Yu Xue

发表

Inhibiting PD-L1 palmitoylation enhances T-cell immune responses against tumours

H. Yao, Jiang Lan, Chushu Li, 2019, Nature Biomedical Engineering.

dbPSP 2.0, an updated database of protein phosphorylation sites in prokaryotes

Yu Xue, Ying Shi, Ying Zhang, 2020, Scientific Data.

Systematic Analysis of Protein Phosphorylation Networks From Phosphoproteomic Data*

Hongyang Wang, H. Zou, Yu Xue, 2012, Molecular & Cellular Proteomics.

Computational analysis of phosphoproteomics: progresses and perspectives.

Yu Xue, Zexian Liu, Jian Ren, 2011, Current protein & peptide science.

Integrated omics in Drosophila uncover a circadian kinome

Yu Xue, Bo Wen, Ying Zhang, 2020, Nature Communications.

Systematic characterization of small RNAome during zebrafish early developmental stages

Qing Yang, Zexian Liu, Yuanwei Zhang, 2014, BMC Genomics.

Systematic Analysis of the Phosphoproteome and Kinase-substrate Networks in the Mouse Testis*

Yu Xue, Zexian Liu, Xuejiang Guo, 2014, Molecular & Cellular Proteomics.

GPS: a novel group-based phosphorylation predicting and scoring method.

Yu Xue, X. Yao, Feng-Feng Zhou, 2004, Biochemical and biophysical research communications.

GPS 2.0, a Tool to Predict Kinase-specific Phosphorylation Sites in Hierarchy *S

Yu Xue, Changjiang Jin, X. Yao, 2008, Molecular & Cellular Proteomics.

PhosSNP for Systematic Analysis of Genetic Polymorphisms That Influence Protein Phosphorylation*

Zineng Yuan, Zhaolei Zhang, Yu Xue, 2009, Molecular & Cellular Proteomics.

A summary of computational resources for protein phosphorylation.

Yu Xue, Changjiang Jin, X. Yao, 2010, Current protein & peptide science.

GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection.

Yu Xue, Changjiang Jin, Zexian Liu, 2011, Protein engineering, design & selection : PEDS.

Computational Prediction of Post-Translational Modification Sites in Proteins

Yu Xue, Zexian Liu, Jian Ren, 2011 .

DOG 1.0: illustrator of protein domain structures

Yu Xue, Changjiang Jin, X. Yao, 2009, Cell Research.

GPS-PUP: computational prediction of pupylation sites in prokaryotic proteins.

Yu Xue, Zexian Liu, Jian Ren, 2011, Molecular Biosystems.

Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs

Jinyan Li, Ziding Zhang, Yu Xue, 2015, PloS one.

HemI: A Toolkit for Illustrating Heatmaps

Yu Xue, Zexian Liu, Wankun Deng, 2014, PloS one.

GPS-PAIL: prediction of lysine acetyltransferase-specific modification sites from protein sequences

Yu Xue, Ying Zhang, Chenwei Wang, 2016, Scientific Reports.

Mal-Lys: prediction of lysine malonylation sites in proteins integrated sequence-based features with mRMR feature selection

Ling-Yun Wu, Yu Xue, Yan Xu, 2016, Scientific Reports.

Systematic study of protein sumoylation: Development of a site‐specific predictor of SUMOsp 2.0

Yu Xue, Andrew Shaw, Changjiang Jin, 2009, Proteomics.

PLMD: An updated data resource of protein lysine modifications.

Yu Xue, Ying Zhang, Shaofeng Lin, 2017, Journal of genetics and genomics = Yi chuan xue bao.

Reconfiguring phosphorylation signaling by genetic polymorphisms affects cancer susceptibility.

Zexian Liu, Yongbo Wang, Jian Ren, 2015, Journal of molecular cell biology.

GPS-SNO: Computational Prediction of Protein S-Nitrosylation Sites with a Modified GPS Algorithm

Zexian Liu, Changjiang Jin, Xinjiao Gao, 2010, PloS one.

CSS-Palm 2.0: an updated software for palmitoylation sites prediction.

Changjiang Jin, Xinjiao Gao, Xuebiao Yao, 2008, Protein engineering, design & selection : PEDS.

[Post-translational modification (PTM) bioinformatics in China: progresses and perspectives].

Ao Li, Lu Xie, Jian Ren, 2015, Yi chuan = Hereditas.

Guidelines for the use and interpretation of assays formonitoring autophagy (3rd edition)

Sangeeta Khare, Xin Qi, Ying Wang, 2016 .

Computationally characterizing and comprehensive analysis of zinc-binding sites in proteins.

Zexian Liu, Yongbo Wang, Yu Xue, 2014, Biochimica et Biophysica Acta.

THANATOS: an integrative data resource of proteins and post-translational modifications in the regulation of autophagy

Zexian Liu, Yongbo Wang, Wankun Deng, 2018, Autophagy.

Towards a better understanding of the novel avian-origin H7N9 influenza A virus in China

Zexian Liu, Yongbo Wang, Tianshun Gao, 2013, Scientific Reports.

Ubiquitin and Ubiquitin-Like Conjugations in Complex Diseases: A Computational Perspective

Yu Xue, Zexian Liu, Yongbo Wang, 2013 .

GPS-PBS: A Deep Learning Framework to Predict Phosphorylation Sites that Specifically Interact with Phosphoprotein-Binding Domains

Yu Xue, Shaofeng Lin, Chenwei Wang, 2020, Cells.

Enhanced Purification of Ubiquitinated Proteins by Engineered Tandem Hybrid Ubiquitin-binding Domains (ThUBDs)*

Z. Deng, Yu Xue, Lingyan Ping, 2016, Molecular & Cellular Proteomics.

Enhanced Purification of Ubiquitinated Proteins by Engineered Tandem Hybrid Ubiquitin-binding Domains (ThUBDs)*

Z. Deng, Yu Xue, Lingyan Ping, 2016, Molecular & Cellular Proteomics.

Phosphoproteome-based kinase activity profiling reveals the critical role of MAP2K2 and PLK1 in neuronal autophagy

Yu Xue, Wankun Deng, Lili Ma, 2017, Autophagy.

Phosphoproteome Analysis Reveals Phosphorylation Underpinnings in the Brains of Nurse and Forager Honeybees (Apis mellifera)

Yu Xue, Han Cheng, Bin Han, 2017, Scientific Reports.

Dysbindin as a novel biomarker for pancreatic ductal adenocarcinoma identified by proteomic profiling

Yu Xue, X. Yao, Dongmei Wang, 2016, International journal of cancer.

PTMsnp: A Web Server for the Identification of Driver Mutations That Affect Protein Post-translational Modification

Yu Xue, Zhixiang Zuo, Shaofeng Lin, 2020, Frontiers in Cell and Developmental Biology.

DeepPhagy: a deep learning framework for quantitatively measuring autophagy activity in Saccharomyces cerevisiae

Yu Xue, Ying Zhang, Chenwei Wang, 2020, Autophagy.

Yu Xue, Yong E. Zhang, Shunping He, 2015, Molecular Genetics and Genomics.

An integrative multi-omics approach uncovers the regulatory role of CDK7 and CDK4 in autophagy activation induced by silica nanoparticles

Yu Xue, Ying Zhang, Chenwei Wang, 2020, Autophagy.

Pan-Cancer Analysis Reveals the Functional Importance of Protein Lysine Modification in Cancer Development

Yu Xue, Zhixiang Zuo, Bosu Hu, 2018, Front. Genet..

Mechanism of cargo recognition by retromer-linked SNX-BAR proteins

Yu Xue, Wankun Deng, D. Billadeau, 2020, PLoS biology.

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1

Mark R. Marten, Erinna F. Lee, Dana L. Miller, 2021, Autophagy.

Computational identification of protein kinases and kinase-specific substrates in plants.

Yu Xue, Zexian Liu, Han Cheng, 2015, Methods in molecular biology.

Computational identification of protein kinases and kinase-specific substrates in plants.

Yu Xue, Zexian Liu, Han Cheng, 2015, Methods in molecular biology.

Analysis of phosphorylation sites on autophagy proteins

Yu Xue, Di Miao, Zexian Liu, 2015, Protein & Cell.

GPS-MBA: Computational Analysis of MHC Class II Epitopes in Type 1 Diabetes

Qing Yang, Yu Xue, Chuang Ma, 2012, PloS one.

WocEA: The visualization of functional enrichment results in word clouds.

Yu Xue, Ying Zhang, Shaofeng Lin, 2018, Journal of genetics and genomics = Yi chuan xue bao.

A genome‐wide analysis of sumoylation‐related biological processes and functions in human nucleus

Guoliang Chen, Fengfeng Zhou, Xuebiao Yao, 2005, FEBS letters.

Yu Xue, Yong E. Zhang, Shunping He, 2015, Zeitschrift für Induktive Abstammungs- und Vererbungslehre.

iUUCD 2.0: an update with rich annotations for ubiquitin and ubiquitin-like conjugations

Ying Zhang, Yu Xue, Yang Xu, 2017, Nucleic Acids Res..

Posttranscriptional regulation of de novo lipogenesis by glucose-induced O-GlcNAcylation.

F. He, Yu Xue, C. Peng, 2021, Molecular cell.

GPS: a comprehensive www server for phosphorylation sites prediction

Yu Xue, Guoliang Chen, Fengfeng Zhou, 2005, Nucleic Acids Res..

CPLM: a database of protein lysine modifications

Yu Xue, Qing Yang, Han Cheng, 2013, Nucleic Acids Res..

GPS 5.0: An Update on the Prediction of Kinase-specific Phosphorylation Sites in Proteins

Yu Xue, Chenwei Wang, Haodong Xu, 2020, Genom. Proteom. Bioinform..

GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs

Qi Zhao, Yu Xue, Yong Zhao, 2014, Nucleic Acids Res..

MeMo: a web tool for prediction of protein methylation modifications

Yu Xue, Hu Chen, Zhirong Sun, 2006, Nucleic Acids Res..

SUMO Substrates and Sites Prediction Combining Pattern Recognition and Phylogenetic Conservation

F. Zhou, Yu Xue, X. Yao, 2004, q-bio/0409011.

CPSS: a computational platform for the analysis of small RNA deep sequencing data

Yu Xue, Bo Xu, Huan Zhang, 2012, Bioinform..

MiCroKiTS 4.0: a database of midbody, centrosome, kinetochore, telomere and spindle

Yu Xue, Zexian Liu, Yongbo Wang, 2014, Nucleic Acids Res..

Computational prediction of methylation types of covalently modified lysine and arginine residues in proteins

Ying Zhang, Yu Xue, Yongbo Wang, 2016, Briefings Bioinform..

GPS-Lipid: a robust tool for the prediction of multiple lipid modification sites

Yubin Xie, Yueyuan Zheng, Jian Ren, 2016, Scientific Reports.

IBS: an illustrator for the presentation and visualization of biological sequences

Qi Zhao, Yu Xue, Yong Zhao, 2015, Bioinform..

Proteome-wide prediction of PKA phosphorylation sites in eukaryotic kingdom.

Changjiang Jin, Xinjiao Gao, Xuebiao Yao, 2008, Genomics.

Phosphorylation of SNX27 by MAPK11/14 links cellular stress–signaling pathways with endocytic recycling

Yu Xue, Guohui Li, Wankun Deng, 2021, The Journal of cell biology.

Phosphoproteomics‐based network medicine

Zexian Liu, Yongbo Wang, Yu Xue, 2013, The FEBS journal.

GPS-ARM: Computational Analysis of the APC/C Recognition Motif by Predicting D-Boxes and KEN-Boxes

Qing Yang, Zexian Liu, Jian Ren, 2012, PloS one.

SUMOsp: a web server for sumoylation site prediction

Yu Xue, Ying Xu, Fengfeng Zhou, 2006, Nucleic Acids Res..

Prediction of Nepsilon-acetylation on internal lysines implemented in Bayesian Discriminant Method.

Changjiang Jin, Xuebiao Yao, Yu Xue, 2006, Biochemical and biophysical research communications.

GPS-Palm: a deep learning-based graphic presentation system for the prediction of S-palmitoylation sites in proteins

Yu Xue, Di Peng, Peiran Jiang, 2020, Briefings Bioinform..

dbPAF: an integrative database of protein phosphorylation in animals and fungi

Shaofeng Lin, Zexian Liu, Wankun Deng, 2016, Scientific Reports.

Systematic analysis of the in situ crosstalk of tyrosine modifications reveals no additional natural selection on multiply modified residues

Zexian Liu, Yongbo Wang, Tianshun Gao, 2014, Scientific Reports.

EPSD: a well-annotated data resource of protein phosphorylation sites in eukaryotes

Shaofeng Lin, Yu Xue, Yiran Tu, 2020, Briefings Bioinform..

EKPD: a hierarchical database of eukaryotic protein kinases and protein phosphatases

Yu Xue, Qing Yang, Han Cheng, 2013, Nucleic Acids Res..

Systematic analysis of the Plk-mediated phosphoregulation in eukaryotes

Yu Xue, Jun Cao, Zexian Liu, 2013, Briefings Bioinform..

WERAM: a database of writers, erasers and readers of histone acetylation and methylation in eukaryotes

Yu Xue, Yang Xu, Shaofeng Lin, 2016, Nucleic Acids Res..

Atg9-centered multi-omics integration reveals new autophagy regulators in Saccharomyces cerevisiae

Cheng Chang, Yu Xue, Ying Shi, 2021, Autophagy.

dbPPT: a comprehensive database of protein phosphorylation in plants

Yu Xue, Han Cheng, Zexian Liu, 2014, Database J. Biol. Databases Curation.

PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory

Yu Xue, Ao Li, Huanqing Feng, 2006, BMC Bioinformatics.

iEKPD 2.0: an update with rich annotations for eukaryotic protein kinases, protein phosphatases and proteins containing phosphoprotein-binding domains

Yu Xue, Haodong Xu, Shaofeng Lin, 2018, Nucleic Acids Res..

dbPSP: a curated database for protein phosphorylation sites in prokaryotes

Ying Zhang, Yu Xue, Zexian Liu, 2015, Database J. Biol. Databases Curation.

Inhibiting PD-L1 palmitoylation enhances T-cell immune responses against tumours

H. Yao, Jiang Lan, Chushu Li, 2019, Nature Biomedical Engineering.

Phosphoproteomic Analysis of the Highly-Metastatic Hepatocellular Carcinoma Cell Line, MHCC97-H

Yu Xue, Zexian Liu, Han Cheng, 2015, International journal of molecular sciences.

The E3 ubiquitin ligase HECTD3 regulates ubiquitination and degradation of Tara.

Jian Yu, Yu Xue, Changjiang Jin, 2008, Biochemical and biophysical research communications.

Stable Isotope Metabolic Labeling-based Quantitative Phosphoproteomic Analysis of Arabidopsis Mutants Reveals Ethylene-regulated Time-dependent Phosphoproteins and Putative Substrates of Constitutive Triple Response 1 Kinase*

Henry Lam, Yu Xue, Han Cheng, 2013, Molecular & Cellular Proteomics.

UUCD: a family-based database of ubiquitin and ubiquitin-like conjugation

Yu Xue, Qing Yang, Han Cheng, 2012, Nucleic Acids Res..

GPS-CCD: A Novel Computational Program for the Prediction of Calpain Cleavage Sites

Zexian Liu, Xinjiao Gao, Jian Ren, 2011, PloS one.

HybridSucc: A Hybrid-learning Architecture for General and Species-specific Succinylation Site Prediction

Yu Xue, Haodong Xu, Wankun Deng, 2020, Genom. Proteom. Bioinform..

Predicting lysine‐malonylation sites of proteins using sequence and predicted structural features

Alan Wee-Chung Liew, Yaoqi Zhou, Yuedong Yang, 2018, J. Comput. Chem..

CGDB: a database of circadian genes in eukaryotes

Yu Xue, Ying Zhang, Shujing Li, 2016, Nucleic Acids Res..

Database Resources of the BIG Data Center in 2019

Tao Zhang, An-Yuan Guo, Ge Gao, 2018, Nucleic acids research.

PTMD: A Database of Human Disease-associated Post-translational Modifications

Yu Xue, Haodong Xu, Shaofeng Lin, 2018, Genom. Proteom. Bioinform..

Prediction of N e -acetylation on internal lysines implemented in Bayesian Discriminant Method

Changjiang Jin, Xuebiao Yao, Yu Xue, 2006 .

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021

Zhang Zhang, An-Yuan Guo, Xing Yan, 2020, Nucleic Acids Res..

Analysis of phosphorylation sites on autophagy proteins

Yu Xue, Di Miao, Zexian Liu, 2015, Protein & Cell.

NBA-Palm: prediction of palmitoylation site implemented in Naïve Bayes algorithm

Yu Xue, Hu Chen, Zhirong Sun, 2006, BMC Bioinformatics.

CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS)

Yu Xue, Ying Xu, Fengfeng Zhou, 2006, Bioinform..

Erratum to: Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition) (Autophagy, 12, 1, 1-222, 10.1080/15548627.2015.1100356

Sara W. Bird, Erinna F. Lee, Michael D. Kim, 2016 .

Author Correction: Inhibiting PD-L1 palmitoylation enhances T-cell immune responses against tumours

H. Yao, Jiang Lan, Chushu Li, 2019, Nature Biomedical Engineering.

Editorial :Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). DOI: 10.1080/15548627.2015.1100356;WOS:000373595400001; 2-s2.0-85013763791&;PMID: 26799652

Lee, Duchen, Izzo, 2016 .

Computational analyses of TBC protein family in eukaryotes.

Yu Xue, Changjiang Jin, X. Yao, 2008, Protein and peptide letters.

Phosphoproteome Analysis Reveals Phosphorylation Underpinnings in the Brains of Nurse and Forager Honeybees (Apis mellifera)

Yu Xue, Han Cheng, Bin Han, 2017, Scientific Reports.

dbPSP: a curated database for protein phosphorylation sites in prokaryotes

Y. Zhang, Yu Xue, Ying Zhang, 2015, Database J. Biol. Databases Curation.

MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore

Yu Xue, Zhaolei Zhang, Zexian Liu, 2009, Nucleic Acids Res..

An efficient site-directed mutagenesis method for ColE1-type ori plasmid.

Yu Xue, Xin Cai, Changjiang Jin, 2007, Analytical Biochemistry.

HSPPIP: An Online Tool for Prediction of Protein-Protein Interactions in Humans

Yu Xue, Changjiang Jin, Xuebiao Yao, 2006, ICIC.

MBA: a literature mining system for extracting biomedical abbreviations

Yu Xue, Yun Xu, YuZhong Zhao, 2009, BMC Bioinformatics.

GPS-YNO2: computational prediction of tyrosine nitration sites in proteins.

Zexian Liu, Xinjiao Gao, Jian Ren, 2011, Molecular bioSystems.

CPLA 1.0: an integrated database of protein lysine acetylation

Yu Xue, Yanhong Zhou, Jun Cao, 2010, Nucleic Acids Res..

CSS-Palm 2.0: an updated software for palmitoylation sites prediction.

Yu Xue, Changjiang Jin, X. Yao, 2008, Protein engineering, design & selection : PEDS.

Predicting lysine‐malonylation sites of proteins using sequence and predicted structural features

Alan Wee-Chung Liew, Yaoqi Zhou, Yuedong Yang, 2018, J. Comput. Chem..

DeepNitro: Prediction of Protein Nitration and Nitrosylation Sites by Deep Learning

Yu Xue, Yong Zhao, Li Chen, 2018, Genom. Proteom. Bioinform..

Proteome-Wide Analysis of Amino Acid Absence in Composition and Plasticity

Yu Xue, Yun Xu, YuZhong Zhao, 2008, ICIC.

A new method for classifying different phenotypes of kidney transplantation

Yu Xue, Zexian Liu, Linyan Wang, 2016, Cell Biology and Toxicology.

A general user interface for prediction servers of proteins' post-translational modification sites

Ying Xu, Fengfeng Zhou, Xuebiao Yao, 2006, Nature Protocols.

Phosphoproteome-based kinase activity profiling reveals the critical role of MAP2K2 and PLK1 in neuronal autophagy

Yu Xue, Wankun Deng, Lili Ma, 2017, Autophagy.

GPS-PUP: computational prediction of pupylation sites in prokaryotic proteins.

Yu Xue, Zexian Liu, Jian Ren, 2011, Molecular bioSystems.

Ubiquitin and Ubiquitin-Like Conjugations in Complex Diseases: A Computational Perspective

Yu Xue, Zexian Liu, Yongbo Wang, 2013 .

Prediction of novel pre-microRNAs with high accuracy through boosting and SVM

Yu Xue, Bo Xu, Yong Zhai, 2011, Bioinform..

Ray Wu, fifth business or father of DNA sequencing?

Hui Shen, Yu Xue, Yongbo Wang, 2016, Protein & Cell.

Comprehensive and reliable phosphorylation site mapping of individual phosphoproteins by combination of multiple stage mass spectrometric analysis with a target-decoy database search.

Xuebiao Yao, Xinning Jiang, Mingliang Ye, 2009, Analytical chemistry.

GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection.

Yu Xue, Changjiang Jin, Zexian Liu, 2011, Protein engineering, design & selection : PEDS.

MeMo: a web tool for prediction of protein methylation modifications

Yu Xue, X. Yao, Zhirong Sun, 2006, Nucleic Acids Res..