DR. ZHAO, Zhongying (趙中應)

SELECTED PUBLICATIONS

2018
1. Runsheng Li, Xiaoliang Ren, Yu Bi, Qiutao Ding, Vincy Wing Sze Ho, Zhongying Zhao^* Species-specific sampling of partial D-loop as a novel Non-Coding Region (NCR) in the mitochondrial genome. DNA Research. Under revision.
2. Long Chen^#, Vincy Wing Sze Ho^#, Ming-Kin Wong^#, Xiaotai Huang^#, Lu-yan Chan, Hon Chun Kaoru Ng, Xiaoliang Ren, Hong Yan & Zhongying Zhao^* 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: 29567658
3. 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^* Genomic bases of recombination suppression in the hybrid between hermaphroditic Caenorhabditis briggsae and gonochoristic C. nigoni. Nucleic Acids Res. 2018 Feb 16;46(3):1295-1307. doi: 10.1093/nar/gkx1277. PMID: 29325078

2017


4. An X, Shao J, Zhang H, Ren X, Ho VWS, Li R, Wong MK, Zhao Z^* (2017) Comparative proteome analysis between C . briggsae embryos and larvae reveals a role of chromatin modification proteins in embryonic cell division. Scientific Reports. 2017 Jun 27;7(1):4296. doi: 10.1038/s41598-017-04533-8. PMID:28655887
5. 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
6. 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

2016

7. 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
8. 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
9. Ren-E Huang^*, Runsheng Li, Zhongying Zhao^* (2016) Discovery of a free-living nematode phylogenetically related to vertebrate parasites of the genus Strongyloides (Nematoda: Strongyloidoidea): morphological, anatomical and molecular characterisation. Invertebrate Systematics. 2016. In press. Paper access
10. Chen Long, Zhongying Zhao, Hong Yan^* (2016) A Probabilistic Relaxation Labeling (PRL) Based Method for C. elegans Cell Tracking in Microscopic Image Sequences. IEEE Journal of Selected Topics in Signal Processing. 2016 February issue;Page(s):185 – 192. Paper access
11. 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

2015

12. Huang RE^*, Ye W, Ren X, and Z Zhao^* (2015) Morphological and Molecular Characterization of Phasmarhabditis huizhouensis sp. nov. (Nematoda: Rhabditidae), a New Rhabditid Nematode from South China. PLoS One. 2015 Dec 16;10(12):e0144386. doi: 10.1371/journal.pone.0144386. PMID:26674768
13. Jie Hu^*, Zhongying Zhao, Hari Krishna Yalamanchili, Junwen Wang, Kenny Ye, Xiaodan Fan^* (2015) Bayesian detection of embryonic gene expression onset in C. elegans. Annals of Applied Statistics. 2015, Vol. 9, No. 2, 950-968. Paper access
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. Runsheng Li, Chia-Ling Hsieh, Amanda Young, Zhihong Zhang, Xiaoliang Ren and Zhongying Zhao^* (2015)
    Illumina Synthetic Long Read Sequencing Allows Recovery of Missing Sequences even in the “Finished” C. elegans Genome. Scientific Reports. 2015 ;5:10814. doi: 10.1038/srep10814. PMID: 26039588
16. Yu Bi^1#, Xiaoliang Ren^1#, Cheung Yan, Jiaofang Shao, Dongying Xie and Zhongying Zhao^* (2015) A Genome-Wide Hybrid Incompatibility Landscape between Caenorhabditis briggsae and C. nigoni. PLoS Genet. 2015 Feb 18;11(2):e1004993. doi: 10.1371/journal.pgen.1004993. eCollection 2015 Feb. PMID: 25692300

2014

17. Huang RE, Ren X, Qiu Y, Zhao Z* (2014) Description of Caenorhabditis sinica sp. n. (Nematoda: Rhabditidae), a nematode species used in comparative biology for C. elegans. PLoS One. 2014 Nov 6;9(11):e110957. PMID: 25375770
18. 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
19. He K, Zhou T, Shao J, Ren X, Zhao Z, Liu D* (2014) Dynamic regulation of genetic pathways and targets during aging in Caenorhabditis elegans. Aging (Albany NY). 2014 Mar;6(3):215-30. PMID: 24739375
20. He K, Shao J, Zhao Z, Liu D* (2014) The comprehensive transcriptional analysis in Caenorhabditis elegans by integrating ChIP-seq and gene expression data. Genet Res (Cambridge). 2014 Jan;96:e005. PMID: 25023089
21. 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

2013

22. 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
23. 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. elegans. J Biol Chem. 2013 Nov 15;288(46):33411-26. PMID: 24097988
24. Long Chen*, Leanne Lai Hang Chan, Zhongying Zhao and Hong Yan (2013) A novel cell nuclei segmentation method based on bi-directional prediction. BMC Bioinformatics. 2013 Nov 19;14:328. PMID: 24252066
25. Huang X*, Chen L, Chim H, Chan LL, Zhao Z, Yan H (2013) Boolean genetic network model for the control of C. elegans early embryonic cell cycles. Biomed Eng Online. 2013;12 Suppl 1:S1. Epub 2013 Dec 9. PMID: 24564942

2012

26. Yan C, Bi Y, Yin D, Zhao Z* (2012) A method for rapid and simultaneous mapping of genetic Loci and introgression sizes in nematode species. PLoS One. 2012;7(8):e43770. PMID: 22952761
27. 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

2010

28. Zhao Z*, Boyle TJ, Liu Z, Murray JI, Wood WB, Waterston RH. (2010) A negative regulatory loop between microRNA and Hox gene controls posterior identities in Caenorhabditis elegans. PLoS Genet. 2010 Sep 2;6(9). pii: e1001089. PMID: 20824072
29. Zhao Z*, Flibotte S, Murray JI, Blick D, Boyle TJ, Gupta B, Moerman DG, Waterston RH. (2010) New tools for investigating the comparative biology of Caenorhabditis briggsae and C. elegans. Genetics. 2010 Mar;184(3):853-63. Epub 2009 Dec 14. PMID: 20008572

2008

30. Murray JI, Bao Z, Boyle TJ, Boeck ME, Mericle BL, Nicholas TJ, Zhao Z, Sandel MJ, Waterston RH.(2008) Automated analysis of embryonic gene expression with cellular resolution in C. elegans. Nat Methods. 2008 Aug;5(8):703-9. Epub 2008 Jun 29. PMID: 18587405
31. Bao Z#, Zhao Z#, Boyle TJ, Murray JI, Waterston RH.(2008) Control of cell cycle timing during C. elegans embryogenesis. Dev Biol. 2008 Jun 1;318(1):65-72. Epub 2008 Mar 13. PMID: 18430415
32. Zhao Z*, Boyle TJ, Bao Z, Murray JI, Mericle B, Waterston RH. (2008) Comparative analysis of embryonic cell lineage between Caenorhabditis briggsae and Caenorhabditis elegans. Dev Biol. 2008 Feb 1;314(1):93-9. Epub 2007 Nov 22. PMID: 18164284

2007

33. Hunt-Newbury R, Viveiros R, Johnsen R, Mah A, Anastas D, Fang L, Halfnight E, Lee D, Lin J, Lorch A, McKay S, Okada HM, Pan J, Schulz AK, Tu D, Wong K, Zhao Z, Alexeyenko A, Burglin T, Sonnhammer E, Schnabel R, Jones SJ, Marra MA, Baillie DL, Moerman DG. (2007) High-throughput in vivo analysis of gene expression in Caenorhabditis elegans. PLoS Biol. 2007 Sep;5(9):e237.PMID: 17850180
34. Zhao Z*, Thomas JH, Chen N, Sheps JA, Baillie DL. (2007) Comparative genomics and adaptive selection of the ATP-binding-cassette gene family in Caenorhabditis species. Genetics. 2007 Mar;175(3):1407-18. Epub 2006 Dec 28. PMID: 17194779

2005

35. Zhao Z*, Fang L, Chen N, Johnsen RC, Stein L, Baillie DL. (2005) Distinct regulatory elements mediate similar expression patterns in the excretory cell of Caenorhabditis elegans. J Biol Chem. 2005 Nov 18;280(46):38787-94. Epub 2005 Sep 13. PMID: 16159881
36. Chen N, Pai S, Zhao Z, Mah A, Newbury R, Johnsen RC, Altun Z, Moerman DG, Baillie DL, Stein LD. (2005) Identification of a nematode chemosensory gene family. Proc Natl Acad Sci U S A. 2005 Jan 4;102(1):146-51. Epub 2004 Dec 23. PMID: 15618405

2004

37. Zhao Z, Sheps JA, Ling V, Fang LL, Baillie DL. (2004) Expression analysis of ABC transporters reveals differential functions of tandemly duplicated genes in Caenorhabditis elegans. J Mol Biol. 2004 Nov 19;344(2):409-17. PMID: 15522294
38. Zhao Z*, Fang LL, Johnsen R, Baillie DL. (2004) ATP-binding cassette protein E is involved in gene transcription and translation in Caenorhabditis elegans. Biochem Biophys Res Commun. 2004 Oct 8;323(1):104-11. PMID: 15351708
39. Sheps JA, Ralph S, Zhao Z, Baillie DL, Ling V. (2004) The ABC transporter gene family of Caenorhabditis elegans has implications for the evolutionary dynamics of multidrug resistance in eukaryotes. Genome Biol. 2004;5(3):R15. Epub 2004 Feb 11.PMID: 15003118

2003

40. McKay SJ, Johnsen R, Khattra J, Asano J, Baillie DL, Chan S, Dube N, Fang L, Goszczynski B, Ha E, Halfnight E, Hollebakken R, Huang P, Hung K, Jensen V, Jones SJ, Kai H, Li D, Mah A, Marra M, McGhee J, Newbury R, Pouzyrev A, Riddle DL, Sonnhammer E, Tian H, Tu D, Tyson JR, Vatcher G, Warner A, Wong K, Zhao Z, Moerman DG. (2004) Gene expression profiling of cells, tissues, and developmental stages of the nematode C. elegans. Cold Spring Harb Symp Quant Biol. 2003;68:159-69. Review. PMID: 15338614

*Corresponding author, ^# Equal contributor