PROF. ZHAO, Zhongying (趙中應)

Professor
EDUCATION

Postdoc (University of Washington)
Ph.D. (Simon Fraser University)

OVERVIEW

Professor Zhongying Zhao obtained his BSc and MSc at the Department of Biology from Anhui Normal University and Beijing Normal University in Anhui and Beijing, China, respectively. He earned his PhD at the Department of Molecular Biology and Biochemistry at Simon Fraser University in BC, Canada. He joined HKBU in 2010 after he completed his postdoc training at the Department of Genome Sciences at the University of Washington, Seattle, WA, USA for 5 years. He is mainly interested in genetic, genomic and cellular characterization of developmental behaviors, at cellular level with exceptional temporal resolution.

His research activities are mainly funded by Hong Kong Research Grant Council (RGC). As a PI or a Principle coordinator (PC), he has so far secured nine RGC grants to support his research, including seven General Research Funds (GRFs), one NSFC/RGC Joint Research Scheme fund and one Early Career Scheme (ECS) project since 2011. He has established wide collaborations both locally, regionally and internationally, which helped him win RGC Collaborative Research Fund as the PC.

CURRENT RESEARCH INTERESTS

  • Application of cutting-edge genomic technologies in genome assembly, genome finishing and annotation
  • Development of automated tools for characterization of cell morphologies and signaling pathways during embryogenesis
  • Molecular and genetic characterization of hybrid incompatibilities between nematode species
  • Developmental dynamics of signaling pathways during nematode embryogenesis

SELECTED PUBLICATIONS

  1. Jianfeng Cao, Guoye Guan, Vincy Wing Sze Ho, Ming-Kin Wong, Lu-Yan Chan, Chao Tang*, Zhongying Zhao* & Hong Yan* Establishment of morphological atlas of Caenorhabditis elegans embryo using deep-learning-based 4D segmentation. Nature Communications. 2020. DOI: 10.1038/s41467-020-19863-x.
  2. Shoudong Zhang, Runsheng Li, Li Zhang, Shengjie Chen, Min Xie, Liu Yang, Yiji Xia, Christine H Foyer, Zhongying Zhao*, Hon-Ming Lam* New insights into Arabidopsis transcriptome complexity revealed by direct sequencing of native RNAs. Nucleic Acids Res. 2020 Jul 11;gkaa588. doi: 10.1093/nar/gkaa588 PMID: 32652016.
  3. Runsheng Li, Xiaoliang Ren, Qiutao Ding, Yu Bi, Dongying Xie, Zhongying Zhao* Direct full-length RNA sequencing reveals unexpected transcriptome complexity during C. elegans development. Genome Research. 2020 Feb;30(2):287-298. doi: 10.1101/gr.251512.119 PMID: 32024662.
  4. Bi Y, Ren X, Li R, Ding Q, Xie D, Zhao Z* (2019) Specific Interactions Between Autosome and X Cause Hybrid Male Sterility in Caenorhabditis Species. Genetics. 2019 May 7. pii: genetics.302202.2019. doi: 10.1534/genetics.119.302202. PMID: 31064822
  5. Sun J, Mu H, Ip JCH, Li R, Xu T, Accorsi A, Sánchez Alvarado A, Ross E, Lan Y, Sun Y, Castro-Vazquez A, Vega IA, Heras H, Ituarte S, Van Bocxlaer B, Hayes KA, Cowie RH, Zhao Z, Zhang Y, Qian PY, Qiu JW (2019) Signatures of Divergence, Invasiveness, and Terrestrialization Revealed by Four Apple Snail Genome. Mol Biol Evol. 2019 Jul 1;36(7):1507-1520. doi: 10.1093/molbev/msz084. PMID: 30980073
  6. Runsheng Li, Xiaoliang Ren, Yu Bi, Qiutao Ding, Vincy Wing Sze Ho, Zhongying Zhao* (2018) Species-specific sampling of partial D-loop as a novel Non-Coding Region (NCR) in the mitochondrial genome. DNA Research. 2018 Dec 1;25(6):577-586. doi: 10.1093/dnares/dsy026. PMID: 30085012
  7. Long Chen#, Vincy Wing Sze Ho#, Ming-Kin Wong#, Xiaotai Huang#, Lu-yan Chan, Hon Chun Kaoru Ng, Xiaoliang Ren, Hong Yan & Zhongying Zhao* (2018) Automated inference of signaling interactions at cellular resolution for every cell cycle of embryogenesis . Genetics. 2018 Mar 22. pii: genetics.300820.2018. doi: 10.1534/genetics. PMID:29567658Highlight in Genetics. Data access
  8. Xiaoliang Ren#, Runsheng Li#, Xiaolin Wei#, Yu Bi, Vincy Wing Sze Ho, Qiutao Ding, Zhihong Zhang, Chia-Ling Hsieh, Amanda Young, Jianyang Zeng*, Xiao Liu*Zhongying Zhao* (2018) Genomic bases of recombination suppression in the hybrid between hermaphroditic Caenorhabditis briggsae and gonochoristic C. nigoniNucleic Acids Res. 2018 Feb 16;46(3):1295-1307. doi: 10.1093/nar/gkx1277. PMID: 29325078
  9. Huang XT, Zhu Y, Chan LHL, Yan H* (2017) Inference of cellular level signaling networks using single-cell gene expression data in Caenorhabditis elegans reveals mechanisms of cell fate specification. Bioinformatics. 2017 May 15;33(10):1528-1535. doi: 10.1093/bioinformatics/btw796. PMID: 28011782
  10. Guan D, Yan B, Thieme C, Hua J, Zhu H, Boheler KR, Zhao Z, Kragler F*, Xia Y*, Zhang S*. (2017) PlaMoM: a comprehensive database compiles plant mobile macromolecules. Nucleic Acids Res. 2017 Jan 4;45(D1):D1021-D1028. doi: 10.1093/nar/gkw988. PMID: 27924044
  11. Li R#, Ren X#, Bi Y, Ho VW, Hsieh CL, Young A, Zhang Z, Lin T, Zhao Y, Miao L, Sarkies P*, Zhao Z.* (2016) Specific Downregulation of Spermatogenesis Genes Targeted by 22G RNAs in Hybrid Sterile Males Associated with an X-Chromosome Introgression. Genome Res. PMID:27197225
  12. Wong MK, Guan D, Ng KH, Ho VW, An X, Li R, Ren X, Zhao Z. * (2016) Timing of Tissue-specific Cell Division Requires a Differential Onset of Zygotic Transcription during Metazoan Embryogenesis. J Biol Chem. 2016;Apr 7. pii:jbc.M115.705426. PMID: 27056332
  13. Huang XT, Zhu Y, Chan LL, Zhao Z, Yan H. (2016) An integrative C. elegans protein-protein interaction network with reliability assessment based on a probabilistic graphical model. Mol Biosyst. 2016 Jan;12(1):85-92. doi: 10.1039/c5mb00417a. PMID: 26555698
  14. WS Ho#, MKWong#, XM An#, DG Guan#, JF Shao, HC Ng, XL Ren, K He, J Liao, Y Ang, L Chen, X Huang, B Yan, Y Xia, LH Chan, KL Chow, H Yan and Z Zhao* (2015) Systems-level quantification of division timing reveals a common genetic architecture between asynchrony and fate asymmetry. Molecular Systems Biology. 2015;11(6):814. doi: 10.15252/msb.20145857. PMID:26063786 Data access PMID:26063786 Data access
  15. Yu Bi1#, Xiaoliang Ren1#, Cheung Yan, Jiaofang Shao, Dongying Xie and Zhongying Zhao* (2015) A Genome-Wide Hybrid Incompatibility Landscape between Caenorhabditis briggsae and C. nigoniPLoS Genet. 2015 Feb 18;11(2):e1004993. doi: 10.1371/journal.pgen.1004993. eCollection 2015 Feb. PMID: 25692300
  16. Guan D, Shao J, Zhao Z , Wang P, Qin J, Deng Y, Boheler KR, Wang J, Yan B* (2014) PTHGRN: unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data. Nucleic Acids Res. 2014 Jul;42. PMID: 24875471
  17. Daogang Guan, Jiaofang Shao, Youping Deng, Zhongying Zhao, Yan Liang, Junwen Wang, Bin Yan* (2014) CMGRN: a web server for constructing multi-level gene regulatory networks using ChIP-seq and gene expression data. Bioinformatics. 2014 Jan 21. PMID: 24389658
  18. Hari Krishna Yalamanchili, Bin Yan, Zhongying Zhao, Francis YL Chin, Mulin Jun Li, Jing Qin and Junwen Wang* (2013) Gapped Alignment Algorithm for Gene Regulatory Network Inference from High Throughput Temporal Data. Bioinformatics. 2014 Feb 1;30(3):377-83. Epub 2013 Nov 27. PMID: 24285602
  19. Shao J, He K, Wang H, Ho WS, Ren X, An X, Wong MK, Yan B, Xie D, Stamatoyannopoulos J*, Zhao Z* (2013) Collaborative Regulation of Development but Independent Control of Metabolism by Two Epidermis Specific Transcription Factors in C. elegansJ Biol Chem. 2013 Nov 15;288(46):33411-26. PMID: 24097988
  20. Murray JI, Boyle TJ, Preston E, Vafeados D, Mericle B, Weisdepp P, Zhao Z, Bao Z, Boeck M, Waterston RH, Flibotte S, Murray JI, Blick D, Boyle TJ, Gupta B, Moerman DG, Waterston RH. (2012) Multidimensional regulation of gene expression in the Caenorhabditis briggsae embryo. Genome Res. 2012 Jul;22(7):1282-94. Epub 2012 Apr 16. PMID: 22508763

*Corresponding author, # Equal contributor

CONTACT DETAILS

Office: RRS 822
Office Tel: (+852) 3411 7058       Email: zyzhao@hkbu.edu.hk
External Website Link: http://www.hkbu.edu.hk/~zyzhao/research.html