Jian Ren

发表

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.

Systematic characterization of small RNAome during zebrafish early developmental stages

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

An integrated overview of spatiotemporal organization and regulation in mitosis in terms of the proteins in the functional supercomplexes

Junjie U. Guo, Jian Ren, Yueyuan Zheng, 2014, Front. Microbiol..

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

Yu Xue, Changjiang Jin, X. Yao, 2008, 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 .

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

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

Single-base mapping of m6A by an antibody-independent method

Cai-Guang Yang, Chuan He, I. A. Roundtree, 2019, Science Advances.

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.

SARS-Cov-2-, HIV-1-, Ebola-neutralizing and anti-PD1 clones are predisposed

Zhenhai Zhang, Changqing Chang, Jian Ren, 2020, bioRxiv.

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

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

BBCancer: an expression atlas of blood-based biomarkers in the early diagnosis of cancers

Zhixiang Zuo, Jian Ren, Yubin Xie, 2019, Nucleic Acids Res..

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

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

lnCAR: A Comprehensive Resource for lncRNAs from Cancer Arrays.

Zhixiang Zuo, Jian Ren, Yueyuan Zheng, 2019, Cancer research.

Expression and regulation of long noncoding RNAs during the osteogenic differentiation of periodontal ligament stem cells in the inflammatory microenvironment

Zhixiang Zuo, Jian Ren, Yan Li, 2017, Scientific Reports.

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.

IDEA: a web server for Interactive Differential Expression Analysis with R Packages

Zhixiang Zuo, Jian Ren, Yubin Xie, 2018, bioRxiv.

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

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

TERC suppresses PD-L1 expression by downregulating RNA binding protein HuR

Haiying Liu, Junjiu Huang, Yong Zhao, 2022, Science China Life Sciences.

TIRSF: a web server for screening gene signatures to predict Tumor immunotherapy response

Zhixiang Zuo, Jian Ren, Yubin Xie, 2022, Nucleic Acids Res..

Proposed modifications and incorporation of plasma Epstein‐Barr virus DNA improve the TNM staging system for Epstein‐Barr virus‐related nasopharyngeal carcinoma

Ying Sun, Jun Ma, Li Tian, 2018, Cancer.

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

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

A Cisplatin Derivative Tetra-Pt(bpy) as an Oncotherapeutic Agent for Targeting ALT Cancer

Zepeng Zhang, Haiying Liu, Junjiu Huang, 2017, Journal of the National Cancer Institute.

VSOLassoBag: a variable-selection oriented LASSO bagging algorithm for biomarker discovery in omic-based translational research.

Jian Ren, Yubin Xie, Yanru Zeng, 2023, Journal of genetics and genomics = Yi chuan xue bao.

Single AAV-Mediated CRISPR-SaCas9 Inhibits HSV-1 Replication by Editing ICP4 in Trigeminal Ganglion Neurons

J. Cui, Junjiu Huang, Z. Songyang, 2020, Molecular therapy. Methods & clinical development.

A systematic simulation of the effect of salicylic acid on sphingolipid metabolism

Jian Ren, N. Yao, Qi Zhao, 2014, bioRxiv.

RM2Target: a comprehensive database for targets of writers, erasers and readers of RNA modifications

Jian Zheng, Yin Zhang, Jian Ren, 2022, Nucleic Acids Res..

N6-methyladenosine Modulates Nonsense-mediated mRNA Decay in Human Glioblastoma.

Q. Cao, Delin Chen, Jian Ren, 2019, Cancer research.

Single-base mapping of m6A by an antibody-independent method

Zhang Zhang, Chuan He, Jian Ren, 2019, Science Advances.

DeepOMe: A Web Server for the Prediction of 2′-O-Me Sites Based on the Hybrid CNN and BLSTM Architecture

Jian Ren, Yubin Xie, Xiaotong Luo, 2021, Frontiers in Cell and Developmental Biology.

SPENCER: a comprehensive database for small peptides encoded by noncoding RNAs in cancer patients

Zhixiang Zuo, Jian Ren, Yubin Xie, 2021, Nucleic Acids Res..

RPS: a comprehensive database of RNAs involved in liquid–liquid phase separation

Zhixiang Zuo, Jian Ren, Yubin Xie, 2021, Nucleic Acids Res..

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

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

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022

Zhenglin Du, Shuhui Song, Haoteng Yan, 2021, Nucleic Acids Res..

YY1 Positively Regulates Transcription by Targeting Promoters and Super-Enhancers through the BAF Complex in Embryonic Stem Cells

Jianlong Wang, Jian Ren, Qian Ma, 2018, Stem cell reports.

TIGER: A Web Portal of Tumor Immunotherapy Gene Expression Resource

Zhixiang Zuo, Jian Ren, Zhihang Chen, 2022, bioRxiv.

m6ASNP: a tool for annotating genetic variants by m6A function

Jian Ren, Shuai Jiang, Li Chen, 2018, GigaScience.

m 6 ASNP : a tool for annotating genetic variants by m 6 A function

Shuai Jiang, Yubin Xie, Yueyuan Zheng, 2018 .

m6AVar: a database of functional variants involved in m6A modification

Peng Nie, Jian Ren, Di Peng, 2017, Nucleic Acids Res..

Differential Alternative Splicing Genes in Response to Boron Deficiency in Brassica napus

Chungui Lu, G. Ding, Lei Shi, 2019, Genes.

PGC1α protects against hepatic steatosis and insulin resistance via enhancing IL10‐mediated anti‐inflammatory response

Chaohui Yu, Z. Ju, Jian Ren, 2020, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

The m6A reader YTHDC1 regulates muscle stem cell proliferation via PI4K–Akt–mTOR signalling

Z. Ju, Jian Ren, Yubin Xie, 2023, Cell proliferation.

Conformation Selective Antibody Enables Genome Profiling and Leads to Discovery of Parallel G-Quadruplex in Human Telomeres.

Yuanlong Ge, Yong Zhao, Ding Li, 2016, Cell chemical biology.

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

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

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

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

CrossICC: iterative consensus clustering of cross-platform gene expression data without adjusting batch effect

Zexian Liu, Yu Sun, Kaiyu Zhu, 2020, Briefings Bioinform..

m6A RNA modification controls autophagy through upregulating ULK1 protein abundance

J. Cui, Junjiu Huang, Jian Ren, 2018, Cell Research.

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.

Mutation profiling in chinese patients with metastatic colorectal cancer and its correlation with clinicopathological features and anti-EGFR treatment response

Fang Wang, Fenghua Wang, Yu-hong Li, 2016, Oncotarget.

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023

Zhenglin Du, Shuhui Song, Yun Xiao, 2022, Nucleic Acids Res..

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.

Firmiana: towards a one-stop proteomic cloud platform for data processing and analysis

Jun Qin, Quan Zhou, Peng Li, 2017, Nature Biotechnology.

Expression and regulation of long noncoding RNAs during the osteogenic differentiation of periodontal ligament stem cells in the inflammatory microenvironment

Zhixiang Zuo, Jian Ren, Yan Li, 2017, Scientific Reports.

dbPSP: a curated database for protein phosphorylation sites in prokaryotes

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

MesKit: a tool kit for dissecting cancer evolution of multi-region tumor biopsies through somatic alterations

Zhixiang Zuo, Jian Ren, Yubin Xie, 2021, GigaScience.

RPFdb: a database for genome wide information of translated mRNA generated from ribosome profiling

Yan Wang, Zhi Xie, Hongyu Li, 2015, Nucleic Acids Res..

A systematic simulation of the effect of salicylic acid on sphingolipid 1 metabolism 2 3 4

Jian Ren, N. Yao, Qi Zhao, 2014 .

VirusMap: A visualization database for the influenza A virus.

Zhixiang Zuo, Jian Ren, Yueyuan Zheng, 2017, Journal of genetics and genomics = Yi chuan xue bao.

Image-driven classification of functioning and nonfunctioning pituitary adenoma by deep convolutional neural networks

Jian Ren, Yubin Xie, Y. Mou, 2021, Computational and structural biotechnology journal.

Dynamic metabonomic and microbiological response of rats to lincomycin exposure: an integrated microbiology and metabonomics analysis

Jian Ren, Meicun Yao, Q. Liao, 2015 .

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

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

RBMX is required for activation of ATR on repetitive DNAs to maintain genome stability

Xiaocui Li, Haiying Liu, Yong Zhao, 2020, Cell Death & Differentiation.

autoRPA: A web server for constructing cancer staging models by recursive partitioning analysis

Qi Zhao, Yubin Xie, Huiqin Li, 2020, Computational and structural biotechnology journal.

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..

IBS 2.0: an upgraded illustrator for the visualization of biological sequences

Jian Ren, Yubin Xie, Xiaotong Luo, 2022, Nucleic Acids Res..

A de novo substructure generation algorithm for identifying the privileged chemical fragments of liver X receptorβ agonists

Zhihong Liu, Jian Ren, Jun Xu, 2017, Scientific Reports.

RMVar: an updated database of functional variants involved in RNA modifications

Yubin Xie, Jian Ren, Zhixiang Zuo, 2020, Nucleic Acids Res..

dbPSP: a curated database for protein phosphorylation sites in prokaryotes

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

MeRIPseqPipe: an integrated analysis pipeline for MeRIP-seq data based on Nextflow

Zhixiang Zuo, Jian Ren, Kaiyu Zhu, 2022, Bioinform..

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

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

A de novo substructure generation algorithm for identifying the privileged chemical fragments of liver X receptorβ agonists

Jian Ren, Jun Xu, Zhihong Liu, 2017, Scientific Reports.

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

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

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

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

m6A RNA modification controls autophagy through upregulating ULK1 protein abundance

J. Cui, Junjiu Huang, Jian Ren, 2018, Cell Research.

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.