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PUBLICATIONS
2022
Yubin Xie, Huiqin Li, Xiaotong Luo, Hongyu Li, Qiuyuan Gao, Luowanyue Zhang, Yuyan Teng, Qi Zhao, Zhixiang Zuo, Jian Ren*.
IBS 2.0: an upgraded illustrator for the visualization of biological sequences
Nucleic Acids Research.
17 May 2022 DOI: 10.1093/nar/gkac373
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Li Chen, Tianjian Chen, Ya Zhang, Haichen Lin, Ruihan Wang, Yihang Wang, Hongyu Li, Zhixiang Zuo*, Jian Ren*, Yubin Xie*.
TIRSF: a web server for screening gene signatures to predict Tumor immunotherapy response
Nucleic Acids Research.
12 May 2022 DOI: 10.1093/nar/gkac374
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2021
Mengni Liu, Huiqin Li, Xiaotong Luo, Jieyi Cai, Tianjian Chen, Yubin Xie*, Jian Ren*, Zhixiang Zuo*.
RPS: a comprehensive database of RNAs involved in liquid–liquid phase separation
Nucleic Acids Research.
28 October 2021 DOI: 10.1093/nar/gkab986
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Xiaotong Luo, Yuantai Huang, Huiqin Li, Yihai Luo, Zhixiang Zuo*, Jian Ren*, Yubin Xie*.
SPENCER: a comprehensive database for small peptides encoded by noncoding RNAs in cancer patients.
Nucleic Acids Research.
27 September 2021 DOI: 10.1093/nar/gkab822
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Mengni Liu, Jianyu Chen, Xin Wang, Chengwei Wang, Xiaolong Zhang, Yubin Xie, Zhixiang Zuo, Jian Ren*, Qi Zhao*.
MesKit: a tool kit for dissecting cancer evolution of multi-region tumor biopsies through somatic alterations.
GigaScience.
21 May 2021 DOI: 10.1093/GIGASCIENCE/GIAB036
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Li Hongyu, Chen Li, Huang Zaoli, Luo Xiaotong, Li Huiqin, Ren Jian*, Xie Yubin*.
DeepOMe: A Web Server for the Prediction of 2′-O-Me Sites Based on the Hybrid CNN and BLSTM Architecture.
Frontiers in Cell and Developmental Biology.
14 May 2021 DOI: 10.3389/fcell.2021.686894
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2020
Yubin Xie, Xiaotong Luo, Huiqin Li, Qingxian Xu, Zhihao He, Qi Zhao*, Zhixiang Zuo*, Jian Ren*.
autoRPA: A web server for constructing cancer staging models by recursive partitioning analysis.
Computational and Structural Biotechnology Journal. 10 November 2020. DOI: 10.1016/j.csbj.2020.10.038
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Di Peng, Huiqin Li, Bosu Hu, Hongwan Zhang, Li Chen, Shaofeng Lin, Zhixiang Zuo, Yu Xue, Jian Ren* and Yubin Xie*. PTMsnp: A Web Server for the Identification of Driver Mutations That Affect Protein Post-translational Modification. Frontiers in Cell and Developmental Biology. 10 November 2020. DOI: 10.3389/fcell.2020.593661
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Xiaotong Luo, Huiqin Li, Jiaqi Liang, Qi Zhao, Yubin Xie*, Jian Ren*, Zhixiang Zuo*. RMVar: an updated database of functional variants involved in RNA modifications. Nucleic Acids Research. 06 October 2020. DOI: 10.1093/nar/gkaa811
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2019
Zuo ZX, Hu HJ, Xu QX, Luo XT, Peng D, Zhu KY, Zhao Q*, Xie YB*, Ren J*. BBCancer: an expression atlas of blood-based biomarkers in the early diagnosis of cancers. Nucleic Acids Research. 29 October 2019. DOI: 10.1093/nar/gkz942
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Zhang Y, Xie Y, Liu W, Deng W, Peng D, Wang C, Xu H, Ruan C, Deng Y, Guo Y, Lu C, Yi C, Ren J*, Xue Y*. DeepPhagy: a deep learning framework for quantitatively measuring autophagy activity in Saccharomyces cerevisiae. Autophagy. Jun 12 2019. DOI: 10.1080/15548627.2019.1632622
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Zheng YY, Xu QX, Liu MN, Hu HJ, Xie YB, Zuo ZX*, Ren J*. lnCAR: a comprehensive resource for lncRNAs from Cancer Arrays. Cancer Res February 20 2019 DOI: 10.1158/0008-5472.CAN-18-2169.
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2018
Xie YB, Luo XT, Li YP, Chen L, Ma WB, Huang JJ, Cui J, Zhao Y, Xue Y, Zuo ZX*, Ren J*. DeepNitro: Prediction of Protein Nitration and Nitrosylation Sites by Deep Learning. Genomics, Proteomics & Bioinformatics. 2018; 16(4): 294-306.
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Jin SH, Zhang XY, Miao YY, Liang PP, Zhu KY, She YC, Wu YX, Liu DA, Huang JJ, Ren J* & Cui J*. m6A RNA modification controls autophagy through upregulating ULK1 protein abundance. Cell Research. 2018.
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Chen L, Miao YY, Liu MN, Zeng YR, Gao ZJ, Peng D, Hu BS, Li X, Zheng YY, Xue y, Zuo ZX, Xie YB* and Ren J*. Pan-Cancer Analysis Reveals the Functional Importance of Protein Lysine Modification in Cancer Development. Frontiers in Genetics. 2018; 9:254.
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Jiang S, Xie YB, He ZH, Zhang Y, Zhao YL, Chen L, Zheng YY, Miao YY, Zuo
ZX* and Ren J*. m6ASNP: a tool for annotating genetic variants by m6A function. GigaScience. 2018;
https://doi.org/10.1093/gigascience/giy035.
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2017
Zhang QB, Chen L, Cui SM, Li Y, Zhao Q, Cao W, Lai SX, Yin SJ, Zuo ZX*
and Ren J*. Expression and regulation of long noncoding RNAs during the osteogenic differentiation of
periodontal ligament stem cells in the inflammatory microenvironment. Scientific Reports.
2017;7:13991.
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Zheng YY, Nie P, Peng D, He ZH, Liu MN, Xie YB, Miao YY, Zuo ZX* and Ren
J*. m6AVar: a database of functional variants involved in m6A modification. Nucleic Acids
Research. 2018; 46(D1): D139-145.
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Peng H, Liu ZH, Yan X, Ren J* and Xu J*. A de novo substructure
generation algorithm for identifying the privileged chemical fragments of liver X receptorβ agonists.
Scientific Reports. 2017; 7:11121.
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Feng JW, Ding C, Qiu NQ, Ni XT, Zhan DD, Liu WL, Xia X, Li P, Lu BX, Zhao
Q, Nie P, Song L, Zhou Q, Lai M, Guo GG, Zhu WM, Ren J*, Shi TL* and Qin J*. Firmiana: towards a one-stop
proteomic cloud platform for data processing and analysis. Nature Biotechnology. 35, 409–412
(2017) | doi:10.1038/nbt.3825.
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Xie YB, Luo XT, He ZH, Zheng YY, Zuo ZX, Zhao Q, Miao YY and Ren J*.
VirusMap: A visualization database for the influenza A virus. Journal of Genetics and Genomics.
2017; Vol 44, Issue 4.
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2016
Xie YB, Zheng YY, Li HY, Luo XT, He ZH, Cao S, Shi Y, Zhao Q, Xue Y, Zuo
ZX, Ren J*. GPS-Lipid: a robust tool for the prediction of multiple lipid modification sites. Scientific
Reports. 2016; 6:28249.
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Xie SQ, Nie P, Wang Y, Wang H, Li H, Yang Z, Liu Y*, Ren J*, Xie Z*.
RPFdb: a database for genome wide information of translated mRNA generated from ribosome profiling.
Nucleic Acids Research. 2016; 44:D254-D258.
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2015
Liu WZ, Xie YB, Ma JY, Luo XT, Nie P, Zuo ZX, Lahrmann U, Zhao Q, Zheng
YY, Zhao Y, Xue Y* and Ren J*. IBS: an illustrator for the presentation and visualization of biological
sequences.
Bioinformatics. 2015; 31(20):3359-61
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[ ESI Hot Paper ]
Huang ZN, Ma LL, Wang YB, Pan ZC, Ren J, Liu ZX, Xue Y. MiCroKiTS 4.0: a
database of midbody, centrosome, kinetochore, telomere and spindle.
Nucleic Acids Research. 2015;43: D328-D334.
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Jiang W, Liu N, Chen XZ, Sun Y, Li B, Ren XY, Qin WF, Jiang N, Xu YF, Li
YQ, Ren J, Cho WCS, Yun JP, Zeng J, Liu LZ, Li L, Guo Y, Mai HQ, Zeng MS, Kang TB, Jia WH, Shao JY, Ma J.
Genome-Wide Identification of a Methylation Gene Panel as a Prognostic Biomarker in Nasopharyngeal Carcinoma.
2864-2873.
Molecular Cancer Therapeutics. 2015;14(12)
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Wang YB, Cheng H, Pan ZC, Ren J, Liu ZX and Xue Y. Reconfiguring
phosphorylation signaling by genetic polymorphisms affects cancer susceptibility.
Journal of Molecular Cell Biology. 2015;7(3):187-202.
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Lin MN, Xie ZY, Zhou YT, Li YM, Ren J, Peng XX, Yao MC, Yang ZZ, Liao QF.
Dynamic metabonomic and microbiological response of rats to lincomycin exposure: an integrated microbiology and
metabonomics analysis.
Rsc Advances. 2015;5(80): 65415-65426.
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Shi C, Yin J, Liu Z, Wu JX, Zhao Q, Ren J, Yao N. A systematic simulation
of the effect of salicylic acid on sphingolipid metabolism.
Frontiers in Plant Science. 2015;6:186.
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2014
Zheng YY, Guo JJ, Li X, Xie YB, Hou MM, Fu XY, Dai SK, Diao RC, Miao YY*
and Ren J*. An integrated overview of spatiotemporal organization and regulation in mitosis in terms of the
proteins in the functional supercomplexes.
Frontiers in Microbiology. 2014; 5: 573
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Zhao Q, Xie YB, Zheng YY, Jiang S, Liu WZ, Mu WP, Liu ZX, Zhao Y, Xue Y*
and Ren J*. GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs.
Nucleic Acids Research. 2014;42: W325-30.
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Liu ZX, Wang YB, Gao TS, Pan ZC, Cheng H, Yang Q, Cheng ZY, Guo AY, Ren J
and Xue Y. CPLM: a database of protein lysine modifications. Nucleic Acids Research.
2014;42:D531-536.
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Cheng H, Deng WK, Wang YB, Ren J, Liu ZX, Xue Y. dbPPT: a comprehensive
database of protein phosphorylation in plants. Database. 2014;2014.
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Wang YB, Dai ZY, Cheng H, Liu ZX, Pan ZC, Deng WK, Gao TS, Li XT, Yao YG,
Ren J and Xue Y. Towards a better understanding of the novel avian-origin H7N9 influenza A virus in China.
Scientific Reports. 2014; 3:2318.
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Pan ZC, Liu ZX, Cheng H, Wang YB, Gao TS, Ullah S, Ren J and Xue Y.
Systematic Analysis of the in Situ Crosstalk of Tyrosine Modifications Reveals No Additional Natural Selection
on Multiply Modified Residues.
Scientific Reports. 2014;4:7331.
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Yao YG, Ma LL, Jia Q, Deng WK, Liu ZX, Zhang YW, Ren J, Xue Y, Jia HB,
Yang Q. Systematic characterization of small RNAome during zebrafish early developmental stages.
BMC Genomics. 2014;15:117.
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2013
Liu ZX#, Ren J#, Cao J#, He J, Yang Q, Ma Q, Gao XJ, Yao XB, Jin CJ, Xue
Y. Systematic analysis of the Plk-mediated phosphoregulation in eukaryotes.
Briefings in Bioinformatics. 2013;14 (3):344-360
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Gao TS, Liu ZX, Wang YB, Cheng H, Yang Q, Guo AY, Ren J and Xue Y. UUCD:
a family-based database of ubiquitin and ubiquitin-like conjugation. Nucleic Acids Research.
2013;41:D445-51
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2012
Song CX, Ye ML, Jiang XN, Han GH, Songyang Z, Tan YX, Wang HY, Ren J*,
Xue Y* & Zou HF*. Systematic analysis of protein phosphorylation networks from phosphoproteomic data.
Molecular & Cellular Proteomics. 2012;11(10):1070-1083.
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Liu ZX, Yuan F, Ren J, Cao J, Zhou YH, Yang Q, Xue Y. GPS-ARM:
Computational Analysis of the APC/C Recognition Motif by Predicting D-Boxes and KEN-Boxes.
Plos One. 2012; 7(3):e34370
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31. Cai RK, Liu ZX, Ren J, Ma C, Gao TS, Zhou YH, Yang Q, Xue Y. GPS-MBA:
computational analysis of MHC class II epitopes in type 1 diabetes.
Plos One. 2012; 7(3):e33884.
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2011
Ren J, Gao XJ, Liu ZX, Cao J, Ma Q, Xue Y. Computational Analysis of
Phosphoproteomics: Progresses and Perspectives.
Current Protein & Peptide Science. 2011;7(12):591-601.
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Liu ZX, Ma Q, Cao J, Gao XJ, Ren J*, Xue Y*. GPS-PUP: computational
prediction of pupylation sites in prokaryotic proteins.
Mol Biosyst. 2011;7(10):2737-2740.
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Liu ZX, Gao X, Ma Q, Cao J, Ren J*, Xue Y*. GPS-CCD: A novel
computational program for prediction of calpain cleavage sites.
Plos One. 2011;6(4):e19001.
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Xue Y*, Liu ZX, Cao J, Ma Q, Gao X, Wang QQ, Jin CJ, Zhou YH, Wen LP, Ren
J*. GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length
selection.
Protein Eng Des Sel. 2011;24(3):255-260.
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Liu ZX, Cao J, Gao XJ, Zhou YH, Wen LP, Yang X, Yao XB, Ren J*, Xue Y*.
CPLA 1.0: an integrated database of protein lysine acetylation.
Nucleic Acids Research. 2011;39:D1029-1034.
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Liu ZX, Gao XJ, Cao J, Ma Q, Ren J, Xue Y. Computational studies of
protein phosphorylation: from site-specific prediction to systematic network analysis.
Amino Acids. 2011;41:S17.
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2010
Xue Y*, Gao XJ, Cao J, Liu ZX, Jin CJ, Wen LP, Yao XB, Ren J*. A Summary
of Computational Resources for Protein Phosphorylation.
Current Protein & Peptide Science. 2010;11(6):485-496.
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Xue Y*, Liu ZX, Gao XJ, Jin CJ, Wen LP, Yao XB, Ren J*. GPS-SNO:
Computational Prediction of Protein S-Nitrosylation Sites with a Modified GPS Algorithm.
Plos One. 2010;5(6): e11290.
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Ren J, Jiang CH, Gao XJ, Liu ZX, Yuan ZN, Jin CJ, Wen LP, Zhang ZL, Xue
Y, Yao XB. PhosSNP for Systematic Analysis of Genetic Polymorphisms That Influence Protein Phosphorylation.
Molecular & Cellular Proteomics. 2010;9(4):623-634.
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Ren J, Liu ZX, Gao XJ, Jin CJ, Ye ML, Zou HF, Wen LP, Zhang ZL, Xue Y,
Yao XB. MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore.
Nucleic Acids Research. 2010;38:D155-D160.
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2009
Ren J, Gao XJ, Jin CJ, Zhu M, Wang XW, Shaw A, Wen LP, Yao XB, Xue Y.
Systematic study of protein sumoylation: Development of a site-specific predictor of SUMOsp 2.0.
Proteomics. 2009;9(12):3409-3412.
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Ren J, Wen LP, Gao XJ, Jin CJ, Xue Y, Yao XB. DOG 1.0: illustrator of
protein domain structures.
Cell Research. 2009;19(2):271-273.
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Han GH, Ye ML, Jiang XN, Chen R, Ren J, Xue Y, Wang FJ, Song CX, Yao XB,
Zou HF. Comprehensive and Reliable Phosphorylation Site Mapping of Individual Phosphoproteins by Combination of
Multiple Stage Mass Spectrometric Analysis with a Target-Decoy Database Search.
Analytical Chemistry. 2009;81(14):5794-5805.
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2008
Ren J, Wen LP, Gao XJ, Jin CJ, Xue Y, Yao XB. CSS-Palm 2.0: an updated
software for palmitoylation sites prediction.
Protein Eng Des Sel. 2008;21(11):639-644.
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Xue Y#, Ren J#, Gao XJ, Jin CJ, Wen LP, Yao XB. GPS 2.0, a tool to
predict kinase-specific phosphorylation sites in hierarchy.
Molecular & Cellular Proteomics. 2008;7(9):1598-1608.
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Gao XJ, Jin CJ, Ren J, Yao XB, Xue Y. Proteome-wide prediction of PKA
phosphorylation sites in eukaryotic kingdom.
Genomics. 2008;92(6):457-463.
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