叶从庭-滨海湿地生态系统教育部重点实验室（厦门大学）

基本信息

: 叶从庭 副教授; 办公地点：环境与生态学院大楼; Congting Ye Assistant Professor; Office Location:CEE Building

详细资料 - 叶从庭副教授

个人履历 Brief CV

武汉科技大学工学学士(2005-2009)
厦门大学工学博士(2009-2015)
美国迈阿密大学访问学者(2013-2014)
厦门大学研究型助理教授(师资博士后)(2016-2019)
厦门大学助理教授(2019-2022)
厦门大学副教授（2023-）
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 (2019-2022)
Associate Professor, Xiamen University (2023-)

研究方向 Research Interests

生物信息学、生态及生物大数据挖掘 Bioinformatics; Data Mining for Ecology and Biology Data

代表性论文 Selected Publications

[1] 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. [2] 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. [3] 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. [4] 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. [5] 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. [6] 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. [7] 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. [8] 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. [9] 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. [10] 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. [11] 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. [12] 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. [13] 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. [14] 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. [15] 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. [16] 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. [17] 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. [18] 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. [19] 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. [20] 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. [21] 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. [22] 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. [23] 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. [24] 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) [25] Hanjie Li, Congting Ye, Guoli Ji, Jiahuai Han*. (2012) Determinants of public T cell responses. Cell Research, 22(1): 33-42. [26] 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.

部分科研课题 Selected Research Programmes

国家自然科学基金-青年科学基金项目:叶从庭—基于单细胞转录组数据的APA位点建模与动态调控研究（61802323），国家自然科学基金委，25万，2019.01-2021.12