纪志梁 JI Zhiliang, Ph.D.
教授,博士生导师
电话：+86-
E-mail: appo@xmu.edu.cn
Website: http://bioinf.xmu.edu.cn



1991-1996 北京清华大学生物科学与技术系理学学士
1997–2000 新加坡国立大学微生物系理学硕士
2000–2004 新加坡国立大学计算科学系理学博士
2003/12 - 2008/7厦门大学生命科学学院副教授
2008/7 - 至今厦门大学生命科学学院教授
1991-1996 Tsinghua University, Bioscience & Biotechnology, B.Sc.
1997–2000 National University of Singapore, Microbiology, M.Sc.
2000–2004 National University of Singapore, Computational Science, Ph.D.
2003/12 - 2008/7 Xiamen University, Associate Professor
2008/7 - now Xiamen University, Professor


研究领域（Research Area)
近年来，课题组的研究重点集中于以下三个方面：（1）系统计算药物毒理学：利用机器学习和网络分析等技术，开展对小分子药物和天然产物的药物不良反应的分子机制研究和理论预测。（2）健康大数据挖掘：基于异质性健康大数据，开发药物信息学数据库及分析软件，开展个体化用药和药物遗传学的理论与应用基础研究。（3）系统生物学与生物大数据分析：开发基于生物芯片、NGS等高通量实验数据分析的新方法和新应用；以文昌鱼为动物模型，通过数据挖掘与网络化分析，系统探索动物器官胚胎发育的分子机制。
We focus our recent research on three areas: (1) Systems Computational Toxicology: We integrate and mine heterogeneous biomedical data for mechanistic exploration and rapid prediction of drug bioactivity, especially toxicity. (2) Individual Medicine: We develop pharmacological databases or tools to facilitate better understanding and prediction of individual drug responses (especially toxicological response). (2) Systems Biology and '-Omics': We develop novel methods and applications to seek biological clues, e.g., molecular mechanisms of organ development and function, from high throughput data, e.g., microarray and RNA-seq, using Amphioxus as animal model.


代表性论文(Selected Publications)
1. Huang LH, He QS, Liu K, Cheng J, Zhong MD, Chen LS, Yao LX, Ji ZL*. ADReCS-Target: target profiles for aiding drug safety research and application. Nucleic Acids Research.2018 Jan; 46: D911-17.
2. Xu Q, Liu K, Lin X, Qin Y, Chen L, Cheng J, Zhong M, He Q, Li Y, Wang T, Pan J, Peng M, Yao L, Ji Z*. ADMETNet: The knowledge base of pharmacokinetics and toxicology network. Journal of Genetics & Genomics.2017 May 20;44(5):273-276.
3. Wei L, Xing P, Shi G, Ji ZL*, Zou Q*. Fast prediction of protein methylation sites using a sequence-based feature selection technique. IEEE/ACM Transactions on Computational Biology and Bioinformatics.2017 Feb 16. doi: 10.1109/TCBB.2017.**.
4. Zhang J, Wang S, Jiang B, Huang L, Ji Z, Li X, Zhou H, Han A, Chen A, Wu Y, Ma H, Zhao W, Zhao Q, Xie C, Sun X, Zhou Y, Huang H, Suleman M, Lin F, Zhou L, Tian F, Jin M, Cai Y, Zhang N, Li Q*. c-Src phosphorylation and activation of hexokinase promotes tumorigenesis and metastasis. Nature Communications. 2017 Jan 5; 8:13732. doi: 10.1038/ncomms13732.
5. Fan F, He Z, Kong LL, Chen Q, Yuan Q, Zhang S, Ye J, Liu H, Sun X, Geng J, Yuan L, Hong L, Xiao C, Zhang W, Sun X, Li Y, Wang P, Huang L, Wu X, Ji Z, Wu Q, Xia NS, Gray NS, Chen L, Yun CH, Deng X, Zhou D*. Pharmacological targeting of kinases MST1 and MST2 augments tissue repair and regeneration. Science Translational Medicine. 2016 Aug 17; 8(352):352ra108. doi: 10.1126/scitranslmed.aaf2304.
6. Shi S^#, Liu K^#, Chen Y^#, Zhang S, Lin J, Gong C, Jin Q, Yang XJ, Chen R*, Ji Z*, Han A*. Competitive inhibition of lysine acetyltransferase 2B by a small motif of the adenoviral oncoprotein E1A. Journal of Biological Chemistry.2016 Jul 1;291(27):14363-72. pii: jbc.M115.697300.
7. Zhang ZF, Ma PF, Jing Y, Yan Y, Cai MC, Zhang MY, Zhang SZ, Peng HX, Ji ZL, Di W, Gu ZY, Gao WQ, Zhuang GL. BET Bromodomain Inhibition as a Therapeutic Strategy in Ovarian Cancer by Downregulating FoxM1. Theranostics. 2016; 6(2): 219-230. doi: 10.7150/thno.13178.
8. Lin S*, Cheng S, Song B, Zhong X, Lin X, Li W, Li L, Zhang Y, Zhang H, Ji Z, Cai M, Zhuang Y, Shi X, Lin L, Wang L, Wang Z, Liu X, Yu S, Zeng P, Hao H, Zou Q, Chen C, Li Y, Wang Y, Xu C, Meng S, Xu X, Wang J, Yang H, Campbell DA, Sturm NR, Dagenais-Bellefeuille S, Morse D. The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis. Science. 2015 Nov 6;350(6261):691-4.
9. Cai MC, Xu Q, Pan YJ, Pan W, Ji N, Li YB, Jin HJ, Liu K and Ji ZL*. ADReCS: an ontology database for aiding standardization and hierarchical classification of adverse drug reaction terms. Nucleic Acids Research.,2015 Jan 28;43: D907-13.
10.Xiang YP, Liu K, Cheng XY, Cheng C, Gong F, Pan JB, Ji ZL*. Rapid Assessment of Adverse Drug Reactions by Statistical Solution of Gene Association Network. IEEE/ACM Transactions on Computational Biology and Bioinformatics.2015 Jul-Aug;12(4):844-50. doi: 10.1109/TCBB.2014.**.
11. Zhang HP, Pan JB, Zhang C, Ji N, Wang H, Ji ZL*. Network understanding of herb medicine via rapid identification of ingredient-target interactions. Scientific Reports.2014 Jan 16;4:3719. doi: 10.1038/srep03719.
12. Wang Q, Wei L, Guan X, Wu Y, Zou Q, Ji ZL*. Briefing in family characteristics of microRNAs and their applications in cancer research. Biochimica et Biophysica Acta-Proteins and Proteomics.2014 Jan;1844(1 Pt B):191-7. doi: 10.1016/j.bbapap.2013.08.002.
13.Pan JB, Ji N, Pan W, Hong R, Wang H, Ji ZL*. High-throughput Identification of Off-Targets for the Mechanistic Study of Severe Adverse Drug Reactions Induced by Analgesics. Toxicology & Applied Pharmacology.2013 Oct 29;274(1):24-34. doi: 10.1016/j.taap.2013.10.017.
14.Pan JB, Hu SC, Wang H, Zou Q, Ji ZL*. PaGeFinder: quantitative identification of spatiotemporal pattern genes. Bioinformatics.2012 Jun 1;28(11):1544-5.


荣誉、奖励及参加学术团体的情况（Honors and awards, Professional service)
“Protein & Peptide Letters”编委（2012-）
卫计委男性生殖健康重点实验室学术委员会委员（2014-)
中国细胞生物学学会功能基因组信息学与系统生物学分会理事（2014-）
中国化学会计算机化学专业委员会委员(2011-)
中国空间科学学会空间生命起源与进化专业委员会委员（2008-）
New Century Excellent Talents of MOE (2006)
Editorial Board Member of journal 'Current Drug Discovery Technologies' (2012-)
Committee Member, Computer Chemistry Committee of China Chemistry Society