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List of works by Yu Xue

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

scientific article published in January 2006

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

article

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

scientific article published on 29 December 2006

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

scientific article published on 13 May 2020

Analysis of phosphorylation sites on autophagy proteins.

scientific article

AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors

scientific article

Atg9-centered multi-omics integration reveals new autophagy regulators in <i>Saccharomyces cerevisiae</i>

scientific article published on 15 March 2021

Bioinformaticians wrestling with the big biomedical data

scientific article published on 18 May 2017

Bioinformatics Commons: The Cornerstone of Life and Health Sciences

article

CPLA 1.0: an integrated database of protein lysine acetylation ⬇️

scientific article published on November 8, 2010

CPLM 4.0: an updated database with rich annotations for protein lysine modifications

scientific article published on 01 January 2022

CPLM: a database of protein lysine modifications.

scientific article

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

scientific article

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

scientific article published on 27 August 2008

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

scientific article published in July 2009

Computational analyses of TBC protein family in eukaryotes.

scientific article published in January 2008

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

scientific article published on January 2015

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

scientific article

Correlated expression of retrocopies and parental genes in zebrafish.

scientific article published on 11 November 2015

DOG 1.0: illustrator of protein domain structures

scientific article published on 01 February 2009

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

scientific article published on 01 August 2018

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

scientific article published on 20 June 2019

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

scientific article published on 9 June 2016

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

scientific article

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

scientific article published on April 2016

Functional characterization of TIP60 sumoylation in UV-irradiated DNA damage response

article

GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy

scientific article

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

scientific article

GPS-ARM: computational analysis of the APC/C recognition motif by predicting D-boxes and KEN-boxes

scientific article

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

scientific article published on 16 June 2016

GPS-MBA: computational analysis of MHC class II epitopes in type 1 diabetes

scientific article

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

scientific article published on 22 December 2016

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

scientific article published on 20 May 2020

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

scientific article published on 18 August 2011

GPS-SNO: computational prediction of protein S-nitrosylation sites with a modified GPS algorithm

scientific article

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

scientific article

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

scientific article

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

scientific article published in December 2004

Genome of Plant Maca (Lepidium meyenii) Illuminates Genomic Basis for High-Altitude Adaptation in the Central Andes

scientific article published on 9 May 2016

HemI: a toolkit for illustrating heatmaps

scientific article

Inhibiting MARSs reduces hyperhomocysteinemia-associated neural tube and congenital heart defects

scientific article published on 31 January 2020

Insulin signaling regulates longevity through protein phosphorylation in Caenorhabditis elegans

scientific article published on 27 July 2021

Integrated omics in Drosophila uncover a circadian kinome

scientific article published on 01 June 2020

MBA: a literature mining system for extracting biomedical abbreviations

scientific article

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

scientific article published on 02 December 2016

MeMo: a web tool for prediction of protein methylation modifications.

scientific article

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

scientific article published on 09 March 2020

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

scientific article

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

scientific article published on 25 September 2009

Open resource of clinical data from patients with pneumonia for the prediction of COVID-19 outcomes via deep learning

scientific article published on 18 November 2020

PLMD: An updated data resource of protein lysine modifications.

scientific article

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

scientific article

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

scientific article published on 01 August 2018

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

scientific article published on 17 July 2018

PhosSNP for systematic analysis of genetic polymorphisms that influence protein phosphorylation

scientific article

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

scientific article published on 16 May 2017

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

scientific article published on 21 September 2017

Phosphoproteomic analysis of the highly-metastatic hepatocellular carcinoma cell line, MHCC97-H

scientific article

Phosphoproteomics-based network medicine.

scientific article published on 28 June 2013

Precision Medicine: What Challenges Are We Facing?

scientific article published on 12 October 2016

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

scientific article published on 14 May 2018

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

scientific article published on 23 March 2011

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

scientific article published on 10 October 2008

Pyruvate Kinase M2 Activates mTORC1 by Phosphorylating AKT1S1

scientific article published on 15 February 2016

Ray Wu, fifth business or father of DNA sequencing?

scientific article published on 15 June 2016

Reconfiguring phosphorylation signaling by genetic polymorphisms affects cancer susceptibility.

scientific article published on 26 February 2015

SUMOsp: a web server for sumoylation site prediction

scientific article

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.

scientific article published on 16 September 2013

Systematic analysis of protein phosphorylation networks from phosphoproteomic data

scientific article

Systematic analysis of the Plk-mediated phosphoregulation in eukaryotes.

scientific article published on 31 July 2012

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

scientific article

Systematic characterization of small RNAome during zebrafish early developmental stages.

scientific article

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

article

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

scientific article published on 20 November 2017

The E3 ubiquitin ligase HECTD3 regulates ubiquitination and degradation of Tara

scientific article

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

scientific article

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

scientific article published on 26 October 2016

WocEA: The visualization of functional enrichment results in word clouds

scholarly article by Wanshan Ning published in July 2018

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

scientific article

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

scientific article published on 24 March 2016

dbPPT: a comprehensive database of protein phosphorylation in plants.

scientific article

dbPSP: a curated database for protein phosphorylation sites in prokaryotes.

scientific article

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

scientific article published in January 2019

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

scientific article

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