Guoli Ji

发表

Determinants of public T cell responses

Jiahuai Han, Hanjie Li, Congting Ye, 2012, Cell Research.

A Sparse Classification Based on a Linear Regression Method for Spectral Recognition

Xi Chen, Guoli Ji, Xiaojing Chen, 2019, Applied Sciences.

Exploiting aberrant mRNA expression in autism for gene discovery and diagnosis

Guoli Ji, Jinting Guan, Yong Zeng, 2015, Human Genetics.

Exploiting aberrant mRNA expression in autism for gene discovery and diagnosis

Guoli Ji, Jinting Guan, Yong Zeng, 2016 .

Aberrant gene expression in autism

James J. Cai, G. Wang, Guoli Ji, 2015 .

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.

Recent Advances in Mathematical Modeling and Simulation of DNA Replication Process

Congting Ye, Guoli Ji, Jinting Guan, 2013 .

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..

detectMITE: A novel approach to detect miniature inverted repeat transposable elements in genomes

Guoli Ji, Congting Ye, Chun Liang, 2016, Scientific Reports.

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.

Commonality in dysregulated expression of gene sets in cortical brains of individuals with autism, schizophrenia, and bipolar disorder

James J. Cai, P. Sham, Guoli Ji, 2019, Translational Psychiatry.

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).

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 .

Overdispersed gene expression in schizophrenia

James J. Cai, Guoli Ji, Guangzao Huang, 2020, npj Schizophrenia.

Overdispersed gene expression characterizes schizophrenic brains

James J. Cai, Guoli Ji, Guangzao Huang, 2018, bioRxiv.

Laser-Induced Breakdown Spectroscopy for Rapid Discrimination of Heavy-Metal-Contaminated Seafood Tegillarca granosa

Xi Chen, Xiaojing Chen, Jing Jiang, 2017, Sensors.

Extraction, isolation and structural characterization of polysaccharides from a red alga Gloiopeltis furcata

Guoli Ji, Guangli Yu, Huashi Guan, 2010 .

Shared and Cell-Type-Specific Gene Expression Patterns Associated With Autism Revealed by Integrative Regularized Non-Negative Matrix Factorization

Guoli Ji, Jinting Guan, Yan Zhuang, 2022, Frontiers in Genetics.

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

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

A Feature Selection Method for Tissue-Specific Alternative Polyadenylation Sites Data in Rice

Guoli Ji, Pengchao Ye, Shuchao Li, 2019, IOP Conference Series: Earth and Environmental Science.

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.

ProbAlign: a re-alignment method for long sequencing reads

Ting Chen, Rui Jiang, Guoli Ji, 2014, bioRxiv.

PlantOrDB: a genome-wide ortholog database for land plants and green algae

Congting Ye, Guoli Ji, C. Liang, 2015, BMC Plant Biology.

Pattern analysis approach reveals restriction enzyme cutting abnormalities and other cDNA library construction artifacts using raw EST data

J. Karro, Guoli Ji, Xiaolin Liu, 2012, BMC Biotechnology.

expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension.

James J. Cai, G. Wang, Guoli Ji, 2014 .

Alternative polyadenylation drives genome-to-phenome information detours in the AMPKα1 and AMPKα2 knockout mice

Jon F. Davis, Xing Fu, Xiaoping Zhou, 2018, Scientific Reports.

DeepAPArice: a deep learning model for poly(A) site intelligent prediction in rice using convolutional neural network

Guoli Ji, Haiyong He, 2022, 2022 IEEE 2nd International Conference on Power, Electronics and Computer Applications (ICPECA).

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

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

scAPAmod: Profiling Alternative Polyadenylation Modalities in Single Cells from Single-Cell RNA-Seq Data

Guoli Ji, Lishan Ye, Hongjuan Fu, 2022, International journal of molecular sciences.

The cell-free DNA methylome captures distinctions between localized and metastatic prostate tumors

Trevor J Pugh, P. Awadalla, A. Wyatt, 2022, Nature Communications.

SRGS: sparse partial least squares-based recursive gene selection for gene regulatory network inference

Guoli Ji, Jinting Guan, Yan Zhuang, 2022, BMC Genomics.

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

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

LemK_MSA: A Multiple Sequence Alignment Method with Sequence Vectorization Based on Lempel-Ziv

Zijiang Yang, Guoli Ji, Jing Ci Yao, 2013 .

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

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

Gene Screening for Autism Based on Cell-type-specific Predictive Models

Yang Wang, Jinting Guan, Guoli Ji, 2020, 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Whole Genome Analysis of Polyadenylation Sites in Long Non-coding RNAs in Oryza Sativa

Guoli Ji, Mengfei Liu, 2021, ICBBT.

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.

Cell Type-Specific Predictive Models Perform Prioritization of Genes and Gene Sets Associated With Autism

Guoli Ji, Jinting Guan, Yibo Zhuang, 2021, Frontiers in Genetics.

WebGMAP: a web service for mapping and aligning cDNA sequences to genomes

Lin Liu, Guoli Ji, Chun Liang, 2009, Nucleic Acids Res..

WebTraceMiner: a web service for processing and mining EST sequence trace files

Gang Wang, Lin Liu, Guoli Ji, 2007, Nucleic Acids Res..

Gene Module Analysis Reveals Cell-Type Specificity and Potential Target Genes in Autism’s Pathogenesis

Guoli Ji, Jinting Guan, Shuchao Li, 2021, Biomedicines.

Aging Shapes the Population-Mean and -Dispersion of Gene Expression in Human Brains

James J. Cai, Guoli Ji, Jinting Guan, 2016, bioRxiv.

Alternative polyadenylation coordinates embryonic development, sexual dimorphism and longitudinal growth in Xenopus tropicalis

Jon F. Davis, M. Griswold, Guoli Ji, 2019, Cellular and Molecular Life Sciences.

Alternative polyadenylation drives genome-to-phenome information detours in the AMPKα1 and AMPKα2 knockout mice

Jon F. Davis, Xing Fu, Xiaoping Zhou, 2018, Scientific Reports.

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..

Aberrant Gene Expression in Humans

Guoli Ji, Yong Zeng, Ence Yang, 2015, PLoS genetics.

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..

Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension

James J. Cai, Guoli Ji, E. Yang, 2014, Front. Genet..

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.

detectIR: A Novel Program for Detecting Perfect and Imperfect Inverted Repeats Using Complex Numbers and Vector Calculation

Guoli Ji, Congting Ye, Chun Liang, 2014, PloS one.

ConiferEST: an integrated bioinformatics system for data reprocessing and mining of conifer expressed sequence tags (ESTs)

Gang Wang, Guoli Ji, Chun Liang, 2007, BMC Genomics.

Aging shapes the population-mean and ‐dispersion of gene expression in human brains

James J. Cai, Guoli Ji, Jinting Guan, 2016, bioRxiv.

Cell Type-Specific Gene Network-Based Analysis Depicts the Heterogeneity of Autism Spectrum Disorder

Guoli Ji, Jinting Guan, Yiping Lin, 2020, Frontiers in Cellular Neuroscience.

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.

Extraction of poly(A) sites from large-scale RNA-Seq data.

Guoli Ji, Chun Liang, Qingshun Quinn Li, 2015, Methods in molecular biology.

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

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

An analytical method for the identification of cell type-specific disease gene modules

Guoli Ji, Jinting Guan, Junchao Gao, 2021, Journal of Translational Medicine.

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.

Human brain cell type-specific gene co-expression associated with autism spectrum disorder

Guoli Ji, Jinting Guan, Shuchao Li, 2019, 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

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.

Comparative Research of Different Dimension Reduction Methods Combined with RWR Network Smoothing in Single Cell RNA-seq Data

Wenbin Ye, Xuesong Xiao, Pengchao Ye, 2020, IOP Conference Series: Earth and Environmental Science.

High throughput TCR sequence alignment using multi-GPU with inter-task parallelization

Qiang Li, Qi Liu, Guoli Ji, 2012, 2012 IEEE-EMBS Conference on Biomedical Engineering and Sciences.

ConiferEST: an integrated bioinformatics system for data reprocessing and mining of conifer expressed sequence tags (ESTs)

G. Wang, Yuansheng Liu, Guoli Ji, 2007, BMC Genomics.

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 .

Single-nucleus gene and gene set expression-based similarity network fusion identifies autism molecular subtypes

Guoli Ji, Jinting Guan, Xilin Gao, 2023, BMC Bioinformatics.

AEGS: identifying aberrantly expressed gene sets for differential variability analysis

Guoli Ji, Congting Ye, Jinting Guan, 2017, Bioinform..

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

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

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.

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.

scIAE: an integrative autoencoder-based ensemble classification framework for single-cell RNA-seq data

Guoli Ji, Jinting Guan, Yang Wang, 2021, Briefings Bioinform..

Alternative polyadenylation coordinates embryonic development, sexual dimorphism and longitudinal growth in Xenopus tropicalis

Jon F. Davis, M. Griswold, Guoli Ji, 2019, Cellular and Molecular Life Sciences.

Messenger RNA Polyadenylation Site Recognition in Green Alga Chlamydomonas Reinhardtii

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

CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis

Jie Zhang, Qi Liu, Pei Li, 2012, Bioinform..

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

Xiaohui Wu, Guoli Ji, Jianti Zheng, 2007 .

An AdaBoost Algorithm for the Identification of Arabidopsis Messenger RNA Polyadenylation Sites

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

Recognition of Plant mRNA Polyadenylation Sites Based on High-Dimensional Space Points' Covering Method

Qingshun Quinn Li, Guoli Ji, Dan Zou, 2008, 2008 International Symposium on Information Science and Engineering.