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| Mailing Address: |
| Department of Ecology and Evolutionary Biology |
| Yale University |
| 165 Prospect Street |
| P. O. Box 208106 |
| New Haven, CT 06520 |
| Email: zhang.zhang@yale.edu |
Zhang Zhang - 章张
Research Interests
My research interests focus on bioinformatics, computational biology, molecular evolution, comparative evolutionary genomics and exploration of Semantic Web and Web 2.0 in biological database and tool interoperation.Projects
- Estimating selective pressure (Ka/Ks, or dN/dS) through more realistic models
- Detecting sequence heterogeneity through clustering algorithms
- Compositional dynamics of GC content, codons, and amino acids
- Data mining, data management, and data integration using Web 2.0
- Scientific Social Community (SSC) for communication, collaboration and knowledge discovery through collective intelligence
- Filamentous Fungal Gene Expression Database
Education & Training
- Postdoctoral Associate in Computational Biology, Bioinformatics and Molecular Evolution, Department of Ecology and Evolutionary Biology, Yale University, 2007~present
2007至今 耶鲁大学 博士后 计算生物学、生物信息、分子进化
- Ph.D. in Computer Science, Institute of Computing Technology and Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China, 2004~2007
2004~2007 中国科学院计算技术研究所与北京基因组研究所联合培养 博士 计算机科学
- M.S. in Computer Science, Nanjing University of Science & Technology, Nanjing, China, 2002~2004
2002~2004 南京理工大学 硕士 计算机科学
- B.S. in Computer Science, Ningxia University, Yinchuan, China, 1998~2002
1998~2002 宁夏大学 学士 计算机科学
Journals Reviewer
BMC Evolutionary Biology, Evolutionary Bioinformatics, Genomics Proteomics & Bioinformatics, Journal of Molecular Evolution, Molecular Biology and EvolutionPublications (*First-author equivalent)
- Zhang, Z., Lopez-Giraldez, F., and Townsend, J.P. LOX: categorizing highly expressed sequence level of expression. In Preparation.
- Zhang, Z., and Townsend, J.P. The Filamentous Fungal Gene Expression Database (FFGED). Under review.
- Zhang, Z., and Townsend, J.P. (2009) Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences, PLoS Computational Biology, 5(6): e1000421.
Software Implementation and Availability: MACML
- Li, J., Zhang, Z.*, Vang S, Yu J, Wong GK, 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.
- Zhang, Z., Cheung, K.H. and Townsend, J.P. (2009) Bringing Web 2.0 to bioinformatics, Briefings in Bioinformatics, 10(1):1-10.
- 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.
- Hu, J., Zhao, X., Zhang, Z.*, and Yu, J. (2007) Compositional dynamics of guanine and cytosine content in prokaryotic genomes, Research in Microbiology, 158(4):363-370.
- Zheng, H., Shi, J., Fang, X., Li, Y., Vang, S., Fan, W., Wang, J., Zhang, Z., Wang, W., Kristiansen, K. et al (2007) FGF: A web tool for Fishing Gene Family in a whole genome database, Nucleic Acids Research, 35:W121-125.
- Zhang, Z., Li, J., Zhao, X., Wang, J., Wong, G. K.-S. and Yu, J. (2006) KaKs_Calculator: calculating Ka and Ks through model selection and model averaging, Genomics Proteomics & Bioinformatics, 4(4):259-263. Software Implementation and Availability: KaKs_Calculator
- Zhang, Z., Li, J. and Yu, J. (2006) Computing Ka and Ks with a consideration of unequal transitional substitutions. BMC Evolutionary Biology, 6, 44.
- Zhang, Z. and Yu, J. (2006) Evaluation of six methods for estimating synonymous and nonsynonymous substitution rates. Genomics Proteomics & Bioinformatics, 4:173-181.
- 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 Research, 34:D572-580.
Conference Presentations
- Zhang, Z., and Townsend, J. P. (2008) Maximum-likelihood estimation of substitution heterogeneity through clustering. The Annual Meeting of the Society for Molecular Biology and Evolution (SMBE), Barcelona, Spain.
- Hu, J., Zhao, X., Zhang, Z., Wong, G. K.-S., and Yu, J. (2005) "The Game of Life" with Four Cards: The Two Parameter Game Has Survived Since 3800 MYA. CAS-MPG Partner Institute for Computational Biology, Shanghai, China.
Software
- MACML (Model Averaging Clustering by Maximum Likelihood; Version 1.1): A program clusters sequences into heterogeneous regions with specific site types, without requiring any prior knowledge.
- KaKs_Calculator (Version 1.2): A program adopts model selection and model averaging to calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates. Several extant algorithms for estimating Ka and Ks are also incorporated into KaKs_Calculator.
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