吳小惠

吳小惠，女，博士學歷，曾任廈門大學航空航天學院自動化系副教授，2021年任蘇州大學巴斯德學院特聘教授，博士生導師。

基本介紹

• 中文名：吳小惠
• 國籍：中國
• 畢業院校：廈門大學
• 學位/學歷：博士
• 職業：教師
• 專業方向：生物信息學
• 任職院校：蘇州大學巴斯德學院 

人物經歷

2021年任蘇州大學巴斯德學院特聘教授，博士生導師。

2011年7月博士畢業於廈門大學系統工程專業（師從吉國力）

2015/09-至今，廈門大學，航空航天學院，副教授

2016/08-2017/08，Universität zu Köln, CECAD，Visiting Scholar

2011/09-2015/08，廈門大學，信息科學與技術學院，助理教授

2009/10-2010/09，Miami University，Department of Botany，Visiting Scholar

研究方向

(1) 生物多組學大數據的信息挖掘

長期致力於生物信息學研究，重點關注RNA加工，特別是基因表達的關鍵步驟—選擇性多聚腺苷化（APA），從海量單細胞轉錄組數據和生物多組學大數據中挖掘與疾病、作物發育、抗逆境等相關的生物標記和基因。

(2) 機器學習模型和分析工具

設計統計模型、機器學習、人工智慧、大數據分析算法，開發高效便捷的生信工具，用於生物多組學大數據分析及基因調控網路研究。

(3) 資料庫和生醫信息平台

結合雲計算、大數據和全文檢索技術，開發用於生物大數據存儲分析與可視化的生物信息平台和資料庫，為生物學者、育種專家、醫務人員等廣大科研工作者提供開放的資源及服務。

學術成果

期刊論文

[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#)

論著章節

[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

會議論文

[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.

承擔項目

• 集成單細胞轉錄組數據的選擇性多聚腺苷化網路建模研究. 國家自然科學基金面上項目. 2019.1-2022.12. 63萬. (61871463, 主持)
• 植物長非編碼RNA選擇性多聚腺苷化及其保守性的全基因組分析. 國家自然科學基金面上項目. 2017.1-2017.12. 16萬. (61673323, 主持)
• 植物非典型poly(A)位點調控機制的全基因組分析. 福建省自然科學基金面上項目. 2017.4-2020.4. 4萬. (2017J01068, 主持)
• 多種真核生物多聚腺苷化信號的識別及其演化研究. 國家自然科學基金青年科學基金項目. 2013.1-2015.12. 25萬. (61201358, 主持)
• 中央高校基本科研業務費 2013.1-2015.12 (2013121025, 主持)
• 高等學校博士學科點專項科研基金新教師類. 2013.1-2015.12 (20120121120038, 主持)
• 福建省自然科學基金面上項目. 2012.1-2014.12 (2012J01154, 主持)

榮譽獎項

• 福建省優秀博士學位論文二等獎 2013
• 廈門市第七屆自然科學優秀學術論文一等獎 2013
• 廈門大學校級優秀博士學位論文 2012
• 廈門大學“田昭武學科交叉獎”一等獎 2012 (團隊成員：吉國力, 吳小惠, 周筍, 劉雲龍, 高雲龍)

招生方向

細胞生物學、生物信息學