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教授 博导 院长
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履历

1.   2012/09 - 至今,  厦门大学,环境与生态学院院长,教授

2.   2010/07 - 2015/06,美国迈阿密大学,植物学系(后为生物学系),教授

3.   2007/07 - 2010/06,美国迈阿密大学,植物学系,副教授(Tenured)

4.   2001/08 - 2007/06,美国迈阿密大学,植物学系,助理教授

5.   1996/09 - 2001/07,美国肯塔基大学,烟草研发中心,研究员

6.   1989/12 - 1991/09,厦门大学,生物系,讲师

7.   1986/09 - 1988/11,厦门大学,生物系,助教

8.   1995/10 - 1996/09,美国肯塔基大学,植物生理/分子生物学,博士后,导师:Arthur G. Hunt

9.   1991/09 - 1995/09,美国肯塔基大学,植物分子生物学/生物化学,哲学博士,导师:Arthur G. Hunt

10. 1983/09 - 1986/09,厦门大学,生化遗传,理学硕士,导师:黄厚哲

11. 1979/09 - 1983/07,厦门大学,植物学,理学学士

研究方向

植物mRNA多聚腺苷化的分子生物学;
红树植物环境适应性的分子生态学;
生物信息学
Plant mRNA Polyadenylation;
Molecular Ecology of Mangrove Adaption;
Bioinformatics

代表性论文

环境适应性及分子生态学研究:

1.    Junjie Yin, Ming Zhou, Zeru Lin, Qingshun Q. Li, Yuan-Ye Zhang*. 2019. Transgenerational effects benefit offspring across diverse environments: a meta‐analysis in plants and animals. Ecology Letters, 22: 1976–1986. https://doi.org/10.1111/ele.13373

2.    Hongmei Qiao, Wenwen Liu, Yihui Zhang*, Yuanye Zhang*, Qingshun Q. Li*.2019. Genetic admixture accelerates invasion via provisioning rapid adaptive evolution, Molecular Ecology. 28:4012-4027. https://doi.org/10.1111/mec.15192

3.    Wenyue Su, Congting Ye, Yihui Zhang, Saiqi Hao, Qingshun Q. Li*.2019. Identification of putative key genes for coastal environments and cold adaptation in mangrove Kandelia obovatathrough transcriptome analysis. Science of the Total Environment. 681:191–201. DOI: 10.1016/j.scitotenv.2019.05.127

4.    Liwei Hong, Wenyue Su, Yuanye Zhang, Congting Ye, Yingjia Shen, Qingshun Q. Li*. 2018. Transcriptome profiling during mangrove viviparity in response to abscisic acid. Scientific Reports, 8:770. DOI:10.1038/s41598-018-19236-x.

5.    Liwei Hong, Liangjie Zhang, Meiling Liu, Shengjie Wang, Linjun He, Wanyu Yang, Jingli Li, Qiaojie Yu, Qingshun Q. Li* & Kefu Zhou*. 2018. Heavy metal rich stone-processing wastewater inhibits the growth and development of plants.International Journal of Phytoremediation. 21:5, 479-486, DOI: 10.1080/15226514.2018.1537241

6.    Neza Repar, Hao Li, Jose S. Aguilar, Qingshun Q. Li, Drobne Damjana, and Yiling Hong*. 2018. Silver nanoparticles induce neurotoxicity in a human embryonic stem cell-derived neuron and astrocyte network. Nanotoxicology, 12:104-116.  DOI: 10.1080/17435390.2018.1425497

7.    Luzhen Chen*, Wenqing Wang, Qingshun Q. Li, Yihui Zhang, Shengchang Yang, Michael J. Osland, Jinliang Huang, and Congjiao Peng. 2017. Mangrove species’ responses to winter air temperature extremes in China.Ecosphere, 8(6): e01865. DOI: 10.1002/ecs2.1865

8.    Xiao-xuan Zhou, Ling-ling Cai, Mei-ping Fu, Li-wei Hong, Ying-jia Shen, Qingshun Q. Li*, 2016. Progress in the Studies of Vivipary on Mangrove Plants. Chinese Journal of Plant Ecology 40(12):1328-1343. 周晓旋, 蔡玲玲, 傅梅萍, 洪礼伟,  沈英嘉,李庆顺*. 2016. 红树植物胎生现象研究进展, 植物生态学报, 40(12):1328-1343. (In Chinese with English abstract) Doi:10.17521/cjpe.2016.0087.

 

mRNA多聚腺苷化机理机制与生物信息学研究:

9.    Zhibo Yu, Juncheng Lin, Qingshun Q. Li*. 2019. Transcriptome analyses of FY mutants reveal its role in mRNA alternative polyadenylation. The Plant Cell. 31(10):2332-2352. https://doi.org/10.1105/tpc.18.00545

10.  Haihui Fu, Peng Wang, Xiaohui Wu, Xiaoxuan Zhou, Guoli Ji, Yingjia Shen, Yahui Gao, Qingshun Q. Li*, Junrong Liang*. 2019. Distinct genome‐wide alternative polyadenylation during the response to silicon availability in the marine diatom Thalassiosira pseudonana. The Plant Journal. 99(1):67-80. DOI: 10.1111/tpj.14309

11.  Congting Ye, Qian Zhou, Xiaohui Wu, Guoli Ji, Qingshun Q. Li. 2019. Genome-wide alternative polyadenylation dynamics in response to biotic and abiotic stresses in rice. Ecotoxicology and Environmental Safety.183:109485. DOI: 10.1016/j.ecoenv.2019.109485.

12.  Congting Ye, Qian Zhou, Xiaohui Wu, Chen Yu, Guoli Ji, Daniel R Saban, Qingshun Q. Li. 2019. scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data. Bioinformatics. https://doi.org/10.1093/bioinformatics/btz701

13.  Congting Ye, Qian Zhou, Yiling Hong, Qingshun Q. Li. 2019.Role of alternative polyadenylation dynamics in acute myeloid leukaemia at single-cell resolution. RNA Biology. 16:6, 785-797. DOI: 10.1080/15476286.2019.1586139

14.  Qian Zhou, Haihui Fu, Dewei Yang, Congting Ye, Sheng Zhu, Juncheng Lin, Wenbin Ye, Guoli Ji, Xinfu Ye, Xiaohui Wu*, Qingshun Q. Li*. 2019. Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies, japonica and indica. The Plant Journal. 98,260-276. https://doi.org/10.1111/tpj.14209.

15.  Jingyi Cao, Congting Ye, Guijie Hao, Carole Dabney-Smith, Arthur G. Hunt, Qingshun Q. Li*. 2019. Root hair single cell type specific profiles of gene expression and alternative polyadenylation under cadmium stress. Frontiers in Plant Science.https://doi.org/10.3389/fpls.2019.00589

16.  Zhixin Zhao, Xiaohui Wu, Guoli Ji, Chun Liang, Qingshun Q. Li*. 2019. Genome-wide comparative analyses of polyadenylation signals in eukaryotes suggest a possible origin of the AAUAAA signal. International Journal of Molecular Sciences. 20(4): 958. Doi: 10.3390/ijms20040958.

17.  Congting Ye, Yuqi Long, Guoli Ji, Qingshun Q. Li*, Xiaohui Wu*. 2018. APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data. Bioinformatics, 34(11):1841-1849. DOI:10.1093/bioinformatics/bty029

18.  Liwei Hong, Congting Ye, Juncheng Lin, Haihui Fu, Xiaohui Wu and Qingshun Q. Li*. 2018. Alternative polyadenylation is involved in auxin-based plant growth and development. Plant Journal, 93:246-258. doi: 10.1111/tpj.13771.

19.  Juncheng Lin, Ruqiang Xu, Xiaohui Wu, Yingjia Shen and Qingshun Q. Li*. 2017. Role of cleavage and polyadenylation specificity factor 100: anchoring poly(A) sites and modulating transcription termination. Plant Journal, 91:829–839. DOI: 10.1111/tpj.13611

20.  Cheng Guo, Matthew Spinelli, Congting Ye, Qingshun Q. Li* and Chun Liang*. 2017. Genome-Wide Comparative Analysis of Miniature Inverted Repeat Transposable Element in 19 Arabidopsis thaliana Accessions. Scientific Reports, 7:2634. DOI: 10.1038/s41598-017-02855-1.

21.  Qingshun Q. Li*, Zhaoyang Liu, Wenjia Lu and Man Liu.  2017. Interplay between Alternative Splicing and Alternative Polyadenylation Defines the Expression Outcome of the Plant Unique OXIDATIVE TOLERANT-6 Gene. Scientific Reports, 7:2052. DOI: 10.1038/s41598-017-02215-z

22.  Haihui Fu, Dewei Yang, Wenyue Su, Liuyin Ma, Yingjia Shen, Guoli Ji, Xinfu Ye*, Xiaohui Wu*, Qingshun Q. Li*. 2016. Genome-wide Dynamics of Alternative Polyadenylation in Rice. Genome Research, 26: 1753-1760. Doi:10.1101/gr.210757.116

23.  Xiaohui Wu*, Yumin Zhang, Qingshun Q. Li *. 2016. PlantAPA: a portal for visualization and analysis of alternative polyadenylation in plants.  Frontiers in Plant Science, 7:889. doi: 10.3389/fpls.2016.00889.

24.  Cheng Guo, Matthew Spinelli, Man Liu, Qingshun Q. Li * and Chun Liang*. 2016. A Genome-wide Study of "Non-3UTR" Polyadenylation Sites in Arabidopsis thaliana.  Scientific Report, 6:28060; doi: 10.1038/srep28060 (2016).

25.  Xiaohui Wu*, Yong Zeng, Jinting Guan, Guoli, Ji, Rongting Huang, Qingshun Q. Li*. 2015. Genome-wide Characterization of Intergenic Polyadenylation Sites Redefines Gene Spaces in Arabidopsis thaliana. BMC Genomics. 16:511. DOI: 10.1186/s12864-015-1691-1

26.  Guoli Ji, Jinting Guan, Yong Zeng, Qingshun Q. Li and Xiaohui Wu*. 2015. Genome-wide identification and predictive modeling of polyadenylation sites in eukaryotes. Briefings in Bioinformatics. 16(2): 304-313. DOI: 10.1093/bib/bbu011

27.  Guoli Ji, Lei Li, Qingshun Q. Li, Xiangdong Wu, Jingyi Fu, Xiaohui Wu*. 2015. PASPA: a web server for mRNA poly(A) site predictions in plants and algae. Bioinformatics,31(10): 1671-3. doi:10.1093/bioinformatics/btv004.

28.  Jinting Guan, Jingyi Fu, Mingcheng Wu, Longteng Chen, Guoli Ji, Qingshun Q. Li, Xiaohui Wu*. 2015. VAAPA: A web platform for visualization and analysis of alternative polyadenylation. Comput Biol Med. 57:20-25. doi: 10.1016/j.compbiomed.2014.11.010

29.  Man Liu, Ruqiang Xu, Carrie Merrill, Liwei Hong, Carol Von Lanken, Arthur G. Hunt* and Qingshun Q. Li*. 2014. Integration of developmental and environmental signals via a polyadenylation factor in plants. PloS One. 9: e115779. doi:10.1371/journal.pone.0115779.

30.  Xiaohui Wu, Bobby Gaffney, Arthur G. Hunt*, and Qingshun Q. Li*. 2014. Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. BMC Genomics. 15:615. DOI: 10.1186/1471-2164-15-615.

31.  Zhixin Zhao, Xiaohui Wu, Praveen Kumar Raj Kumar, Min Dong, Guoli Ji, Qingshun Q. Li* and Chun Liang*. 2014. Bioinformatics analysis of alternative polyadenylation in green alga Chlamydomonas reinhardtii using transcriptome sequences from three different sequencing platforms. Genes Genomics Genetics (G3).4:871-883. DOI: 10.1534/g3.114.010249

32.  Liuyin Ma, Pratap Kumar Pati, Man Liu, Qingshun Q. Li* and Arthur G. Hunt*. 2014. High throughput characterizations of poly(A) site choice in plants. Methods. 67:74-83. http://dx.doi.org/10.1016/j.ymeth.2013.06.037

33.  Liuyin Ma, Cheng Guo and Qingsun Q. Li*. 2014. Role of alternative polyadenylation in epigenetic silencing and antisilencing. Proc. Nat. Acad. Sci. USA, 111:9-10. DOI: 10.1073/pnas.1321025111

34.  William C Ray*, Samuel L Wolock, Nicholas W Callahan, Min Dong, Qingshun Q. Li, Chun Liang, Thomas J. Magliery and Christopher W. Bartlett. 2014. Addressing the unmet need for visualizing Conditional Random Fields in Biological Data. BMC Bioinformatics. 15:202.

35.  Guoli Ji*, Yong Zeng, Jinting Guan, Qingshun Q. Li, Congting Ye, Yunlong Liu. 2013. Recent advances in mathematical modeling and simulation of DNA replication process. Current Bioinformatics. 8:591-602. DOI: 10.2174/15748936113088880005

36.  Denghui Xing, Yajun Wang, Ruqiang Xu, Xinfu Ye, Dewei Yang, Qingshun Q. Li*. 2013. The Regulatory Role of Pcf11-Similar-4 (PCFS4) in Arabidopsis Development by Genome-Wide Physical Interactions with Target Loci. BMC Genomics. 14:598. DOI:10.1186/1471-2164-14-598

37.  Patrick E. Thomas, Xiaohui Wu, Man Liu, Bobby Gaffney, Guoli Ji, Qingshun Q. Li and Arthur G. Hunt*. 2012. Genome-wide control of poly(A) site choice by CPSF30 in Arabidopsis. Plant Cell. 24: 4376-4388. DOI:10.1105/tpc.112.096107

38.  Arthur G. Hunt, Denghui Xing*, Qingshun Q. Li*. 2012. Plant polyadenylation factors: conservation and variety. BMC Genomics. 13:641. DOI: 10.1186/1471-2164-13-641

39.  Xiaohui Wu, Guoli Ji*, Qingshun Q. Li and Sun Zhou. 2012. Comprehensive recognition of messenger RNA polyadenylation patterns in plants. Afr. J. Biotech, 11:3215-3234. DOI: 10.5897/AJB10.2539

40.  Hongwei Zhao, Jun Zheng, Qingshun Q. Li*. 2011. A novel plantin vitro assay system for pre-mRNA cleavage and polyadenylation. Plant Physiology, 157:1546-1554. DOI: 10.1104/pp.111.179465

41.  Yingjia Shen, R. C. Venu, Kan Nobuta, Xiaohui Wu, Varun Notibula, Caghan Demirci, Blake C Meyers, Guo-Liang Wang, Guoli Ji, Qingshun Q. Li*. 2011. Transcriptome Dynamics Through Alternative Polyadenylation in Developmental and Environmental Responses in Plants Revealed by Deep Sequencing. Genome Research, 21:1478-1486. DOI: 10.1101/gr.114744.110

42.  Xiaohui Wu, Man Liu, Bruce Downie, Chun Liang, Guoli Ji, Qingshun Q. Li*, Arthur Hunt*. 2011. The genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. Proc. Nat. Acad. Sci. USA, 108:12533–12538. doi/10.1073/pnas.1019732108

43.  Jianti Zheng, Denghui Xing, Xiaohui Wu, Diana Kroll, Yingjia Shen, Guoli Ji, Qingshun Q. Li*. 2011. Ratio-based analysis of differential mRNA processing and expression of a polyadenylation factor mutant pcfs4using Arabidopsis tiling microarray. PLoS One, 6:e14719. DOI: 10.1371/journal.pone.0014719

44.  Denghui Xing, Qingshun Q. Li*. 2011. Alternative polyadenylation and gene expression regulation in plants. WIREs (Willey Interdisciplinary Reviews) RNA, 2:445-458. (Invited review) DOI: 10.1002/wrna.59

45.  Guoli Ji, Xiaohui Wu, Yingjia Shen, Jiangyin Huang and Qingshun Q. Li*. 2010. A Classification-Based Prediction Models of Messenger RNA Polyadenylation Sites.  Journal of Theoretical Biology, 265:287-296. DOI: 10.1016/j.jtbi.2010.05.015

46.  Guoli Ji*, Xiaohui Wu, Jiangyin Huang, Qingshun Q. Li. 2010. Implementation of a Classification-Based Prediction Model for Plant mRNA Poly(A) Sites. Journal of Computational and Theoretical Nanoscience, 7(5):927-932. DOI: 10.1166/jctn.2010.1440

47.  Hongwei Zhao, Denghui Xing, Qingshun Q. Li*.  2009. Unique features of plant cleavage and polyadenylation specificity factor revealed by proteomic studies. Plant Physiology, 151:1546-1556. DOI: 10.1104/pp.109.142729

48.  Denghui Xing, Hongwei Zhao and Qingshun Q. Li*. 2008. Arabidopsis CLP1-Similar Protein3, an ortholog of human polyadenylation factor CLP1, functions in gametophyte, embryo and post-embryonic development. Plant Physiology, 148:2059-2069. doi/10.1104/pp.108.129817

49.  Yingjia Shen, Yuansheng Liu, Lin Liu, Chun Liang, and Qingshun Q. Li*. 2008. Unique features of nuclear mRNA poly(A) signals and alternative polyadenylation in Chlamydomonas reinhardtii. Genetics,179:167-176. DOI: 10.1534/genetics.108.088971

50.  Denghui Xing, Hongwei Zhao, Ruqiang Xu and Qingshun Q. Li*. 2008. Arabidopsis PCFS4, a homologue of yeast polyadenylation factor Pcf11p, regulates FCA alternative processing and promotes flowering time. Plant Journal, 54:899-910. DOI: 10.1111/j.1365-313X.2008.03455.x

51.  Arthur G. Hunt*, Ruqiang Xu, Balasubrahmanyam Addepalli, Suryadevara Rao, Kevin P. Forbes, Lisa R. Meeks, Denghui Xing, Min Mo, Hongwei Zhao, Amrita Bandyopadhyay, Lavanya Dampanaboina, Amanda Marion, Carol Von Lanken, and Qingshun Q. Li*. 2008. Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling. BMC Genomics, 9:220. DOI: 10.1186/1471-2164-9-220 Highly Accessed

52.  Yingjia Shen, Guoli Ji, Brian J. Haas, Xiaohui Wu, Jianti Zheng, Greg J. Reese, and Qingshun Q. Li*. 2008. Genome level analysis of rice mRNA 3’-end processing signals and alternative polyadenylation. Nucleic Acids Research, 36:3150-3161. DOI: 10.1093/nar/gkn158

53.  Jingxian Zhang, Kil-Young Yun, Ruqiang Xu, Arthur G. Hunt, Irina Artiushin, Kim Delaney, Qingshun Q. Li and Deane L. Falcone*.  2008. A Polyadenylation Factor Subunit Implicated in Regulating Oxidative Signaling in Arabidopsis thaliana. PLoS One, 3:e2410. DOI: 10.1371/journal.pone.0002410

54.  Chun Liang*, Yuansheng Liu, Lin Liu, Adam C. Davis, Yingjia Shen, and Qingshun Q. Li. 2008. Expressed sequence tags with cDNA termini – previously overlooked resources for gene annotation and transcriptome exploration in Chlamydomonas reinhardtii. Genetics, 179:83-93. DOI: 10.1534/genetics.107.085605

55.  Guoli Ji, Jianti Zheng, Yingjia Shen, Xiaohui Wu, Ronghan Jiang, Yun Lin, Johnny C. Loke, Kimberly M. Davis, Greg J. Reese and Qingshun Q. Li*.  2007. Predictive modeling of plant messenger RNA polyadenylation sites. BMC Bioinformatics, 8:43. DOI: 10.1186/1471-2105-8-43 Highly Accessed

56.  Guoli Ji, Xiaohui Wu, Jianti Zheng, Yingjia Shen and Qingshun Q. Li*. 2007. Modeling Plant mRNA Poly(A) sites: Software Design and Implementation. Journal of Computational and Theoretical Nanoscience, 4:1365-1368. DOI: 10.1166/jctn.2007.025

57.  Kim Delaney, Ruqiang Xu, Jingxian Zhang, Qingshun Q. Li, Kil-Young Yun, Deane L. Falcone and Arthur G. Hunt*. 2006. Calmodulin interacts with and regulates the RNA-binding activity of an Arabidopsispolyadenylation factor subunit. Plant Physiology, 140:1507-1521. DOI: 10.1104/pp.105.070672

58.  Balasubrahmanyam Addepalli, Ruqiang Xu, Tomal Dattaroy, Baochun Li, W. Troy Bass, Qingshun Q. Li and Arthur G. Hunt*. 2006. Disease resistance in plants that carry a feedback-regulated yeast poly(A) binding protein gene. Plant Molecular Biology, 61:383 - 397. DOI: 10.1007/s11103-006-0019-6

59.  Ruqiang Xu, Hongwei Zhao, Randy Dinkins, Xiaowen Cheng, George Carberry and Qingshun Q. Li*. 2006. The 73 kD subunit of the cleavage and polyadenylation specificity factor (CPSF) complex affects reproductive development in Arabidopsis.  Plant Molecular Biology, 61:799-815. DOI: 10.1007/s11103-006-0051-6

60.  Johnny C. Loke, Eric Stahlberg, Dave Strenski, Brian J. Haas, P. Chris Wood and Qingshun Q. Li*. 2005. Compilation of mRNA Polyadenylation Signals in Arabidopsis Revealed a New Signal Element and Potential Secondary Structures. Plant Physiology, 138: 1457-1468. DOI: 10.1104/pp.105.060541

 

其他:

61.  Dewei Yang, Xinfu Ye*, Xianghua Zheng, Chaoping Cheng, Ning Ye, Libin Lu, Fenghuang Huang, Qingshun Q. Li *.  2016. Identification and fine mapping of LD1, a single recessive gene playing an essential role in the development of lemma in rice. J. Agricultural Science 154(6)989-1001. DOI:10.1017/S0021859615000866

62.  David A. Francko*, Kenneth G. Wilson, Qingshun Q. Li and Alejandra Equiza. 2011. A topical spray to enhance plant resistance to cold injury and mortality. HortTechnology, 21:109-118.

63.  Denghui Xing, Shuisong Ni, Michael A. Kennedy, Qingshun Q. Li*. 2009. Identification of a plant-specific Zn-sensitive ribonuclease activity. Planta, 230:819-825. DOI 10.1007/s00425-009-0986-3

64.  Ruqiang Xu and Qingshun Q. Li*. 2008. Streamline cloning of genes into binary vectors in Agrobacterium via the Gateway® TOPO vector system. Plant Methods, 4:4. DOI: 10.1186/1746-4811-4-4

65.  Hongyan Xing, Orlando Chambers, Chris B. Lawrence, H. Maelor Davies, Nicholas P. Everett and Qingshun Q. Li*. 2006. Increased pathogen resistance and yield in transgenic plants expressing combinations of the modified antimicrobial peptides based on indolicidin and magainin. Planta, 223:1024-1032. DOI: 10.1007/s00425-005-0143-6


开设课程

分子生物学基础,分子生态学,遗传与进化,生态之美,环境与生态组学技术
Molecular Biology, Molecular Ecology, Genetic and Evolution, Beauty of Ecosystem, Omic Technologies in Environment and Ecology

科研课题


荣誉奖励

1、Sigma Xi-全美科学研究协会评为“最佳研究者”(2011)。

2、被迈阿密大学评为“杰出学者”(2012)。

3、美国肯塔基大学植物学系杰出校友奖(2014)。

4、曾两度做为海外优秀华人学者代表应邀在天安门参加中华人民共和国成立50周年与60周年庆典,受中央领导接见。

5、福建省高层次引进创新创业人才

6、厦门市双百计划人才



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