018 Jan 2;22(1):286-298. (* Correspondence Author & #Lead Contact, +Co-first author)
Zheng LL+, Zhou KR+, Liu S, Zhang DY, Wang ZL, Chen ZR, Yang JH*, Qu LH*. dreamBase: DNA modification, RNA regulation and protein binding of expressed pseudogenes in human health and disease. Nucleic Acids Res. 2018 Jan 4;46(D1):D85-D91. (* Correspondence Author, +Co-first author)
Xuan JJ, Sun WJ, Lin PH, Zhou KR, Liu S, Zheng LL, Qu LH*, Yang JH*. RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data. Nucleic Acids Res. 2018 Jan 4;46(D1):D327-D334. (* Correspondence Author)ESI Highly Cited Paper
2017年
Zhang XQ*+, Wang ZL+, Poon MW+, Yang JH*. Spatial-temporal transcriptional dynamics of long non-coding RNAs in human brain. Hum Mol Genet. 2017 Aug 15;26(16):3202-3211.(* Correspondence Author, +Co-first author)
Zheng LL, Deng KW, Deng AC, Wu J, Yang JH, Lun ZR, Qu LH. Exo-miRExplorer: A Comprehensive Resource for Exploring and Comparatively Analyzing Exogenous MicroRNAs. Front Microbiol. 2017 Feb 1;8:126.
Zhou KR, Liu S, Sun WJ, Zheng LL, Zhou H, Yang JH*, Qu LH*. ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data. Nucleic Acids Res. 2017 Jan 4;45(D1):D43-D50. (* Correspondence Author)ESI Highly Cited Paper
2016年
Huang ZP, Ding Y, Chen J, Wu G, Kataoka M, Hu Y, Yang JH, Liu J, Drakos SG, Selzman CH, Kyselovic J, Qu LH, Dos Remedios CG, Pu WT, Wang DZ. Long non-coding RNAs link extracellular matrix gene expression to ischemic cardiomyopathy. Cardiovasc Res. 2016 Aug 24. pii: cvw201.
Guo YH, Wang LQ, Li B, Xu H, Yang JH, Zheng LS, Yu P, Zhou AD, Zhang Y, Xie SJ, Liang ZR, Zhang CM, Zhou H, Qu LH. Wnt/β-catenin pathway transactivates microRNA-150 that promotes EMT of colorectal cancer cells by suppressing CREB signaling. Oncotarget. 2016 Jul 5;7(27):42513-4252
Zheng LL, Xu WL, Liu S, Sun WJ, Li JH, Wu J, Yang JH*, Qu LH*. tRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers. Nucleic Acids Res. 2016 Jul 8;44(W1):W185-93. (* Correspondence Author)
Wang ZL+, Li B,+ Piccolo SR, Zhang XQ, Li JH, Zhou H, Yang JH*, Qu LH*. Integrative analysis reveals clinical phenotypes and oncogenic potentials of long non-coding RNAs across 15 cancer types. Oncotarget. 2016 Jun 7;7(23):35044-55. (* Correspondence Author,+Co-first author)
Zheng LL, Li JH, Wu J, Sun WJ, Liu S, Wang ZL, Zhou H, Yang JH*, Qu LH*. deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data. Nucleic Acids Res. 2016 Jan 4;44(D1):D196-202. (* Correspondence Author) ESI Highly Cited Paper
Sun WJ, Li JH, Liu S, Wu J, Zhou H, Qu LH*, Yang JH*. RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data. Nucleic Acids Res. 2016 Jan 4;44(D1):D259-65. (* Correspondence Author)ESI Highly Cited Paper
2015年
Liu S, Li JH, Wu J, Zhou KR, Zhou H, Yang JH*, Qu LH*. StarScan: a web server for scanning small RNA targets from degradome sequencing data. Nucleic Acids Res. 2015 Jul 1;43(W1):W480-6. (* Correspondence Author)
Li JH, Liu S, Zheng LL, Wu J, Sun WJ, Wang ZL, Zhou H, Qu LH*, Yang JH*. Discovery of Protein-lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets. Front Bioeng Biotechnol. 2015 Jan 14;2:88. (* Correspondence Author, research paper invited by Carlo Maria Croce)
2014年
Zhang YJ, Yang JH, Shi QS, Zheng LL, Liu J, Zhou H, Zhang H, Qu LH. Rapid birth-and-death evolution of imprinted snoRNAs in the Prader-Willi syndrome locus: implications for neural development in Euarchontoglires. PLoS One. 2014 Jun 19;9(6):e100329.
Gou LT+, Dai P+, Yang JH+, Xue Y, Hu YP, Zhou Y, Kang JY, Wang X, Li H, Hua MM, Zhao S, Hu SD, Wu LG, Shi HJ, Li Y, Fu XD, Qu LH, Wang ED, Liu MF. Pachytene piRNAs instruct massive mRNA elimination during late spermiogenesis. Cell Res. 2014 Jun;24(6):680-700. (+Co-first author)Cover Paper, Research Highlight in Cell Res.
Wen JZ, Liao JY, Zheng LL, Xu H, Yang JH, Guan DG, Zhang SM, Zhou H, Qu LH. A contig-based strategy for the genome-wide discovery of microRNAs without complete genome resources. PLoS One. 2014 Feb 7;9(2):e88179.
Li JH, Liu S, Zhou H, Qu LH*, Yang JH*. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 2014 Jan;42:D92-7. (* Correspondence Author)ESI Highly Cited Paper
Wen JZ, Liao JY, Zheng LL, Xu H, Yang JH, Guan DG, Zhang SM, Zhou H, Qu LH. A Contig-Based Strategy for the Genome-Wide Discovery of MicroRNAs without Complete Genome Resources. PLoS One. 2014 Feb 7;9(2):e88179.
2013年
Yang JH, Li JH, Jiang S, Zhou H, Qu LH. ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucleic Acids Res. 2013 Jan;41:D177-87. ESI Highly Cited Paper
Xiao ZD, Diao LT, Yang JH, Xu H, Huang MB, Deng YJ, Zhou H, Qu LH. Deciphering the transcriptional regulation of microRNA genes in humans with ACTLocater. Nucleic Acids Res. 2013 Jan 7;41(1):e5.
Zheng LL, Wen YZ, Yang JH, Liao JY, Shao P, Xu H, Zhou H, Wen JZ, Lun ZR, Ayala FJ, Qu LH. Comparative transcriptome analysis of small noncoding RNAs in different stages of Trypanosoma brucei. RNA. 2013 Jul;19(7):863-75.
Shao P, Liao JY, Guan DG, Yang JH, Zheng LL, Jing Q, Zhou H, Qu LH. Drastic expression change of transposon-derived piRNA-like RNAs and microRNAs in early stages of chicken embryos implies a role in gastrulation. RNA Biol. 2012 Feb;9(2):212-
2011年
Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH. starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res. 2011 Jan;39:D202-9. ESI Highly Cited Paper
2010年
Yang JH, Shao P, Zhou H, Chen YQ, Qu LH. deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res. 2010 Jan;38:D123-30.
Zhang Y, Guan DG, Yang JH, Shao P, Zhou H, Qu LH. ncRNAimprint: a comprehensive database of mammalian imprinted noncoding RNAs. RNA. 2010 Oct;16(10):1889-901.
2010以前
Zhang H+, Yang JH+, Zheng YS+, Zhang P, Chen X, Wu J, Xu L, Luo XQ, Ke ZY, Zhou H, Qu LH, Chen YQ. Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach. PLoS One. 2009 4(9):e6849. (+ co-first author)
Shao P+, Yang JH+, Zhou H, Guan DG, Qu LH. Genome-wide analysis of chicken snoRNAs provides unique implications for the evolution of vertebrate snoRNAs. BMC Genomics. 2009 Feb 22;10:86. (+ co-first author)
Yang JH, Zhang XC, Huang ZP, Zhou H, Huang MB, Zhang S, Chen YQ, Qu LH. snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome. Nucleic Acids Res. 2006;34(18):5112-23.
