助理教授
办公电话:
邮箱:yec@xmu.edu.cn

履历

  • 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-现在)

  • 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)


研究方向

  • 生物大数据分析与挖掘、生物信息算法及工具、组学数据处理与分析

  • Mining and Analysis of Biology Data, Development of Bioinformatics Algorithms and Tools, Genomics and Transcriptomics Data Processing and Analysis


代表性论文

[27] 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

[26] 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.

[25] 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.

[24] 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.

[23] 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.

[22] 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.

[21] 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.

[20] 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.

[19] 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.

[18] 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.

[17] 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.

[16] 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.

[15] 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.

[14] 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.

[13] 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.

[12] 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.

[11] 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.

[10] 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.

[09] 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.

[08] 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.

[07] 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.  

[06] 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.

[05] 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.

[04] 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.

[03] 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)

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

[01] 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.


开设课程

生物信息学(Bioinformatics)

数理统计(Mathematical Statistics)


科研课题

  • 国家自然科学基金青年项目, 基于单细胞转录组数据的APA位点建模与动态调控研究 (61802323), 2019/01-2021/12, 25万元, 主持.

  • 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.

  • 国家自然科学基金面上项目, 集成单细胞转录组数据的选择性多聚腺苷化网络建模研究 (61871463), 2019/01-2022/12, 63万元, 参与.

  • 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.

  • 国家自然科学基金青年项目, 水稻mRNA选择性多聚腺苷化在高温干旱胁迫中调控作用研究(31801268), 2019/01-2021/12, 25万元, 参与.

  • 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.

  • 厦门大学校长基金, 基于向量计算的重复序列识别算法研究 (20720170076), 2017/01-2019/12, 30万元, 主持.

  • 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.

  • 基础创新科研基金, 植物选择性多聚腺苷化位点预测及其网络平台构建 (201112G018), 2011/06-2013/06, 10万元, 主持.

  • 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.

荣誉奖励


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