吴清发 中国科学技术大学生命科学学院教授

吴清发，中国科学技术大学生命科学学院教授，博士生导师。主要从事基因组和转录组学数据分析以及RNA沉默抗病毒机制研究、非编码RNA的签定和功能分析。

教育及工作经历：

1999年开始在中国科学院遗传与发育生物学研究所/北京基因组研究所攻读博士学位，作为技术骨干参与“人类基因组计划中国部分”的序列解析和数据分析工作。期间作为交流博士生，在丹麦哥本哈根大学Panum医学院功能基因组中心从事人类疾病基因的定位克隆工作。

2004年4月到2006年10月，在美国西北大学从事博士后研究, 主要进行人造血干细胞转录谱的研究工作。

2006年10月-2010年10月，在美国加州大学河滨分校从事病毒和宿主相互作用的系统生物学研究工作。

2010年10月起任中国科学技术大学生命科学学院教授。

学术兼职：

1、中国细胞生物学学会会员。 

研究方向：

论文专著： 

[1]Guo D, Xu W, Cui T, Rong Q, Wu Q*. Protein-coding circular RNA enhances antiviral immunity via JAK/STAT pathway in Drosophila. mBio. 2024. 19:e0146924

[2]Chen D, Shi C, Xu W, Rong Q, Wu Q*. Regulation of phase separation and antiviral activity of Cactin by glycolytic enzyme PGK via phosphorylation in Drosophila. mBio. 2024. 15:e01378-23. 

[3]Rong Q, Xi Z, Guo D, Xu W, Zhang L, Wu Q*. Regulation of ubiquitination and antiviral activity of Cactin by deubiquitinase Usp14 in Drosophila. J Virol. 2024. 98(5):e0017724. 

[4]Cui T, Bai Q*, Yu W, Guo D, Ban Y, Chen K, Raza Ali, Zhou G, Wu Q*. Chromosome-levelgenome assembly and population genomic analysis provide novel insights into the immunity and evolution of Sogatella furcifera. Genomics. 2023. 115: 110729. 

[5]Yan W, Zhu Y, Liu W, Zou C, Jia B, Chen ZQ, Han Y, Wu J, Yang DL, Zhang Z, Xie L,Chen B, Li R, Ding SW*, Wu Q*, Guo Z*. Discovery of aphid-transmitted Rice tiller inhibition virus from native plants through metagenomic sequencing. PLoS Pathogen. 2023.19(3):e1011238.

[6]Zhang, Liqin; Xu, Wen; Gao, Xinlei; Li, Wenjie; Qi, Shuishui; Guo, Dongyang; Ajayi, Olugbenga Emmanuel; Ding, Shou-Wei; Wu, Qingfa*.lncRNA Sensing of a Viral Suppressor of RNAi Activates Non-canonical Innate Immune Signaling in Drosophila.Cell Host & Microbe, 2020, 27(1): 115-128. 

[7]Yao, Ziting; Zou, Chengwu; Peng, Na; Zhu, Yu; Bao, Yixue; Zhou, Qiujuan; Wu, Qingfa; Chen, Baoshan; Zhang, Muqing.Virome Identification and Characterization of Fusarium sacchari and F. andiyazi: Causative Agents of Pokkah Boeng Disease in Sugarcane.Frontiers in Microbiology, 2020, 11: 240.

[8]Fang, Tao; Zhu, Yanjie; Xu, Anlan; Zhang, Yanli; Wu, Qingfa; Huang, Guoying; Sheng, Wei*; Chen, Mingwu*.Functional analysis of the congenital heart disease-associated GATA4 H436Y mutation in vitro.Molecular Medicine Reports, 2019, 20(3): 2325-2331.

[9]Gao, Xinlei; Fu, Yating; Ajayi, Olugbenga Emmanuel; Guo, Dongyang; Zhang, Liqin; Wu, Qingfa*.Identification of genes underlying phenotypic plasticity of wing size via insulin signaling pathway by network-based analysis in Sogatella furcifera.BMC Genomics, 2019, 20: 396.

[10]Deng Lu; Gao Xinlei; Liu Bingjie; He Xueyan; Xu Jiahui; Qiang Jiankun; Wu Qingfa; Liu Suling*。NMT1 inhibition modulates breast cancer progression through stress-triggered JNK pathway.Cell Death & Disease, 2018, 9(12): 1143. 

[11]Akinyemi Ibukun A; Wang Fang; Chang Zhao-Xia; Wu Qingfa*。Genome characterization of the newly identified maize-associated totivirus Anhui.Archives of Virology, 2018, 163(10): 2929-2931.

[12]Zeng Zhen; Fu Yating; Guo Dongyang; Wu Yuxuan; Ajayi Olugbenga Emmanuel; Wu Qingfa*。Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host.BMC Genomics, 2018, 19(1): 688.

[13] Han Yanhong*; Wu Qingfa*; Ding Shou-Wei*.Templating Antiviral RNAi in Insects.Cell Host & Microbe, 2018, 23(3): 290-292.

[14]Chang Zhao-Xia; Akinyemi Ibukun A; Guo Dong-Yang; Wu Qingfa.Characterization and comparative analysis of microRNAs in the rice pest Sogatella furcifera.PLos One, 2018, 13(9): e0204517.

[15]Wang Lin#; Tang Nan#; Gao Xinlei; Chang Zhaoxia; Zhang Liqin; Zhou Guohui; Guo Dongyang; Zeng Zhen; Li Wenjie; Akinyemi A.Ibukun; Yang Huanming; Wu Qingfa*.Genome sequence of a rice pest, the white-backed planthopper (Sogatella furcifera).GigaScience, 2017, 6: 1-9.

[16]Cao, Linyan; Gao, Chun-Hui; Zhu, Jiade; Zhao, Liping; Wu, Qingfa; Li, Min; Sun, Baolin*.Identification and functional study of type III-A CRISPR-Cas systems in clinical isolates of Staphylococcus aureus.International Journal of Medical Microbiology, 2016, 306(8): 686-696.

[17]Akinyemi, Ibukun A; Wang, Fang; Zhou, Benguo; Qi, Shuishui; Wu, Qingfa*.Ecogenomic survey of plant viruses infecting Tobacco by Next generation sequencing.Virology Journal, 2016, 13(1): 181-181.

[18]Wang, Lin; Tang, Nan; Gao, Xinlei; Guo, Dongyang; Chang, Zhaoxia; Fu, Yating; Akinyemi, Ibukun A; Wu, Qingfa.Understanding the immune system architecture and transcriptome responses to southern rice black-streaked dwarf virus in Sogatella furcifera.Scientific Reports, 2016, 6: 36254-36254.

[19]Chang, Zhao-Xia; Tang, Nan; Wang, Lin; Zhang, Li-Qing; Akinyemi, Ibukun A; Wu, Qing-Fa.Identification and characterization of microRNAs in the white-backed planthopper, Sogatella furcifera.Insect Science, 2016, 23(3): 452-468. 

[20]Li, Gaopeng; Wu, Xiaoli; Qian, Wenchang; Cai, Huayong; Sun, Xinbao; Zhang, Weijie; Tan, Sheng; Wu, Zhengsheng; Qian, Pengxu; Ding, Keshuo; Lu, Xuefei; Zhang, Xiao; Yan, Hong; Song, Haifeng; Guang, Shouhong; Wu, Qingfa; Lobie, Peter E.; Shan, Ge; Zhu, Tao*.CCAR1 5' UTR as a natural miRancer of miR-1254 overrides tamoxifen resistance.Cell Research, 2016, 26(6): 655-673.

[21]Yang, Yan-Qing; Yang, Wei; Yao, Yuan; Ma, Hong-Di; Wang, Yin-Hu; Li, Liang; Wu, Qingfa; Gershwin, M Eric; Lian, Zhe-Xiong.Dysregulation of peritoneal cavity B1a cells and murine primary biliary cholangitis.Oncotarget, 2016, 7(19): 26992-27006.

[22]Yu, Li-Yan; Cheng, Wang; Zhou, Kang; Li, Wei-Fang; Yu, Hong-Mei; Gao, Xinlei; Shen, Xudong; Wu, Qingfa; Chen, Yuxing*; Zhou, Cong-Zhao*.Structures of an all-alpha protein running along the DNA major groove.Nucleic Acids Research, 2016, 44(8): 3936-3945.

[23] Wang Fang; Wu Qingfa; Zhou Benguo; Gao Zenliang; Xu DF.FirstReport of Turnip yellows virus in Tobacco in China.Plant Disease, 2015, 11(12): 1870-1870.

[24]Yu, Hongmei; Qi, Shuishui; Chang, Zhaoxia; Rong, Qiqi; Akinyemi, Ibukun A; Wu, Qingfa*.Complete genome sequence of a novel velarivirus infecting areca palm in China.Archives of Virology, 2015, 160(9): 2367-2370.

[25]Liang, Pengbo; Navarro, Beatriz; Zhang, Zhixiang; Wang, Hongqing; Lu, Meiguang; Xiao, Hong; Wu, Qingfa; Zhou, Xueping; Di Serio, Francesco; Li, Shifang.Identification and characterization of a novel geminivirus with a monopartite genome infecting apple trees.Journal of General Virology, 2015, 96(8): 2411-2420.

[26]Zhang, Qi; Zhang, Liqin; Gao, Xinlei; Qi, Shuishui; Chang, Zhaoxia; Wu, Qingfa*.DIP1 plays an antiviral role against DCV infection in Drosophila melanogaster.Biochem Biophys Res Commun, 2015, 460(2): 222-226.

[27]Wang Lin; Gao Chunhui; Hu Songnian; Hu Songnian; Wu Qingfa*.Identification of genetic variations associated with epsilon-poly-lysine biosynthesis in Streptomyces albulus ZPM by genome sequencing.Scientific Reports, 2015, 5(9201): 1-9.

[28]Li, Zhaoyong; Huang, Chuan; Bao, Chun; Chen, Liang; Lin, Mei; Wang, Xiaolin; Zhong, Guolin; Yu, Bin; Hu, Wanchen; Dai, Limin; Zhu, Pengfei; Chang, Zhaoxia; Wu, Qingfa; Zhao, Yi; Jia, Ya; Xu, Ping; Liu, Huijie; Shan, Ge.Exon-intron circular RNAs regulate transcription in the nucleus.Nat Struct Mol Biol, 2015, 22(4): 240-251.

[29]Wu, Qingfa*; Ding, Shou-Wei*; Zhang, Yongjiang; Zhu, Shuifang*.Identification of viruses and viroids by next-generation sequencing and homology-dependent and homology-independent algorithms.Annual Review of Phytopathology, 2015, 53: 425-444.

[30]Hu, Hai-Xi; Jiang, Yong-Liang; Zhao, Meng-Xi; Cai, Kun; Liu, Sanling; Wen, Bin; Lv, Pei; Zhang, Yonghui; Peng, Junhui; Zhong, Hui; Yu, Hong-Mei; Ren, Yan-Min; Zhang, Zhiyong; Tian, Changlin; Wu, Qingfa; Oliveberg, Mikael; Zhang, Cheng-Cai; Chen, Yuxing; Zhou, Cong-Zhao.Structural insights into HetR-PatS interaction involved in cyanobacterial pattern formation.Scientific Reports, 2015, 5: 16470-16470.

[31]Liu, Ying; Chen, Chunying; Qian, Pengxu; Lu, Xuefei; Sun, Baoyun; Zhang, Xiao; Wang, Liming; Gao, Xingfa; Li, Han; Chen, Zhiyun; Tang, Jinglong; Zhang, Weijie; Dong, Jinquan; Bai, Ru; Lobie, Peter E; Wu, Qingfa; Liu, Suling; Zhang, Huafeng; Zhao, Feng; Wicha, Max S; Zhu, Tao; Zhao, Yuliang.Gd-metallofullerenol nanomaterial as non-toxic breast cancer stem cell-specific inhibitor.Nature Communications, 2015, 6: 5988-5988.

     [32]Zhang, Zhixiang; Qi, Shuishui; Tang, Nan; Zhang, Xinxin; Chen, Shanshan; Zhu, Pengfei; Ma, Lin; Cheng, Jinping; Xu, Yun; Lu, Meiguang; Wang, Hongqing; Ding, Shou-Wei; Li, Shifang*; Wu, Qingfa*. Discovery of replicating circular RNAs by RNA-seq and computational algorithms.PLOS Pathogens.2014, 10(12): e1004553. doi:10.1371/journal.ppat.1004553 (& Corresponding author） 

[33]Liu Huijie; Wang Xueren; Wang Horng-Dar; Wu Jinjing; Ren Jing; Meng Lingfeng; Wu Qingfa; Dong Hansheng; Wu Jing; Kao Tzu-Yu; Ge Qian; Wu Zheng-xing; Yuh Chiou-Hwa; Shan Ge.Escherichia coli noncoding RNAs can affect gene expression and physiology of Caenorhabditis elegans.Nat Commun. 2012;3:1073.

[34]Wu Q , Wang Y , Cao M, Pantaleo V, Burgyan J, Li WX, Ding SW.Homology-independent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm.Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3938-43. Epub 2012 Feb 15.(# Co-first author） 

[35]Han Yan-Hong#; Luo Ying-Jun#; Wu Qingfa#*; Jovel Juan; Wang Xiao-Hong; Aliyari Roghiyh; Han Chenggui; Li Wan-Xiang; Ding Shou-Wei*. RNA-based immunity terminates viral infection in adult Drosophila in the absence of viral suppression of RNA interference: characterization of viral small interfering RNA populations in wild-type and mutant flies.Journal of Virology, 2011, 85(24): 13153-13163..Epub 2011 Sep 28.( #Co-first author，& Co-corresponding author) 

[36]Wang Xian-Bing; Jovel Juan; Udomporn  Petchthai; Wang Ying; Wu Qingfa; Li Wan-Xiang; Gasciolli Virginie; Vaucheret Herve; Ding Shou-Wei.The 21-nucleotide, but not 22-nucleotide, viral secondary small interfering RNAs direct potent antiviral defense by two cooperative argonautes in Arabidopsis thaliana.Plant Cell, 2011, 23(4): 1625-1638.. Epub 2011 Apr 5.

[37]Wu Qingfa; Wang Xianbing; Ding Shou-Wei.Viral suppressors of RNA-based viral immunity: host targets.Cell Host Microbe, 2010, 8(1): 12-5. 

[38]Yu Bin; Bi Liu; Zhai Jixian; Agarwal Manu; Li Shengben; Wu Qingfa; Ding Shou-Wei; Meyers Blake; Vaucheret Herve; Chen Xuemei.siRNAs compete with miRNAs for methylation by HEN1 in Arabidopsis.Nucleic Acids Research, 2010, 38(17): 5844-5850.

[39]Wu Qingfa; Luo Yingjun; Lu Rui; Lau Nelson; Lai Eric; Li Wan-Xiang; Ding Shou-Wei.Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs.Proceedings of the National Academy of Sciences of the United States of America, 2010, 107(4): 1606-1611.

[40]Wang Xian-Bing; Wu Qingfa; Ito Takao; Cillo Fabrizio; Li Wan-Xiang; Chen Xuemei; Yu Jia-Lin; Ding Shou-Wei.RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana.Proceedings of the National Academy of Sciences of the United States of America, 2010, 107(1): 484-489.

[41]Kim Yeong#; Wu Qingfa#; Chen Jun; Xuan Zhenyu; Jung Yong-Chul; Zhang Michael; Rowley Janet; Wang San Ming.The transcriptome of human CD34+ hematopoietic stem-progenitor cells.Proceedings of the National Academy of Sciences of the United States of America, 2009, 106(20): 8278-8283. Epub 2009 Apr 30.(# Co-first author） 

[42]Aliyari Roghiyh#; Wu Qingfa#; Li Hong-Wei; Wang Xiao-Hong; Li Feng; Green Lance; Han Cliff; Li Wan-Xiang; Ding; Shou-Wei.Mechanism of induction and suppression of antiviral immunity directed by virus-derived small RNAs in Drosophila.Cell Host Microbe. 2008 Oct 16;4(4):387-397.(#Co-first author）

[43]Lu Jian; Shen Yang; Wu Qingfa; Kumar Supriya; He Bin; Shi Suhua; Carthew Richard; Wang San Ming; Wu Chung-I.The birth and death of microRNA genes in Drosophila. Nature Genetics, 2008 Mar;40(3):351-355. Epub 2008 Feb 17

[44]Wu Qingfa#; Kim Yeong#; Lu Jian; Xuan Zhenyu; Chen Jun; Zheng Yonglan; Zhou Tom; Zhang Michael; Wu Chung-I; Wang San Ming.Poly A- transcripts expressed in HeLa cells. PLoS One. 2008 Jul 30;3(7):e2803.(# Co-first author）

[45]Ge X, Rubinstein WS, Jung YC, Wu Q Genome-wide analysis of antisense transcription with Affymetrix exon array. BMC Genomics. 2008 Jan 22;9:27.

[46]Ge Xijin; Wu Qingfa; Wang San Ming.SAGE detects microRNA precursors.BMC Genomics. 2006 Nov 7;7:285.

[47]Wu, Qingfa; Tommerup, Niels; Ming Wang, San; Hansen, Lars.A novel primate specific gene, CEI, is located in the homeobox gene IRXA2 promoter in Homo sapiens.Gene. 2006 Apr 26;371(2):167-173. Epub 2006 Mar 3.

[48]Ge Xijin; Wu Qingfa; Jung Yong-Chul; Chen Jun; Wang San Ming.A large quantity of novel human antisense transcripts detected by LongSAGE.Bioinformatics. 2006 Oct 15;22(20):2475-2479. Epub 2006 Aug 7.

[49]Ge Xijin; Jung Yong-Chul; Wu Qingfa; Kibbe Warren; Wang San Ming.Annotating nonspecific SAGE tags with microarray data. Genomics. 2006 Jan;87(1):173-180. Epub 2005 Nov 28.

[50]Wang Jing#; Zhang Meng#; Wu Qingfa#; Huang Wei#; Shen Yan#; Yu Jun; Qiang Boqing; Chen Zhu; Yang Huanming. "Beijing Region" (3pter-D3S3397) of the Human Genome: Complete sequence and analysis. Science in China Series C-Life Sciences. 2005, 48(4): 311-329. (#Co-first author)

[51]Wu Qingfa; Niebuhr Erik; Yang Huanming; Hansen Lars. Determination of the 'critical region' for cat-like cry of Cri-du-chat syndrome and analysis of candidate genes by quantitative PCR. Eur J Hum Genet, 2005, 13(4): 475-85.

[52]Yu Jun; Wang Jun; Lin Wei; Li Songgang; Li Heng; Zhou Jun; Ni Peixiang; Dong Wei; Hu Songnian; Zeng Changqing; Zhang Jianguo; Zhang Yong; Li Ruiqiang; Xu Zuyuan; Li Shengting; Li Xianran; Zheng Hongkun; Cong Lijuan; Lin Liang; Yin Jianning; Geng Jianing; Li Guangyuan; Shi Jianping; Liu Juan; Lv Hong; Li Jun; Wang Jing; Deng Yajun; Ran Longhua; Shi Xiaoli; Wang Xiyin; Wu Qingfa; Li Changfeng; Ren Xiaoyu; Wang Jingqiang; Wang Xiaoling; Li Dawei; Liu Dongyuan; Zhang Xiaowei; Ji Zhendong.The Genomes of Oryza sativa: a history of duplications.PLoS Biol. 2005 Feb;3(2):e38. Epub 2005 Feb 1.

[53]Wu Qingfa#; Xu Zuyuan#; Wei Tian; Zeng Haipang; Li Jingxiang; Gang Haixue; Sun Min; Jiang Fangbo; Wang Xiang; Dong Wei; Yang Ling; Wang Jian.Development of Taqman RT-nested PCR system for clinical SARS-CoV detection.Journal of Virological Methods, 2004, 119(1): 17-23.(# Co-first author）

[54]Xia Q, Zhou Z, Lu C, Cheng D, Dai F, Li B, Zhao P, Zha X, Cheng T, Chai C, Pan G, Xu J, Liu C, Lin Y, Qian J, Hou Y, Wu Z, Li G, Pan M, Li C, Shen Y, Lan X, Yuan L, Li T, Xu H, Yang G, Wan Y, Zhu Y, Yu M, Shen W, Wu D, Xiang Z, Yu J, Wang J, Li R, Shi J, Li H, Li G, Su J, Wang X, Li G, Zhang Z, Wu Q, Li J, Zhang Q, Wei N, Xu J, Sun H, Dong L, Liu D, Zhao S, Zhao X, Meng Q, Lan F, Huang X, Li Y, Fang L, Li C, Li D, Sun Y, Zhang Z, Yang Z, Huang Y, Xi Y, Qi Q, He D, Huang H, Zhang X, Wang Z, Li W, Cao Y, Yu Y, Yu H, Li J, Ye J, Chen H, Zhou Y, Liu B, Wang J, Ye J, Ji H, Li S, Ni P, Zhang J, Zhang Y, Zheng H, Mao B, Wang W, Ye C, Li S, Wang J, Wong GK, Yang H; Biology Analysis Group.A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science. 2004 Dec 10;306(5703):1937-40.

[55]International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature. 2004, 431: 931 – 945

[56]Wu Qingfa#; Zhang Yilin#; Lu Hong; Wang Jing; He Ximiao; Liu Yong; Ye Chen; Lin Wei; Hu Jianfei; Ji Jia; Xu Jing; Ye Jie; Hu Yongwu; Chen Wenjun; Li Songgang; Wang Jun; Wang Jian; Bi Shengli; Yang Huanming.The E protein is a multifunctional membrane protein of SARS-CoV. Genomics Proteomics Bioinformatics, 2003, 1(2): 131-144.( #Co-first author）

[57]Bi, Shengli; Qin, E'de; Xu, Zuyuan; Li, Wei; Wang, Jing; Hu, Yongwu; Liu, Yong; Duan, Shumin; Hu, Jianfei; Han, Yujun; Xu, Jing; Li, Yan; Yi, Yao; Zhou, Yongdong; Lin, Wei; Xu, Hong; Li, Ruan; Zhang, Zizhang; Sun, Haiyan; Zhu, Jingui; Yu, Man; Fan, Baochang; Wu, Qingfa; Lin, Wei; Tang, Lin; Yang, Baoan; Li, Guoqing; Peng, Wenming; Li, Wenjie; Jiang, Tao; Deng, Yajun; Liu, Bohua; Shi, Jianping; Deng, Yongqiang; Wei, Wei; Liu, Hong; Tong, Zongzhong; Zhang, Feng; Zhang, Yu; Wang, Cui'e; Li, Yuquan.Complete genome sequences of the SARS-CoV: the BJ Group (Isolates BJ01-BJ04). Genomics Proteomics Bioinformatics, 2003, 1(3): 180-192.

[58]Qin E'de; He Xionglei; Tian Wei; Liu Yong; Li Wei; Wen Jie; Wang Jingqiang; Fan Baochang; Wu Qingfa; Chang Guohui; Cao Wuchun; Xu Zuyuan; Yang Ruifu; Wang Jing; Yu Man; Li Yan; Xu Jing; Si Bingyin; Hu Yongwu; Peng Wenming; Tang Lin; Jiang Tao; Shi Jianping; Ji Jia; Zhang Yu; Ye Jia; Wang Cui'e; Han Yujun; Zhou Jun; Deng Yajun; Li Xiaoyu; Hu Jianfei; Wang Caiping; Yan Chunxia; Zhang Qingrun; Bao Jingyue; Li Guoqing; Chen Weijun; Fang Lin; Li Changfeng; Lei Meng; Li Dawei; Tong Wei; Tian Xiangjun.A genome sequence of novel SARS-CoV isolates: the genotype, GD-Ins29, leads to a hypothesis of viral transmission in South China. Genomics Proteomics Bioinformatics. 2003 ，1(2):101-107.

[59]Ren, Yi; Ding, Hui-guo; Wu, Qing-fa; Chen, Wei-jun; Chen, Dong; Bao, Zhi-ying; Yang, Ling; Zhao, Chun-hui; Wang, Jian。[Detection of SARS-CoV RNA in stool samples of SARS patients by nest RT-PCR and its clinical value].Acta Academiae Medicinae Sinicae, 2003, 25(3): 368-371. 

[60]Wu Q, Dong W, Qi X, Bao W, Niu Y, Zhang Y, Zhang H, Chen C, Liu B, Hu S, Wang J, Yang H. Genomic Structure of Metabotropic glutamate receptor 7 and comparison of genomic structures of extracellular domains of mGluR family. Chinese Science Bulletin. 2002, 47:508-515

[61]International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. 2001, 409: 860-921

发表中文论文

[1]付亚亭, 郭冬阳, 吴清发. 组织蛋白酶D有助于SRBSDV在白背飞虱体内复制[J]. 生物学杂志, 2023, 40 (05): 20-23.

[2]席志崇, 王帅利, 赵开亮, 李龙龙, 胡孔旺, 吴清发. 人CD48亚型特异性抗体的鉴定及其表征分析[J]. 基因组学与应用生物学, 2023, 42 (07): 757-766.

[3]吴梦, 齐水水, 徐雯, 吴清发. 果蝇原肌球蛋白2抗果蝇C病毒作用研究[J]. 基因组学与应用生物学, 2022, 41 (Z2): 2089-2098.

[4]胡孔旺, 王宜文, 陆明, 李龙龙, 吴清发, 李昊. 循环肿瘤细胞检测在胃癌新辅助化疗决策中的应用[J]. 肿瘤, 2018, 38 (12): 1130-1136+1154. 

[5]动物遗传学-吴清发-果蝇RNA沉默免疫机制研究 张琪; 韩艳红; 齐水水; 张耀; 丁守伟; 吴清发 中国遗传学会第九次全国会员代表大会暨学术研讨会论文摘要汇编（2009-2013） 2013-09-18

[6]家蚕(Bombyx mori)全基因组框架图 夏庆友; 周泽扬; 鲁成; 程道军; 代方银; 李斌; 赵萍; 查幸福; 程廷才; 柴春利; 潘国庆; 许金山; 刘春; 林英; 钱吉凤; 侯勇; 吴正理; 李关荣; 潘敏慧; 李春峰; 沈以红; 蓝希钳; 袁联伟; 李田; 徐汉福; 杨光伟; 万永继; 朱勇; 余茂德; 沈卫德; 吴大洋; 向仲怀; 于军; 王俊; 李瑞强; 石剑萍; 李恒; 李光远; 苏建宁; 王晓玲; 李国庆; 张增金; 吴清发; 李俊; 张庆鹏; 韦宁; 徐建哲; 孙海波; 董乐; 刘东源; 赵胜利; 赵晓兰; 孟庆顺; 兰锋镝; 黄显刚; 李源哲; 方林; 李昌锋; 李大为; 孙永巧; 张振鹏; 杨峥; 黄艳清; 奚艳; 亓秋辉; 贺丹丹; 黄海燕; 张晓伟; 王智强; 李文杰; 曹玉竹; 余迎朴; 俞鸿; 李金宏; 叶杰华; 陈欢; 周雁; 刘斌; 王晶; 叶葭; 纪海; 李胜霆; 倪培相; 张建国; 张勇; 郑洪坤; 毛炳宇; 王文; 叶辰; 李松岗; 汪建; Gane Ka-Shu Wong; 杨焕明 蚕学通讯 2008-12-15

[7]空气和空调器样本中SARS冠状病毒的检测 杜宗敏; 王效义; 戴二黑; 刘海洪; 韩延平; 庞昕; 翟俊辉; 杨瑞馥; 吴清发; 李京湘; 杨玲; 汪建 中国消毒学杂志 2005-06-15

[8]逆转录套式PCR检测粪便样本中的SARS冠状病毒 戴二黑; 李京湘; 杜宗敏; 吴清发; 王效义; 杨玲; 刘海洪; 庞昕; 韩延平; 翟俊辉; 江凌晓; 陈泽良; 邱茂锋; 王津; 王宏霞; 郭兆彪; 汪建; 杨瑞馥 微生物学免疫学进展 2004-12-20

[9]应用套式RT-PCR检测SARS患者血液样品中SARS冠状病毒 王效义; 戴二黑; 杜宗敏; 刘海洪; 韩延平; 庞昕; 翟俊辉; 江凌晓; 陈泽良; 邱茂峰; 王津; 王宏霞; 郭兆彪; 杨瑞馥; 吴清发; 李京湘; 杨玲; 汪建 生物技术通讯 2004-10-30

[10]人类基因组3pter-p26区域的序列比较分析 罗春清; 李彦; 张晓伟; 张以琳; 张海青; 陈冲; 吴清发; 徐祖元; 崔鹏; 胡松年; 王俊; 杨焕明; 董伟 中国科学(C辑:生命科学) 2004-08-20

[11]传染性非典型肺炎患者不同病程粪便标本中SARS-CoV的分离与鉴定 田薇; 邓亚军; 吴清发; 王绪敏; 杨玲; 张峰; 刘晨辉; 包其郁; 汪建; 杨焕明; 刘明旭 世界华人消化杂志 2004-05-15

[12]RT-PCR测定SARS患者粪便及漱口液中SARS CoV RNA及其临床意义 任翊; 丁惠国; 吴清发; 陈唯军; 陈东; 任珍; 杨玲; 赵春惠; 汪健 中华微生物学和免疫学杂志 2003-12-30

[13]SARS相关病毒(BJ01株)的全序列及其比较分析 秦鄂德; 祝庆余; 于曼; 范宝昌; 常国辉; 司炳银; 杨保安; 彭文明; 姜涛; 刘伯华; 邓永强; 刘洪; 张雨; 王翠娥; 李豫川; 甘永华; 李晓萸; 吕富双; 谭刚; 曹务春; 杨瑞馥; 汪建; 李蔚; 徐祖元; 李彦; 吴清发; 林伟; 陈维军; 唐琳; 邓亚军; 韩玉军; 李昌峰; 雷蒙; 李国庆; 李文杰; 吕宏; 石建萍; 童宗中; 张峰; 李松岗; 刘斌; 刘斯奇; 董伟; 王俊; 黄家树; 于军; 杨焕明 科学通报 2003-06-15

[14]AKINYEMI A. Ibukun; 齐水水; 常朝霞; 吴清发*.利用高通量测序在草莓中发现马铃薯X病毒属的新成员SMYEaV1.中国科技论文在线. 

[15]齐水水; 姜冬梅; 祝鹏飞; AKINYEMI A. Ibukun; 李世访; 吴清发*.利用小RNA深度测序鉴定锦紫苏类病毒.中国科技论文在线.

荣誉奖励：

资料更新中……

 

我科学家首次发现苹果中具有核酶活性的环状rna 

本报讯近日，中国农业科学院植物保护研究所研究员李世访研究团队与中国科学技术大学吴清发教授研究团队合作，在世界上首次发现苹果中存在具有核酶活性的环状rna。

上世纪80年代，在研究苹果上一种危害严重的病害——苹果锈果病时，中国农业科学院兴城果树研究所的果树病毒专家刘福昌研究员和日本果树病毒专家小金泽硕城均从苹果中分离到一种特殊环状rna。但是，限于检测及分析技术的限制，一直未能揭示出它的真面目。

2012年，在一次国际会议中，李世访结识了专门从事生物信息学研究的吴清发，并决定共同探究苹果中环状rna的真面目。

研究团队采用了高通量测序（ngs）技术结合生物信息学分析的策略。他们重新编译了pfor2程序，其运行速度比pfor提高了3~8倍，从而能够处理高通量测序获得的大量数据。通过对含有环状rna的苹果锈果样品进行高通量测序，经过几个月的摸索和反复验证，终于拿到了该环状rna的全序列。

序列分析发现，该环状rna由434个核苷酸组成，是一种迄今为止从未见过报道的新的环状rna。自中国报道后，美国、意大利等国研究人员的检测结果也为此提供了有力的佐证。有意思的是，生化实验表明，该环状rna正、负链均具有核酶活性，能够进行自我剪切。该研究为今后从植物和动物中发现更多环状rna提供了新的思路和技术手段。

来源：中国科学报 2015-01-14 06:45

2014.12.12，我院吴清发教授研究组在PLoS Pathogens上在线发表论文

2014.12.12，我院吴清发教授研究组在PLoS Pathogens上在线发表题为：“Discovery of Replicating Circular RNAs by RNA-Seq and Computational Algorithms”的论文，PLoS Pathog 10(12): e1004553.

作者： Zhixiang Zhang, Shuishui Qi, Nan Tang, Xinxin Zhang, Shanshan Chen, Pengfei Zhu, Lin Ma,Jinping Cheng, Yun Xu, Meiguang Lu, Hongqing Wang, Shou-Wei Ding, Shifang Li, Qingfa Wu

Abstract:

Replicating circular RNAs are independent plant pathogens known as viroids, or act to modulate the pathogenesis of plant and animal viruses as their satellite RNAs. The rate of discovery of these subviral pathogens was low over the past 40 years because the classical approaches are technical demanding and time-consuming. We previously described an approach for homology-independent discovery of replicating circular RNAs by analysing the total small RNA populations from samples of diseased tissues with a computational program known as progressive filtering of overlapping small RNAs (PFOR). However, PFOR written in PERL language is extremely slow and is unable to discover those subviral pathogens that do not trigger in vivo accumulation of extensively overlapping small RNAs. Moreover, PFOR is yet to identify a new viroid capable of initiating independent infection. Here we report the development of PFOR2 that adopted parallel programming in the C++ language and was 3 to 8 times faster than PFOR. A new computational program was further developed and incorporated into PFOR2 to allow the identification of circular RNAs by deep sequencing of long RNAs instead of small RNAs. PFOR2 analysis of the small RNA libraries from grapevine and apple plants led to the discovery of Grapevine latent viroid (GLVd) and Apple hammerhead viroid-like RNA (AHVd-like RNA), respectively. GLVd was proposed as a new species in the genus Apscaviroid, because it contained the typical structural elements found in this group of viroids and initiated independent infection in grapevine seedlings. AHVd-like RNA encoded a biologically active hammerhead ribozyme in both polarities, and was not specifically associated with any of the viruses found in apple plants. We propose that these computational algorithms have the potential to discover novel circular RNAs in plants, invertebrates and vertebrates regardless of whether they replicate and/or induce the in vivo accumulation of small RNAs.

来源：中国科技大学生命科学学院 2015-03-15