(u): Undergraduate students; (g): Graduate students; (v): visiting scholar;*: Corresponding author;

Publications from the Work at Ohio University (1-12)

  1. Hua, Z.*, and Yu, P.(g)(2019). Diversifying evolution of the ubiquitin-26s proteasome system in Brassicaceae and Poaceae. Int J Mol Sci, 20, 3226; https://doi.org/10.3390/ijms20133226
  2. Hua, Z.*, and Early, M.J.(u)(2019). Closing Target Trimming and CTTdocker programs for discovering hidden superfamily loci in genomes. PLoS ONE, 14, e0209468; https://doi.org/10.1371/journal.pone.0209468
  3. Hua, Z.*(2019). Using CTT for comprehensive superfamily gene annotations. Protocols.io. 2019. https://dx.doi.org/10.17504/protocols.io.zf4f3qw
  4. Marshall, R.S., Hua, Z., Mali, S., McLoughlin, F., and Vierstra, R.D. (2019). ATG8-Binding UIM proteins define a new class of autophagy adaptors and receptors.Cell 177, 766-781; https://doi.org/10.1016/j.cell.2019.02.009
  5. Hua, Z.*, and Gao, Z.(v)(2019). Adaptive and degenerative evolution of the S-Phase Kinase-Associated Protein 1-Like family in Arabidopsis thaliana. PeerJ7, e6740;https://doi.org/10.7717/peerj.6740
  6. Ruan, B.^, Hua, Z.^, Zhao, J.^, Zhang, B., Ren, D., Liu, C., Yang, S., Zhang, A., Jiang, H., Yu, H., Hu, J., Zhu, L., Chen, G., Shen, L., Dong, G., Zhang, G., Zeng, D., Guo, L., Qian, Q., and Gao, Z. (2019). OsACL-A2 negatively regulates cell death and disease resistance in rice. Plant Biotechnology Journal17, 1344-1356 (^ Co-first author); https://doi.org/10.1111/pbi.13058
  7. Hua, Z.* (2019). Data Oriented Genomics Techniques (Book). figshare https://doi.org/10.6084/m9.figshare.7557065.v1
  8. Zhang, G., and Hua, Z.*(2018). Genome comparison implies the role of Wsm2 in membrane trafficking and protein degradation.PeerJ6, e4678; https://doi.org/10.7717/peerj.4678
  9. Hua, Z.*, and Early, M.J.(u) (2018). Closing Target Trimming: a Perl package for discovering hidden superfamily loci in genomes. biooRxiv 490490; https://doi.org/10.1101/490490
  10. Hua, Z.*, Doroodian, P.(u), and Vu, W.(u)(2018). Contrasting duplication patterns reflect functional diversities of ubiquitin and ubiquitin-like protein modifiers in plants. Plant Journal95, 296-311; https://doi.org/10.1111/tpj.13951
  11. Haak, D.C., Fukao, T., Grene, R., Hua, Z., Ivanov, R., Perrella, G., and Li, S. (2017). Multilevel Regulation of Abiotic Stress Responses in Plants. Frontiers in Plant Science8, 1564; https://doi.org/10.3389/fpls.2017.01564
  12. Hua, Z., and Vierstra, R.D. (2016). Ubiquitin Goes Green. Trends in Cell Biology26, 3-5; https://doi.org/10.1016/j.tcb.2015.12.001
  13. Hua, Z., Pool, J.E., Schmitz, R.J., Schultz, M.D., Shiu, S.H., Ecker, J.R., and Vierstra, R.D. (2013). Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis. Proc Natl Acad Sci USA110, 16927-16932; https://doi.org/10.1073/pnas.1316009110
  14. Christians, M.J., Gingerich, D.J., Hua, Z., Lauer, T.D., and Vierstra, R.D. (2012). The light-response BTB1 and BTB2 proteins assemble nuclear ubiquitin ligases that modify phytochrome B and D signaling in Arabidopsis. Plant Physiol160, 118-134; https://doi.org/10.1104/pp.112.199109
  15. Hua, Z., Zou, C., Shiu, S.H., and Vierstra, R.D. (2011). Phylogenetic comparison of F-Box (FBX) gene superfamily within the plant kingdom reveals divergent evolutionary histories indicative of genomic drift. PLoS ONE6, e16219; https://doi.org/10.1371/journal.pone.0016219
  16. Hua, Z., and Vierstra, R.D. (2011). The cullin-RING ubiquitin-protein ligases. Annu Rev Plant Biol62, 299-334; https://doi.org/10.1146/annurev-arplant-042809-112256
  17. Miller, M.J., Barrett-Wilt, G.A., Hua, Z., and Vierstra, R.D. (2010). Proteomic analyses identify a diverse array of nuclear processes affected by small ubiquitin-like modifier conjugation in Arabidopsis. Proc Natl Acad Sci USA107, 16512-16517; https://doi.org/10.1073/pnas.1004181107
  18. International Brachypodium Initiative (including Hua, Z. and Vierstra, R.D.) (2010). Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature463, 763-768;https://doi.org/10.1038/nature08747
  19. Meng, X., Hua, Z., Sun, P., and Kao, T.H. (2011). The amino terminal F-box domain of Petunia inflataS-locus F-box protein is involved in the S-RNase-based self-incompatibility mechanism. AoB Plants2011, plr016; https://doi.org/10.1093/aobpla/plr016
  20. Kubo, K., Entani, T., Takara, A., Wang, N., Fields, A.M., Hua, Z., Toyoda, M., Kawashima, S., Ando, T., Isogai, A., Kao, T.H., and Takayama, S. (2010). Collaborative non-self recognition system in S-RNase-based self-incompatibility. Science330, 796-799; https://doi.org/10.1126/science.1195243
  21. Fields, A.M., Wang, N., Hua, Z., Meng, X., and Kao, T.H. (2010). Functional characterization of two chimeric proteins between a Petunia inflataS-locus F-box protein, PiSLF2, and a PiSLF-like protein, PiSLFLb-S2. Plant Mol Biol74, 279-292; https://doi.org/10.1007/s11103-010-9672-x
  22. Meng, X., Hua, Z., Wang, N., Fields, A.M., Dowd, P.E., and Kao, T.H. (2009). Ectopic expression of S-RNase of Petunia inflatain pollen results in its sequestration and non-cytotoxic function. Sex Plant Reprod22, 263-275; https://doi.org/10.1007/s00497-009-0114-3
  23. Hua, Z., Fields, A., and Kao, T.H. (2008). Biochemical models for S-RNase-based self-incompatibility. Mol Plant1, 575-585; https://doi.org/10.1093/mp/ssn032
  24. Hua, Z., and Kao, T.H. (2008). Identification of major lysine residues of S(3)-RNase of Petunia inflatainvolved in ubiquitin-26S proteasome-mediated degradation in vitro. Plant J54, 1094-1104; https://doi.org/10.1111/j.1365-313X.2008.03487.x
  25. Hua, Z., Meng, X., and Kao, T.H. (2007). Comparison of Petunia inflata S-Locus F-box protein (Pi SLF) with Pi SLF like proteins reveals its unique function in S-RNase based self-incompatibility. Plant Cell19, 3593-3609; https://doi.org/10.1105/tpc.107.055426
  26. Hua, Z., and Kao, T.H. (2006). Identification and characterization of components of a putative petunia S-locus F-box-containing E3 ligase complex involved in S-RNase-based self-incompatibility. Plant Cell18, 2531-2553; https://doi.org/10.1105/tpc.106.041061
  27. Hua, Z., Zhu, X., Lin, H., Gao, Z., Qian, Q., Yan, M., and Huang, D. (2001). [Studies of the integration and expression of exogenes in transgenic rice obtained via particle bombardment transformation]. J Genetics Genomics(formerly Acta Genetica Sinica) 28, 1012-1018.
  28. Hua, Z., and Huang, D.N. (1999). Genetic mode of exogenes in transgenic plants. J Integr Plant Biol(formerly Acta Bot Sin) 41, 1-5.
  29. Huang, D., Li, J., Zhang, S., Xue, R., Yang, W., Hua, Z., Xie, X., and Wang, X. (1998). New technology to examine and improve the purity of hybrid rice with herbicide resistant gene. Chin Sci Bull43, 784-787; https://doi.org/10.1007/BF02898961


Computational Programs in Bioinformatics from the work at Ohio University

  1. Hua, Z.*, and Early, M.J.*(u)(2018). CTT Perl Package, https://github.com/hua-lab/ctt.git
  2. Hua, Z.*(2019) CTTdocker Package, https://github.com/hua-lab/cttdocker.git




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