吳清發，中國科學技術大學生命科學學院教授，博士生導師。主要從事基因組和轉錄組學數據分析以及RNA沉默抗病毒機制研究、非編碼RNA的簽定和功能分析。

教育及工作經歷：

1999年開始在中國科學院遺傳與發育生物學研究所/北京基因組研究所攻讀博士學位，作為技術骨干參與“人類基因組計劃中國部分”的序列解析和數據分析工作。期間作為交流博士生，在丹麥哥本哈根大學Panum醫學院功能基因組中心從事人類疾病基因的定位克隆工作。

2004年4月到2006年10月，在美國西北大學從事博士后研究, 主要進行人造血干細胞轉錄譜的研究工作。

2006年10月-2010年10月，在美國加州大學河濱分校從事病毒和宿主相互作用的系統生物學研究工作。

2010年10月起任中國科學技術大學生命科學學院教授。

學術兼職：

1、中國細胞生物學學會會員。 

研究方向：

論文專著： 

[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

發表中文論文

[1]付亞亭, 郭冬陽, 吳清發. 組織蛋白酶D有助于SRBSDV在白背飛虱體內復制[J]. 生物學雜志, 2023, 40 (05): 20-23.

[2]席志崇, 王帥利, 趙開亮, 李龍龍, 胡孔旺, 吳清發. 人CD48亞型特異性抗體的鑒定及其表征分析[J]. 基因組學與應用生物學, 2023, 42 (07): 757-766.

[3]吳夢, 齊水水, 徐雯, 吳清發. 果蠅原肌球蛋白2抗果蠅C病毒作用研究[J]. 基因組學與應用生物學, 2022, 41 (Z2): 2089-2098.

[4]胡孔旺, 王宜文, 陸明, 李龍龍, 吳清發, 李昊. 循環腫瘤細胞檢測在胃癌新輔助化療決策中的應用[J]. 腫瘤, 2018, 38 (12): 1130-1136+1154. 

[5]動物遺傳學-吳清發-果蠅RNA沉默免疫機制研究 張琪; 韓艷紅; 齊水水; 張耀; 丁守偉; 吳清發 中國遺傳學會第九次全國會員代表大會暨學術研討會論文摘要匯編（2009-2013） 2013-09-18

[6]家蠶(Bombyx mori)全基因組框架圖 夏慶友; 周澤揚; 魯成; 程道軍; 代方銀; 李斌; 趙萍; 查幸福; 程廷才; 柴春利; 潘國慶; 許金山; 劉春; 林英; 錢吉鳳; 侯勇; 吳正理; 李關榮; 潘敏慧; 李春峰; 沈以紅; 藍希鉗; 袁聯偉; 李田; 徐漢福; 楊光偉; 萬永繼; 朱勇; 余茂德; 沈衛德; 吳大洋; 向仲懷; 于軍; 王俊; 李瑞強; 石劍萍; 李恒; 李光遠; 蘇建寧; 王曉玲; 李國慶; 張增金; 吳清發; 李俊; 張慶鵬; 韋寧; 徐建哲; 孫海波; 董樂; 劉東源; 趙勝利; 趙曉蘭; 孟慶順; 蘭鋒鏑; 黃顯剛; 李源哲; 方林; 李昌鋒; 李大為; 孫永巧; 張振鵬; 楊崢; 黃艷清; 奚艷; 亓秋輝; 賀丹丹; 黃海燕; 張曉偉; 王智強; 李文杰; 曹玉竹; 余迎樸; 俞鴻; 李金宏; 葉杰華; 陳歡; 周雁; 劉斌; 王晶; 葉葭; 紀海; 李勝霆; 倪培相; 張建國; 張勇; 鄭洪坤; 毛炳宇; 王文; 葉辰; 李松崗; 汪建; Gane Ka-Shu Wong; 楊煥明 蠶學通訊 2008-12-15

[7]空氣和空調器樣本中SARS冠狀病毒的檢測 杜宗敏; 王效義; 戴二黑; 劉海洪; 韓延平; 龐昕; 翟俊輝; 楊瑞馥; 吳清發; 李京湘; 楊玲; 汪建 中國消毒學雜志 2005-06-15

[8]逆轉錄套式PCR檢測糞便樣本中的SARS冠狀病毒 戴二黑; 李京湘; 杜宗敏; 吳清發; 王效義; 楊玲; 劉海洪; 龐昕; 韓延平; 翟俊輝; 江凌曉; 陳澤良; 邱茂鋒; 王津; 王宏霞; 郭兆彪; 汪建; 楊瑞馥 微生物學免疫學進展 2004-12-20

[9]應用套式RT-PCR檢測SARS患者血液樣品中SARS冠狀病毒 王效義; 戴二黑; 杜宗敏; 劉海洪; 韓延平; 龐昕; 翟俊輝; 江凌曉; 陳澤良; 邱茂峰; 王津; 王宏霞; 郭兆彪; 楊瑞馥; 吳清發; 李京湘; 楊玲; 汪建 生物技術通訊 2004-10-30

[10]人類基因組3pter-p26區域的序列比較分析 羅春清; 李彥; 張曉偉; 張以琳; 張海青; 陳沖; 吳清發; 徐祖元; 崔鵬; 胡松年; 王俊; 楊煥明; 董偉 中國科學(C輯:生命科學) 2004-08-20

[11]傳染性非典型肺炎患者不同病程糞便標本中SARS-CoV的分離與鑒定 田薇; 鄧亞軍; 吳清發; 王緒敏; 楊玲; 張峰; 劉晨輝; 包其郁; 汪建; 楊煥明; 劉明旭 世界華人消化雜志 2004-05-15

[12]RT-PCR測定SARS患者糞便及漱口液中SARS CoV RNA及其臨床意義 任翊; 丁惠國; 吳清發; 陳唯軍; 陳東; 任珍; 楊玲; 趙春惠; 汪健 中華微生物學和免疫學雜志 2003-12-30

[13]SARS相關病毒(BJ01株)的全序列及其比較分析 秦鄂德; 祝慶余; 于曼; 范寶昌; 常國輝; 司炳銀; 楊保安; 彭文明; 姜濤; 劉伯華; 鄧永強; 劉洪; 張雨; 王翠娥; 李豫川; 甘永華; 李曉萸; 呂富雙; 譚剛; 曹務春; 楊瑞馥; 汪建; 李蔚; 徐祖元; 李彥; 吳清發; 林偉; 陳維軍; 唐琳; 鄧亞軍; 韓玉軍; 李昌峰; 雷蒙; 李國慶; 李文杰; 呂宏; 石建萍; 童宗中; 張峰; 李松崗; 劉斌; 劉斯奇; 董偉; 王俊; 黃家樹; 于軍; 楊煥明 科學通報 2003-06-15

[14]AKINYEMI A. Ibukun; 齊水水; 常朝霞; 吳清發*.利用高通量測序在草莓中發現馬鈴薯X病毒屬的新成員SMYEaV1.中國科技論文在線. 

[15]齊水水; 姜冬梅; 祝鵬飛; AKINYEMI A. Ibukun; 李世訪; 吳清發*.利用小RNA深度測序鑒定錦紫蘇類病毒.中國科技論文在線.

榮譽獎勵：

資料更新中……

 

我科學家首次發現蘋果中具有核酶活性的環狀rna 

本報訊近日，中國農業科學院植物保護研究所研究員李世訪研究團隊與中國科學技術大學吳清發教授研究團隊合作，在世界上首次發現蘋果中存在具有核酶活性的環狀rna。

上世紀80年代，在研究蘋果上一種危害嚴重的病害——蘋果銹果病時，中國農業科學院興城果樹研究所的果樹病毒專家劉福昌研究員和日本果樹病毒專家小金澤碩城均從蘋果中分離到一種特殊環狀rna。但是，限于檢測及分析技術的限制，一直未能揭示出它的真面目。

2012年，在一次國際會議中，李世訪結識了專門從事生物信息學研究的吳清發，并決定共同探究蘋果中環狀rna的真面目。

研究團隊采用了高通量測序（ngs）技術結合生物信息學分析的策略。他們重新編譯了pfor2程序，其運行速度比pfor提高了3~8倍，從而能夠處理高通量測序獲得的大量數據。通過對含有環狀rna的蘋果銹果樣品進行高通量測序，經過幾個月的摸索和反復驗證，終于拿到了該環狀rna的全序列。

序列分析發現，該環狀rna由434個核苷酸組成，是一種迄今為止從未見過報道的新的環狀rna。自中國報道后，美國、意大利等國研究人員的檢測結果也為此提供了有力的佐證。有意思的是，生化實驗表明，該環狀rna正、負鏈均具有核酶活性，能夠進行自我剪切。該研究為今后從植物和動物中發現更多環狀rna提供了新的思路和技術手段。

來源：中國科學報 2015-01-14 06:45

2014.12.12，我院吳清發教授研究組在PLoS Pathogens上在線發表論文

2014.12.12，我院吳清發教授研究組在PLoS Pathogens上在線發表題為：“Discovery of Replicating Circular RNAs by RNA-Seq and Computational Algorithms”的論文，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.

來源：中國科技大學生命科學學院 2015-03-15