Qingshun Quinn Li, Ph.D.

Ph.D. (1995) University of Kentucky

2015-present Professor, Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, California, USA.

2013-2015 Professor, Department of Biology, Miami University, Oxford, Ohio.

2010-2013 Professor, Botany Department, Miami University, Oxford, Ohio.

2011-2013 Director, The Cell, Molecular and Structural Biology Ph.D. Graduate Program, Miami University, Oxford, Ohio.

2007-2010 Associate Professor, Botany Department, Miami University, Oxford, Ohio.

2001-2007 Assistant Professor, Botany Department, Miami University, Oxford, Ohio.

Genetics

Bioinformatics

Research Interests:

1.Mechanism of mRNA polyadenylation and its role in gene expression regulation

Messenger RNA polyadenylationis one of the critical steps in eukaryotic gene expression. The poly(A) tail of a mature mRNA is essential for its function, including mRNA translatability, stability and translocation to cytoplasm. The process also affects pre-mRNA splicing and transcription termination. Recent studies have linked mRNA polyadenylation to other cellular processes, e.g. pathogen invasion and cancer development.

I am interested to elucidate mRNA polyadenylation mechanisms at genetic, transcriptome, and molecular levels. We have used functional genomic tools to study the functions of this set of genes in model plantArabidopsis. Funded byUS National Science FoundationandUS National Instate of Health, we have studied the biochemical, genetic and molecular functions of some polyadenylation factors, and their role in plant gene expression regulations in gametophyte development and stress responses.

Aided by powerful RNA-sequencing technologies, we are performing large-scale analyses of alternative polyadenylation to discover the full landscape of polyadenylation from single cells to whole organisms. There are over 70% genes using alternative polyadenylation (APA) to regulate their expression. Role of such extensive APA in cells and organisms is just being revealed.Accompany with multi-omics tools, it has been demonstrated that APA are linked to many cellular processes, including circadian regulation of gene expression, epigenetic control, and quantitative traits, etc.The theme of APA as a hub of fine-tuning gene expression regulation at the transcriptome level has emerged.

2.Role of exosomes in neuronal cell communication on Alzheimer and Alzheimer-like disease models using iPSC derived cells.

My research interests are extendedto include gene expression regulation and communication of human iPSC (induced pluripotent stem cells), particularly in neuronal disease models like Alzheimer’s disease (AD).AD and related dementias are a global crisis facing the aging population.AD is characterized in part by massive neuronal loss in the brain. However, how these neurons get lost is not understood.

Microglia,the resident immune cells of the central nerve system,have long been suspected to play a role in AD pathogenicity.The interactions among microglia, astrocyte, neuron and extracellular matrix significantly are influenced byextracellular vesicles (EVs). Generated by the endosomal system of a cell, EVs are lipid bilayer membrane vesicles, 30 to 200 nm in diameter.Their role involved in cell-to-cell communications is supported by the fact that EVscontain active biomolecules, including proteins, mRNA and miRNA that are capable of modulating gene expression in recipient cells.Microglia-derived microvesicles have been reported to regulate neuronal excitability too. Theyrepresent a relatively new field of research in neurodegenerative diseases.

We have employed multi-omics tools to first study the components of the microglia derived EVs associated with specific AD-like model cells derived from patients and normal control individuals. Delineation of these potential markers and their functions in regulating gene expression, particularly related to neuronal degeneration, are of great interests. The results of these research could lead to new insight on neuronal gene expression regulation and offer potential targets for drug design in the near future.

Best Faculty Mentor Award, Graduate College of Biomedical Sciences, Western University of Health Sciences, 2017.

Distinguished Alumnus, Department of Plant and Soil Sciences, University of Kentucky, 2014.

Distinguished Scholar, Miami University 2012.

Researcher of the Year, Sigma Xi, Miami University 2011.

·Editorial Board Member,Frontiers in Plant Science

·Editorial Board Member,Scientific Reports

·Review Editor, Computational Genomics section forFrontiers in Genetics, Frontiers in Plant Science,andFrontiers in Bioengineering and Biotechnology.

1. Biomedical sciences related publications (*corresponding author):

Wenyue Su#, Qian Zhou#, Yubin Wang#, Athar Chishti,Qingshun Q. Li,Sujay Dayal, Shayan Shiehzadegan, Ariel Cheng, Clare Moore, Xiaoning Bi and Michel Baudry*. 2020. Deletion of the Capn1 gene results in alterations in several signaling pathways related to Alzheimer’s disease, protein quality control and synaptic plasticity in mouse brain.Frontiers in Genetics, 11:334.DOI: 10.3389/fgene.2020.00334

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

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

Kristopher J. L. Irizarry*,Adam Chan, Derek Kettle, Steven Kezian, Dominic Ma, LouisPalacios,Qingshun Q. Li,Calvin L. Keelerand Yvonne Drechsler.2017. Bioinformatics Analysis of Chicken miRNAs Associated with Monocyte to Macrophage Differentiation and Subsequent IFN Stimulated Activation.MicroRNA, 6:53-70.DOI:10.2174/2211536605666161129122803.

2.mRNA polyadenylations relatedpublications:

Juncheng Lin#, Zhibo Yu#, Liwei Hong, Yiru Chu, Yingjia Shen,Qingshun Q. Li*. 2021.Alternative polyadenylated mRNAs behave as asynchronous rhythmic transcription inArabidopsis.RNA Biology, in press, 2021.DOI: 10.1080/15476286.2021.1933732

Yi-Zhe Zhang#, Juncheng Lin#, Zhizhong Ren#, Chun-Xiang Chen#, Daisuke Miki#, Si-Si Xie, Jian Zhang, Ya-Nan Chang, Jing Jiang,Qingshun Q. Li*, Jian-Kang Zhu*, Cheng-Guo Duan*. 2021.Genome‐wide distribution and functions of the AAE complex in epigenetic regulation inArabidopsis,J. Integrative Plant Biology, 63(4):707-722.DOI: 10.1111/jipb.13068

Juncheng Lin, Congting Ye,Qingshun Q. Li*.2021. QPAT-seq, a Rapid and Deduplicatable Method for the Quantification of Poly(A) Site Usages. In series:Methods in Enzymology. Book title: “mRNA 3’ End Processing and Stability.”Tian B. (Editor). Elsevier Inc.

Xiaohui Wu, Arthur G. Hunt,Qingshun Q. Li*.2020. Genome-wide determination of poly(A) sites inMedicago truncatula: evolutionary conservation of alternative poly(A) site choice. In book:The Model LegumeMedicago truncatula. Frans J. de Bruijn (Editor). Chapter 12.6.3, Pp911-920.John Wiley and Sons, Inc. USA. ISBN 9781119409168.

Xuan Wu#, Jie Wang#, Xiaohui Wu, Yiling Hong,Qingshun Q. Li*. 2020.Heat shock responsive gene expression modulated by poly(A) tail length via translation efficiency.Frontiers in Plant Science, 11:1255. DOI: 10.3389/fpls.2020.01255

Juncheng Lin#, Fu-Yu Hung#, Congting Ye, Liwei Hong, Yuan-Hsin Shih, Keqiang Wu*,Qingshun Q. Li*. 2020.HDA6-dependent histone deacetylation regulates mRNA polyadenylation in Arabidopsis.Genome Research,30:1407–1417.DOI:10.1101/gr.255232.119

Congting Ye, Juncheng Lin,Qingshun Q. Li*. 2020. Discovery of alternative polyadenylation dynamics in single cell types.Computational and Structural Biotechnology Journal, 18:1012-1019.DOI: 10.1016/j.csbj.2020.04.009 (Invited review)

Congting Ye*#, Qian Zhou#, Xiaohui Wu, Chen Yu, Guoli Ji,Qingshun Q. Li. 2019. scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data.Bioinformatics,36(4):1262-1264.DOI: 10.1093/bioinformatics/btz701

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

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

Jingyi Cao, Congting Ye, Guijie Hao, Carole Dabney-Smith, Arthur G. Hunt,Qingshun Q. Li*. 2019. Root hair single cell type specific alternative polyadenylation under cadmium stress.Frontiers in Plant Science, 10:589.DOI:10.3389/fpls.2019.00589

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, 20:958. DOI:10.3390/ijms20040958.

Haihui Fu, Peng Wang, Xiaohui Wu, Xiaoxuan Zhou，Guoli Ji, Yingjia Shen,Qingshun Q. Li*, Junrong Liang*. 2019. Distinct genome-wide alternative polyadenylation during silicon response of marine diatomThalassiosira pseudonana.PlantJournal,99:67-80. DOI: 10.1111/tpj.14309

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

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 subspeciesJaponicaandIndica.Plant Journal,98(2):260-276.DOI: 10.1111/tpj.14209.

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, 34:1841-1849. DOI:10.1093/bioinformatics/bty029

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

Juncheng Lin, Ruqiang Xu, Xiaohui Wu, Yingjia Shen andQingshun Q. Li*. 2017. Role of Cleavage and Polyadenylation Specificity Factor 100: Anchoring Poly(A) Sites and Terminating Transcription inArabidopsis.Plant Journal,91:829–839. DOI: 10.1111/tpj.13611

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 UniqueOXIDATIVE TOLERANT-6Gene.Scientific Reports, 7:2052. DOI: 10.1038/s41598-017-02215-z

Kristopher J. L. Irizarry*, Adam Chan, Derek Kettle, Steven Kezian, Dominic Ma, Louis Palacios,Q. Quinn Li, Calvin L. Keeler and Yvonne Drechsler. Bioinformatics Analysis of Chicken miRNAs Associated with Monocyte to Macrophage Differentiation and Subsequent IFN Stimulated Activation.MicroRNA, 6:1-19.DOI:10.2174/2211536605666161129122803.

Haihui Fu, Dewei Yang, Wenyue Su, Liuyin Ma, Yingjia Shen, Guoli Ji, Xinfu Ye*, Xiaohui Wu*,Q. Quinn Li*. 2016. Genome-wide Dynamics of Alternative Polyadenylation in Rice.Genome Research, 26: 1753-1760.Link to Abstract

Xiaohui Wu*, Yumin Zhang,Q. Quinn 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.Download paper

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

Dewei Yang, Xinfu Ye*, Xianghua Zheng, Chaoping Cheng, Ning Ye, Libin Lu, Fenghuang Huang, Q Quinn Li*. 2016. Identification and fine mapping ofLD1,a single recessive geneplaying an essential role in the development of lemma in rice.J. Agricultural Science154(6)989-1001. DOI:10.1017/S0021859615000866

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

Guoli Ji, Jinting Guan, Yong Zeng, Q. Quinn 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/bbu011Download abstract

Guoli Ji, Lei Li, Q. Quinn 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.Download abstract

Jinting Guan, Jingyi Fu, Mingcheng Wu, Longteng Chen, Guoli Ji, Q. Quinn 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.2014.11.010Download abstract

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

Jingyi Cao, Q. Quinn Li*. 2015.Poly(A) Tag Library Construction from 10 ng Total RNA. Pp185-194.In “Polyadenylation in Plants” Editors: A.G. Hunt and Q.Q. Li. Series:Methods in Molecular BiologyVol 1255; Series Editor: John Walker. Humana Press, Springer Publishing Group, USA.

Hongwei Zhao*, Xinfu Ye, Q. Quinn Li..2015.Characterization of plant polyadenylation complexes by using tandem affinity purification. Pp 69-78. In “Polyadenylation in Plants” Editors: A.G. Hunt and Q.Q. Li. Series:Methods in Molecular BiologyVol 1255; Series Editor: John Walker. Humana Press, Springer Publishing Group, USA.

Hongwei Zhao*, Q. Quinn Li. 2015.In vitro analysis of cleavage and polyadenylation in Arabidopsis. Pp 79-90. In “Polyadenylation in Plants” Editors: A.G. Hunt and Q.Q. Li. Series:Methods in Molecular BiologyVol 1255; Series Editor: John Walker. Humana Press, Springer Publishing Group, USA.

Denghui Xing*, Q. Quinn Li. 2015.RADPRE: a computational program for identification of differential mRNA processing including alternative polyadenylation. Pp 57- 68. In “Polyadenylation in Plants” Editors: A.G. Hunt and Q.Q. Li. Series:Methods in Molecular BiologyVol 1255; Series Editor: John Walker. Humana Press, Springer Publishing Group, USA.

Xiaohui Wu, Guoli Ji, Q. Quinn Li*. 2015.Computational analysis of plant polyadenylation signals. Pp 3-12. In “Polyadenylation in Plants” Editors: A.G. Hunt and Q.Q. Li. Series:Methods in Molecular BiologyVol 1255; Series Editor: John Walker. Humana Press, Springer Publishing Group, USA.

Xiaohui Wu*, Guoli Ji, Q. Quinn Li. 2015.Prediction of plant polyadenylation sites. Pp 13-24. In “Polyadenylation in Plants” Editors: A.G. Hunt and Q.Q. Li. Series:Methods in Molecular BiologyVol 1255; Series Editor: John Walker. Humana Press, Springer Publishing Group, USA.

Xiaohui Wu*, Guoli Ji, Q. Quinn Li. 2015.Poly(A) Tag deep sequencing data processing to extract poly(A) sites. Pp 39-48. In “Polyadenylation in Plants” Editors: A.G. Hunt and Q.Q. Li. Series:Methods in Molecular BiologyVol 1255; Series Editor: John Walker. Humana Press, Springer Publishing Group, USA.

Min Dong, Q. Quinn Li, and Chun Liang*. 2015.Extraction of poly(A) sites from RNA-seq data. Pp 25-38. In “Polyadenylation in Plants” Editors: A.G. Hunt and Q.Q. Li. Series:Methods in Molecular BiologyVol 1255; Series Editor: John Walker. Humana Press, Springer Publishing Group, USA.

Man Liu, Xiaohui Wu, Q. Quinn Li*. 2015.DNA/RNA hybrid primer mediated poly(A) tag library construction for Illumina sequencing. Pp 175-184. In “Polyadenylation in Plants” Editors: A.G. Hunt and Q.Q. Li. Series:Methods in Molecular BiologyVol 1255; Series Editor: John Walker. Humana Press, Springer Publishing Group, USA.

Xiaohui Wu, Bobby Gaffney, Arthur G. Hunt*, and Q. Quinn Li *. Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice.BMC Genomics. 15:615.Download paper

William C Ray*, Samuel L Wolock, Nicholas W Callahan, Min Dong, Q. Quinn 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.Download paper

Zhixin Zhao, Xiaohui Wu, Praveen Kumar Raj Kumar, Min Dong, Guoli Ji, Q. Quinn 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(5):871-883.Download paper

Liuyin Ma, Pratap Kumar Pati, Man Liu, Q. Quinn Li* and Arthur G. Hunt*. 2014. High throughput characterizations of poly(A) site choice in plants.Methods, 67(1):74-83.Download paper

Liuyin Ma, Cheng Guo and Q Quinn Li*. 2014. Role of alternative polyadenylation in epigenetic silencing and antisilencing.Proc. Nat. Acad. Sci. USA, 111:9-10.Download paper

Denghui Xing, Yajun Wang, Ruqiang Xu, Xinfu Ye, Dewei Yang, Q. Quinn 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.Download paper

Guoli Ji*, Yong Zeng, Jinting Guan, Q. Quinn Li, Congting Ye, Yunlong Liu. 2013. Recent advances in mathematical modeling and simulation of DNA replication process.Current Bioinformatics, 8:591-602.Download paper

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

Arthur G. Hunt, Denghui Xing*, Q. Quinn Li*. 2012. Plant polyadenylation factors: conservation and variety.BMC Genomics, 13:641.Download paper

Hongwei Zhao, Jun Zheng, Q. Quinn Li*. 2011. A novel plant in vitro assay system for pre-mRNA cleavage and polyadenylation.Plant Physiology, 157:1546-1554.Download paper

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

Xiaohui Wu, Man Liu, Bruce Downie, Chun Liang, Guoli Ji, Q. Quinn 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.Download paper

Jianti Zheng, Denghui Xing, Xiaohui Wu, Diana Kroll, Yingjia Shen, Guoli Ji*, Q. Quinn Li*. 2011. Ratio-based analysis of differential mRNA processing and expression of a polyadenylation factor mutant pcfs4 using Arabidopsis tiling microarray.PLoS One, 6:e14719.Download paper

Denghui Xing, Q. Quinn Li*. 2010. Alternative polyadenylation and gene expression regulation in plants.WIREs (Willey Interdisciplinary Reviews) RNA, 2:445-458. (Invited review)Download paper

Guoli Ji*, Xiaohui Wu, Yingjia Shen, Jiangyin Huang, Zhoujing Wang and Q. Quinn Li. 2010. Classification-Based Prediction Models of Messenger RNA Polyadenylation Sites.Journal of Theoretical Biology, 265:287-296.Abstract

Guoli Ji*, Xiaohui Wu, Jiangyin Huang, Q. Quinn 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.Abstract

Hongwei Zhao, Denghui Xing, Q. Quinn Li*. 2009. Unique features of plant cleavage and polyadenylation specificity factor revealed by proteomic studies.Plant Physiology, 151:1546-1556.Download paper

Denghui Xing, Shuisong Ni, Michael A. Kennedy, Q. Quinn Li*. 2009. Identification of a plant-specific Zn-sensitive ribonuclease activity.Planta, 230:819-825.Download paper

Denghui Xing and Q. Quinn Li*. 2009. Alternative polyadenylation: a mechanism maximizing transcriptome diversity in higher eukaryotes.Plant Signaling and Behavior, 4:440-442.Download paper

Denghui Xing, Hongwei Zhao and Q. Quinn Li *. 2008. Arabidopsis CLPS3, an ortholog of human polyadenylation factor CLP1, functions in gametophyte, embryo and post-embryonic development.Plant Physiology,148:2059-2069.Download paper

Denghui Xing, Hongwei Zhao, Ruqiang Xu and Q. Quinn Li* . 2008 . Arabidopsis PCFS4, a homologue of yeast polyadenylation factor Pcf11p, regulates FCA alternative processing and promotes flowering time.Plant Journal, 54:899-910.Download paper

Chun Liang*, Yuansheng Liu, Lin Liu, Adam C. Davis, Yingjia Shen, and Q. Quinn Li . 2008 ESTs with cDNA termini - previously overlooked resources for gene annotation and transcriptome exploration in Chlamydomonas reinhardtii. Genetics, 179:83-93 .Download paper

Yingjia Shen, Guoli Ji, Brian J. Haas, Xiaohui Wu, Jianti Zheng, Greg J. Reese, and Q. Quinn Li* . 2008 Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation. Nucleic Acids Research, 36:3150-3161. Download paper

Yingjia Shen, Yuansheng Liu, Lin Liu, Chun Liang, and Q. Quinn 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).Download paper

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 Q. Quinn Li *. 2008 Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling. BMC Genomics, 9:220. Highly accessed at BMC Genomics webpageDownload paper

Ruqiang Xu and Q. Quinn Li*. 2008. Streamline cloning of genes into binary vectors in Agrobacterium via the Gateway® TOPO vector system.Plant Methods, 4:4.Download paper

Jingxian Zhang, Kil-Young Yun , Ruqiang Xu, Arthur G. Hunt, Irina Artiushin, Kim Delaney, Q. Quinn Li and Deane L. Falcone*. 2008. Differential RNA processing implicated in responses of Arabidopsis thaliana to oxidative stress: a stress-tolerant mutant is deficient in a calmodulin-regulated RNA-binding protein.PLoS One, 3:e2410.Download paper

Guoli Ji, Xiaohui Wu, Jianti Zheng, Yingjia Shen and Q. Quinn Li*. 2007. Modeling Plant mRNA Poly(A) sites: Software Design and Implementation.J. Computational Theoretical Nanoscience, 4:1365-1368.

Guoli Ji, Jianti Zheng, Yingjia Shen, Xiaohui Wu, Ronghan Jiang, Yun Lin, Johnny C. Loke, Kimberly M. Davis, Greg J. Reese and Q. Quinn Li*. 2007. Predictive modeling of plant messenger RNA polyadenylation sites.BMC Bioinformatics, 8:43 (doi:10.1186/1471-2105-8-43). Highly accessed at BMC Bioinformatics webpageDownload paper

Kim Delaney, Ruqiang Xu, Jingxian Zhang, Q. Quinn Li, Kil-Young Yun, Deane L. Falcone and Arthur G. Hunt*. 2006. Calmodulin interacts with and regulates the RNA-binding activity of an Arabidopsis polyadenylation factor subunit. Plant Physiology, 140:1507-1521.

Addepalli Balasubrahmanyam, Ruqiang Xu, Tomal Dattaroy, Baochun Li, W. Troy Bass, Q. Quinn 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.

Ruqiang Xu, Hongwei Zhao, Randy Dinkins, Xiaowen Cheng, George Carberry and Q. Quinn 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.

Hongyan Xing, Orlando Chambers, Chris B. Lawrence, H. Maelor Davies, Nicholas P. Everett and Q. Quinn 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.

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

Ruqiang Xu, Xinfu Ye, Q. Quinn Li. 2004. AtCPSF73-II gene encoding an Arabidopsis homolog of CPSF 73 kDa subunit is critical for early embryo development. Gene, 324: 35-45.

Q. Quinn Li, Carol von Lanken, Jianjun Yang, Chris B. Lawrence and Arthur G. Hunt. 2000. The yeast polyadenylate binding protein ( PAB1 ) gene acts as a disease lesion mimic gene when expressed in plants. Plant Molecular Biology, 42:335-344.

Jaydip Dasgupta, Q. Quinn Li and Arthur G. Hunt. 1998. Identification and characterization of two distinctive RNA-binding activities in pea nuclear extracts. Journal of Plant Biochemistry and Biotechnology, 7: 1-5.

Jaydip Dasgupta, Q. Quinn Li, A. Brian Thomson and Arthur G. Hunt. 1998. Characterization of cDNAs encoding a novel plant poly(A) polymerase.Plant Molecular Biology, 37: 729-734.

Q. Quinn Li, Jaydip Dasgupta and Arthur G. Hunt. 1998. Polynucleotide phosphorylase is a component of a novel plant poly(A) polymerase.Journal of Biological Chemistry, 273: 17539-17543.

Q. Quinn Li and Arthur G. Hunt. 1997. The Polyadenylation of RNA in Plants. Plant Physiology, 115: 321-326.

Q. Quinn Li, Jaydip Dasgupta and Arthur G. Hunt. 1996. A plant poly(A ) polymerase requires a novel RNA binding protein for activity. Journal of Biological Chemistry, 271:19831-35

Jaydip Dasgupta, Q. Quinn Li, A. Brian Thomson and Arthur G. Hunt, 1995. Characterization of a poly(A) polymerase from plants. Plant Science, 110: 215-226.

Q. Quinn Li and Arthur G. Hunt. 1995. A near upstream element in a plant polyadenylation signal consists of more than six bases. Plant Molecular Biology, 28: 927-934.

3. Selected publications of other interests

Saiqi Hao, Wenyue Su,Qingshun Q. Li*.2021.Adaptive roots of mangroveAvicennia marina: structure and gene expression analyses of pneumatophores.Science of the Total Environment.757:143994.DOI: 10.1016/j.scitotenv.2020.143994

Yuan-Ye Zhang*, Junjie Yin, Ming Zhou, Zeru Lin,Qingshun Q. Li.2020. Adaptive transgenerational effects remain significant.Ecology Letter, 23(11):1719-1920.DOI:10.1111/ele.13589

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 Letter, 22:1976-1986. DOI: 10.1111/ele.13373

Hongmei Qiao#, Wenwen Liu#, Yihui Zhang*, Yuan-Ye Zhang*,Qingshun Q. Li*.2019. Genetic admixture accelerates invasion via provisioning rapid adaptive evolution.Molecular Ecology, 28:4012-4027.DOI: 10.1111/mec.15192

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

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.

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

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

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 Ecology40(12):1328-1343.(In Chinese with English abstract)Doi:10.17521/cjpe.2016.0087

Gail J. Pruss, Christopher B. Lawrence, Troy Bass, Q. Quinn Li, Lewis H. Bowman and Vicki Vance. 2004. The viral suppressor of RNA silencing confers enhanced resistance to multiple pathogens. Virology, 320:107-120. (Cover image)

Ruqiang Xu and Q. Quinn Li. 2003. A RING-H2 zinc finger protein gene RIE1 is essential for seed development in Arabidopsis. Plant Molecular Biology, 53:37-50. (Cover image)

Q. Quinn Li, Christopher B. Lawrence, H. Maelor Davies and Nicholas P. Everett. 2002. A tridecapeptide possesses both antimicrobial and protease-inhibitory activities. Peptides23: 1-6

Urvee A. Desai, Gargi Sur, Sylvia Daunert, Ruth A. Babbitt, and Q. Quinn Li. 2002. Expression and affinity purification of recombinant proteins from plants.Protein Expression and Purification, 25: 195-202.

Q. Quinn Li, Chris B. Lawrence, Hongyan Xing, Ruth A. Babbitt, W. Troy Bass Indu B. Maiti and Nicholas P. Everett. 2001. Enhanced disease resistance conferred by expression of an antimicrobial peptide magainin analogue in transgenic tobacco. Planta, 212: 635-639

Songhai Shen, Q. Quinn Li , Shengyang He, Debao Li, Kenneth Barker and Arthur G. Hunt. 2000. Conversion of compatible plant-pathogen interactions into incompatible interactions by expression of the Pseudomonas syringae pv. syringae 61 hrmA gene in transgenic tobacco plants. Plant Journal, 23:205-213.

4. Patents

Dave Francko, Ken Wilson, Q. Quinn Li, Alejandra Equiza. Plant Cryoprotectant Compositions and Methods of Use. US Patent 8580708 (Nov. 12, 2013). This patent has been used for commercial production. The product is under trademark Freezepruf.

Nicholas P. Everett, Q. Quinn Li , Christopher Lawrence, H. Maelor Davies. 2007. Peptides with enhanced stability to protease degradation. US Patent #7,214,766.

Q. Quinn Li, Songhai Shen, Arthur G. Hunt and Shengyang He. 2002. Use of hrmA proteins and their genes for broad range protection of plants against bacterial, viral and fungal pathogens. US Patent #6342654

Arthur G. Hunt, Glen B. Collins, Q. Quinn Li, Christopher B. Lawrence and Santanu Dasgupta. 2002. Use of bacterial acetate kinase and their genes for protection of plants against different pathogens. US Patent # 6476293

Arthur G. Hunt, Q. Quinn Li, Jianjun Yang and Carol von Lanken. 2000. Use of yeast poly(A) binding proteins and their genes for broad range protection of plants against bacterial, fungal and viral pathogens. US Patent #6018106.