Present Address:
Beijing Institute of Genomics, Chinese Academy of Sciences
Beijing, China
Email: zhangzhang(AT)big.ac.cn
http://cbb.big.ac.cn

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.

Education & Professional Experience

  • Research Scientist, King Abdullah University of Science and Technology, Kingdom of Saudi Arabia, 2009~2011

  • Postdoctoral Associate in Computational Biology, Bioinformatics and Molecular Evolution, Department of Ecology and Evolutionary Biology, Yale University, 2007~2009

  • Ph.D. in Computer Science, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China, 2004~2007

  • M.S. in Computer Science, Nanjing University of Science & Technology, Nanjing, China, 2002~2004

  • B.S. in Computer Science, Ningxia University, Yinchuan, China, 1998~2002

Journals Reviewer

BMC Bioinformatics, BMC Evolutionary Biology, Evolutionary Bioinformatics, Genomics Proteomics & Bioinformatics, Journal of Molecular Evolution, Molecular Biology and Evolution

Journal Publications (*First-author equivalent)

  1. 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. Software Implementation and Availability: LOX
  2. Zhang, Z. and Townsend, J.P. (2010) The Filamentous Fungal Gene Expression Database (FFGED). Fungal Genetics and Biology, 47(3):199-204.
  3. 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.
    SciVee: 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
  4. 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.
  5. Zhang, Z., Cheung, K.H. and Townsend, J.P. (2009) Bringing Web 2.0 to bioinformatics. Briefings in Bioinformatics, 10(1):1-10.
  6. 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.
  7. 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. 
  8. Zheng, H., Shi, J., Fang, X., Li, Y., Vang, S., Fan, W., Wang, J., Zhang, Z., Wang, W., Kristiansen, K. and Wang, J. (2007) FGF: A web tool for Fishing Gene Family in a whole genome database. Nucleic Acids Research, 35:W121-125.
  9. 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
  10. Zhang, Z., Li, J. and Yu, J. (2006) Computing Ka and Ks with a consideration of unequal transitional substitutions. BMC Evolutionary Biology, 6, 44.   
  11. Zhang, Z. and Yu, J. (2006) Evaluation of six methods for estimating synonymous and nonsynonymous substitution rates. Genomics Proteomics & Bioinformatics, 4:173-181.  
  12. 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 Publications

  1. Zhang, Z. and Townsend, J.P. (2009) Evolving directions in bioinformatics: data integration, analysis and sharing. The International Conference of Genomics, Beijing, China.
  2. Zhang, Z. and Townsend, J.P. (2009) Modeling sequence heterogeneity through maximum-likelihood model averaging. The International Conference of Genomics, Beijing, China.
  3. 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.
  4. 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

  1. LOX (Level Of eXpression; Version 1.2): A program employs Markov Chain Monte Carlo to estimate level of expression from census sequencing data sets with multiple treatments or samples.

    Download LOX1.2 for Linux/Mac/Windows

  2. 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.

    Download MACML1.1 for Linux/Mac/Windows

  3. 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.

    Download KaKs_Calculator1.2 for Linux/Mac/Windows

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Last update: October 24, 2009 (EST)