OUR PUBLICATIONS
In Press
| [] ♦ | Li Y, Zheng Y, Huang J, Nie R, Wu Q, Zuo Z, Yuan S, Yu K, Liang C, Pan Y, Zhao B, Xu Y, Zhang Q, Zheng Y, Chen J, Zeng Z, Wei W, Liu Z†, Xu R†, Luo H†. CAF-macrophage crosstalk in tumour microenvironments governs the response to immune checkpoint blockade in gastric cancer peritoneal metastases. Gut, 2024, 10.1136/gutjnl-2024-333617. (PMID: 39537239) |
| [] ♦ | Zou Y, Duan H, Deng Z, Xiang R, Zhao J, Zhang Z, Hu W, Yang Y, Yan Z, Wen S, Liu Z, Zhang G, Mou Y, Li D, Jiang X. Single-cell atlas profiling revealed cellular characteristics and dynamic changes after PD-1 blockade therapy of brain metastases from laryngeal squamous cell carcinoma. Molecular and Cellular Biochemistry, 2024. Online ahead of print. (PMID: 39085744) |
2024
| [141] ♦ | Qin J, Huang X, Gou S, Zhang S, Gou Y, Zhang Q, Chen H, Sun L, Chen M, Liu D, Han C, Tang M, Feng Z, Niu S, Zhao L, Tu Y, Liu Z, Xuan W, Dai L, Jia D, Xue Y. Ketogenic diet reshapes cancer metabolism through lysine β-hydroxybutyrylation. Nature Metabolism, 2024, 6(8):1505-1528. (PMID: 39134903) |
| [140] ♦ | Luo X, Lu Y, Wang Y, Huang R, Liu J, Jin Y, Liu Z, Liu Z, Huang Q, Pu H, Zeng Z, Xu R, Zhao Q, Wu Q. M6A-modified lncRNA FAM83H-AS1 promotes colorectal cancer progression through PTBP1. Cancer Letters, 2024, 598:217085. (PMID: 38964733) |
| [139] ♦ | Xie R, Cao B, Wu Z, Ouyang Y, Chen H, Zhai W, Liu Z†, Xu M†, Guo G†. dbEBV: A database of Epstein-Barr virus variants and their correlations with human health. Computational and Structural Biotechnology Journal, 2024, 23:2076-2082. (PMID: 38803518) |
| [138] ♦ | Qian Z, Pan Y, Li X, Chen Y, Wu H, Liu Z, Kosar M, Bartek J, Wang Z, Xu R. Modulator of TMB-associated immune infiltration (MOTIF) predicts immunotherapy response and guides combination therapy. Science Bulletin, 2024, 69(6):803-822. (PMID: 38320897) |
| [137] ♦ | Liang T, Chen H, Liu L, Zheng Y, Ma Z, Min L, Zhang J, Wu L, Ma J, Liu Z, Zhang Q, Luo K, Hu D, Ji T, Yu X. Antibody Profiling of Pan-Cancer Viral Proteome Reveals Biomarkers for Nasopharyngeal Carcinoma Diagnosis and Prognosis. Molecular & Cellular Proteomics, 2024, 23(3):100729. (PMID: 38309569) |
| [136] ♦ | Liu D, Cao F, Xu Z, Zhao C, Liu Z, Pang J, Liu Z, Moghiseh M, Butler A, Liang S, Fan W, Yang J. Selective Organ-Targeting Hafnium Oxide Nanoparticles with Multienzyme-Mimetic Activities Attenuate Radiation-Induced Tissue Damage. Advanced Materials, 2023, 36(19):e2308098. (PMID: 37777858) |
| [135] ♦ | Guo G, Li J, Zheng Y, Liu Z†, Lin H†. Breast-conserving surgery is associated with a lower incidence of suicide among females with breast cancer in the United States: A population-based retrospective cohort study. International Journal of Surgery, 2024, 110(3):1392-1401. (PMID: 38215250) |
| [134] ♦ | Wu Q, Qi J, Liu Z, Luo X, Yu K, Lu Y, Wang Y, Jin Y, Liu J, Huang L, Zeng Z, Zheng Y, Xu R†, Liu Z†. HIPK3 maintains sensitivity to platinum drugs and prevents disease progression in gastric cancer. Cancer Letters, 2024, 216643. (PMID: 38246220) |
2023
| [133] ♦ | Yuan S, Nie R, Huang Y, Chen Y, Wang S, Sun X, Li Y, Liu Z, Chen Y, Yao Y, Xu Y, Qiu H, Liang Y, Wang W, Liu Z, Zhao Q, Xu R, Zhou Z, Wang F. Residual circulating tumor DNA after adjuvant chemotherapy effectively predicts recurrence of stage II-III gastric cancer. Cancer Communications, 2023, 43(12):1312-1325. (PMID: 37837629) |
| [132] ♦ | Zheng Y, Pan Y, Liao K, Yu K, Wu Q, Chen Y, Deng Y, Sun H, Pu H, Ju H†, Xu R†, Liu Z†. Pan-cancer landscape of tumour endothelial cells pinpoints insulin receptor as a novel antiangiogenic target and predicts immunotherapy response. Clinical and Translational Medicine, 2023, 13(12):e1501. (PMID: 38037528) |
| [131] ♦ | Li J, Wang J, Tian T, Liu J, Zheng Y, Mo H, Sheng H, Chen Y, Wu Q, Han Y, Liao K, Pan Y, Zeng Z, Liu Z, Yang W, Xu R, Ju H. The liver microenvironment orchestrates FGL1-mediated immune escape and progression of metastatic colorectal cancer. Nature Communications, 2023, 14(1):6690. (PMID: 37872170) |
| [130] ♦ | Qiu M, Wang C, Wu Z, Zhao Q, Zhao Z, Huang C, Wu W, Yang L, Zhou Z, Zheng Y, Pan H, Liu Z, Zeng Z, Luo H, Wang F, Wang F, Yang S, Huang M, Lian Z, Zhang H, Xu R. Dynamic single-cell mapping unveils Epstein‒Barr virus-imprinted T-cell exhaustion and on-treatment response. Signal Transduction and Targeted Therapy, 2023, 8(1):370. (PMID: 37735150) |
| [129] ♦ | Liu J, Zhou W, Luo X, Chen Y, Wong C, Liu Z, Zheng J, Mo H, Chen J, Li J, Zhong M, Xu Y, Zhang Q, Pu H, Wu Q, Jin Y, Wang Z, Xu R, Luo H. Long noncoding RNA Regulating ImMune Escape regulates mixed lineage leukaemia protein-1-H3K4me3-mediated immune escape in oesophageal squamous cell carcinoma. Clinical and Translational Medicine, 2023, 13(9):e1410. (PMID: 37712124) |
| [128] ♦ | Pang J, Zhu D, Liu Y, Liu D, Zhao C, Zhang J, Li S, Liu Z, Li X, Huang P, Wen S, Yang J. A Cyclodiaryliodonium NOX Inhibitor for the Treatment of Pancreatic Cancer via Enzyme-Activatable Targeted Delivery by Sulfated Glycosaminoglycan Derivatives. Advanced Healthcare Materials, 2023, 12(17):e2203011. (PMID: 36841552) |
| [127] ♦ | Zhao G, Luo T, Liu Z, Li J. Development and validation of focal adhesion-related genes signature in gastric cancer. Frontiers in Genetics, 2023, 14:1122580. (PMID: 36968601) |
| [126] ♦ | Li X, Zhou Y, Jiang Q, Huang J, Liu Z, Li Y, Guo G. A novel scoring model based on RNA modification "writers" can predict the prognosis and guide immunotherapy in gastric cancer. Functional & Integrative Genomics, 2023, 23(2):162. (PMID: 37188931) |
| [125] ♦ | Xu L, Wang D, Zhao L, Yang Z, Liu X, Li X, Yuan T, Wang Y, Huang T, Bian N, He Y, Chen X, Tian B, Liu Z, Luo F, Si W, Gao G, Ji W, Niu Y, Wei J. C9orf72 poly(PR) aggregation in nucleus induces ALS/FTD-related neurodegeneration in cynomolgus monkeys. Neurobiology of Disease, 2023, 184:106197. (PMID: 37328037) |
| [124] ♦ | Hong Y, Yuan Y, Liu Z, Liu Z†, Zhang Y†. A Pan-Cancer Analysis of Prognostic and Immunological Roles for Cell Death Genes. Genes (Basel), 2023, 14(6):1178. (PMID: 37372358) |
| [123] ♦ | Hu J, Huang R, Liang C, Wang Y, Wang M, Chen Y, Wu C, Zhang J, Liu Z, Zhao Q, Liu Z, Wang F, Yuan S. TRIM50 Inhibits Gastric Cancer Progression by Regulating the Ubiquitination and Nuclear Translocation of JUP. Molecular Cancer Research, 2023, 21(10):1107-1119. (PMID: 37409971) |
| [122] ♦ | Liu Z#, Wang P#, Zhang Q#, Li S, Zhang Y, Guo Y, Jia C, Shao T, Li L, Cheng H, Wang Z. iHypoxia: An Integrative Database of Protein Expression Dynamics in Response to Hypoxia in Animals. Genomics, Proteomics & Bioinformatics, 2023, 21(2):267-277. (PMID: 36503126) |
| [121] ♦ | Yuan J, Zhang Y, Hua X, Hong H, Shi W, Liu K, Liu Z†, Huang P†. Genetically predicted vitamin C levels significantly affect patient survival and immunotypes in multiple cancer types. Frontiers in Immunology, 2023, 14:1177580. (PMID: 37283769) |
| [120] ♦ | Han Y, Zhang Y, Pan Y, Zheng X, Liao K, Mo H, Sheng H, Wu Q, Liu Z, Zeng Z, Yang W, Yuan S, Huang P, Ju H, Xu R. IL-1β-associated NNT acetylation orchestrates iron-sulfur cluster maintenance and cancer immunotherapy resistance. Molecular Cell, 2023, 83(11):1887-1902.e8. (PMID: 37244254) |
| [119] ♦ | Chen Y, Wang Z, Jin Y, Zhao Q, Liu Z, Zuo Z, Ju H, Cui C, Yao J, Zhang Y, Li M, Feng J, Tian L, Xia X, Feng H, Yao S, Wang F, Li Y, Wang F, Xu R. An immunogenic and oncogenic feature-based classification for chemotherapy plus PD-1 blockade in advanced esophageal squamous cell carcinoma. Cancer Cell, 2023, 41(5):919-932.e5. (PMID: 37059106) |
| [118] ♦ | Liu J#, Liu Z#, Li J, Zeng Z, Wang J, Luo X, Wong C, Zheng J, Pu H, Mo H, Sheng H, Wu Q, Li H, Wan G, Li B, Wang D†, Xu R†, Ju H†. The macrophage-associated lncRNA MALR facilitates ILF3 liquid-liquid phase separation to promote HIF1α signaling in esophageal cancer. Cancer Research, 2023, 83(9):1476-1489. (PMID: 36264156) |
| [117] ♦ | Zhang X#, Liu Z#, , Zhang Y#, Xu L, Chen M, Zhou Y, Yu J, Li X, Zhang N. SEPT2 crotonylation promotes metastasis and recurrence in hepatocellular carcinoma and is associated with poor survival. Cell & Bioscience, 2023, 13(1):63. (PMID: 36949517) |
| [116] ♦ | Zhang X, Cheng L, Gao C, Chen J, Liao S, Zheng Y, Xu L, He J, Wang D, Fang Z, Zhang J, Yan M, Luan Y, Chen S, Chen LK, Xia X, Deng C, Chen G, Li W, Liu Z†, Zhou P†. Androgen Signaling Contributes to Sex Differences in Cancer by Inhibiting NF-κB Activation in T Cells and Suppressing Anti-Tumor Immunity. Cancer Research, 2023, 83(6):906-921. (PMID: 36634207) |
| [115] ♦ | Zhao C, Liu Z, Chang C, Chen Y, Zhang Q, Zhang X, Andreou C, Pang J, Liu Z†, Wang D†, Kircher MF, Yang J†. Near-Infrared Phototheranostic Iron Pyrite Nanocrystals Simultaneously Induce Dual Cell Death Pathways via Enhanced Fenton Reactions in Triple-Negative Breast Cancer. ACS Nano, 2023, 17(5):4261-4278. (PMID: 36706095) |
| [114] ♦ | Cheng R, Li F, Zhang M, Xia X, Wu J, Gao X, Zhou H, Zhang Z, Huang N, Yang X, Zhang Y, Shen S, Kang T, Liu Z, Xiao F, Yao H, Xu J, Yan C, Zhang N. A novel protein RASON encoded by a lncRNA controls oncogenic RAS signaling in KRAS mutant cancers. Cell Research, 2023, 33(1):30-45. (PMID: 36241718) |
| [113] ♦ | Yu K, Liu Z, Cheng H, Li S, Zhang Q, Liu J, Ju H, Zuo Z, Zhao Q, Kang S†, Liu Z†. dSCOPE: a software to detect sequences critical for liquid-liquid phase separation. Briefings in Bioinformatics, 2023, 24(1):bbac550. (PMID: 36528388) |
| [112] ♦ | Yu K, Wang Y, Zheng Y, Liu Z, Zhang Q, Wang S, Zhao Q, Zhang X, Li X, Xu R†, Liu Z†. qPTM: an updated database for PTM dynamics in human, mouse, rat and yeast. Nucleic Acids Research, 2023, 51(D1):D479-D487. (PMID: 36165955) |
2022
| [111] ♦ | Liu X, Zheng Y, Xiao M, Chen X, Zhu Y, Xu C, Wang F, Liu Z, Cao K. SRSF10 stabilizes CDC25A by triggering exon 6 skipping to promote hepatocarcinogenesis. Journal of Experimental & Clinical Cancer Research, 2022, 41(1):353. (PMID: 36539837) |
| [110] ♦ | Wang Y, Ruan D, Wang Z, Yu K, Rong D, Liu Z, Wang F, Hu J, Jin Y, Wu Q, Pu H, Wang M, Xu R, Zeng Z. Targeting the cholesterol-RORα/γ axis inhibits colorectal cancer progression through degrading c-myc. Oncogene, 2022, 41(49):5266-5278. (PMID: 36316442) |
| [109] ♦ | Liu Z#, Zhang X#, Zhao Q#, Chen Y, Sheng H, He C, Sun Y, Lai M, Wu M, Zuo Z, Wang W, Zhou Z, Wang F, Li Y, Xu R†, Qiu M†. Whole-exome sequencing among Chinese patients with hereditary diffuse gastric cancer. JAMA Network Open, 2022, 5(12):e2245836. (PMID: 36484990) |
| [108] ♦ | Zhang X, Qian Z, Wang Y, Zhang Q, Yu K, Zheng Y, Liu Z, Zhao Q, Liu Z†. DrugCVar: a platform for evidence-based drug annotation for genetic variants in cancer. Bioinformatics, 2022, 38(11):3094-3098. (PMID: 35426945) |
| [107] ♦ | Chen L, Zheng Y, Yu K, Chen S, Wang W, Gale RP, Liu Z†, Liang Y†. Changing causes of death in persons with haematological cancers 1975-2016. Leukemia, 2022, 36(7):1850-1860. (PMID: 35577905) |
| [106] ♦ | Liang J, Li Z, Yue C, Hu Z, Cheng H, Liu Z, Guo W. Multi-modal optimization to identify personalized biomarkers for disease prediction of individual patients with cancer. Briefings in Bioinformatics, 2022, 23(5):bbac254. (PMID: 35858208) |
| [105] ♦ | Luo X, He M, Liu J, Zheng J, Wu Q, Chen Y, Meng Q, Luo K, Chen D, Xu R, Zeng Z†, Liu Z†, Luo H†. LncRNA TMPO-AS1 promotes esophageal squamous cell carcinoma progression by forming biomolecular condensates with FUS and p300 to regulate TMPO transcription. Experimental & Molecular Medicine, 2022, 54(6):834-847. (PMID: 35760875) |
| [104] ♦ | Xu Y, Lei B, Zhang Q, Lei Y, Li C, Li X, Yao R, Hu R, Liu K, Wang Y, Cui Y, Wang L, Dai J, Li L, Ni W, Zhou P†, Liu Z†, Hu S†. ADDAGMA: A database for domestic animal gut microbiome atlas. Computational and Structural Biotechnology Journal, 2022, 20: 891–898. (PMID: 35222847) |
| [103] ♦ | Zhang W, Chen S, Du Q, Bian P, Chen Y, Liu Z, Zheng J, Sai K, Mou Y, Chen Z, Fan X, Jiang X. CircVPS13C promotes pituitary adenoma growth by decreasing the stability of IFITM1 mRNA via interacting with RRBP1. Oncogene, 2022, 41(11):1550-1562. (PMID: 35091683) |
| [102] ♦ | Lin J, Hu P, Wang Y, Tan Y, Yu K, Liao K, Wu Q, Li T, Meng Q, Lin J, Liu Z, Pu H, Ju H, Xu R, Qiu M. Phosphorylated NFS1 weakens oxaliplatin-based chemosensitivity of colorectal cancer by preventing PANoptosis. Signal Transduction and Targeted Therapy, 2022, 7(1):54. (PMID: 35221331) |
| [101] ♦ | Xiong W, He W, Wang T, He S, Xu F, Wang Z, Wang X, Guo H, Ling J, Zhang H, Liu Y, Xing K, Li M, Zhang H, Li J, Niu N, Xue J, Zhan Q, Liu Z, Bei J, Huang P, Liu J, Xia L, Xia X. Smad4 Deficiency Promotes Pancreatic Cancer Immunogenicity by Activating the Cancer-Autonomous DNA-Sensing Signaling Axis. Advanced Science, 2022, 9(7):e2103029. (PMID: 35064757) |
| [100] ♦ | Xue H, Zhang Q, Wang P, Cao B, Jia C, Cheng B, Shi Y, Guo W, Wang Z, Liu Z†, Cheng H†. qPTMplants: an integrative database of quantitative post-translational modifications in plants. Nucleic Acids Research, 2022, 50(D1):D1491-D1499. (PMID: 34718741) |
| [99] ♦ | Liu S#, Sun X#, Chen Q#, Liu Z#, Bian L#, Yuan L, Xiao B, Lu Z, Li X, Yan J, Yan S, Li J, Bei J, Mai H, Tang L. Development and validation of a transcriptomics-based gene signature to predict distant metastasis and guide induction chemotherapy in locoregionally advanced nasopharyngeal carcinoma. European Journal of Cancer, 2022, 163:26-34. (PMID: 35032814) |
2021
| [98] ♦ | Liu B, Zhang Q, Wang J, Cao S, Zhou Z, Liu Z†, Cheng H†. iCAV: an integrative database of cancer-associated viruses . Database, 2021, 2021(2021):baab079. (PMID: 34907423) |
| [97] ♦ | Pan L, Huang X, Liu Z#, Ye Y, Li R, Zhang J, Wu G, Bai R, Zhuang L, Wei L, Li M, Zheng Y, Su J, Deng J, Deng S, Zeng L, Zhang S, Wu C, Che X, Wang C, Chen R, Lin D, Zheng J. Inflammatory cytokine-regulated tRNA-derived fragment tRF-21 suppresses pancreatic ductal adenocarcinoma progression. Journal of Clinical Investigation, 2021, 131(22):e148130. (PMID: 34779408) |
| [96] ♦ | Li L, Bai L, Lin H, Dong L, Zhang R, Cheng X, Liu Z, Ouyang Y, Ding K. Multiomics analysis of tumor mutational burden across cancer types. Computational and Structural Biotechnology Journal, 2021, 19:5637-5646. (PMID: 34745455) |
| [95] ♦ | Su J, Wu G, Ye Y, Zhang J, Zeng L, Huang X, Zheng Y, Bai R, Zhuang L, Li M, Pan L, Deng J, Li R, Deng S, Zhang S, Zuo Z, Liu Z, Lin J, Lin D, Zheng J. NSUN2-mediated RNA 5-methylcytosine promotes esophageal squamous cell carcinoma progression via LIN28B-dependent GRB2 mRNA stabilization. Oncogene, 2021, 40(39):5814-5828. (PMID: 34345012) |
| [94] ♦ | Li W, Wang C, Tao L, Yan Y, Zhang M, Liu Z, Li Y, Zhao H, Li X, He X, Xue Y, Dong M. Insulin signaling regulates longevity through protein phosphorylation in Caenorhabditis elegans. Nature Communications, 2021, 12(1):4568. (PMID: 34315882) |
| [93] ♦ | Ruan D, Li T, Wang Y, Meng Q, Li Y, Yu K, Wang M, Lin J, Luo L, Wang D, Lin J, Bai L, Liu Z, Zhao Q, Wu X, Ju H, Xu R. FTO downregulation mediated by hypoxia facilitates colorectal cancer metastasis. Oncogene, 2021, 40(33):5168-5181. (PMID: 34218271) |
| [92] ♦ | Meng Q, Lu Y, Ruan D, Yu K, Chen Y, Xiao M, Wang Y, Liu Z, Xu R, Ju H, Qiu M. DNA methylation regulator-mediated modification patterns and tumor microenvironment characterization in gastric cancer. Molecular Therapy-Nucleic Acids, 2021, 24:695-710. (PMID: 33996253) |
| [91] ♦ | Sui Q, Liu D, Jiang W, Tang J, Kong L, Han K, Liao L, Li Y, Ou Q, Xiao B, Liu G, Ling Y, Chen J, Liu Z, Zuo Z, Pan Z, Zhou P, Zheng J, Ding P. Dickkopf 1 impairs the tumor response to PD-1 blockade by inactivating CD8+ T cells in deficient mismatch repair colorectal cancer. Journal for ImmunoTherapy of Cancer, 2021, 9(3):e001498. (PMID: 33782107) |
| [90] ♦ | Wu Q, Luo X, Liu J, Lu Y, Wang Y, Qi J, Liu Z, Huang Q, Liu Z, Lu J, Jin Y, Pu H, Hu P, Zheng J, Zeng Z, Ju H, Xie D, Zhao Q, Xu R. MYC-Activated LncRNA MNX1-AS1 Promotes the Progression of Colorectal Cancer by Stabilizing YB1. Cancer Research, 2021, 81(10):2636-2650. (PMID: 33782099) |
| [89] ♦ | Zheng Y, Chen Y, Yu K, Yang Y, Wang X, Yang X, Qian J, Liu Z†, Wu B. Fatal Infections Among Cancer Patients: A Population-Based Study in the United States. Infectious Diseases and Therapy, 2021, 10(2):871-895. (PMID: 33761114) |
| [88] ♦ | Li S, Yu K, Wu G, Zhang Q, Wang P, Zheng J, Liu Z, Wang J, Gao X, Cheng H. pCysMod: Prediction of Multiple Cysteine Modifications Based on Deep Learning Framework. Frontiers in Cell and Developmental Biology, 2021, 9:617366. (PMID: 33732693) |
| [87] ♦ | You X, Tian J, Zhang H, Guo Y, Yang J, Zhu C, Song M, Wang P, Liu Z, Cancilla J, Lu W, Glorieux C, Wen S, Du H, Huang P, Hu Y. Loss of mitochondrial aconitase promotes colorectal cancer progression via SCD1-mediated lipid remodeling. Molecular Metabolism, 2021, 48:101203. (PMID: 33676027) |
| [86] ♦ | Zeng Z, Lu J, Wang Y, Sheng H, Wang Y, Chen Z, Wu Q, Zheng J, Chen Y, Yang D, Yu K, Mo H, Hu J, Hu P, Liu Z, Ju H, Xu R. The lncRNA XIST/miR-125b-2-3p axis modulates cell proliferation and chemotherapeutic sensitivity via targeting Wee1 in colorectal cancer. Cancer Medicine, 2021, 10(7):2423-2441. (PMID: 33666372) |
| [85] ♦ | Que Y, Zhang X, Liu Z, Zhao J, Pan Q, Wen X, Xiao W, Xu B, Hong D, Guo T, Shen L, Fan W, Chen H, Weng D, Xu H, Zhou P, Zhang Y, Niu X, Zhang X. Frequent amplification of HDAC genes and efficacy of HDAC inhibitor chidamide and PD-1 blockade combination in soft tissue sarcoma. Journal for ImmunoTherapy of Cancer, 2021, 9(2):e001696. (PMID: 33637599) |
| [84] ♦ | Wang P, Zhang Q, Li S, Cheng B, Xue H, Wei Z, Shao T, Liu Z†, Cheng H†, Wang Z. iCysMod: an integrative database for protein cysteine modifications in eukaryotes. Briefings in Bioinformatics, 2021, 22(5):bbaa400. (PMID: 33406221) |
| [83] ♦ | 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, 22(3):bbaa082. (PMID: 32496513) |
| [82] ♦ | Huang N, Li F, Zhang M, Zhou H, Chen Z, Ma X, Yang L, Wu X, Zhong J, Xiao F, Yang X, Zhao K, Li X, Xia X, Liu Z, Gao S, Zhang N. An Upstream Open Reading Frame in Phosphatase and Tensin Homolog Encodes a Circuit Breaker of Lactate Metabolism. Cell Metabolism, 2021, 33(1):128-144.e9. (PMID: 33406399) |
| [81] ♦ | 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, 2021, 70(5):890-899. (PMID: 32816920) |
2020
| [80] ♦ | Jiang L, Wang YJ, Zhao J, Uehara M, Hou Q, Kasinath V, Ichimura T, Banouni N, Dai L, Li X, Greiner DL, Shultz LD, Zhang X, Sun ZJ, Curtin I, Vangos NE, Yeoh ZC, Geffken EA, Seo HS, Liu Z, Heffron GJ, Shah K, Dhe-Paganon S, Abdi R. Direct Tumor Killing and Immunotherapy through Anti-SerpinB9 Therapy. Cell, 2020, 183(5):1219-1233.e18. (PMID: 33242418) |
| [79] ♦ | 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) |
| [78] ♦ | 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) |
| [77] ♦ | 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) |
| [76] ♦ | 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) |
| [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] ♦ | Luo T, Li Y, Nie R, Liang C, Liu Z, Xue Z, Chen G, Jiang K, Liu Z, Lin H, Li C, Chen Y. Development and validation of metabolism-related gene signature in prognostic prediction of gastric cancer. Computational and Structural Biotechnology Journal, 2020, 18: 3217-3229. (PMID: 33209209) |
| [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) |
| [64] ♦ | 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 Rice Young Panicles. Genomics, Proteomics & Bioinformatics, 2020, 18(3):305-320. (PMID: 33147495) |
2019
| [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 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) |
| [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) |
| [51] ♦ | 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) |
2018
| [50] ♦ | 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) |
| [49] ♦ | 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) |
| [48] ♦ | 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) |
| [47] ♦ | 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) |
| [46] ♦ | 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) |
| [45] ♦ | 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) |
| [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) |