SYSUCC Sun Yat-sen University Cancer Center

OUR PUBLICATIONS


2020

[80] ♦ Zhao Q, Chen Y, Wu Q, Zhang C, Liu M, Wang Y, Feng Y, Hu J, Fu J, Yang H, Qi J, Wang Z, Lu Y, Sheng H, Liu Z, Zuo Z, Zheng J, Yun J, Bei J, Jia W, Lin D, Xu R, Wang F. Systematic analysis of the transcriptome in small-cell carcinoma of the oesophagus reveals its immune microenvironment. Clinical & Translational Immunology, 2020, 9(10): e1173. (PMID: 33033616)
[79] ♦ Yu K, Zhang Q, Liu Z, Du Y, Gao X, Zhao Q, Li X, Cheng H, Liu Z. Deep learning based prediction of reversible HAT/HDAC-specific lysine acetylation. Briefings in Bioinformatics, 2020, 21(5):1798-1805. (PMID: 32978618)
[78] ♦ Zhao Q, Sun Y, Liu Z, Zhang H, Li X, Zhu K, Liu Z, Ren J, Zuo Z. CrossICC: Iterative consensus clustering of cross-platform gene expression data without adjusting batch effect. Briefings in Bioinformatics, 2020, 21(5):1818-1824. (PMID: 32978617)
[77] ♦ Hu P, Li T, Lin J, Qiu M, Wang D, Liu Z, Chen Z, Yang L, Zhang X, Zhao Q, Chen Y, Lu Y, Wu Q, Pu H, Zeng Z, Xie D, Ju H, Luo H, Xu R. VDR-SOX2 signaling promotes colorectal cancer stemness and malignancy in an acidic microenvironment. Signal Transduction and Targeted Therapy, 2020, 5(1):183. (PMID: 32900990)
[76] ♦ Huang J, Chen P, Liu K, Liu J, Zhou B, Wu R, Peng Q, Liu Z, Li C, Kroemer G, Lotze M, Zeh H, Kang R, Tang D. CDK1/2/5 inhibition overcomes IFNG-mediated adaptive immune resistance in pancreatic cancer. Gut, 2020, 10.1136/gutjnl-2019-320441. (PMID: 32816920)
[75] ♦ Liu Z, Zhao Q, Zuo Z, Yuan S, Yu K, Zhang Q, Zhang X, Sheng H, Ju H, Cheng H, Wang F, Xu R, Liu Z. Systematic analysis of the aberrances and functional implications of ferroptosis in cancer. iScience, 2020, 23(7):101302. (PMID: 32629423)
[74] ♦ Zhang Q, Yu K, Li S, Zhang X, Zhao Q, Zhao X, Liu Z, Cheng H, Liu Z, Li X. gutMEGA: a database of the human gut MEtaGenome Atlas. Briefings in Bioinformatics, 2020, in press. (PMID: 32496513)
[73] ♦ Li S, Yu K, Wang D, Zhang Q, Liu Z, Zhao L, Cheng H. Deep learning based prediction of species-specific protein S-glutathionylation sites. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2020, 1868(7):140422. (PMID: 32234550)
[72] ♦ Liu S#, Bian L#, Liu Z#, Chen Q#, Sun X#, Sun R, Luo D, Li X, Xiao B, Yan J, Lu Z, Yan S, Yuan L, Tang L, Li J, Mai H. Development and Validation of the Immunoscore to Predict Distant Metastasis in Patients with Nasopharyngeal Carcinoma. Journal for ImmunoTherapy of Cancer, 2020, 8(1):e000205. (PMID: 32303611)
[71] ♦ Liu J#, Liu Z#, Wu Q#, Lu Y#, Wong C#, Miao L, Wang Y, Wang Z, Jin Y, He M, Ren C, Wang D, Chen D, Pu H, Feng L, Li B, Xie D, Zeng M, Huang P, Lin A, Lin D, Xu R, Ju H. Long Noncoding RNA AGPG Regulates PFKFB3-Mediated Tumor Glycolytic Reprogramming. Nature Communications, 2020, 11(1):1507. (PMID: 32198345)
[70] ♦ Liu Z, Chen M, Zhang Q, Zhang Y, An X, Luo Y, Liu X, Liu S, Liu Q, Yang T, Liu Y, Liu B, Zhou A, Li M, Liu Y, Liu Z, Zhong Q. ZIC2 is downregulated and represses tumor growth via the regulation of STAT3 in breast cancer. International Journal of Cancer, 2020, 147(2):505-518. (PMID: 32064600)
[69] ♦ Yang D, Chen Z, Yu K, Lu J, Wu Q, Wang Y, Ju H, Xu R, Liu Z, Zeng Z. METTL3 promotes the progression of gastric cancer via MYC target. Frontiers in Oncology, 2020, 10:115. (PMID: 32175271)
[68] ♦ Wang Y, Lu J, Wang F, Wang Y, He M, Wu Q, Lu Y, Yu H, Chen Z, Zhao Q, Liu J, Chen Y, Wang D, Sheng H, Liu Z, Zeng Z, Xu R, Ju H. Inhibition of fatty acid catabolism augments the efficacy of oxaliplatin-based chemotherapy in gastrointestinal cancers. Cancer Letters, 2020, 473:74-89. (PMID: 31904482)
[67] ♦ Wang Y, Lu J, Wu Q, Jin Y, Wang D, Chen Y, Liu J, Luo X, Meng Q, Pu H, Wang Y, Hu P, Liu Z, Zeng Z, Zhao Q, Deng R, Zhu X, Ju H, Xu R. LncRNA LINRIS stabilizes IGF2BP2 and promotes the aerobic glycolysis in colorectal cancer. Molecular Cancer, 2020, 18(1):174. (PMID: 31791342)
[66] ♦ Mei X, Qi D, Zhang T, Zhao Y, Jin L, Hou J, Wang J, Lin Y, Xue Y, Zhu P, Liu Z, Huang L, Nie J, Si W, Ma J, Ye J, Finnell RH, Saiyin H, Wang H, Zhao J, Zhao S, Xu W. Inhibiting MARSs reduces hyperhomocysteinemia-associated neural tube and congenital heart defects. EMBO Molecular Medicine, 2020, 12(3):e9469. (PMID: 32003121)
[65] ♦ Luo H, Zhao Q, Wei W, Zheng L, Yi S, Li G, Wang W, Sheng H, Pu H, Mo H, Zuo Z, Liu Z, Li C, Xie C, Zeng Z, Li W, Hao X, Liu Y, Cao S, Liu W, Gibson S, Zhang K, Xu G, Xu R. Circulating tumor DNA methylation profiles enable early diagnosis, prognosis prediction, and screening for colorectal cancer. Science Translational Medicine, 2020, 12(524):eaax7533. (PMID: 31894106)


2019

[64] ♦ Zhu Y, He D, Bo H, Liu Z, Xiao M, Xiang L, Zhou J, Liu Y, Liu X, Gong L, Ma Y, Zhou Y, Zhou M, Xiong W, Yang F, Xing X, Li R, Li W, Cao K. The MRVI1-AS1/ATF3 signaling loop sensitizes nasopharyngeal cancer cells to paclitaxel by regulating the Hippo-TAZ pathway. Oncogene, 2019, 38(32):6065-6081. (PMID: 31273338)
[63] ♦ Zhang J, Bai R, Li M, Ye H, Wu C, Wang C, Li S, Tan L, Mai D, Li G, Pan L, Zheng Y, Su J, Ye Y, Fu Z, Zheng S, Zuo Z, Liu Z, Zhao Q, Che X, Xie D, Jia W, Zeng MS, Tan W, Chen R, Xu RH, Zheng J, Lin D. Excessive miR-25-3p maturation via N6-methyladenosine stimulated by cigarette smoke promotes pancreatic cancer progression. Nature Communications, 2019, 10(1):1858. (PMID: 31015415)
[62] ♦ He W, Liang B, Wang C, Li S, Zhao Y, Huang Q, Liu Z, Yao Z, Wu Q, Liao W, Zhang S, Liu Y, Xiang Y, Liu J, Shi M. MSC-regulated lncRNA MACC1-AS1 promotes stemness and chemoresistance through fatty acid oxidation in gastric cancer. Oncogene, 2019, 38(23):4637-4654. (PMID: 30742067)
[61] ♦ Wang Y, Lu Y, Liu J, Jin Y, Bi H, Zhao Q, Liu Z, Li Y, Hu J, Sheng H, Jiang Y, Zhang C, Tian F, Chen Y, Pan Z, Chen G, Zeng Z, Liu K, Ogasawara M, Yun J, Ju H, Feng J, Xie D, Gao S, Jia W, Kopetz S, Xu R, Wang F. AMPKα1 confers survival advantage of colorectal cancer cells under metabolic stress by promoting redox balance through the regulation of glutathione reductase phosphorylation. Oncogene, 2019, 39(3):637-650. (PMID: 31530934)
[60] ♦ You R, Liu Y, Lin D, Li Q, Yu T, Zou X, Lin M, Zhang X, He G, Yang Q, Zhang Y, Xie Y, Jiang R, Wu C, Zhang C, Cui C, Wang J, Wang Y, Zhuang A, Guo G, Hua Y, Sun R, Yun J, Zuo Z, Liu Z, Zhu X, Kang T, Qian C, Mai H, Sun Y, Zeng M, Feng L, Zeng Y, Chen M. Clonal Mutations Activate the NF-κB Pathway to Promote Recurrence of Nasopharyngeal Carcinoma. Cancer Research, 2019, 79(23):5930-5943. (PMID: 31484669)
[59] ♦ Chen Z, Qi J, Wu Q, Lu J, Liu Z, Wang Y, Hu P, Li T, Lin J, Wu X, Miao L, Zeng Z, Xie D, Ju H, Xu R, Wang F. Eukaryotic initiation factor 4A2 promotes experimental metastasis and oxaliplatin resistance in colorectal cancer. Journal of Experimental & Clinical Cancer Research, 2019, 38(1):196. (PMID: 31088567)
[58] ♦ Wang F, Zhao Q, Wang Y, Jin Y, He M, Liu Z, Xu R. Evaluation of POLE and POLD1 Mutations as Biomarkers for Immunotherapy Outcomes Across Multiple Cancer Types. JAMA Oncology, 2019, 5(10):1504-1506. (PMID: 31415061)
[57] ♦ Liu Z#, Yu K#, Dong J#, Zhao L#, Liu Z, Zhang Q, Li S, Du Y, Cheng H. Precise prediction of calpain cleavage sites and their aberrance caused by mutations in cancer. Frontiers in Genetics, 2019, 10:715. (PMID: 31440276)
[56] ♦ Liu Z, Yu K, Zheng J, Lin H, Zhao Q, Zhang X, Feng W, Wang L, Xu J, Xie D, Zuo Z, Liu Z, Zheng Q. Dysregulation, functional implications and prognostic ability of the circadian clock across cancers. Cancer Medicine, 2019, 8(4):1710-1720. (PMID: 30791227)
[55] ♦ Zhu L, Cheng H, Peng G, Wang S, Zhang Z, Ni E, Fu X, Zhuang C, Liu Z, Zhou H. Ubiquitinome Profiling Reveals the Landscape of Ubiquitination Regulation in Young Panicles. Genomics, Proteomics & Bioinformatics, 2019, In press. (PMID: )
[54] ♦ Tan L, Mai D, Zhang B, Jiang X, Zhang J, Bai R, Ye Y, Li M, Pan L, Su J, Zheng Y, Liu Z, Zuo Z, Zhao Q, Li X, Huang X, Yang J, Tan W, Zheng J, Lin D. PIWI-interacting RNA-36712 restrains breast cancer progression and chemoresistance by interaction with SEPW1 pseudogene SEPW1P RNA. Molecular Cancer, 2019, 18(1):9. (PMID: 30636640)
[53] ♦ Ju H, Lu Y, Chen D, Zuo Z, Liu Z, Wu Q, Mo H, Wang Z, Wang D, Pu H, Zeng Z, Li B, Xie D, Huang P, Hung M, Chiao P, Xu R. Modulation of Redox Homeostasis by Inhibition of MTHFD2 in Colorectal Cancer: Mechanisms and Therapeutic Implications. Journal of the National Cancer Institute, 2019, 111(6):584–596. (PMID: 30534944)
[52] ♦ Yu K, Zhang Q, Liu Z, Zhao Q, Zhang X, Wang Y, Wang Z, Jin Y, Li X, Liu Z, Xu R. qPhos: a database of protein phosphorylation dynamics in humans. Nucleic Acids Research, 2019, 47(D1):D451-D458. (PMID: 30380102)


2018

[51] ♦ Mai D, Ding P, Tan L, Zhang J, Pan Z, Bai R, Li C, Li M, Zhou Y, Tan W, Zhou Z, Li Y, Zhou A, Ye Y, Pan L, Zheng Y, Su J, Zuo Z, Liu Z, Zhao Q, Li X, Huang X, Li W, Wu S, Jia W, Zou S, Wu C, Xu R, Zheng J, Lin D. PIWI-interacting RNA-54265 is oncogenic and a potential therapeutic target in colorectal adenocarcinoma. Theranostics, 2018, 8(19):5213-5230. (PMID: 30555542)
[50] ♦ Wei X, Wu Q, Chen D, Zeng Z, Lu J, Liu Z, Ju H, Ren C, Pan Z, Wang F, Xu R. The Clinical and Biomarker Association of Programmed Death Ligand 1 and its Spatial Heterogeneous Expression in Colorectal Cancer. Journal of Cancer, 2018, 9(23):4325-4333. (PMID: 30519336)
[49] ♦ Zhang Q#,†, Yu K, Liu Z, Wang D, Zhao Y, Yin S, Liu Z. Prediction of prkC-mediated protein serine/threonine phosphorylation sites for bacteria. PLoS One, 2018, 13(10):e0203840. (PMID: 30278050)
[48] ♦ Sang L, Ju H, Liu G, Tian T, Ma G, Lu Y, Liu Z, Pan R, Li R, Piao H, Marks J, Yang L, Yan Q, Wang W, Shao J, Zhou Y, Zhou T, Lin A. LncRNA CamK-A Regulates Ca2+-Signaling-Mediated Tumor Microenvironment Remodeling. Molecular Cell, 2018, 72(1):71-83. (PMID: 30220561)
[47] ♦ Li S, Zhuang Z, Wu T, Lin J, Liu Z, Zhou L, Dai T, Lu L, Ju H. Nicotinamide nucleotide transhydrogenase-mediated redox homeostasis promotes tumor growth and metastasis in gastric cancer. Redox Biology, 2018, 18:246-255. (PMID: 30059901)
[46] ♦ Wang Y, Zeng Z, Lu J, Wang Y, Liu Z, He M, Zhao Q, Wang Z, Li T, Lu Y, Wu Q, Yu K, Wang F, Pu H, Li B, Jia W, Shi M, Xie D, Kang T, Huang P, Ju H, Xu R. CPT1A-mediated fatty acid oxidation promotes colorectal cancer cell metastasis by inhibiting anoikis. Oncogene, 2018, 37(46):6025-6040. (PMID: 29995871)
[45] ♦ Wang D#, Liu Z#, Lu Y#, Bao H, Wu X, Zeng Z, Liu Z, Zhao Q, He C, Lu J, Wang Z, Qiu M, Wang F, Wang F, Li Y, Wang X, Shao Y, Xu R. Liquid biopsies to track trastuzumab resistance in metastatic HER2-positive gastric cancer. Gut, 2019, 68(7):1152-1161. (PMID: 30269082)
[44] ♦ Liu Z, Zhang Q, Bu C, Wang D, Yu K, Gan Z, Chang J, Cheng Z, Liu Z. Quantitative dynamics of proteome, acetylome and succinylome during stem cells differentiation into hepatocyte-like cells. Journal of Proteome Research, 2018, 17(7):2491-2498. (PMID: 29882676)
[43] ♦ Wang F, Liu D, Zhao Q, Chen G, Liu X, Wang Y, Su H, Qin Y, He Y, Zou Q, Liu Y, Lin Y, Liu Z, Bei J, Xu R. The genomic landscape of small cell carcinoma of the esophagus. Cell Research, 2018, 28(7):771-774. (PMID: 29728688)
[42] ♦ Liu G, Liu R, Yan J, An X, Jiang W, Ling Y, Chen J, Bei J, Zuo X, Cai M, Liu Z, Zuo Z, Liu J, Pan Z, Ding P. The Heterogeneity Between Lynch-Associated and Sporadic MMR Deficiency in Colorectal Cancers. Journal of the National Cancer Institute, 2018, 110(9):975-984. (PMID: 29471527)
[41] ♦ Lu Y#, Ju H#, Liu Z#, Chen D, Wang Y, Zhao Q, Wu Q, Zeng Z, Qiu H, Hu P, Wang Z, Zhang D, Wang F, Xu R. ME1 regulates NADPH homeostasis to promote gastric cancer growth and metastasis. Cancer Research, 2018, 78(8):1972-1985. (PMID: 29654155)
[40] ♦ Deng W, Ma L, Zhang Y, Zhou J, Wang Y, Liu Z, Xue Y. THANATOS: an integrative data resource of proteins and post-translational modifications in the regulation of autophagy. Autophagy, 2018, 14(2):296-310. (PMID: 29157087)


2016

[39] ♦ Deng W, Wang C, Zhang Y, Xu Y, Zhang S, Liu Z, Xue Y. GPS-PAIL: prediction of lysine acetyltransferase-specific modification sites from protein sequences. Scientific Reports, 2016, 6:39787. (PMID: 28004786)
[38] ♦ Zhu D#, Liu Z#, Pan Z, Qian M, Wang L, Zhu T, Xue Y, Wu D. A new method for classifying different phenotypes of kidney transplantation. Cell Biology and Toxicology, 2016, 32(4):323-32. (PMID: 27278387)
[37] ♦ Ullah S, Lin S, Xu Y, Deng W, Ma L, Zhang Y, Liu Z, Xue Y. dbPAF: an integrative database of protein phosphorylation in animals and fungi. Scientific Reports, 2016, 6:23534. (PMID: 27010073)
[36] ♦ Gao Y, Li Y, Zhang C, Zhao M, Deng C, Lan Q, Liu Z, Su N, Wang J, Xu F, Xu Y, Ping L, Chang L, Gao H, Wu J, Xue Y, Deng Z, Peng J, Xu P. Enhanced Purification of Ubiquitinated Proteins by Engineered Tandem Hybrid Ubiquitin-binding Domains (ThUBDs). Molecular & Cellular Proteomics, 2016, 15(4):1381-96. (PMID: 26842620)
[35] ♦ He C, Bian Y, Xue Y, Liu Z, Zhou K, Yao C, Lin Y, Zou H, Luo F, Qu Y, Zhao J, Ye M, Zhao S, Xu W. Pyruvate Kinase M2 Activates mTORC1 by Phosphorylating AKT1S1. Scientific Reports, 2016, 6:21524. (PMID: 26876154)
[34] ♦ Klionsky DJ, .., Liu Z, ... Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). Autophagy, 2016, 12(1):1-222. (PMID: 26799652)


2015

[33] ♦ Feng W, Zhang W, Wang H, Ma L, Miao D, Liu Z, Xue Y, Deng H, Yu L. Analysis of phosphorylation sites on autophagy proteins. Protein Cell, 2015, 6(9):698-701. (PMID: 26081468)
[32] ♦ Pan Z, Wang B, Zhang Y, Wang Y, Ullah S, Liu Z, Xue Y. dbPSP: a curated database for protein phosphorylation sites in prokaryotes. Database, 2015, 2015:bav031. (PMID: 25841437)
[31] ♦ Tian M, Cheng H, Wang Z, Su N, Liu Z, Hong X, Xue Y, Xu P. Phosphoproteomic analysis of the highly metastatic hepatocellular carcinoma cell line MHCC97-H. International Journal of Molecular Sciences, 2015, 16(2):4209-25. (PMID: 25690035)
[30] ♦ Wang Y, Cheng H, Pan Z, Ren J, Liu Z, Xue Y. Reconfiguring phosphorylation signaling by genetic polymorphisms affects cancer susceptibility. Journal of Molecular Cell Biology, 2015, 7(3):187-202. (PMID: 25722345) COVER STORY
[29] ♦ Huang Z, Ma L, Wang Y, Pan Z, Ren J, Liu Z, Xue Y. MiCroKiTS 4.0: a database of midbody, centrosome, kinetochore, telomere and spindle. Nucleic Acids Research, 2015, 43:D328-34. (PMID: 25392421)


2014

[28] ♦ Cheng H, Deng W, Wang Y, Ren J, Liu Z, Xue Y. dbPPT: a comprehensive database of protein phosphorylation in plants. Database, 2014, 2014:bau121. (PMID: 25534750)
[27] ♦ Pan Z#, Liu Z#, Cheng H, Gao T, Ullah S, Ren J, 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. (PMID: 25476580)
[26] ♦ Li Z, Wu P, Zhao Y, Liu Z, Zhao W. Prediction of serine/threonine phosphorylation sites in bacteria proteins Advances in Experimental Medicine and Biology, 2015, 827:275-85. (PMID: 25387970)
[25] ♦ Deng W, Wang Y, Liu Z, Cheng H, Xue Y. HemI: A Toolkit for Illustrating Heatmaps. PLoS One, 2014, 9(11):e111988. (PMID: 25372567)
[24] ♦ Qi L#, Liu Z#, Wang J, Cui Y, Guo Y, Zhou T, Zhou Z, Guo X, Xue Y, Sha J. Systematic analysis of the phosphoproteome and kinase-substrate networks in the mouse testis. Molecular & Cellular Proteomics, 2014, 13(12):3626-38. (PMID: 25293948)
[23] ♦ Zhao Q, Xie Y, Zheng Y, Jiang S, Liu W, Mu W, Liu Z, Zhao Y, Xue Y, Ren J. GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs. Nucleic Acids Research, 2014, 42:W325-30. (PMID: 24880689)
[22] ♦ Yao Y, Ma, L, Jia Q, Deng W, Liu Z, Zhang Y, Ren J, Xue Y, Jia H, Yang Q. Systematic characterization of small RNAome during zebrafish early developmental stages. BMC Genomics, 2014, 15(1): 117. (PMID: 24507755)
[21] ♦ Wang Y#, Liu Z#, Cheng H, Gao T, Pan Z, Yang Q, Guo A, Xue Y. EKPD: a hierarchical database of eukaryotic protein kinases and protein phosphatases. Nucleic Acids Research, 2014, 42: D496-D502. (PMID: 24214991)
[20] ♦ Liu Z, Wang Y, Gao T, Pan Z, Cheng H, Yang Q, Cheng Z, Guo A, Ren J, Xue Y. CPLM: a database of protein lysine modifications. Nucleic Acids Research, 2014, 42: D531-D536. (PMID: 24214993)


2013

[19] ♦ Wang Y#, Dai Z#, Cheng H#, Liu Z#, Pan Z#, Deng W#, Gao T, Li X, Yao Y, Ren J, Xue Y. Towards a better understanding of the novel avian-origin H7N9 influenza A virus in China. Scientific Reports, 2013, 3:2318. (PMID: 23897131)
[18] ♦ Liu Z, Wang Y, Xue Y. Phosphoproteomics-based network medicine. FEBS Journal, 2013, 280(22): 5696-5704. (PMID: 23751130)
[17] ♦ Liu Z, Wang Y, Zhou C, Xue Y, Zhao W, Liu H. Computationally characterizing and comprehensive analysis of zinc-binding sites in proteins. BBA - Proteins and Proteomics, 2014, 1844(1 Pt B): 171-180. (PMID: 23499845)
[16] ♦ Wang H, Zeng F, Liu Q, Liu H, Liu Z, Niu L, Teng M, Li X. The structure of the ARE-binding domains of Hu antigen R (HuR) undergoes conformational changes during RNA binding. Acta Crystallographica Section D, 2013, D69, 373–380. (PMID: 23519412)
[15] ♦ Gao T#, Liu Z#, Wang Y, Cheng H, Yang Q, Guo A, Ren J, Xue Y. UUCD: a family-based database of ubiquitin and ubiquitin-like conjugation. Nucleic Acids Research, 2013, 41: D445-D451. (PMID: 23172288)
[14] ♦ Liu Z#, Ren J#, Cao J#, He J, Yao X, Jin C, Xue Y. Systematic analysis of the Plk-mediated phosphoregulation in eukaryotes. Briefings in Bioinformatics, 2013, 14(3):344-360. (PMID: 22851512)


2012

[13] ♦ Song C, Ye M, Liu Z, Cheng H, Jiang X, Han G, Songyang Z, Tan Y, Wang H, Ren J, Xue Y, Zou H. Systematic analysis of protein phosphorylation networks from phosphoproteomic data. Molecular & Cellular Proteomics, 2012, 11(10):1070-83. (PMID: 22798277)
[12] ♦ Liu Z#, Yuan F#, Ren J, Cao J, Zhou Y, Yang Q, Xue Y. GPS-ARM: Computational analysis of APC/C recognition motif by predicting D-boxes and KEN-boxes. PLoS One, 2012, 7(3): e34370. (PMID: 22479614)
[11] ♦ Cai, R#, Liu Z#, Ren J, Ma, C, Gao, T, Zhou Y, Yang Q, Xue Y. GPS-MBA: Computational analysis of MHC Class II Epitopes in Type 1 Diabetes. PLoS One, 2012, 7(3): e33884. (PMID: 22479466)


2011

[10] ♦ Liu Z#, Ma Q#, Cao J, Gao X, Ren J, Xue Y. GPS-PUP: GPS-PUP: Computational prediction of pupylation sites in prokaryotic proteins. Molecular BioSystems, 2011, 7(10): 2737-2740. (PMID: 21850344)
[9] ♦ Ren J, Gao X, Liu Z, Ma Q, Cao J, Xue Y. Computational Analysis of Phosphoproteomics: Progresses and Perspectives. Current Protein & Peptide Science, 2011, 12, 591-601. (PMID: 21827424)
[8] ♦ Liu Z#, Cao J#, Gao X, Ma Q, Ren J, Xue Y. GPS-CCD: A novel computational program for the prediction of calpain cleavage sites. PLoS One, 2011, 6(4):e19001. (PMID: 21533053)
[7] ♦ Liu Z, Cao J, Ma Q, Gao X, Ren J, Xue Y. GPS-YNO2: Computational prediction of tyrosine nitration sites in proteins. Molecular BioSystems, 2011, 7(4): 1197-1204. (PMID: 21258675) TOP TEN ACCESSED ARTICLES in August, 2011 from the Molecular Biosystems
[6] ♦ Xue Y, Liu Z, Cao J, Ma Q, Gao X, Wang Q, Jin C, Zhou Y, Wen L, Ren J. GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection. Protein Engineering, Design and Selection, 2011, 24(3): 255-260. (PMID: 21062758)
[5] ♦ Liu Z, Cao J, Gao X, Zhou Y, Wen L, Yang X, Yao X, Ren J, Xue Y. CPLA 1.0: an integrated database of protein lysine acetylation. Nucleic Acids Research, 2011, 39: D1029-D1034. (PMID: 21059677)


2010

[4] ♦ Xue Y, Liu Z, Gao X, Jin C, Wen L, Yao X, Ren J. GPS-SNO: computational prediction of protein S-nitrosylation sites with a modified GPS algorithm. PLoS One, 2010, 5(6):e11290. (PMID: 20585580)
[3] ♦ Xue Y, Gao X, Cao J, Liu Z, Jin C, Wen L, Yao X, Ren J. summary of computational resources for protein phosphorylation. Current Protein & Peptide Science, 2010, 11, 485-496. (PMID: 20491621)
[2] ♦ Ren J, Jiang C, Gao X, Liu Z, Yuan Z, Jin C, Wen L, Zhang Z, Xue Y, Yao X. PhosSNP for systematic analysis of genetic polymorphisms that influence protein phosphorylation. Molecular & Cellular Proteomics, 2010, 9, 623-634. (PMID: 19995808)
[1] ♦ Ren J, Liu Z, Gao X, Jin C, Ye M, Zou H, Wen L, Zhang Z, Xue Y, Yao X. MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore. Nucleic Acids Research, 2010, 38, D155-160. (PMID: 19783819)