Brief CV

• B.S., Wuhan University of Science and Technology (2005-2009)

• Ph.D., Xiamen University (2009-2015)

• Visiting Scholar, Miami University (2013-2014)

• Research Assistant Professor, Xiamen University (2016–2019)

• Assistant Professor, Xiamen University (2019-present)

Research Interests

• Mining and Analysis of Biology Data

• Development of Bioinformatics Algorithms and Tools

• Genomics and Transcriptomics Data Processing and Analysis

Selected Publications

• Juncheng Lin#, Fu-Yu Hung#, Congting Ye, Liwei Hong, Yuan-Hsin Shih, Keqiang Wu*, Qingshun Quinn Li*. (2020) From chromatin to mature RNA: histone deacetylation affects alternative polyadenylation in Arabidopsis. Genome Research. DOI: 10.1101/gr.255232.119

• Congting Ye, Juncheng Lin, Qingshun Q. Li*. (2020) Discovery of alternative polyadenylation dynamics from single cell types. Computational and Structural Biotechnology Journal, 18: 1012-1019.

• Congting Ye^#*, Qian Zhou^#, Xiaohui Wu, Chen Yu, Guoli Ji, Daniel R. Saban, Qingshun Q. Li. (2020) scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data. Bioinformatics, 36(4): 1262-1264.

• Pengchao Ye, Wenbin Ye, Congting Ye, Shuchao Li, Lishan Ye, Guoli Ji, Xiaohui Wu*. (2020) scHinter: Imputing dropout events for single-cell RNA-seq data with limited sample size. Bioinformatics, 36(3): 789-797.

• Sheng Zhu^#, Wenbin Ye^#, Lishan Ye, Hongjuan Fu, Congting Ye, Xuesong Xiao, Yuanhaowei Ji, Weixu Lin, Guoli Ji, Xiaohui Wu*. (2020) PlantAPAdb: a comprehensive database for alternative polyadenylation sites in plants. Plant Physiology, 182(1): 228-242.

• 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.

• Wenyue Su, Congting Ye, Yihui Zhang, Qingshun Q. Li*. (2019) Identification of putative key genes for coastal environments and cold adaptation in mangrove Kandelia obovata through transcriptome analysis. Science of The Total Environment, 681:191-201.

• Moliang Chen, Guoli Ji, Hongjuan Fu, Qianmin Lin, Congting Ye, Wenbin Ye, Yaru Su, Xiaohui Wu*. (2019) A survey on identification and quantification of alternative polyadenylation sites from RNA-seq data. Briefings in bioinformatics, DOI: 10.1093/bib/bbz068.

• 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.

• Qian Zhou^#, Haihui Fu^#, Dewei Yang, Congting Ye, Sheng Zhu, Juncheng Lin, Wenbin Ye, Guoli Ji, Xinfu Ye, Xiaohui Wu* and 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.

• Zhu Sheng, Xiaohui Wu*, Hongjuan Fu, Congting Ye, Moliang Chen, Zhihua Jiang*, Guoli Ji*. (2019) Modeling of genome-wide polyadenylation signals in Xenopus tropicalis. Frontiers in Genetics. 10:647.

• 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, 10:589.

• Guoli Ji, Moliang Chen, Wenbin Ye, Sheng Zhu, Congting Ye, Yaru Su, Haonan Peng, Xiaohui Wu*. (2018) TSAPA: identification of tissue-specific alternative polyadenylation sites in plants. Bioinformatics, 34(12): 2123-2125.

• 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.

• Jinting Guan, Moliang Chen, Congting Ye, James J. Cai, Guoli Ji*. (2018) AEGS: identifying aberrantly expressed gene sets for differential variability analysis. Bioinformatics, 34(5): 881-883.

• Liwei Hong, Wenyue Su, Yuan-Ye Zhang, Congting Ye, Yingjia Shen, Qingshun Q. Li*. (2018) Transcriptome profiling during mangrove viviparity in response to abscisic acid. Scientific Reports, 8(770): 1-12.

• Liwei Hong, Congting Ye, Juncheng Lin, Haihui Fu, Xiaohui Wu, Qingshun Q. Li*. (2018) Alternative polyadenylation is involved in auxin-based plant growth and development. The Plant Journal, 93(2): 246-258.

• Guoli Ji, Qianmin Lin, Yuqi Long, Congting Ye, Wenbin Ye, Xiaohui Wu*. (2017) PAcluster: Clustering polyadenylation site data using canonical correlation analysis. Journal of Bioinformatics and Computational Biology, 15(5): 1-19.

• Cheng Guo, Matthew R. Spinelli, Congting Ye, Qingshun Q. Li, Chun Liang*. (2017) Genome-Wide Comparative Analysis of Miniature Inverted Repeat Transposable Elements in 19 Arabidopsis thaliana Ecotype Accessions. Scientific Reports, 7(2634): 1-12.

• Congting Ye, Guoli Ji*, Chun Liang*. (2016) detectMITE: A novel approach to detect miniature inverted repeat transposable elements in genomes. Scientific Reports, 6(19688): 1-11.

• Lei Li, Guoli Ji*, Congting Ye, Changlong Shu, Jie Zhang, Chun Liang*. (2015) PlantOrDB: a genome-wide ortholog database for land plants and green algae. BMC Plant Biology, 15(1): 1-11.  

• Congting Ye, Guoli Ji*, Lei Li, Chun Liang*. (2014) detectIR: a novel program for detecting perfect and imperfect inverted repeats using complex numbers and vector calculation. PLoS ONE, 9(11): e113349.

• Guoli Ji*, Yong Zeng, Zijiang Yang, Congting Ye, Jingci Yao. (2014) A multiple sequence alignment method with sequence vectorization. Engineering Computations, 31(2): 283-296.

• Guoli Ji, Yong Zeng, Jinting Guang, Qingshun Q. Li, Congting Ye, Yunlong Liu*. (2013) Recent Advances in Mathematical Modeling and Simulation of DNA Replication Process. Current Bioinformatics, 8(5): 591-602.

• Hanjie Li^#, Congting Ye^#, Guoli Ji*, Xiaohui Wu, Zhe Xiang, Yuanyue Li, Yonghao Cao, Xiaolong Liu, Daniel C. Douek, David A. Price*, Jiahuai Han*. (2012) Recombinatorial Biases and Convergent Recombination Determine Interindividual TCR beta Sharing in Murine Thymocytes. Journal of Immunology, 189(5): 2404-2413. (co-first author)

• Hanjie Li, Congting Ye, Guoli Ji, Jiahuai Han*. (2012) Determinants of public T cell responses. Cell Research, 22(1): 33-42.

• Guoli Ji*, Congting Ye, Zijiang Yang, Zhenya Guo. (2009) A Novel Method for Progressive Multiple Sequence Alignment Based on Lempel-Ziv. Neural Information Processing, Pt 1, Proceedings, Lecture Notes in Computer Science. pp. 151-158.

Teaching Experience

• Bioinformatics

• Mathematical Statistics

Research Funding

• Modeling the alternative polyadenylation sites and dynamics based on single cell RNA-seq data, National Natural Science Foundation of China (No. 61802323), 2019/01-2021/12, Principal Investigator.

• Network modeling of alternative polyadenylation by integrating single-cell transcriptome data, National Natural Science Foundation of China (No. 61871463), 2019/01-2022/12, Major Participant.

• mRNA alternative polyadenylation regulation of rice under high temperature and drought stresses, National Natural Science Foundation of China (No. 31801268), 2019/01-2021/12, Major Participant.

• Detection of repeats based on vector computation, Fundamental Research Funds for the Central Universities in China from Xiamen University (No. 20720170076), 2017/01-2019/12, Principal Investigator.

• Prediction of plant alternative polyadenylation sites and its web-platform construction, Fundamental Research Funds for the Central Universities in China from Xiamen University (No. 201112G018), 2011/06-2013/06, Principal Investigator.