吴小惠副教授 研究方向：生物信息学
系别：
联系电话：
电子邮箱：xhuister@xmu.edu.cn



个人简介
研究成果
承担项目
学术奖励


2011年7月博士毕业于厦门大学系统工程专业，主要研究方向为生物信息学。
2015/09-至今，厦门大学，航空航天学院，副教授
2016/08-2017/08，Universit?t zu K?ln, CECAD，Visiting Scholar
2011/09-2015/08，厦门大学，信息科学与技术学院，助理教授
2009/10-2010/09，Miami University，Department of Botany，Visiting Scholar




代表性期刊论文：
[1] Zhou Q, Fu H, Yang D, Ye C, Zhu S, Lin J, Ye W, Ji G, Ye X, Wu X*, Li QQ*: Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies Japonica and Indica. The Plant Journal 2019, 0(ja). (JCR2#, Top)
[2] Ye W, Long Y, Ji G, Su Y, Ye P, Fu H, Wu X*: Cluster analysis of replicated alternative polyadenylation data using canonical correlation analysis. BMC Genomics 2019, 20(75):1-15. (JCR2#)
[3] Ye C, Long Y, Ji G, Li QQ*, Wu X*: APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data. Bioinformatics 2018, 34(11):1841-1849. (JCR2#, Top)
[4] Ji G, Ye W, Su Y, Chen M, Huang G, Wu X*: AStrap: identification of alternative splicing from transcript sequences without a reference genome. Bioinformatics 2018:bty1008-bty1008. (JCR2#, Top)
[5] Ji G, Chen M, Ye W, Zhu S, Ye C, Su Y, Peng H, Wu X*: TSAPA: identification of tissue-specific alternative polyadenylation sites in plants. Bioinformatics 2018, 34(12):2123-2125. (JCR2#, Top)
[6] Ji G, Lin Q, Long Y, Ye C, Ye W, Wu X*: PAcluster: Clustering polyadenylation site data using canonical correlation analysis. J Bioinf Comput Biol 2017, 15(5):19. (JCR4#)
[7] Fu H, Yang D, Su W, Ma L, Shen Y, Ji G, Ye X*, Wu X*, Li QQ*: Genome-wide dynamics of alternative polyadenylation in rice. Genome Res 2016, 26(12):1753-1760. (JCR1#, Top)
[8] Wu, X.*, Zhang, Y., and Li, Q. Q.* (2016) PlantAPA: a portal for visualization and analysis of alternative polyadenylation in plants. Frontiers in Plant Science 7 (JCR2#)
[9] Wu, X.*, Zeng, Y., Guan, J., Ji, G., Huang, R., and Li, Q. Q.* (2015) Genome-wide characterization of intergenic polyadenylation sites redefines gene spaces in Arabidopsis thaliana. BMC Genomics 16, 015-1691 (JCR2#)
[10] Ji, G., Li, L., Li, Q. Q., Wu, X., Fu, J., Chen, G., and Wu, X.* (2015) PASPA: a web server for mRNA poly(A) site predictions in plants and algae. Bioinformatics 31, 1671-1673 (JCR2#, Top)
[11] Ji, G., Huang, G., Yang, Z., Wu, X., Chen, X., and Yuan, M. (2015) Using consensus interval partial least square in near infrared spectra analysis. Chemometrics Intellig. Lab. Syst. 144, 56-62 (JCR3#)
[12] Ji, G., Guan, J., Zeng, Y., Li, Q. Q., and Wu, X.* (2015) Genome-wide identification and predictive modeling of polyadenylation sites in eukaryotes. Briefings in Bioinformatics 16, 304-313 (JCR1#, Top)
[13] Zhao, Z., Wu, X., Raj Kumar, P. K., Dong, M., Ji, G., Li, Q. Q., and Liang, C. (2014) Bioinformatics Analysis of Alternative Polyadenylation in Green Alga Chlamydomonas reinhardtii Using Transcriptome Sequences from Three Different Sequencing Platforms. G3: Genes|Genomes|Genetics 4, 871-883 (JCR3#)
[14] Wu, X., Gaffney, B., Hunt, A., and Li, Q. (2014) Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. BMC Genomics 15, 615 (JCR2#)
[15] Wu, X.*, Ji, G., and Zeng, Y. (2012) In silico prediction of mRNA poly(A) sites in Chlamydomonas reinhardtii. Mol. Genet. Genomics 287, 895-907 (JCR3#)
[16] Thomas, P. E., Wu, X., Liu, M., Gaffney, B., Ji, G., Li, Q. Q., and Hunt, A. G. (2012) Genome-Wide Control of Polyadenylation Site Choice by CPSF30 in Arabidopsis. Plant Cell 24, 4376-4388 (JCR1#, Top)
[17] Li, H. J., Ye, C. T., Ji, G. L., Wu, X. H., Xiang, Z., Li, Y. Y., Cao, Y. H., Liu, X. L., Douek, D. C., Price, D. A., and Han, J. H. (2012) Recombinatorial Biases and Convergent Recombination Determine Interindividual TCR beta Sharing in Murine Thymocytes. J. Immunol. 189, 2404-2413 (JCR2#)
[18] Zheng, J., Xing, D., Wu, X., Shen, Y., Kroll, D. M., Ji, G., and Li, Q. Q. (2011) Ratio-based analysis of differential mRNA processing and expression of a polyadenylation factor mutant pcfs4 using Arabidopsis Tiling microarray. PLoS ONE 6, 10 (JCR3#)
[19] Wu, X., Liu, M., Downie, B., Liang, C., Ji, G., Li, Q. Q., and Hunt, A. G. (2011) Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. Proc. Natl. Acad. Sci. USA 108, 12533-12538 (JCR1#, Top)
[20] Shen, Y., Venu, R. C., Nobuta, K., Wu, X., Notibala, V., Demirci, C., Meyers, B. C., Wang, G.-L., Ji, G., and Li, Q. Q. (2011) Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing. Genome Res. 21, 1478-1486 (JCR1#, Top)
[21] Ji, G., Wu, X., Shen, Y., Huang, J., and Li, Q. Q. (2010) A classification-based prediction model of messenger RNA polyadenylation sites. J. Theor. Biol. 265, 287-296 (JCR3#)
[22] Shen, Y., Ji, G., Haas, B. J., Wu, X., Zheng, J., Reese, G. J., and Li, Q. Q. (2008) Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation. Nucleic Acids Res. 36, 3150-3161 (JCR1#, Top)
[23] Ji, G., Zheng, J., Shen, Y., Wu, X., Jiang, R., Lin, Y., Loke, J. C., Davis, K. M., Reese, G. J., and Li, Q. Q. (2007) Predictive modeling of plant messenger RNA polyadenylation sites. BMC Bioinformatics 8, 43 (JCR3#)
论著章节：

[1]Wu, X., Ji, G., and Li, Q. Q. (2015) Poly(A)-Tag Deep Sequencing Data Processing to Extract Poly(A) Sites. In Polyadenylation in Plants : Methods and Protocols Vol. 1255 pp. 39-48, Springer New York, New York
[2]Wu, X., Ji, G., and Li, Q. Q. (2015) Prediction of Plant mRNA Polyadenylation Sites. In Polyadenylation in Plants : Methods and Protocols Vol. 1255 pp. 13-23
[3]Wu, X., Ji, G., and Li, Q. Q. (2015) Computational Analysis of Plant Polyadenylation Signals. In Polyadenylation in Plants : Methods and Protocols Vol. 1255 pp. 3-11
[4]Liu, M., Wu, X., and Li, Q. Q. (2015) DNA/RNA Hybrid Primer Mediated Poly(A) Tag Library Construction for Illumina Sequencing. In Polyadenylation in Plants : Methods and Protocols Vol. 1255 pp. 175-184, Springer New York, New York

部分会议论文：

[1]Wang, Y., Sun, C., Hong, H., and Wu, X. * (2015) Genome-wide analysis of the associations between polyadenylation sites and repeated sequences in Arabidopsis thaliana. In Biomedical Engineering and Informatics (BMEI), 2015 8th International Conference on pp. 537-541
[2]Wu, X., Tang, M., Yao, J., Lin, S., Xiang, Z., and Ji, G. (2012) PATMAP: Polyadenylation Site Identification from Next-Generation Sequencing Data. In Hybrid Artificial Intelligent Systems Vol. 7208 pp. 485-496, Springer Berlin / Heidelberg, Salamanca
[3]Ji, G., Xiang, Z., Wu, X., Lin, S., Tang, M., and Yao, J. (2012) High-throughput antibody sequence alignment based on GPU computing. In 27th Annual ACM Symposium on Applied Computing, SAC 2012, March 26, 2012 - March 30, 2012 pp. 1417-1418, Association for Computing Machinery, Trento, Italy
[4]Wu, X., Liu, Q., Tang, M., Zhang, H., Yao, J., and Ji, G. (2011) Identification of mRNA poly(A) signal patterns. In 2011 International Symposium on Innovations in Intelligent Systems and Applications (INISTA 2011)
[5]Ji, G., Wu, X., Li, Q., and Zheng, J. (2010) Messenger RNA polyadenylation site recognition in green alga Chlamydomonas Reinhardtii. Lecture Notes in Computer Science 6063, 17-26
[6]Ji, G., Wu, X., Xing, D., and Li, Q. Q. (2009) PROBER: segmentation and differential analysis tool for tiling microarray data. In Proceedings of the 2009 2nd International Conference on Biomedical Engineering and Informatics (BMEI) p. 5 pp.


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. 国家自然科学基金面上项目. 2019.1-2022.12. 63万. (**, 主持)
植物长非编码RNA选择性多聚腺苷化及其保守性的全基因组分析. 国家自然科学基金面上项目. 2017.1-2017.12. 16万. (**, 主持)
植物非典型poly(A)位点调控机制的全基因组分析. 福建省自然科学基金面上项目. 2017.4-2020.4. 4万. (2017J01068, 主持)
多种真核生物多聚腺苷化信号的识别及其演化研究. 国家自然科学基金青年科学基金项目. 2013.1-2015.12. 25万. (**, 主持)
中央高校基本科研业务费 2013.1-2015.12 (, 主持)
高等学校博士学科点专项科研基金新教师类. 2013.1-2015.12 (038, 主持)
福建省自然科学基金面上项目. 2012.1-2014.12 (2012J01154, 主持)


福建省优秀博士学位论文二等奖 2013
厦门市第七届自然科学优秀学术论文一等奖 2013
厦门大学校级优秀博士学位论文 2012
厦门大学“田昭武学科交叉奖”一等奖 2012 (团队成员：吉国力, 吴小惠, 周笋, 刘云龙, 高云龙)