Xiaohui Wu

发表

scNPF: an integrative framework assisted by network propagation and network fusion for preprocessing of single-cell RNA-seq data

Guoli Ji, Pengchao Ye, Wenbin Ye, 2019, BMC Genomics.

SCNMLRR: Single Cell Clustering Based on Low-rank Non-negative Matrix Factorization

Guoli Ji, Xiaohui Wu, Xin Wei, 2020, ICBBS.

Learning association for single-cell transcriptomics by integrating profiling of gene expression and alternative polyadenylation

Sheng Zhu, Guoli Ji, Wenbin Ye, 2021, bioRxiv.

PlantAPAdb: A Comprehensive Database for Alternative Polyadenylation Sites in Plants1[CC-BY]

Sheng Zhu, Congting Ye, Guoli Ji, 2019, Plant Physiology.

Genome level analysis of rice mRNA 3′-end processing signals and alternative polyadenylation

Guoli Ji, Jianti Zheng, Yingjia Shen, 2008, Nucleic acids research.

A classification-based prediction model of messenger RNA polyadenylation sites.

Guoli Ji, Jiangyin Huang, Yingjia Shen, 2010, Journal of theoretical biology.

Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation

Guoli Ji, Chun Liang, Bruce Downie, 2011, Proceedings of the National Academy of Sciences.

Genome-Wide Control of Polyadenylation Site Choice by CPSF30 in Arabidopsis[C][W][OA]

Guoli Ji, Xiaohui Wu, Q. Li, 2012, Plant Cell.

Genome-wide characterization of intergenic polyadenylation sites redefines gene spaces in Arabidopsis thaliana

Guoli Ji, Jinting Guan, Yong Zeng, 2015, BMC Genomics.

Prediction of plant mRNA polyadenylation sites.

Guoli Ji, Xiaohui Wu, Q. Li, 2015, Methods in molecular biology.

Modeling of Genome-Wide Polyadenylation Signals in Xenopus tropicalis

Sheng Zhu, Congting Ye, Guoli Ji, 2019, Front. Genet..

Ratio-Based Analysis of Differential mRNA Processing and Expression of a Polyadenylation Factor Mutant pcfs4 Using Arabidopsis Tiling Microarray

Guoli Ji, Xiaohui Wu, Q. Li, 2011, PloS one.

Using consensus interval partial least square in near infrared spectra analysis

Guangzao Huang, Mingshun Yuan, Xiaohui Wu, 2015 .

A two-layer model for gene clustering using poly(A) site data

Congting Ye, Guoli Ji, Wenbin Ye, 2017, 2017 3rd IEEE International Conference on Control Science and Systems Engineering (ICCSSE).

Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice

Xiaohui Wu, Q. Li, A. Hunt, 2014, BMC Genomics.

Role of cleavage and polyadenylation specificity factor 100: anchoring poly(A) sites and modulating transcription termination

Xiaohui Wu, Q. Li, Y. Shen, 2017, The Plant journal : for cell and molecular biology.

Cluster analysis of replicated alternative polyadenylation data using canonical correlation analysis

Guoli Ji, Pengchao Ye, Wenbin Ye, 2019, BMC Genomics.

Computational analysis of plant polyadenylation signals.

Guoli Ji, Xiaohui Wu, Q. Li, 2015, Methods in molecular biology.

Comprehensive recognition of messenger RNA polyadenylation patterns in plants

Guoli Ji, Xiaohui Wu, Q. Li, 2012 .

Alternative polyadenylation is involved in auxin‐based plant growth and development

Congting Ye, Xiaohui Wu, Q. Li, 2018, The Plant journal : for cell and molecular biology.

In silico prediction of mRNA poly(A) sites in Chlamydomonas reinhardtii

Guoli Ji, Yong Zeng, Xiaohui Wu, 2012, Molecular Genetics and Genomics.

Chapter 2 Prediction of Plant mRNA Polyadenylation Sites

Guoli Ji, Xiaohui Wu, Q. Li, 2018 .

The full-length transcriptome of Spartina alterniflora reveals the complexity of high salt tolerance in monocotyledonous halophyte.

Sheng Zhu, Guoli Ji, Wenbin Ye, 2020, Plant & cell physiology.

The full-length transcriptome of Spartina alterniflora reveals the complexity of high salt tolerance in monocotyledonous halophyte

Sheng Zhu, Guoli Ji, Wenbin Ye, 2019, bioRxiv.

PlantAPA: A Portal for Visualization and Analysis of Alternative Polyadenylation in Plants

Xiaohui Wu, Q. Li, Yumin Zhang, 2016, Front. Plant Sci..

PolyAtailor: measuring poly(A) tail length from short-read and long-read sequencing data

Xiaohui Wu, L. Hao, Mengfei Liu, 2022, Briefings Bioinform..

Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice

Xiaohui Wu, Q. Li, A. Hunt, 2014, BMC Genomics.

A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-seq, and Single-cell RNA-seq

Congting Ye, Wenbin Ye, Xiaohui Wu, 2022, bioRxiv.

stAPAminer: Mining Spatial Patterns of Alternative Polyadenylation for Spatially Resolved Transcriptomic Studies

Sheng Zhu, Guoli Ji, Pengchao Ye, 2022, bioRxiv.

Genome-wide characterization of intergenic polyadenylation sites redefines gene spaces in Arabidopsis thaliana

Guoli Ji, Jinting Guan, Yong Zeng, 2015, BMC Genomics.

APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data

Xiaohui Wu, Qingshun Quinn Li, Guoli Ji, 2018, Bioinform..

Bioinformatics Analysis of Alternative Polyadenylation in Green Alga Chlamydomonas reinhardtii Using Transcriptome Sequences from Three Different Sequencing Platforms

Guoli Ji, Xiaohui Wu, Q. Li, 2014, G3: Genes, Genomes, Genetics.

Regulatory network-based imputation of dropouts in single-cell RNA sequencing data

Andreas Beyer, Ana Carolina Leote, Xiaohui Wu, 2019, bioRxiv.

Heat Shock Responsive Gene Expression Modulated by mRNA Poly(A) Tail Length

Xiaohui Wu, Q. Li, Yiling Hong, 2020, Frontiers in Plant Science.

PAcluster: Clustering polyadenylation site data using canonical correlation analysis

Xiaohui Wu, Guoli Ji, Congting Ye, 2017, J. Bioinform. Comput. Biol..

Genome-wide identification and predictive modeling of polyadenylation sites in eukaryotes

Yong Zeng, Xiaohui Wu, Qingshun Quinn Li, 2015, Briefings Bioinform..

Alternative 3′ UTRs contributes to post-transcriptional gene expression regulation under high salt stress

Sheng Zhu, Guoli Ji, Wenbin Ye, 2022, bioRxiv.

A survey on identification and quantification of alternative polyadenylation sites from RNA-seq data

Guoli Ji, Congting Ye, Hongjuan Fu, 2020, Briefings Bioinform..

Distinct genome-wide alternative polyadenylation during the response to silicon availability in the marine diatom Thalassiosira pseudonana.

Guoli Ji, Peng Wang, Junrong Liang, 2019, The Plant journal : for cell and molecular biology.

Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing.

B. Meyers, Guoli Ji, Xiaohui Wu, 2011, Genome research.

QuantifyPoly(A): reshaping alternative polyadenylation landscapes of eukaryotes with weighted density peak clustering

Guoli Ji, Congting Ye, Wenbin Ye, 2021, Briefings Bioinform..

scNPF: an integrative framework assisted by network propagation and network fusion for preprocessing of single-cell RNA-seq data

Guoli Ji, Pengchao Ye, Wenbin Ye, 2019, BMC genomics.

Genome-Wide Comparative Analyses of Polyadenylation Signals in Eukaryotes Suggest a Possible Origin of the AAUAAA Signal

Guoli Ji, Xiaohui Wu, Q. Li, 2019, International journal of molecular sciences.

Recombinatorial Biases and Convergent Recombination Determine Interindividual TCRβ Sharing in Murine Thymocytes

Yuanyue Li, Jiahuai Han, D. Douek, 2012, The Journal of Immunology.

scLINE: A multi-network integration framework based on network embedding for representation of single-cell RNA-seq data

Guoli Ji, Huoyou Li, Xuesong Xiao, 2021, J. Biomed. Informatics.

Genome-wide dynamics of alternative polyadenylation in rice

Guoli Ji, Xinfu Ye, Yingjia Shen, 2016, Genome research.

Genome-wide alternative polyadenylation dynamics in response to biotic and abiotic stresses in rice.

Congting Ye, Guoli Ji, Xiaohui Wu, 2019, Ecotoxicology and environmental safety.

This information is current as Sharing in Murine Thymocytes β TCR Recombination Determine Interindividual Recombinatorial Biases and Convergent

Guoli Ji, Congting Ye, Daniel C. Douek, 2012 .

Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies, japonica and indica

Sheng Zhu, Congting Ye, Guoli Ji, 2019, The Plant journal : for cell and molecular biology.

A Pipeline to Identify Novel 3’ UTRs and Widespread Intergenic Transcription by Combination of Polyadenylation Sites and RNA-seq Data

Guoli Ji, Xiaohui Wu, Yibo Zhuang, 2020, ICBBS.

scAPAdb: a comprehensive database of alternative polyadenylation at single-cell resolution

Sheng Zhu, Guoli Ji, Wenbin Ye, 2021, Nucleic Acids Res..

scAPAtrap: identification and quantification of alternative polyadenylation sites from single-cell RNA-seq data

Tao Liu, Guoli Ji, Congting Ye, 2020, Briefings Bioinform..

Cluster analysis of replicated alternative polyadenylation data using canonical correlation analysis

Guoli Ji, Pengchao Ye, Wenbin Ye, 2019, BMC Genomics.

Data Analysis of Arabidopsis Tiling Array

Xiaohui Wu, Guoli Ji, Qingshun Quinn Li, 2009, 2009 First International Conference on Information Science and Engineering.

PROBER: Segmentation and Differential Analysis Tool for Tiling Microarray Data

Xiaohui Wu, Qingshun Quinn Li, Guoli Ji, 2009, 2009 2nd International Conference on Biomedical Engineering and Informatics.

Alternative 3'-untranslated regions regulate high salt tolerance of Spartina alterniflora.

Sheng Zhu, Guoli Ji, Wenbin Ye, 2023, Plant physiology.

PASPA: a web server for mRNA poly(A) site predictions in plants and algae

Gong Chen, Lei Li, Xiaohui Wu, 2015, Bioinform..

Predictive modeling of plant messenger RNA polyadenylation sites

Xiaohui Wu, Qingshun Quinn Li, Guoli Ji, 2007, BMC Bioinformatics.

Poly(A)-tag deep sequencing data processing to extract poly(A) sites.

Xiaohui Wu, Guoli Ji, Qingshun Quinn Li, 2015, Methods in molecular biology.

scHinter: imputing dropout events for single-cell RNA-seq data with limited sample size

Guoli Ji, Congting Ye, Xiaohui Wu, 2019, Bioinform..

A normalization method based on variance and median adjustment for massive mRNA polyadenylation data

Y. Wang, Guoli Ji, Xiaohui Wu, 2013 .

scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data

Xiaohui Wu, Qingshun Quinn Li, Guoli Ji, 2019, Bioinform..

Genome-wide analysis of the associations between polyadenylation sites and repeated sequences in Arabidopsis thaliana

Cheng Sun, Xiaohui Wu, Yuntian Wang, 2015, 2015 8th International Conference on Biomedical Engineering and Informatics (BMEI).

VAAPA: A web platform for visualization and analysis of alternative polyadenylation

Guoli Ji, Jinting Guan, Xiaohui Wu, 2015, Comput. Biol. Medicine.

In silico prediction of mRNA poly(A) sites in Chlamydomonas reinhardtii

Guoli Ji, Yong Zeng, Xiaohui Wu, 2012, Molecular Genetics and Genomics.

PATMAP: Polyadenylation Site Identification from Next-Generation Sequencing Data

Junfeng Yao, Xiaohui Wu, Zhe Xiang, 2012, HAIS.

Identification of mRNA poly(A) signal patterns

Qi Liu, Junfeng Yao, Xiaohui Wu, 2011, 2011 International Symposium on Innovations in Intelligent Systems and Applications.

DNA/RNA hybrid primer mediated poly(A) tag library construction for Illumina sequencing.

Xiaohui Wu, Q. Li, Man Liu, 2015, Methods in molecular biology.

Implementation of a classification-based prediction model for plant mRNA Poly(A) sites

Xiaohui Wu, Qingshun Quinn Li, Guoli Ji, 2008, 2008 3rd International Conference on Bio-Inspired Computing: Theories and Applications.

Identification of secondary structures surrounding plant polyadenylation sites

Xiaohui Wu, Sien Yang, 2022, Other Conferences.

Messenger RNA Polyadenylation Site Recognition in Green Alga Chlamydomonas Reinhardtii

Xiaohui Wu, Qingshun Quinn Li, Guoli Ji, 2010, ISNN.

Modeling Plant mRNA Poly(A) Sites: Software Design and Implementation

Xiaohui Wu, Guoli Ji, Jianti Zheng, 2007 .