Education

1991-1996, B.Sc., Tsinghua University, Bioscience & Biotechnology;

1997-2000, M.Sc., National University of Singapore, Microbiology;

2000-2004, PhD., National University of Singapore, Computational Science.

Professional Experience

2003-2008, Associate Professor, Xiamen University;

2008-present, Professor, Xiamen University.

Research Area

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.

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 Research. 2015, 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 ONE. 2013, 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 Pharmacology. 2014, 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 Research. 2007, 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.