Xiaohui Wu
Tel. 13459029440 Email: xhuister@xmu.edu.cn
Dr. Xiaohui Wu received her bachelor degree and PhD degree in Automation from Xiamen University in 2006 and 2011, respectively. She is currently an Associate Professor in the Department of Automation, Xiamen University. Her research centers around bioinformatics.
She has authored (or co-authored) more than 60 peer-reviewed publications. As the first or corresponding author, she has published 20 peer-reviewed papers in journals ranked with Chinese Academy of Sciences JCR Q1/Q2 (including 13 top Journal papers), such as PNAS (IF:9.412), Genome Research (IF:11.093), Briefings in Bioinformatics (IF:8.99) and Bioinformatics (IF:5.61).
For scientific contributions please visit my Google Scholar profile: https://scholar.google.com/citations?user=ALru2t4AAAAJ&hl=en.
Qualifications
2011/07 PhD, Department of Automation, Xiamen University
2006/07 BSc, Department of Automation, Xiamen University
Experience
2015/07 - Present Professor, Soochow University
2015/08 - 2021/06 Associate Professor, Xiamen University
2011/09 - 2015/07 Assistant Professor, Xiamen University
2016/08 - 2017/08 Guest Scientist, University of Cologne
2009/10 - 2010/10 Guest Student, Miami University
Research Interests
(1) Single-cell sequencing data analysis
(2) Machine learning for big data analysis
(3) Omics data mining in RNA processing and gene expression regulation
(4) Construction of database or websites related to biomedical data
Grants (PI)
(1) Network modeling of alternative polyadenylation by integrating single-cell transcriptome data, 61871463, National Natural Science Foundation of China, 2019.1-2022.12,¥ 630K (In progress).
(2) Genome level analysis of the pattern and conservation of alternative polyadenylation of long noncoding RNAs in plants, 61673323, National Natural Science Foundation of China, 2017.1-2017.12, ¥ 160K (Closed).
(3) Identification and evolutional study of poly(A) signals in eukaryotes, 61201358, National Natural Science Foundation of China, 2013.1-2015.12, ¥ 250K (Closed).
(4) Research on molecular mechanism of autism based on big gene data, XDHT2020131A, 2020.05.01-2021.04.30, ¥ 450K (In progress).
(5) Genome-wide analysis of the regulatory mechanism of noncanonical poly(A) sites in plants, 2017J01068, Natural Science Foundation of Fujian Province of China, 2017.4-2020.4, ¥ 40K (Closed).
(6) Identification and evolutional study of poly(A) signals in eukaryotes, 2012J01154, Natural Science Foundation of Fujian Province of China, 2012.1-2014.12, ¥ 50K (Closed).
(7) Genome-wide analysis of polyadenylation signals and polyadenylation signal variations in eukaryotic genomes, 20120121120038, the Specialized Research Fund for the Doctoral Program of Higher Education of China, 2013.1-2015.12, ¥ 40K (Closed).
(8) Genome-wide analysis of the association of alternative polyadenylation and SNPs, 2013121025, Fundamental Research Funds for the Central Universities in China, 2013.1-2015.12, ¥ 270K (Closed).
Selected Papers (First/Corresponding Author)
(1) Wu X, Liu M, Downie B, Liang C, Ji G, Li QQ*, Hunt AG*: Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. Proc Natl Acad Sci USA2011, 108(30):12533-12538.
[ 2010IF: 9.771, JCR-Q1, Top Journal, Cited 232# ]
(2) 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 Res2016, 26(12):1753-1760.
[ 2016IF: 11.922, JCR-Q1, Top Journal, Cited 40# ]
(3) Wu X*, Liu T, Ye C, Ye W, Ji G: scAPAtrap: identification and quantification of alternative polyadenylation sites from single-cell RNA-seq data. Briefings in Bioinformatics 2020.
[ 2019IF: 8.99, JCR-Q1, Top Journal ]
(4) Chen M, Ji G, Fu H, Lin Q, Ye C, Ye W, Su Y, Wu X*: A survey on identification and quantification of alternative polyadenylation sites from RNA-seq data. Briefings in Bioinformatics2020, 21(4):1261–1276.
[ 2019IF: 8.99, JCR-Q1, Top Journal ]
(5) Ji G, Guan J, Zeng Y, Li QQ, Wu X*: Genome-wide identification and predictive modeling of polyadenylation sites in eukaryotes. Briefings in Bioinformatics 2015, 16(2):304-313.
[ 2015IF: 8.399, JCR-Q1, Top Journal, Cited 29# ]
(6) Ye P, Ye W, Ye C, Li S, Ye L, Ji G, Wu X*: scHinter: Imputing dropout events for single-cell RNA-seq data with limited sample size. Bioinformatics2020, 36(3):789–797.
[ 2019IF: 5.61, JCR-Q1, Top Journal ]
(7) Ji G, Ye W, Su Y, Chen M, Huang G, Wu X*: AStrap: identification of alternative splicing from transcript sequences without a reference genome. Bioinformatics2019, 35(15):2654-2656.
[ 2019IF: 5.61, JCR-Q1, Top Journal ]
(8) Ye W, Liu T, Ye C, Fu H, Ji G*, Wu X*: movAPA: Modeling and visualization of dynamics of alternative polyadenylation across biological samples. Bioinformatics 2020 (online).
[ 2019IF: 5.61, JCR-Q1, Top Journal ]
(9) Ye C, Long Y, Ji G, Li QQ*, Wu X*: APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data. Bioinformatics2018, 34(11):1841-1849.
[ 2018IF: 4.531, JCR-Q1, Top Journal, Cited 40# ]
(10) 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. Bioinformatics2018, 34(12):2123-2125.
[ 2018IF: 4.531, JCR-Q1, Top Journal ]
(11) Ji G, Li L, Li QQ, Wu X, Fu J, Chen G, Wu X*: PASPA: a web server for mRNA poly(A) site predictions in plants and algae. Bioinformatics2015, 31(10):1671-1673.
[ 2015IF: 5.766, JCR-Q1, Top Journal ]
(12) Zhu S, Ye W, Ye L, Fu H, Ye C, Xiao X, Ji Y, Lin W, Ji G, Wu X*: PlantAPAdb: A Comprehensive Database for Alternative Polyadenylation Sites in Plants.Plant Physiol 2020, 182(1):228-242.
[ 2019IF: 6.902, JCR-Q1, Top Journal ]
(13) Zhou Q, Fu H, Yang D, Ye C, Zhu S, Lin J, Ye W, Ji G, Ye X, Wu X*, Li Q*: Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies Japonica and Indica. The Plant Journal2019, 98(2):260-276.
[ 2019IF: 6.141, JCR-Q1, Top Journal ]
(14) Ye W, Wang T, Wei W, Lou S, Lan F, Zhu S, Li Q, Ji G, Lin C, Wu X*, Ma L*: The full-length transcriptome of Spartina alterniflora reveals the complexity of high salt tolerance in monocotyledonous halophyte. Plant and Cell Physiology2020, 61(5):882-896.
[ 2019IF: 4.062, JCR-Q2 ]
(15) Wu X*, Zhang Y, Li QQ*: PlantAPA: a portal for visualization and analysis of alternative polyadenylation in plants. Frontiers in Plant Science2016, 7.
[ 2016IF: 4.291, JCR-Q2 ]
(16) 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.
[ 2019IF: 3.594, JCR-Q2 ]
(17) Ye W, Ji G, Ye P, Long Y, Xiao X, Li S, Su Y, Wu X*: scNPF: an integrative framework assisted by network propagation and network fusion for preprocessing of single-cell RNA-seq data. BMC Genomics2019, 20(1):347.
[ 2019IF: 3.594, JCR-Q2 ]
(18) Wu X*, Zeng Y, Guan J, Ji G, Huang R, Li QQ*: Genome-wide characterization of intergenic polyadenylation sites redefines gene spaces in Arabidopsis thaliana. BMC Genomics 2015, 16(511):1-14.
[ 2015IF: 3.867 JCR-Q2 ]
(19) Wu X, Gaffney B, Hunt A*, Li Q*: Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. BMC Genomics 2014, 15(1):615.
[ 2014IF: 3.986, JCR-Q2 ]
(20) Zhu S, Wu X*, Fu H, Ye C, Chen M, Jiang Z*, Ji G*: Polyadenylation Signals in Xenopus tropicalis. Frontiers in Genetics2019, 10(647).
[ 2019IF: 3.258, JCR-Q2 ]
(21) Polyadenylation in Plants : Methods and Protocols. Springer2015. [Book Chapters]
(22) The Model Legume Medicago truncatula. John Wiley & Sons2019. [Book Chapter]
Selected Co-author Papers (in Top Journals)
(23) Ye C*, Zhou Q, Wu X, Yu C, Ji G, Saban DR, Li QQ*: scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data. Bioinformatics2019, 36(4):1262-1264.
[ 2019IF: 8.99, JCR-Q1, Top Journal ]
(24) Li H, Ye C, Ji G*, Wu X, Xiang Z, Li Y, Cao Y, Liu X, Douek D, Price D, Han J*: Recombinatorial Biases and Convergent Recombination Determine Interindividual TCR beta Sharing in Murine Thymocytes. J Immunol 2012, 189(5):2404-2413.
[ 2011IF: 5.788, JCR-Q1, Top Journal ]
(25) Thomas PE, Wu X, Liu M, Gaffney B, Ji G, Li QQ, Hunt AG*: Genome-Wide Control of Polyadenylation Site Choice by CPSF30 in Arabidopsis. Plant Cell 2012, 24(11):4376-4388.
[ 2011IF: 8.987, JCR-Q1, Top Journal ]
(26) Fu H, Wang P, Wu X, Zhou X, Ji G, Shen Y, Gao Y, Li QQ*, Liang J*: Distinct genome-wide alternative polyadenylation during the response to silicon availability in the marine diatom Thalassiosira pseudonana. The Plant Journal 2019, 99(10):67-80.
[ 2019IF: 6.141, JCR-Q1, Top Journal ]
(27) Lin J, Xu R, Wu X, Shen Y, Li QQ*: Role of Cleavage and Polyadenylation Specificity Factor 100: Anchoring Poly(A) Sites and Modulating Transcription Termination. The Plant Journal 2017, 91:829-839.
[ 2019IF: 6.141, JCR-Q1, Top Journal ]
(28) Hong L, Ye C, Lin J, Fu H, Wu X, Li QQ*: Alternative polyadenylation is involved in auxin-based plant growth and development. The Plant Journal 2017, 93(2):246-258.
[ 2019IF: 6.141, JCR-Q1, Top Journal ]
(29) Shen Y, Venu RC, Nobuta K, Wu X, Notibala V, Demirci C, Meyers BC, Wang G-L, Ji G, Li QQ*: Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing. Genome Res 2011, 21(9):1478-1486.
[ 2010IF=13.588, JCR-Q1, Top Journal ]
(30) Shen Y, Ji G, Haas BJ, Wu X, Zheng J, Reese GJ, Li QQ*: Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation. Nucleic Acids Res 2008, 36(9):3150-3161.
[ 2015IF=9.202, JCR-Q1, Top Journal ]
Courses Taught
2012/09 - 2020/07Fundamentals of Bioinformatics (32 class hours, Undergraduate)
2012/09 - 2020/07Bioinformatics (48 class hours, Graduate)
2012/09 - 2020/07Statistical Modeling and R Language (32 class hours, Graduate)
2020/02 - 2020/06Literature Retrieval and English Paper Writing (16 class hours, Graduate)
Awards and Honours
2012/04 First Prize of Tian Zhaowu Interdisciplinary Award of Xiamen University (Team Award)
2012/10 Excellent Doctoral Dissertation, Xiamen University
2013/04 First Prize of the 7th Natural Science Outstanding Academic Paper of Xiamen
2013/06 Second Prize of Excellent Doctoral Dissertation, Fujian
Professional Service Activities
2020/10 Secretary General of Xiamen Systems Engineering Association
2021/03 Associate Editor for Computational Genomics (specialty section of Frontiers in Genetics, Frontiers in Bioengineering and Biotechnology and Frontiers in Plant Science)