简介

主要研究领域：

代表论著：

简介

职 称: 研究员

职 务: 博士生导师

研究方向: 生物信息学/计算生物学

教育及工作经历

1998－2002 宁夏大学 计算机科学 学士

2002－2004 南京理工大学 计算机科学 硕士

2004－2007 中国科学院计算技术研究所 计算机科学 博士

2007－2009 美国耶鲁大学（Yale University） 博士后

2009－2011 沙特阿卜杜拉国王理工大学（King Abdullah University of Science and Technology） 研究科学家

2011－至今 中国科学院北京基因组研究所“百人计划”研究员

主要研究领域：

本项目组的主要研究方向是生物信息学/计算生物学。目前的研究内容包括：（1）基因组组分动力学和计算分子进化学研究；（2）海量生物数据的整合和挖掘；（3）基于Web 2.0/3.0的基因组信息学数据共享系统研究；（4）生物信息学的Semantic Web Service和生物数据的标准化研究。

代表论著：

JOURNAL PUBLICATIONS (*First-author equivalent)

1. Zhang, Z., Li, J., Cui, P., Ding, F., Li, A., Townsend, J.P., and Yu, J. (2011) Codon Deviation Coefficient (CDC): a novel measure for estimating codon usage bias and its statistical significance, under review.

2. Ding, F., Cui, P., Lin, Q., Zhang, L.F., Li, A., Zhang, Z., Hu, S.N., and Yu, J. (2011) Distinct contributions of DNA replication and transcription to mutation rates in human genomes, under review.

3. Zhang, Z. and Yu, J. (2011) On the organizational dynamics of the genetic code, Genomics Proteomics Bioinformatics, in press.

4. Zhang, Z. and Yu, J. (2010) Modeling compositional dynamics based on GC and purine contents of protein-coding sequences, Biology Direct, 5, 63.

5. Qu, H.Z., Wu, H., Zhang, T.W., Zhang, Z., Hu, S.N., and Yu, J. (2010) Nucleotide compositional asymmetry between leading and lagging strands of eubacterial genomes, Research in Microbiology, 161(10):838-846.

6. Wang, D.P., Zhang, Y.B., Zhang, Z., Zhu, J., and Yu, J. (2010) KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies, Genomics Proteomics Bioinformatics, 8(1):77-80.

7. Zhang, Z., Lopez-Giraldez, F. and Townsend, J.P. (2010) LOX: inferring Level Of eXpression from diverse methods of census sequencing, Bioinformatics, 26(15):1918-1919.

8. Zhang, Z. and Townsend, J.P. (2010) The Filamentous Fungal Gene Expression Database (FFGED), Fungal Genetics and Biology, 47(3):199-204.

9. Zhang, Z. and Townsend, J.P. (2009) Maximum-likelihood model averaging to profile clustering of sites types across discrete linear sequences, PLoS Computational Biology, 5(6):e1000421.

10. Li, J., Zhang, Z.*, Vang, S, Yu, J, Wong, G.K., and Wang, J. (2009) Correlation between Ka/Ks and Ks is related to substitution model and evolutionary lineage, Journal of Molecular Evolution, 68(4):414-423.

11. Zhang, Z., Cheung, K.-H., and Townsend, J.P. (2009) Bringing Web 2.0 to bioinformatics, Briefings in Bioinformatics, 10(1):1-10.

12. Hu, J., Zhao, X., Zhang, Z.* and Yu, J. (2007) Compositional dynamics of guanine and cytosine content in prokaryotic genomes, Research in Microbiology, 154(4):363-370.

13. Zhao, X., Zhang, Z.*, Yan, J. and Yu, J. (2007) GC content variability of eubacteria is governed by the pol III alpha subunit, Biochem Biophys Res Commun, 356(1): 20-25.

14. Zheng, H., Shi, J., Fang, X., Li, Y., Vang, S., Fan, W., Wang, J., Zhang, Z., Wang, W., Kristiansen, K., Wang, J. (2007) FGF: A web tool for Fishing Gene Family in a whole genome database, Nucleic Acids Res, 34: W121-W125.

15. Zhang, Z., Li, J., Zhao, X., Wang, J., Wong, G.K. and Yu, J. (2006) KaKs_Calculator: calculating Ka and Ks through model selection and model averaging, Genomics Proteomics Bioinformatics, 4(4): 259-263.

16. Zhang, Z., Li, J. and Yu, J. (2006) Computing Ka and Ks with a consideration of unequal transitional substitutions, BMC Evolutionary Biology, 6, 44.

17. Zhang, Z. and Yu, J. (2006) Evaluation of six methods for estimating synonymous and nonsynonymous substitution rates, Genomics Proteomics Bioinformatics, 4(3):173-181.

18. Li, H., Coghlan, A., Ruan, J., Coin, L.J., Heriche, J.K., Osmotherly, L., Li, R., Liu, T., Zhang, Z., Bolund, L., Wong, G.K., Zheng, W., Dehal, P., Wang, J. and Durbin, R. (2006) TreeFam: a curated database of phylogenetic trees of animal gene families, Nucleic Acids Res, 34:D572-580.

BOOK CHAPTER

19. Zhang, Z., Bajic, V.B., Yu, J., Cheung, K.-H., and Townsend, J.P. (2011) Data integration in bioinformatics: current efforts and challenges. In Bioinformatics: Mahdavi, M.A. (ed.), The InTech Open Access Publisher, submitted.

CONFERENCE PRESENTATION

1. Zhang, Z., Cui, P., Ding, F., Li, A., and Yu, J. (2010) A mutation-selection model for composition dynamics. The Cold Spring Harbor Asia Conference on Computational Biology, Suzhou, China.

2. Zhang, Z. and Townsend, J.P. (2009) Evolving directions in bioinformatics: data integration, analysis and sharing. The International Conference of Genomics, Beijing, China.

3. Zhang, Z. and Townsend, J.P. (2009) Modeling sequence heterogeneity through maximum-likelihood model averaging. The International Conference of Genomics, Beijing, China.

4. Zhao, X., Zhang, Z. and Yu, J. (2009) The correlation between genomic GC content and DNA polymerase III in eubacteria. The International Conference of Genomics, Beijing, China.

5. Zhang, Z. and Townsend, J.P. (2008) Maximum-likelihood estimation of substitution heterogeneity through clustering. The Annual Meeting of the Society of Molecular Biology and Evolution (SMBE), Barcelona, Spain.

6. Hu, J., Zhao, X., Zhang, Z., Wong, G.K. and Yu, J. (2005) “The Game of Life” with Four Cards: The Two Parameter Game Has Survived Since 3800 MYA, Symposium “Stories DNA tells” in CAS-MPG Partner Institute for Computational Biology, Beijing, China.