Publications

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JOURNAL PUBLICATIONS (*Corresponding author; #First-author equivalent)

In preparation

  1. Increasing participations in biological knowledge wikis through contribution quantification and explicit authorship, in preparation.
  2. RiceWiki: a wiki-based system for harnessing collective intelligence for rice gene annotations, in preparation.
  3. Differential patterns of codon usage bias and its statistical significance in human tissue-specific genes, in preparation.
  4. Zhang, Z. and Yu, J. A universal equilibrium of physicochemical properties across and within genomes, in preparation.

Published

  1. Cui, P., Ding, F., Lin, Q., Zhang, L., Li, A., Zhang, Z., Hu, S. and Yu, J. (2012) Distinct contributions of replication and transcription to mutation rate variation of human genomes, Genomics Proteomics Bioinformatics, 10, 4-10.
  2. Zhang, Z., Li, J., Cui, P., Ding, F., Li, A., Townsend, J.P. and Yu, J. (2012) Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance, BMC Bioinformatics, 13, 43.
  3. Zhang, Z.*, Xiao, J., Wu, J., Zhang, H., Liu, G., Wang, X. and Dai, L. (2012) ParaAT: A parallel tool for constructing multiple protein-coding DNA alignments, Biochem Biophys Res Commun, 419, 779-781.
  4. Wu, H., Zhang, Z., Hu, S. and Yu, J. (2012) On the molecular mechanism of GC content variation among eubacterial genomes, Biology Direct, 7, 2.
  5. Zhang, Z. and Yu, J. (2011) On the organizational dynamics of the genetic code, Genomics Proteomics Bioinformatics, 9, 21-29.
  6. Zhang, Z. and Yu, J. (2010) Modeling compositional dynamics based on GC and purine contents of protein-coding sequences, Biology Direct, 5, 63.
  7. Zhang, Z. and Townsend, J.P. (2010) The filamentous fungal gene expression database (FFGED), Fungal Genetics Biology, 47, 199-204.
  8. Zhang, Z., Lopez-Giraldez, F. and Townsend, J.P. (2010) LOX: inferring Level Of eXpression from diverse methods of census sequencing, Bioinformatics, 26, 1918-1919.
  9. Wang, D., Zhang, Y., 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, 77-80.
  10. Qu, H., Wu, H., Zhang, T., Zhang, Z., Hu, S. and Yu, J. (2010) Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomes, Res Microbiol, 161, 838-846.
  11. Zhang, Z. and Townsend, J.P. (2009) Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences, PLoS Comput Biol, 5, e1000421.
  12. Zhang, Z., Cheung, K.H. and Townsend, J.P. (2009) Bringing Web 2.0 to bioinformatics, Briefings in Bioinformatics, 10, 1-10.
  13. 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, J Mol Evol, 68, 414-423.
  14. Zheng, H., Shi, J., Fang, X., Li, Y., Vang, S., Fan, W., Wang, J., Zhang, Z., Wang, W. and Kristiansen, K. (2007) FGF: a web tool for Fishing Gene Family in a whole genome database, Nucleic Acids Res, 35, W121-125.
  15. 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, 20-25.
  16. Hu, J., Zhao, X., Zhang, Z.# and Yu, J. (2007) Compositional dynamics of guanine and cytosine content in prokaryotic genomes, Res Microbiol, 158, 363-370.
  17. Zhang, Z. and Yu, J. (2006) Evaluation of six methods for estimating synonymous and nonsynonymous substitution rates, Genomics Proteomics Bioinformatics, 4, 173-181.
  18. Zhang, Z., Li, J., Zhao, X.Q., 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, 259-263.
  19. Zhang, Z., Li, J. and Yu, J. (2006) Computing Ka and Ks with a consideration of unequal transitional substitutions, BMC Evolutionary Biology, 6, 44.
  20. Li, H., Coghlan, A., Ruan, J., Coin, L.J., Hériché, J.-K., Osmotherly, L., Li, R., Liu, T., Zhang, Z., Bolund, L., Wong, G.K.-S., 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-D580.

BOOK CHAPTER

  1. Zhang, Z., Bajic, V.B., Yu, J., Cheung, K.-H. and Townsend, J.P. (2011) Data Integration in Bioinformatics: Current Efforts and Challenges. In Mahdavi, M.A. (ed), Bioinformatics - Trends and Methodologies. InTech - Open Access Publisher, Rijeka, Croatia.