学术论文

代表性论文（第一或通讯作者）

2024

• Wang X#, Lian Q#, Dong H, Xu S, Su Y, Wu X* Benchmarking algorithms for gene set scoring of single-cell ATAC-seq data Genomics, Proteomics & Bioinformatics FullText | PubMed
• Zhang Y#, Hu C#, Wu X*, Song J* Calib-RT: an open source python package for peptide retention time calibration in DIA mass spectrometry data Bioinformatics FullText | PubMed | Tool
• Bi X#, Ye W#, Chen X, Yang N, Wu X* vizAPA: visualizing dynamics of alternative polyadenylation from bulk and single-cell data Bioinformatics FullText | PubMed | Tool
• Bi X#, Zhu S#, Liu F, Wu X* Dynamics of alternative polyadenylation in single root cells of Arabidopsis thaliana Frontiers in Plant Science FullText

2023

• Ye W, Lian Q, Ye C, Wu X* A survey on methods for predicting polyadenylation sites from DNA sequences, bulk RNA-seq and single-cell RNA-seq Genomics, Proteomics & Bioinformatics FullText | PubMed
• Wang T#, Ye W#, Zhang J, Li H, Zeng W, Zhu S, Ji G, Wu X*, Ma L* Alternative 3′ UTRs regulate post-transcriptional gene expression under high salt stress in Spartina alterniflora Plant Physiology FullText | PubMed
• Ji G, Tang Q, Zhu S, Zhu J, Ye P, Xia S, Wu X* stAPAminer: mining spatial patterns of alternative polyadenylation for spatially resolved transcriptomic studies Genomics, Proteomics & Bioinformatics FullText | PubMed | Tool
• Xu S, Kang L, Bi X, Wu X* Integrative Analysis of Gene Expression and Alternative Polyadenylation from Single-Cell RNA-seq Data Bioinformatics Research and Applications. ISBRA 2023. Lecture Notes in Computer Science FullText

2022

• Zhu S, Lian Q, Ye W, Qin W, Wu Z, Ji G, Wu X* scAPAdb: a comprehensive database of alternative polyadenylation at single-cell resolution Nucleic Acids Research FullText | PubMed | Database
• Liu M, Hao L, Yang S, Wu X* PolyAtailor: measuring poly(A) tail length from short-read and long-read sequencing data Briefings in Bioinformatics FullText | PubMed | Tool
• Leote AC#, Wu X#, Beyer A* Regulatory network-based imputation of dropouts in single-cell RNA sequencing data PLOS Computational Biology FullText | PubMed | Tool

2021

• 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 FullText | PubMed | Tool
• Ye W#, Liu T#, Fu H, Ye C, Ji G*, Wu X* movAPA: Modeling and visualization of dynamics of alternative polyadenylation across biological samples Bioinformatics FullText | PubMed | Tool

2020

• 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 Bioinformatics FullText | PubMed | Code
• 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 Bioinformatics FullText | PubMed | Tool
• 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 Physiology FullText | PubMed | Database
• 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 Physiology FullText | PubMed | Database

2019

• 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 FullText | PubMed | Tool
• 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 FullText | PubMed
• Zhu S, Wu X*, Fu H, Ye C, Chen M, Jiang Z*, Ji G* Modeling of genome-wide polyadenylation signals in Xenopus tropicalis Frontiers in Genetics FullText | PubMed
• 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 FullText | PubMed | Tool
• 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 Genomics FullText | PubMed | Tool

2018

• 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 FullText | PubMed | Tool
• Ye C, Long Y, Ji G, Li QQ*, Wu X* APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data Bioinformatics FullText | PubMed | Tool

Before 2018

• 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 Research, 2016 FullText | PubMed

• Wu X*, Zhang Y, Li QQ* PlantAPA: a portal for visualization and analysis of alternative polyadenylation in plants Frontiers in Plant Science, 2017 FullText | PubMed

• 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 FullText | PubMed

• 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 Bioinformatics, 2015 FullText | PubMed | Tool

• 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 FullText | PubMed

• 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 FullText | PubMed

• Wu X*, Ji G, Zeng Y In silico prediction of mRNA poly(A) sites in Chlamydomonas reinhardtii Mol Genet Genomics, 2012 FullText | PubMed

• 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 USA, 2011 FullText | PubMed

代表性论文（合作作者）

• Ye C*, Zhao D, Ye W, Wu X, Li Q, Lin J*. 2021. QuantifyPoly(A): reshaping alternative polyadenylation landscapes of eukaryotes with weighted density peak clustering. Briefings in Bioinformatics bbab268.*
• Ye C*#, Zhou Q#, Wu X, Yu C, Ji G, Saban DR, Li QQ. 2019. scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data. Bioinformatics 36(4):1262-1264.
• Li H#, Ye C#, Ji G*, Wu X, Xiang Z, Li Y, Cao Y, Liu X, Douek D, Price D, Han J*. 2012. Recombinatorial biases and convergent recombination determine interindividual TCR beta sharing in Murine Thymocytes. Journal of Immunol 189(5):2404-2413.
• Thomas PE, Wu X, Liu M, Gaffney B, Ji G, Li QQ*, Hunt AG*. 2012. Genome-wide control of polyadenylation site choice by CPSF30 in Arabidopsis. Plant Cell 24(11):4376-4388.
• Fu H, Wang P, Wu X, Zhou X, Ji G, Shen Y, Gao Y, Li QQ*, Liang J*. 2019. Distinct genome-wide alternative polyadenylation during the response to silicon availability in the marine diatom Thalassiosira pseudonana. Plant Journal 99(10):67-80.
• Lin J, Xu R, Wu X, Shen Y, Li QQ*. 2017. Role of cleavage and polyadenylation specificity factor 100: anchoring poly(A) sites and modulating transcription termination. Plant Journal 91:829-839.
• Hong L, Ye C, Lin J, Fu H, Wu X, Li QQ*. 2017. Alternative polyadenylation is involved in auxin-based plant growth and development. Plant Journal 93(2):246-258.
• Shen Y, Venu RC, Nobuta K, Wu X, Notibala V, Demirci C, Meyers BC, Wang G-L, Ji G, Li QQ*. 2011. Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing. Genome Research 21(9):1478-1486.
• Shen Y, Ji G, Haas BJ, Wu X, Zheng J, Reese GJ, Li QQ*. 2008. Genome level analysis of rice mRNA 3’-end processing signals and alternative polyadenylation. Nucleic Acids Research 36(9):3150-3161.