{"id":19,"date":"2019-05-22T16:06:47","date_gmt":"2019-05-22T20:06:47","guid":{"rendered":"http:\/\/sites.miamioh.edu\/zhao-genetics-genomics-lab\/?page_id=19"},"modified":"2021-12-20T10:35:15","modified_gmt":"2021-12-20T15:35:15","slug":"publications","status":"publish","type":"page","link":"https:\/\/sites.miamioh.edu\/zhao-genetics-genomics-lab\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"\n


H-index: 18 (Google Scholar)\u00a0 \u00a0 Citations: 5172 (December 2021)<\/strong>
Google Scholar Page:
https:\/\/scholar.google.com\/citations?user=DpXQ5k0AAAAJ&hl=en<\/a> <\/p>\n\n\n\n

**undergraduate student; *graduate student; <\/strong>\u2020<\/strong><\/sup>Corresponding Author <\/strong><\/p>\n\n\n\n

2021<\/strong><\/p>\n\n\n\n

8. Zhao M.\u2020<\/strong>, Ku J.C., Yang D.*, Yin L.*, Liu B.*, Ferrell T.J.**, Stoll C.E.**, Guo W.*, Zhang X., Wang D., Wang C.R., and Lisch D.\u2020<\/strong> 2021. The mop1<\/em> mutation affects the recombination landscape in maize. Proc Natl Acad Sci U S A. <\/em>https:\/\/www.pnas.org\/content\/118\/7\/e2009475118. (Recommended by Faculty Opinions<\/a>)<\/p>\n\n\n\n

7. Zhao M.\u2020<\/strong>, Liu S., Ma J. 2021. Asymmetric Evolution of Transposable Elements in Brassica oleracea. <\/em>The Brassica oleracea <\/em>genome. Compendium of Plant Genomes. Springer, Cham. p. 77-90.<\/p>\n\n\n\n

6. Liu B.*, Iwata-Otsubo A., Yang D.*, Baker R.L., Liang C., Jackson S.A., Liu S., Ma J., and Zhao M.\u2020<\/strong> 2021. Analysis of CACTA transposase genes unveils the mechanism of intron loss and distinct small RNA silencing pathways underlying divergent evolution of Brassica<\/em> genome. Plant J<\/em>. 105: 34-48. [PDF]<\/a><\/p>\n\n\n\n

2020<\/strong><\/p>\n\n\n\n

5. Zhang X., Zhao M.<\/strong>, McCarty D.R., and Lisch D. 2020. Transposable elements employ distinct integration strategies with respect to transcriptional landscapes in eukaryotic genomes. Nucleic Acids Res<\/em>. 48: 6685-6698. [PDF]<\/a><\/p>\n\n\n\n

4. Wang D., Zhang J., Zuo T., Zhao M.<\/strong>, Lisch D., and Peterson T. 2020. Small RNA-mediated de novo<\/em> silencing of Ac\/Ds<\/em> transposons is initiated by alternative transposition in maize. Genetics<\/em>. 215: 393-406. [PDF]<\/a>
<\/p>\n\n\n\n

3. Burgess D., Li H., Zhao M.<\/strong>, Kim S.Y., and Lisch D. 2020. Silencing of Mu<\/em> elements in maize involves distinct populations of small RNAs and distinct patterns of DNA methylation. Genetics<\/em>. 215: 379-391. [PDF]<\/a><\/p>\n\n\n\n

2. Zhang X., Zhao, M.<\/strong>, and Lisch D. 2020. Cost-effective profiling of Mutator<\/em> transposon insertions in maize by next-generation sequencing. Methods Mol Biol.<\/em> 2072: 39-50. [PDF]<\/a><\/p>\n\n\n\n

2018<\/strong><\/p>\n\n\n\n

1. Zhao M.\u2020<\/strong>, Zhang B., Ma J., and Lisch D. 2018. Genome-wide estimation of evolutionary distance and phylogenetic analysis of homologous genes. Bio-protocol<\/em> 8(23): e3097. [PDF]<\/a><\/p>\n\n\n\n

Prior to Miami (2011-2018)<\/strong><\/h3>\n\n\n\n

22. Zhao M.<\/strong>, Zhang B., Lisch D., and Ma J. 2017. Patterns and consequences of subgenome differentiation provide insights into the nature of paleopolyploidy in plants. Plant Cell <\/em>29: 2974-2994. [PDF]<\/a><\/p>\n\n\n\n

21. Zhao M.<\/strong>, and Ma J. 2017. Transposable Elements. In: Nguyen H., Bhattacharyya M. (eds). The Soybean Genome. Compendium of Plant Genomes. Springer, Cham. p. 171-181. [PDF]<\/a><\/p>\n\n\n\n

20. Zhang D.#<\/sup>, Zhao M.#<\/sup><\/strong>, Li S.#<\/sup>, Sun L., Wang W., Cai C., Dierking E., and Ma J. 2017. Plasticity and innovation of regulatory mechanisms underlying seed oil content mediated by duplicated genes in the palaeopolyploid soybean. Plant J<\/em>. 90: 1120-1133. (#<\/sup>Equal contributors<\/strong>) [PDF]<\/a><\/p>\n\n\n\n

19. Li L., Lin F., Wang W., Ping J., Fitzgerald J.C., Zhao M.<\/strong>, Li S., Sun L., Cai C., and Ma J. 2016. Fine mapping and candidate gene analysis of two loci conferring resistance to Phytophthora sojae<\/em> in soybean. Theor<\/em>. Appl<\/em>. Genet<\/em>. 129: 2379-2386. [PDF]<\/a><\/p>\n\n\n\n

18. Sun L., Miao Z., Cai C., Zhang D., Zhao M.<\/strong>, Wu Y., Zhang X., Swarm S.A., Zhou L., Zhang Z.J., Nelson R.L., and Ma J. 2015. GmHs1-1, encoding a calcineurin-like protein, controls hard-seededness in soybean. Nat. Genet.<\/em> 47: 939-943. [PDF]<\/a><\/p>\n\n\n\n

17. Zhao M.<\/strong>, Meyers B.C., Cai C., Xu W., and Ma J. 2015. Evolutionary patterns and co-evolutionary consequences of MIRNA<\/em> genes and microRNA targets triggered by multiple mechanisms of genomic duplications in soybean. Plant Cell<\/em> 27: 546-562. [PDF]<\/a><\/p>\n\n\n\n

16. Zhao M.<\/strong>, Cai C., Zhai J., Lin F., Li L., Shreve J., Thimmapuram J., Hughes T.J., Meyers B.C., and Ma J. 2015. Coordination of microRNAs, phasiRNAs, and NB-LRR<\/em> genes in response to a plant pathogen: insights from analyses of a set of soybean Rps<\/em> gene near-isogenic lines. Plant Gen<\/em>., 10.3835\/plantgenome2014.09.0044. [PDF]<\/a><\/p>\n\n\n\n

15. Chalhoub B., Denoeud F., Liu S., \u2026 Zhao M.<\/strong>, \u2026 Paterson A.H., Guan C., Wincker P. 2014. Early allopolyploid evolution in the post-Neolithic Brassica napus<\/em> oilseed genome. Science<\/em> 345: 950-953. (Annotated and analyzed all TEs in Brassica napus<\/em><\/strong>) [PDF]<\/a><\/p>\n\n\n\n

14. Ping J., Liu Y., Sun L., Zhao M.<\/strong>, Li Y., She M., Sui Y., Lin F., Liu X., Tang Z., Nguyen H., Tian Z., Qiu L., Nelson R.L., Clemente T.E., Specht J.E., and Ma J. 2014. Dt2<\/em> is a Gain-of-Function MADS-Domain Factor Gene That Specifies Semi-Determinacy in Soybean. Plant Cell<\/em> 26: 2831-2842. [PDF]<\/a><\/p>\n\n\n\n

13. Liu S., Liu Y., Yang X., Tong C., Edwards D., Parkin I.A.P., Zhao M.<\/strong>, \u2026, Wang X., Wang J., Chalhoub B., and Paterson A.H. 2014. The Brassica oleracea<\/em> genome reveals the asymmetrical evolution of polyploid genomes. Nat. Commun<\/em>. 5: 3930. (Leading the TE annotation and analysis in the genome<\/strong>) [PDF]<\/a>[<\/a><\/p>\n\n\n\n

12. Lin F.#<\/sup><\/strong>, Zhao M.#<\/sup><\/strong>, Baumann D.D., Ping J., Sun L., Liu Y., Zhang B., Tang Z., Hughes E., Doerge R.W., Hughes T.J., and Ma J. 2014. Molecular response to the pathogen Phytophthora sojae<\/em> among ten soybean near isogenic lines revealed by comparative transcriptpmics. BMC Genomics <\/em>15: 18. (#<\/sup>Equal contributors<\/strong>) [PDF]<\/a><\/p>\n\n\n\n

11. Zhao M.<\/strong>,Du J., Lin F., Tong C., Yu J., Huang S., Wang X., Liu S., and Ma J. 2013. Shifts in evolutionary rate and intensity of purifying selection between two Brassica<\/em> genomes revealed by analyses of orthologous transposons and relics of a whole genome triplication. Plant J<\/em>. 76: 211-222. <\/p>\n\n\n\n

10. Zhao M.<\/strong>, and Ma J. 2013. Co-evolution of plant LTR-retrotransposons and their host genomes. Protein & Cell<\/em> 4: 493-501. [PDF]<\/a><\/p>\n\n\n\n

9. Zhao M.<\/strong>, Zhang B., Liu S., and Ma J. 2013. Transposon expression and potential effect on gene regulation in the Brassica rapa<\/em> and Brassica oleracea<\/em> genomes. Hereditas<\/em> 35: 1014-1022. [PDF]<\/a>[<\/a><\/p>\n\n\n\n

8. Yu J. #<\/sup><\/strong>, Zhao M.#<\/sup><\/strong>,Wang X., Tong C., Huang S., Tehrim S., Liu Y., Hua W., and Liu S. 2013. Bolbase: a comprehensive genomics database for Brassica oleracea<\/em>. BMC Genomics<\/em> 14: 664. (*<\/sup>Equal contributors<\/strong>) [PDF]<\/a><\/p>\n\n\n\n

7. Lin F., Zhao M.<\/strong>, Ping J., Johnson A., Zhang B., Abney T.S., Hughes T., and Ma J. 2013. Molecular mapping of two genes conferring resistance to Phytophthora sojae<\/em> in a soybean landrace PI 567139B. Theor<\/em>. Appl<\/em>. Genet<\/em>. 126: 2177-2185. [PDF]<\/a><\/p>\n\n\n\n

6. Motamayor J.C., Mockaitis K., Schmutz J., Haiminen N., \u2026 Zhao M.<\/strong>, \u2026 Parida L. and Kuhn D.N. 2013. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biol<\/em>. 14: R53. [PDF]<\/a><\/p>\n\n\n\n

5. Tian Z., Zhao M.<\/strong>, She M., Du J., Cannon S.B., Liu X., Xu X., Li M.W., Lam H.M., and Ma J. 2012. Genome-wide characterization of non-reference transposons reveals evolutionary propensities of transposons in soybean. Plant Cell<\/em> 24: 1-15. [PDF]<\/a><\/p>\n\n\n\n

4. Du J., Tian Z., Sui Y., Zhao M.<\/strong>, Song Q., Cannon S.B., Cregan P., and Ma J. 2012. Pericentromeric effects shape the patterns of divergence, retention, and expression of duplicated genes in the palaeopolyploid soybean. Plant Cell<\/em> 24: 21-32. [PDF]<\/a><\/p>\n\n\n\n

3. Wang X., Wang H., Sun R., Wu J., Liu S., \u2026 Zhao M.<\/strong>, \u2026 Xiong Z. and Zhang Z. 2011. The genome of the mesopolyploid crop species Brassica rapa<\/em>. Nat. Genet.<\/em> 43: 1035-1039. [PDF]<\/a><\/p>\n\n\n\n

2. Wang C., Cai L., Dong C., Huang J., Zhao M.<\/strong>, Zhou R., Liu S. 2011. Over-expression of BnERF104<\/em> from Brassica napus<\/em> enhanced transgenic Arabidopsis<\/em> resistance to Sclerotinia sclerotiorum<\/em>. Chin. J. Oil Crop Sci.<\/em> 33: 325-33<\/p>\n\n\n\n

1. Zhang B., Huang J., Liu S., Zhao M.<\/strong>, Wang C., Cai L. 2011. Establishment of a rapid identification method to determine differences in susceptibility of Cercospora Sojina<\/em> Hara by hyphae inoculated on the excised leaf surface. J. Anhui Agri. Sci.<\/em> 39: 12714-12718. <\/p>\n","protected":false},"excerpt":{"rendered":"

H-index: 18 (Google Scholar)\u00a0 \u00a0 Citations: 5172 (December 2021) Google Scholar Page: https:\/\/scholar.google.com\/citations?user=DpXQ5k0AAAAJ&hl=en **undergraduate student; *graduate student; \u2020Corresponding Author 2021 8. Zhao M.\u2020, Ku J.C., Yang D.*, Yin L.*, Liu B.*, Ferrell T.J.**, Stoll C.E.**, Guo W.*, Zhang X., Wang … Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":2740,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_bbp_topic_count":0,"_bbp_reply_count":0,"_bbp_total_topic_count":0,"_bbp_total_reply_count":0,"_bbp_voice_count":0,"_bbp_anonymous_reply_count":0,"_bbp_topic_count_hidden":0,"_bbp_reply_count_hidden":0,"_bbp_forum_subforum_count":0,"footnotes":""},"class_list":["post-19","page","type-page","status-publish","hentry"],"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/sites.miamioh.edu\/zhao-genetics-genomics-lab\/wp-json\/wp\/v2\/pages\/19","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.miamioh.edu\/zhao-genetics-genomics-lab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.miamioh.edu\/zhao-genetics-genomics-lab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.miamioh.edu\/zhao-genetics-genomics-lab\/wp-json\/wp\/v2\/users\/2740"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.miamioh.edu\/zhao-genetics-genomics-lab\/wp-json\/wp\/v2\/comments?post=19"}],"version-history":[{"count":0,"href":"https:\/\/sites.miamioh.edu\/zhao-genetics-genomics-lab\/wp-json\/wp\/v2\/pages\/19\/revisions"}],"wp:attachment":[{"href":"https:\/\/sites.miamioh.edu\/zhao-genetics-genomics-lab\/wp-json\/wp\/v2\/media?parent=19"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}