Publications

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

  1. Li RJ, Liang F, Li W, Zou D, Sun SX, Zhao YB, Zhao WM, Bao YM, Xiao JF, Zhang Z* (2018) MethBank 3.0: a database of DNA methylomes across a variety of species. Nucleic Acids Res, accepted and in press.
  2. Song SH, Tian DM, Li CP, Tang BX, Dong LL, Xiao JF, Bao YM, Zhao WM, He H, Zhang Z* (2018) Genome Variation Map: a data repository of genome variations in BIG Data Center. Nucleic Acids Res, accepted and in press.
  3. Zhang Z* as corresponding author in BIG Data Center Members (2018) Database Resources of the BIG Data Center in 2018. Nucleic Acids Res, accepted and in press. Pubmed.png
  4. Sang J, Wang ZN,..., Hao LL, Zhang Z* (2018) ICG: a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization. Nucleic Acids Res, accepted and in press. Pubmed.png
  5. Zhao ZM, Campbell MC, Li N, Lee DSW, Zhang Z, Townsend JP (2017) Detection of regional variation in selection intensity within protein-coding genes using DNA sequence polymorphism and divergence. Molecular Biology and Evolution, accepted and in press, Pubmed.png
  6. Xia L, Zou D, Sang J, Xu XJ, Yin HY, Li MW, Wu SY, Hu SN, Hao LL, Zhang Z* (2017) Rice Expression Database (RED): an integrated RNA-Seq-derived gene expression database for rice. Journal of Genetics and Genomics, 44(5):235-241. Pubmed.png
  7. Salhi A, Essack M, Alam T,..., Zhang Z*, Bajic V (2017) DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. RNA Biology , 14(7):963-971. Pubmed.png
  8. Wang YQ, ..., Zhang Z*, Zhao WM: GSA: Genome Sequence Archive. Genomics, Proteomics & Bioinformatics 2017, 15(1):14-18. Pubmed.png [Cover Story; Preview]
  9. Xu XJ, Ji ZH, Zhang Z*: CloudPhylo: a fast and scalable tool for phylogeny reconstruction. Bioinformatics 2017, 33 (3):438-440. Pubmed.png
  10. Zhang Z authored in The RNAcentral Consortium: RNAcentral: a comprehensive database of non-coding RNA sequences. Nucleic Acids Res 2017, 45(D1):D128-D134. Pubmed.png
  11. Zhang, Z.* as Corresponding author in BIG Data Center Members (2017) The BIG Data Center: from deposition to integration to translation, Nucleic Acids Res, 45(D1):D18-D24. Pubmed.png
  12. Zhang, Z. authored in The RNAcentral Consortium. (2017) RNAcentral: a comprehensive database of non-coding RNA sequences., Nucleic Acids Res, 45(D1):D128-D134. Pubmed.png
  13. Zhao W, Zhang S, Tang B, Chen T, Hao L, Sang J, Li R, Xiao J, Zhang Z: Constructing the international database management system for omics big data. Big Data Research 2016, 2(6):43-52. (In Chinese)
  14. Xue, Y.,...,Zhang, Z., Huang, K., Yu, J. (2016) Precision Medicine: What Challenges Are We Facing?, Genomics Proteomics Bioinformatics, 14(5):253-261. Pubmed.png
  15. Yin, H.Y, Wang, G.Y., Ma, L.N., Yi, S.V., Zhang, Z.* (2016) What signatures dominantly associate with gene age? Genome Biology and Evolution, 8(10):3083-9.Pubmed.png
  16. Sun, S.X., Xiao, J.F., Zhang, H.Y.*, Zhang, Z.* (2016) Pangenome evidence for higher codon usage bias and stronger translational selection in core genes of Escherichia coli, Frontiers in Microbiology, 7:1180. Pubmed.png
  17. Yin, H.Y., Ma, L.N., Wang, G.Y., Li, M.W., Zhang, Z.*. (2016) Old genes experience stronger translational selection than young genes, Gene, 590(1):29–34.Pubmed.png
  18. Wang, G.Y., Sun, S.X., Zhang, Z.* (2016) Randomness in sequence evolution increases over time, PLoS One, 11(5): e0155935.Pubmed.png
  19. Zhang, Z.* as corresponding author in The IC4R Project Consortium (2016) Information Commons for Rice (IC4R), Nucleic Acids Research, 44(D1):D1172-80. Pubmed.png
  20. Zou, D., Ma, L.N., Yu, J.*, Zhang, Z.* (2015) Biological databases for human research, Genomics Proteomics Bioinformatics, 13(1):55-63. Pubmed.png
  21. Zhang, Y., Chen, L.L., Zhang, Z. (2015) The Curation and Analysis of Rice Stress-Resistance Genes Based on RiceWiki, Hans Journal of Computational Biology, 5(3):29-40. Pdf.gif
  22. Bai, B., Zhao, W.-M.,..., Zhang, Z.,..., Wang, G.-D., and Zhang, Y.-P. (2015) DoGSD: the dog and wolf genome SNP database, Nucleic Acids Research, 43:D777-83. Pubmed.png
  23. Ma, L.N., Li, A., Zou, D., Xu, X.J., Xia, L., Yu, J., Bajic, V.B., and Zhang, Z*. (2015) LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs, Nucleic Acids Research, 43:D187-92. Pubmed.png
  24. Zou, D., Sun, S., Li, R., Liu, J., Zhang, J., Zhang, Z.* (2015) MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data, Nucleic Acids Research, 43:D54-8. Pubmed.png
  25. Kang, Y., Gu, C., Yuan, L., Wang, Y., Zhu, Y., Li, X., Luo, Q., Xiao, J., Jiang, D., Qian, M., Ahmed, K.A., Chen, F., Zhang, Z.*, Yu, J.* (2014) Flexibility and Symmetry of Prokaryotic Genome Rearrangement Reveal Lineage-Associated Core-Gene-Defined Genome Organizational Frameworks, MBio, 25:5(6), e01867-14. Pubmed.png
  26. Xu, P., Zhang, X., Wang, X., ..., Zhang, Z., Yu, J., and Sun, X. (2014) Genome sequence and genetic diversity of the common carp, Cyprinus carpio, Nature Genetics, 46(11):1212-9. Pubmed.png
  27. Wu, G., Zhu, J., Yu, J., Zhou, L., Huang, J.H., and Zhang, Z.* (2014) Evaluation of five methods for genome-wide circadian gene identification, Journal of Biological Rhythms, 29(4):231-42. Pubmed.png
  28. Zhang, Z.*, Zhu, W.M., and Luo, J.C. (2014) Bringing biocuration to China, Genomics Proteomics Bioinformatics, 12(4):153-5. Pubmed.png
  29. Ma, L.N., Cui, P., Zhu, J., Zhang, Z.H., and Zhang, Z.* (2014) Translational selection in human: more pronounced in housekeeping genes, Biology Direct, 9,17. Pubmed.png
  30. Wu, J.Y., Xiao, J.F., Zhang, Z., Wang, X.M., Hu, S.N., and Yu, J. (2014) Ribogenomics: the science and knowledge of RNA, Genomics, Proteomics & Bioinformatics, 12(2):57-63. Pubmed.png
  31. Zhao, Y.B., Jia, X.M., Yang, J.H., Ling, Y.C., Zhang, Z., Yu, J., Wu, J.Y., and Xiao, J.F. (2014) PanGP: A tool for quickly analyzing bacterial pan-genome profile, Bioinformatics, 30(9):1297-9. Pubmed.png
  32. Wu, H., Fang, Y.J., Yu, J.*, and Zhang, Z.* (2014) The quest for a unified view of bacterial land colonization, The ISME Journal, 8(7),1358-69. Pubmed.png
  33. Zhang, Z.*, Sang, J. Ma, L.N., Wu, G., Wu, H., Huang, D.W., Zou, D., Liu, S.Q., Li, A., Hao, L.L., Tian, M., Xu, C., Wang, X.M., Wu, J.Y., Xiao, J.F., Dai, L., Chen, L.-L., Hu, S.N., and Yu, J. (2014) RiceWiki: a wiki-based database for community curation of rice genes, Nucleic Acids Research, 42(D1),D1222-D1228. Pubmed.png
  34. Wu, J.Y., Xiao, J.F., Wang, L.P., Zhong, J., Yin, H.Y., Wu, S.X., Zhang, Z., Yu, J. (2013) Systematic analysis of intron size and abundance parameters in diverse lineages, Sci China Life Sci, 56(10),968-974. Pubmed.png
  35. Zhang, Z., Wong, G.K. and Yu, J. (2013) Protein coding, In: Encyclopedia of Life Sciences (eLS). John Wiley & Sons Ltd, Chichester. DOI: 10.1002/9780470015902.a0005017.pub2
  36. Dai, L., Tian, M., Wu, J.Y., Xiao, J.F., Wang, X.M., Townsend, J.P. and Zhang, Z.* (2013) AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification, Bioinformatics, 29(14),1837-1839. Pubmed.png
  37. Ma, L.N., Bajic, V.B., and Zhang, Z.* (2013) On the classification of long non-coding RNAs, RNA Biology, 10(6),1-10. Pubmed.png
  38. Tong, X., Yang, Y., Wang, W., Bai, Z., Ma, L., Zheng, X., Sun, H., Zhang, Z., Zhao, M., Yu, J., Ge, R.L.(2013) Expression profiling of abundant genes in pulmonary and cardiac muscle tissues of Tibetan Antelope (Pantholops hodgsonii), Gene, 523(2),187–191. Pubmed.png
  39. Dai, L., Xu, C., Tian, M., Sang, J., Zou, D., Li, A., Liu, G.C., Chen, F., Wu, J.Y., Xiao, J.F., Wang, X.M., Yu, J., and Zhang, Z.* (2013) Community intelligence in knowledge curation: an application to managing scientific nomenclature, PLoS ONE, 8(2), e56961.Pubmed.png
  40. Zhang, Z., and Yu. J. (2013) Does the genetic code have a eukaryotic origin? Genomics Proteomics Bioinformatics, 11(1),41-55.Pubmed.png
  41. Chen, M., Xiao, J.F., Zhang, Z., Liu, J., Wu, J.Y., and Yu, J. (2013) Identification of human HK Genes and gene expression regulation study in cancer from transcriptomics data analysis, PLoS ONE, 8(1), e54082.Pubmed.png
  42. Dai, L., Gao, X., Guo, Y., Xiao, J.F. and Zhang, Z.* (2012) Bioinformatics clouds for big data manipulation, Biology Direct, 7, 43. Highly-accessed.gif [Official Certificate for Highly Accessed] Pubmed.png
  43. Zhang, Z. and Yu, J. (2012) The pendulum model for genome compositional dynamics: from the four nucleotides to the twenty amino acids, Genomics Proteomics Bioinformatics, 10(4), 175-180. [Cover story] Pubmed.png
  44. Wu, H., Qu, H.Z, Wan, N., Zhang, Z., Hu, S.N. and Yu, J. (2012) Strand-biased gene distribution in bacteria is related to both horizontal gene transfer and strand-biased nucleotide composition, Genomics Proteomics Bioinformatics, 10(4), 186-196. Pubmed.png
  45. Cui, P., Liu, W., Zhao, Y., Lin, Q., Zhang, D., Ding, F., Xin, C., Zhang, Z., Song, S., Sun F et al (2012) Comparative analyses of H3K4 and H3K27 trimethylations between the mouse cerebrum and testis, Genomics Proteomics Bioinformatics, 10(2), 82-93. Pubmed.png
  46. 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(1), 4-10. Pubmed.png
  47. 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(4), 779-781.Pubmed.png
  48. 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. Highly-accessed.gif [Official Certificate for Highly Accessed] Pubmed.png
  49. 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.Pubmed.png
  50. 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. Available from: http://www.intechopen.com/articles/show/title/data-integration-in-bioinformatics-current-efforts-and-challenges.
  51. Zhang, Z. and Yu, J. (2011) On the organizational dynamics of the genetic code, Genomics Proteomics Bioinformatics, 9(1-2), 21-29.Pubmed.png
  52. Zhang, Z. and Yu, J. (2010) Modeling compositional dynamics based on GC and purine contents of protein-coding sequences, Biology Direct, 5, 63.Pubmed.png
  53. Zhang, Z. and Townsend, J.P. (2010) The filamentous fungal gene expression database (FFGED), Fungal Genetics Biology, 47(3), 199-204.Pubmed.png
  54. 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.Pubmed.png
  55. 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(1), 77-80.Pubmed.png
  56. 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(10), 838-846.Pubmed.png
  57. 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(6), e1000421.Pubmed.png
  58. Zhang, Z., Cheung, K.H. and Townsend, J.P. (2009) Bringing Web 2.0 to bioinformatics, Briefings in Bioinformatics, 10(1), 1-10.Pubmed.png
  59. 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(4), 414-423.Pubmed.png
  60. 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.Pubmed.png
  61. 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.Pubmed.png
  62. 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.Pubmed.png
  63. Zhang, Z. and Yu, J. (2006) Evaluation of six methods for estimating synonymous and nonsynonymous substitution rates, Genomics Proteomics Bioinformatics, 4, 173-181.Pubmed.png
  64. 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. [Highly cited in GPB] Pubmed.png
  65. Zhang, Z., Li, J. and Yu, J. (2006) Computing Ka and Ks with a consideration of unequal transitional substitutions, BMC Evolutionary Biology, 6, 44. Highly-accessed.gifPubmed.png
  66. 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.Pubmed.png
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