User:Zhang Zhang

Contact Info

 * Mailing address:
 * Zhang Zhang
 * King Abdullah University of Science and Technology
 * P.O. Box 2139, 4700 KAUST
 * Thuwal 23955-6900
 * Kingdom of Saudi Arabia


 * Tel:
 * Fax:
 * Email me through OpenWetWare

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

 * 2009-Present, Research Scientist, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
 * 2007-2009, Postdoctoral Associate, Yale University, New Haven, Connecticut, United States of America

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.

Useful links

 * Introductory tutorial
 * OpenWetWare help pages