User:Zhang Zhang

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Contact Info

Zhang Zhang (an artistic interpretation)
Zhang Zhang (an artistic interpretation)
  • Mailing address:
Zhang Zhang
King Abdullah University of Science and Technology
P.O. Box 2139, 4700 KAUST
Thuwal 23955-6900
Kingdom of Saudi Arabia

Education

  • 2007, Ph.D., Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
  • 2004, M.S., Nanjing University of Science & Technology, Nanjing, China
  • 2002, B.S., Ningxia University, Yinchuan, China

Professional experience

Research interests

  1. Computational Biology and Bioinformatics
  2. Molecular Evolution and Genomics
  3. Data Integration & Mining and Machine Learning

Publications

  • Zhang, Z. and Yu, J. On the organizational dynamics of the genetic code, Genomics, Proteomics & Bioinformatics, accepted.
  • Zhang, Z. and Yu, J. (2010) Modeling compositional dynamics based on GC and purine contents of protein-coding sequences, Biology Direct, 5, 63.
  • 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, in press.
  • 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. [Download LOX]
  • 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.
  • Zhang, Z. and Townsend, J.P. (2010) The Filamentous Fungal Gene Expression Database (FFGED), Fungal Genetics and Biology, 47(3):199-204.
  • 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. [Download MACML]
  • 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.
  • Zhang, Z., Cheung, K.-H. and Townsend, J.P. (2009) Bringing Web 2.0 to bioinformatics, Briefings in Bioinformatics, 10(1):1-10.
  • 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.
  • 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.
  • 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 Res, 34: W121-W125.
  • 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. [Download 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 Res, 34, D572-580.


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