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纪志梁教授博导

发布时间:2015-12-20来源:点击数:10659

 

纪志梁教授博导纪志梁 JI Zhiliang, Ph.D.                              

教授,博士生导师

+86-592-2182897

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. 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 Research2015, 43 (D1): D907-13.

2. 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 Transactions on Computational Biology and Bioinformatics. 2014, 12 (4): 844-850.

3. Zhang HP, Pan JB, Zhang C, Ji N, Wang H, Ji ZL*. Network understanding of herb medicine via rapid identification of ingredient-target interactions. Science Report . 2014 , 4: 3719.

4. 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. 2014 , 1844 (1 Pt B): 191-7.

5. Pan JB, Hu SC, Shi D, Cai MC, Li YB, Zou Q, Ji ZL*. PaGenBase: a pattern gene database for the global and dynamic understanding of gene function. PLoS ONE2013, 8 (12): e80747. doi: 10.1371/journal.pone.0080747.

6. 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 Pharmacology2014, 274 (1): 24-34.

7. Pan JB, Hu SC, Wang H, Zou Q, Ji ZL*. PaGeFinder: quantitative identification of spatiotemporal pattern genes. Bioinformatics. 2012,  28 (11): 1544-5.

8. Xiao SJ, Zhang C, Ji ZL*. TiSGeD: a Database for Tissue-Specific Genes. Bioinformatics. 2010,  26 (9): 1273-5.

9. Quan Y, Ji ZL*, Wang X, Tartakoff AM, Tao T*. Evolutionary and Transcriptional Analysis of Karyopherin Superfamily Proteins. Molecular & Cellular Proteomics. 2008, 7(7): 1254-69.

10. Xu JR, Zhang JX, Han BC, Liang L, Ji ZL*. CytoSVM: An Advanced Server for Identification of Cytokine-Receptor Interactions. Nucleic Acids Research2007, 35: W538-42.

11. Zhang JX, Huang WJ, Huang WH, Wang Y, Zhao R, Han BC, Liu QF, Chen YZ, Ji ZL*. DITOP: Drug-Induced Toxicity Related Protein Database. Bioinformatics. 2007, 23 (13): 1710–1712.

12. Wang YP, Liang L, Han BC, Quan Y, Wang X, Tao T, Ji ZL*. GEPS: Gene Expression Pattern Scanner. Nucleic Acids Research. 2006, 34: W492-W497.

 

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