1.        Fangnan Peng, Wenxin Zhang, Wenjie Zeng, Jian-Kang Zhu, Daisuke Miki*, Gene targeting in Arabidopsis via an all-in-one strategy that uses a translational enhancer to aid Cas9 expression. Plant Biotechnology Journal, 18(4): 892-894. (2020) (* Corresponding author)

2.        Wen-Feng Nie, Mingguang Lei, Mingxuan Zhang, Kai Tang, Huan Huang, Cuijun Zhang, Daisuke Miki, Pan Liu, Yu Yang, Xingang Wang, Heng Zhang, Zhaobo Lang, Na Liu, Xuechen Xu, Ramesh Yelagandula, Huiming Zhang, Zhidan Wang, Xiaoqiang Chai, Andrea Andreucci, Jing-Quan Yu, Frederic Berger, Rosa Lozano-Duran, Jian-Kang Zhu, Histone acetylation recruits the SWR1 complex to regulate active DNA demethylation in Arabidopsis. Proc. Natl. Acad. Sci. USA, 116(33): 16641-16650. (2019)

3.        Changsong Zou, Leiting Li, Daisuke Miki, Delin Li, Qiming Tang, Lihong Xiao, Santosh Rajput, Ping Deng, Li Peng, Wei Jia, Ru Huang, Meiling Zhang, Yidan Sun, Jiamin Hu, Xing Fu, Patrick S. Schnable, Yuxiao Chang, Feng Li, Hui Zhang, Baili Feng, Xinguang Zhu, Renyi Liu, James C. Schnable, Jian-Kang Zhu, Heng Zhang, The genome of broomcorn millet. Nature Communications, 10(1): 436. (2019)

4.        Dong-Lei Yang, Guiping Zhang, Lili Wang, Jingwen Li, Dachao Xu, Cuiru Di, Kai Tang, Lan Yang, Liang Zeng, Daisuke Miki, Cheng-Guo Duan, Huiming Zhang, Jian-Kang Zhu, Four putative SWI2/SNF2 chromatin remodelers have dual roles in regulating DNA methylation in Arabidopsis. Cell Discovery, 4(55): (2018)

5.        Haifeng Zhu, Wenxiang Xie, Dachao Xu, Daisuke Miki, Kai Tang, Chao-Feng Huang, Jian-Kang Zhu, DNA demethylase ROS1 negatively regulates the imprinting of DOGL4 and seed dormancy in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA, 115(42): E9962-9970. (2018)

6.        Daisuke Miki？*, Wenxin Zhang？, Wenjie Zeng, Zhengyan Feng, Jian-Kang Zhu*, CRISPR/Cas9-mediated gene targeting in Arabidopsis using sequential transfromation. Nature Communications, 9(1): 1967. (2018) (？ These authors contributed equally to this work; * Corresponding authors)

7.        Rong Yang, Zhimin Zheng, Qing Chen, Lan Yang, Huan Huang, Daisuke Miki, Wenwu Wu, Liang Zeng, Jun Liu, Jin-Xing Zhou, Joe Ogas, Jian-Kang Zhu, Xin-Jian He, Heng Zhang, The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci. Genome Biology, 18(1): 103. (2017)

8.        Daisuke Miki？*, Peiying Zhu？, Wencan Zhang？, Yanfei Mao, Zhengyan Feng, Huan Huang, Hui Zhang, Yanqiang Li, Renyi Liu, Huiming Zhang, Yijun Qi, Jian-Kang Zhu, Efficient Generation of diRNAs Requires Components in the Posttranscriptional Gene Silencing Pathway. Scientific Reports, 7(1): 301. (2017) (？ These authors contributed equally to this work; * Corresponding author)

9.        Cheng-Guo Duan, Xingang Wang, Shaojun Xie, Li Pan, Daisuke Miki, Kai Tang, Chuan-Chih Hsu, Mingguang Lei, Yingli Zhong, Yueh-Ju Hou, Zhijuan Wang, Zhengjing Zhang, Satendra K Mangrauthia, Huawei Xu, Heng Zhang, Brian Dilkes, W Andy Tao, Jian-Kang Zhu, A pair of transposon-derived proteins function in a histone acetyltransferase complex for active DNA demethylation. Cell Research, 27(2): 226-240. (2017)

10.    Yu Yang, Honggui La, Kai Tang, Daisuke Miki, Lan Yang, Bangshing Wang, Cheng-Guo Duan, Wenfeng Nie, Xingang Wang, Siwen Wang, Yufeng Pan, Elizabeth J. Tran, Lizhe An, Huiming Zhang, Jian-Kang Zhu, SAC3B, a central component of the mRNA export complex TREX-2, is required for prevention of epigenetic gene silencing in Arabidopsis. Nucleic Acids Research, 45(1): 181-197. (2017)

11.    Zhimin Zheng, Hasi Yu, Daisuke Miki, Dan Jin, Qingzhu Zhang, Zhonghai Ren, Zhizhong Gong, Heng Zhang, Jian-Kang Zhu, Involvement of Multiple Gene-Silencing Pathways in a Paramutation-like Phenomenon in Arabidopsis. Cell Reports, 11(8): 1160-7. (2015)

12.    Zhaobo Lang, Mingguang Lei, Xingang Wang, Kai Tang, Daisuke Miki, Huiming Zhang, Satendra K. Mangrauthia, Wenshan Liu, Wenfeng Nie, Guojie Ma, Jun Yan, Cheng-Guo Duan, Chuan-Chih Hsu, Chunlei Wang, W. Andy Tao, Zhizhong Gong, Jian-Kang Zhu, The methyl-CpG-binding protein MBD7 facilitates active DNA demethylation to limit DNA hyper-methylation and transcriptional gene silencing. Molecular Cell, 57(6): 971-83. (2015)

13.    Weiqiang Qian？, Daisuke Miki？, Mingguang Lei？, Xiaohong Zhu, Huiming Zhang, Yunhua Liu, Yan Li, Zhaobo Lang, Jing Wang, Kai Tang, Renyi Liu, Jian-Kang Zhu, Regulation of Active DNA Demethylation by An α-Crystallin Domain Protein in Arabidopsis. Molecular Cell, 55(3): 361-71. (2014) (？ These authors contributed equally to this work)

14.    Chizuko Yamamuro, Daisuke Miki, Zhimin Zheng, Jun Ma, Jing Wang, Zhenbiao Yang, Juan Dong, Jian-Kang Zhu, Overproduction of stomatal lineage cells in Arabidopsis mutants defective in active DNA demethylation. Nature Communications, 5(5): 4062. (2014)

15.    Satoshi Naramoto, Marisa Otegui, Natsumaro Kutsuna, Riet de Rycke, Tomoko Dainobu, Michael Karampelias, Keiko Shoda, Masaru Fujimoto, Elena Feraru, Daisuke Miki, Akihiko Nakano, Jiri Friml, Insights into the localization and function of GNOM ARF-GEF at the Golgi apparatus in Arabidopsis thaliana. Plant Cell, 26(7): 3062-76. (2014)

16.    Mingguang Lei, Honggui La, Kun Lu, Pengcheng Wang, Daisuke Miki, Zhizhong Ren, Cheng-Guo Duan, Xingang Wang, Kai Tang, Liang Zeng, Lan Yang, Heng Zhang, Wenfeng Nie, Pan Liu, Jianping Zhou, Renyi Liu, Yingli Zhong, Dong Liu, Jian-Kang Zhu, Arabidopsis EDM2 promotes IBM1 distal polyadenylation and regulates genome DNA methylation patterns. Proc. Natl. Acad. Sci. USA, 111(1): 527-32. (2014)

17.    Chao-Feng Huang, Daisuke Miki, Kai Tang, Hao-Ran Zhou, Zhimin Zheng, Wei Chen, Ze-Yang Ma, Lan Yang, Heng Zhang, Renyi Li, Xin-Jian He, Jian-Kang Zhu, A Pre-mRNA-Splicing Factor Is Required for RNA-Directed DNA Methylation in Arabidopsis. PLoS Genetics, 9 (9): e1003779. (2013)

18.    Weiqiang Qian？, Daisuke Miki？, Heng Zhang, Yunhua Liu, Xi Zhang, Kai Tang, Yunchao Kan, Honggui La, Xiaojie Li, Shaofang Li, Xiaohong Zhu, Xiaobing Shi, Kangling Zhang, Olga Pontes, Xuemei Chen, Renyi Liu, Zhizhong Gong, Jian-Kang Zhu, A Histone Acetyltransferase Regulates Active DNA Demethylation in Arabidopsis. Science, 336 (6087): 1445-48. (2012) (？ These authors contributed equally to this work)

19.    Huiming Zhang, Xiangyang Deng, Daisuke Miki, Sean Cutler, Honggui La, Yueh-Ju Hou, JeeEun Oh, Jian-Kang Zhu, Sulfamethazine Suppresses Epigenetic Silencing in Arabidopsis by Impairing Folate Synthesis. Plant Cell, 24 (3): 1230-41. (2012)

20.    María Isabel Martínez-Macías？, Weiqiang Qian？, Daisuke Miki？, Olga Pontes, Yunhua Liu, Kai Tang, Renyi Liu, Teresa Morales-Ruiz, Rafael R. Ariza, Teresa Roldán-Arjona, Jian-Kang Zhu, A DNA 3’-phosphatase functions in active DNA demethylation in Arabidopsis. Molecular Cell, 45 (3): 357-70. (2012) (？ These authors contributed equally to this work)

21.    Qian Liu, Junguo Wang, Daisuke Miki, Ran Xia, Wenxiang Yu, Junna He, Zhimin Zheng, Jian-Kang Zhu, Zhizhong Gong, DNA replication factor C1 mediates genomic stability and transcriptional gene silencing in Arabidopsis. Plant Cell, 22 (7): 2336-52. (2010)

22.    Zhihuan Gao, Hai-Liang Liu, Lucia Daxinger, Olga Pontes, Xinjian He, Weiqiang Qian, Huixin Lin, Mingtang Xie, Zdravko J. Lorkovic, Shoudong Zhang, Daisuke Miki, Xiangqiang Zhan, Dominique Pontier, Thierry Lagrange, Hailing Jin, Antonius J. M. Matzke, Marjori Matzke, Craig S. Pikaard, Jian-Kang Zhu, An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature, 465 (6): 106-09. (2010)

23.    Letian Chen, Kenji Shiotani, Takashi Togashi, Daisuke Miki, Misa Aoyama, Hann Ling Wong, Tsutomu Kawasaki, Ko Shimamoto, Analysis of the Rac/Rop Small GTPase Family in Rice: Expression, Subcellular Localization and Role in Disease Resistance. Plant and Cell Physiology, 51(4): 585-95. (2010)

24.              Syunichi Urayama, Hiromitsu Moriyama, Nanako Aoki, Yukihiro Nakazawa, Daisuke Miki, Ko Shimamoto, Toshiyuki Fukuhara, Knock-down of OsDCL2 in Rice Negatively Affects Maintenance of the Endogenous dsRNA Virus, Oryza sativa Endornavirus. Plant and Cell Physiology, 51(1): 58-67. (2010)

25.    Xianwu Zheng, Olga Pontes, Jianhua Zhu, Daisuke Miki, Fei Zhang, Wen-Xue Li, Kei Iida, Avnish Kapoor, Craig S. Pikaard, Jian-Kang Zhu, ROS3, an RNA-binding protein required for DNA demethylation in Arabidopsis. Nature, 455(7217): 1259-62. (2008)

26.    Daisuke Miki, Ko Shimamoto, De novo DNA methylation induced by siRNA targeted to endogenous transcribed sequences is gene-specific and OsMet1-independent in rice. The Plant Journal, 56(4): 539-49. (2008)

27.    Yosuke Okano, Daisuke Miki, Ko Shimamoto, Small interfering RNA (siRNA) targeting of endogenous promoters induces DNA methylation, but not necessarily gene silencing, in rice. The Plant Journal, 53(1): 65-77. (2008)

28.    Daisuke Miki, Rika Itoh, Ko Shimamoto, RNA silencing of single and multiple members in a gene family of rice. Plant Physiology, 138(4): 1903-13. (2005)

29.    Satoru Moritoh, Daisuke Miki, Masahiro Akiyama, Mihoko Kawahara, Takeshi Izawa, Hisaji Maki, Ko Shimamoto, RNAi-mediated silencing of OsGEN-L (OsGEN-like), a new member of the RAD2/XPG nuclease family, causes male sterility by defect of microspore development in rice. Plant and Cell Physiology, 46(5): 699-715. (2005)

30.    Daisuke Miki, Ko Shimamoto, Simple RNAi vectors for stable and transient suppression of gene function in rice. Plant and Cell Physiology, 45(4): 490-495. (2004)