EDUCATION

  • Ph. D.School of Life Sciences, University of Science and Technology of China, 09/2008 - 06/2013
  • B. Sc.School of Life Sciences, University of Science and Technology of China, 09/2004 - 07/2008

RESEARCH INTEREST

  • Bioinformatics studies of protein post-translational modifications (PTMs) and PTM proteome
  • Cancer bioinformatics for HTP technologies

ACADEMIC EXPERIENCE

  • 12/2015 - PresentAssociate Professor, Sun Yat-sen University Cancer Center
    • Precision medicine and cancer bioinformatics
  • 07/2013 - 11/2015Postdoctoral research, The CUCKOO Workgroup, Huazhong University of Science and Technology (HUST), Mentor: Dr. Yu Xue
    • Bioinformatics of PTM proteome and PTM related enzymes
  • 07/2008 - 06/2013Graduate research, The CUCKOO Workgroup, USTC, Mentor: Dr. Yu Xue (Now @HUST)
    • Bioinformatics of PTM
  • 10/2007 - 06/2013Undergraduate study and graduate research, Lab of Computational Biology, USTC, Mentor: Dr. Haiyan Liu
    • Design of new fold for proteins
    • The structural dynamics of proteins
    • Structure-based computational analysis of zinc-binding in proteins
  • 10/2006 - 07/2007Undergraduate study, Laboratory of Signaling Transduction and Transcription, USTC, Mentor: Dr. Weihua Xiao
    • Biotechnology for immunology and molecular biology

PUBLICATIONS

  • Books Chapter
  • [3] Cheng H., Wang Y., Liu Z., Xue Y. (2015) Computational identification of protein kinases and kinase-specific substrates in plants. Plant Phosphoproteomics, Schulze, W. X. (Ed.), ISBN: 978-1-4939-2647-3, Methods in Molecular Biology, 1306:195-205, Springer New York. (PMID: 25930704)
  • [2] Gao T., Liu Z., Wang Y., Xue Y. (2013) Ubiquitin and Ubiquitin-Like Conjugations in Complex Diseases: A Computational Perspective. Bioinformatics for Diagnosis, Prognosis and Treatment of Complex Diseases, Bairong Shen (Ed.), ISBN: 978-94-007-7974-7, Translational Bioinformatics, 4:171-187, Springer Netherlands.
  • [1] Xue Y., Liu Z., Cao J., Ren J. (2011) Computational Prediction of Post-Translational Modification Sites in Proteins, Systems and Computational Biology - Molecular and Cellular Experimental Systems, Ning-Sun Yang (Ed.), ISBN: 978-953-307-280-7, DOI: 10.5772/18559, InTech.
  • CN Journals#: (Co-)first author; : (Co-)corresponding author
  • [1] Liu Z., Cai Y., Guo X., Li A., Li T., Qiu J., Ren J., Shi S., Song J., Wang M., Xie L., Xue Y., Zhang Z., Zhao X. (2015) Post-translational modification (PTM) bioinformatics in China: progresses and perspectives. Yi Chuan, 37(7): 621-634. (PMID: 26351162)
  • SCI Journals#: (Co-)first author; : (Co-)corresponding author
  • [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., Zhang Q. (2019) Dysregulation, functional implications and prognostic ability of the circadian clock across cancers. Cancer Medicine, 10.1002/cam4.2035. [Epub ahead of print]. (PMID: 30791227)
  • [55] Zhu L., Cheng H., Peng G., Wang S., Zhang Z., Ni E., Fu X., Zhuang C., Liu Z., Zhou H. (2019) Ubiquitinome Profiling Reveals the Landscape of Ubiquitination Regulation in Young Panicles. Genomics, Proteomics & Bioinformatics, 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. (2019) PIWI-interacting RNA-36712 restrains breast cancer progression and chemoresistance by interaction with SEPW1 pseudogene SEPW1P RNA. Molecular Cancer, 18(1):9. (PMID: 30636640)
  • [53] 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. (2018) PIWI-interacting RNA-54265 is oncogenic and a potential therapeutic target in colorectal adenocarcinoma. Theranostics, 8(19):5213-5230. (PMID: 30555542)
  • [52] 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. (2018) Modulation of Redox Homeostasis by Inhibition of MTHFD2 in Colorectal Cancer: Mechanisms and Therapeutic Implications. Journal of the National Cancer Institute, 10.1093/jnci/djy160. (PMID: 30534944)
  • [51] Wei X., Wu Q., Chen D., Zeng Z., Lu J., Liu Z., Ju H., Ren C., Pan Z., Wang F., Xu R. (2018) The Clinical and Biomarker Association of Programmed Death Ligand 1 and its Spatial Heterogeneous Expression in Colorectal Cancer. Journal of Cancer, 9(23):4325-4333. (PMID: 30519336)
  • [50] Yu K., Zhang Q., Liu Z., Zhao Q., Zhang X., Wang Y., Wang Z., Jin Y., Li X., Liu Z., Xu R. (2018) qPhos: a database of protein phosphorylation dynamics in humans. Nucleic Acids Research, 47(D1):D451-D458. (PMID: 30380102)
  • [49] Zhang Q.#,†, Yu K., Liu Z., Wang D., Zhao Y., Yin S., Liu Z. (2018) Prediction of prkC-mediated protein serine/threonine phosphorylation sites for bacteria. PLoS One, 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. (2018) LncRNA CamK-A Regulates Ca2+-Signaling-Mediated Tumor Microenvironment Remodeling. Molecular Cell, 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. (2018) Nicotinamide nucleotide transhydrogenase-mediated redox homeostasis promotes tumor growth and metastasis in gastric cancer. Redox Biology, 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. (2018) CPT1A-mediated fatty acid oxidation promotes colorectal cancer cell metastasis by inhibiting anoikis. Oncogene, doi: 10.1038/s41388-018-0384-z. (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. (2018) Liquid biopsies to track trastuzumab resistance in metastatic HER2-positive gastric cancer. Gut, doi: 10.1136/gutjnl-2018-316522. (PMID: 30269082)
  • [44] Liu Z., Zhang Q., Bu C., Wang D., Yu K., Gan Z., Chang J., Cheng Z., Liu Z. (2018) Quantitative dynamics of proteome, acetylome and succinylome during stem cells differentiation into hepatocyte-like cells. Journal of Proteome Research, 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. (2018) The genomic landscape of small cell carcinoma of the esophagus. Cell Research, 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. (2018) The Heterogeneity Between Lynch-Associated and Sporadic MMR Deficiency in Colorectal Cancers. Journal of the National Cancer Institute, 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. (2018) ME1 regulates NADPH homeostasis to promote gastric cancer growth and metastasis. Cancer Research, 78(8):1972-1985. (PMID: 29654155)
  • [40] Deng W., Ma L., Zhang Y., Zhou J., Wang Y., Liu Z., Xue Y. (2017) THANATOS: an integrative data resource of proteins and post-translational modifications in the regulation of autophagy. Autophagy, 14(2):296-310. (PMID: 29157087)
  • [39] Deng W., Wang C., Zhang Y., Xu Y., Zhang S., Liu Z., Xue Y. (2016) GPS-PAIL: prediction of lysine acetyltransferase-specific modification sites from protein sequences. Scientific Reports, 6:39787. (PMID: 28004786)
  • [38] Zhu D.#, Liu Z.#, Pan Z., Qian M., Wang L., Zhu T., Xue Y., Wu D. (2016) A new method for classifying different phenotypes of kidney transplantation. Cell Biology and Toxicology, 32(4):323-32. (PMID: 27278387)
  • [37] Ullah S., Lin S., Xu Y., Deng W., Ma L., Zhang Y., Liu Z., Xue Y. (2016) dbPAF: an integrative database of protein phosphorylation in animals and fungi. Scientific Reports, 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. (2016) Enhanced Purification of Ubiquitinated Proteins by Engineered Tandem Hybrid Ubiquitin-binding Domains (ThUBDs). Molecular & Cellular Proteomics, 15(4):1381-96. [Epub ahead of print]. (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. (2016) Pyruvate Kinase M2 Activates mTORC1 by Phosphorylating AKT1S1. Scientific Reports, 6:21524. (PMID: 26876154)
  • [34] Klionsky DJ., ..., Liu Z., ... (2016) Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). Autophagy, 12(1):1-222. (PMID: 26799652)
  • [33] Feng W., Zhang W., Wang H., Ma L., Miao D., Liu Z., Xue Y., Deng H., Yu L. (2015) Analysis of phosphorylation sites on autophagy proteins. Protein Cell, 6(9):698-701. (PMID: 26081468)
  • [32] Pan Z., Wang B., Zhang Y., Wang Y., Ullah S., Liu Z., Xue Y. (2015) dbPSP: a curated database for protein phosphorylation sites in prokaryotes. Database, 2015: bav031. (PMID: 25841437)
  • [31] Tian M., Cheng H., Wang Z., Su N., Liu Z., Hong X., Xue Y., Xu P. (2015) Phosphoproteomic analysis of the highly metastatic hepatocellular carcinoma cell line MHCC97-H. International Journal of Molecular Sciences, 16(2):4209-25. (PMID: 25690035)
  • [30] Wang Y., Cheng H., Pan Z., Ren J., Liu Z., Xue Y. (2015) Reconfiguring phosphorylation signaling by genetic polymorphisms affects cancer susceptibility. Journal of Molecular Cell Biology, 7(3):187-202. (PMID: 25722345) COVER STORY
  • [29] Cheng H., Deng W., Wang Y., Ren J., Liu Z., Xue Y. (2014) dbPPT: a comprehensive database of protein phosphorylation in plants. Database, 2014: bau121. (PMID: 25534750)
  • [28] Pan Z.#, Liu Z.#, Cheng H., Gao T., Ullah S., Ren J., Xue Y. (2014) Systematic analysis of the in situ crosstalk of tyrosine modifications reveals no additional natural selection on multiply modified residues. Scientific Reports, 4:7331. (PMID: 25476580)
  • [27] Li Z., Wu P., Zhao Y., Liu Z., Zhao W. (2015) Prediction of serine/threonine phosphorylation sites in bacteria proteins. Advances in Experimental Medicine and Biology, 827:275-85. (PMID: 25387970)
  • [26] Deng W., Wang Y., Liu Z., Cheng H., Xue Y. (2014) HemI: A Toolkit for Illustrating Heatmaps. PLoS One, 9(11):e111988. (PMID: 25372567)
  • [25] Huang Z., Ma L., Wang Y., Pan Z., Ren J., Liu Z., Xue Y. (2015) MiCroKiTS 4.0: a database of midbody, centrosome, kinetochore, telomere and spindle. Nucleic Acids Research, 43:D328-34. (PMID: 25392421)
  • [24] Qi L.#, Liu Z.#, Wang J., Cui Y., Guo Y., Zhou T., Zhou Z., Guo X., Xue Y., Sha J. (2014) Systematic analysis of the phosphoproteome and kinase-substrate networks in the mouse testis. Molecular & Cellular Proteomics, 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. (2014) GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs. Nucleic Acids Research, 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. (2014) Systematic characterization of small RNAome during zebrafish early developmental stages. BMC Genomics, 15(1): 117. (PMID: 24507755)
  • [21] Wang Y.#, Liu Z.#, Cheng H., Gao T., Pan Z., Yang Q., Guo A., Xue Y. (2014) EKPD: a hierarchical database of eukaryotic protein kinases and protein phosphatases. Nucleic Acids Research, 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. (2014) CPLM: a database of protein lysine modifications. Nucleic Acids Research, 42: D531-D536. (PMID: 24214993)
  • [19] Wang Y.#, Dai Z.#, Cheng H.#, Liu Z.#, Pan Z.#, Deng W.#, Gao T., Li X., Yao Y., Ren J., Xue Y. (2013) Towards a better understanding of the novel avian-origin H7N9 influenza A virus in China. Scientific Reports, 3:2318. (PMID: 23897131)
  • [18] Liu Z., Wang Y., Xue Y. (2013) Phosphoproteomics-based network medicine. FEBS Journal, 280(22): 5696-5704. (PMID: 23751130)
  • [17] Liu Z., Wang Y., Zhou C., Xue Y., Zhao W., Liu H. (2014) Computationally characterizing and comprehensive analysis of zinc-binding sites in proteins. BBA - Proteins and Proteomics, 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. (2013) The structure of the ARE-binding domains of Hu antigen R (HuR) undergoes conformational changes during RNA binding. Acta Crystallographica Section D, D69, 373–380. (PMID: 23519412)
  • [15] Gao T.#, Liu Z.#, Wang Y., Cheng H., Yang Q., Guo A., Ren J., Xue Y. (2013) UUCD: a family-based database of ubiquitin and ubiquitin-like conjugation. Nucleic Acids Research, 41: D445-D451. (PMID: 23172288)
  • [14] Song C., Ye M., Liu Z., Cheng H., Jiang X., Han G., Songyang Z., Tan Y., Wang H., Ren J., Xue Y., Zou H. (2012) Systematic analysis of protein phosphorylation networks from phosphoproteomic data. Molecular & Cellular Proteomics, 11(10):1070-83. (PMID: 22798277)
  • [13] Liu Z.#, Ren J.#, Cao J.#, He J., Yao X., Jin C., Xue Y. (2012) Systematic analysis of the Plk-mediated phosphoregulation in eukaryotes. Briefings in Bioinformatics, 14(3):344-360. (PMID: 22851512)
  • [12] Liu Z.#, Yuan F.#, Ren J., Cao J., Zhou Y., Yang Q., Xue Y. (2012) GPS-ARM: Computational analysis of APC/C recognition motif by predicting D-boxes and KEN-boxes. PLoS One, 7(3): e34370. (PMID: 22479614)
  • [11] Cai, R.#, Liu Z.#, Ren J., Ma, C., Gao, T., Zhou Y., Yang Q., Xue Y. (2012) GPS-MBA: Computational analysis of MHC Class II Epitopes in Type 1 Diabetes. PLoS One, 7(3): e33884. (PMID: 22479466)
  • [10] Liu Z.#, Ma Q.#, Cao J., Gao X., Ren J., Xue Y. (2011) GPS-PUP: GPS-PUP: Computational prediction of pupylation sites in prokaryotic proteins. Molecular BioSystems, 7(10): 2737-2740. (PMID: 21850344)
  • [9] Ren J., Gao X., Liu Z., Ma Q., Cao J., Xue Y. (2011) Computational Analysis of Phosphoproteomics: Progresses and Perspectives. Current Protein & Peptide Science, 12, 591-601. (PMID: 21827424)
  • [8] Liu Z.#, Cao J.#, Gao X., Ma Q., Ren J., Xue Y. (2011) GPS-CCD: A novel computational program for the prediction of calpain cleavage sites. PLoS One, 6(4):e19001. (PMID: 21533053)
  • [7] Liu Z., Cao J., Ma Q., Gao X., Ren J., Xue Y. (2011) GPS-YNO2: Computational prediction of tyrosine nitration sites in proteins. Molecular BioSystems, 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. (2011) GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection. Protein Engineering, Design and Selection, 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. (2011) CPLA 1.0: an integrated database of protein lysine acetylation. Nucleic Acids Research, 39: D1029-D1034. (PMID: 21059677)
  • [4] Xue Y., Liu Z., Gao X., Jin C., Wen L., Yao X., Ren J. (2010) GPS-SNO: computational prediction of protein S-nitrosylation sites with a modified GPS algorithm. PLoS One, 5(6):e11290. (PMID: 20585580)
  • [3] Xue Y., Gao X., Cao J., Liu Z., Jin C., Wen L., Yao X., Ren J. (2010) A summary of computational resources for protein phosphorylation. Current Protein & Peptide Science, 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. (2010) PhosSNP for systematic analysis of genetic polymorphisms that influence protein phosphorylation. Molecular & Cellular Proteomics, 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. (2010) MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore. Nucleic Acids Research, 38, D155-160. (PMID: 19783819)

CONFERENCES

HONORS AND AWARDS