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76. Zhang Z, Zeng W, Zhang W, Li J, Kong D, Zhang L, Wang R, Peng F, Kong Z, Ke Y, Zhang H, Kim C, Zhang H, Botella JR, Zhu JK, Miki D. (2022) Insights into the molecular mechanisms of CRISPR/Cas9-mediated gene targeting at multiple loci in Arabidopsis. Plant Physiol. 190: 2203-2216.

75. Dai L, Singh SK, Gong H, Tang Y, Peng Z, Zhang J, Wu D, Zhang H, He D. (2022) Rhizospheric microbial consortium of Lilium lancifolium Thunb. causes lily root rot under continuous cropping system. Front Microbiol. 13: 981615.

74. Rodrigues-Dos Santos AS, Rebelo-Romao I, Zhang H, Vílchez JI. (2022) Discerning Transcriptomic and Biochemical Responses of Arabidopsis thaliana Treated with the Biofertilizer Strain Priestia megaterium YC4-R4: Boosting Plant Central and Secondary Metabolism. Plants (Basel) 11: 3039.

73. Lv S, Yang Y, Yu G, Peng L, Zheng S, Singh SK, Vílchez JI, Kaushal R, Zi H, Yi D, Wang Y, Luo S, Wu X, Zuo Z, Huang W, Liu R, Du J, Macho AP, Tang K, Zhang H * (2022) Dysfunction of histone demethylase IBM1 in Arabidopsis causes autoimmunity and reshapes the root microbiome. ISME J. 16: 2513-2524.

72. He D, Singh SK, Peng L, Kaushal R, Vílchez JI, Shao C, Wu X, Zheng S, Morcillo RJL, Paré PW, Zhang H * (2022) Flavonoid-attracted Aeromonas sp. from the Arabidopsis root microbiome enhances plant dehydration resistance. ISME J. 16: 2622-2632.

71. Yang Y, Chen S, Wu X, Peng L, Vílchez JI, Kaushal R, Liu X, Singh SK, He D, Yuan F, Lv S, Morcillo RJL, Wang W, Huang W, Lei M, Zhu J-K, Paré PW, Zhang H * (2022) Plant latent defense response to microbial non-pathogenic factors antagonizes compatibility. Natl. Sci. Rev. 9(8): nwac109.

70. Singh SK, Sun Y, Yang Y, Zuo Z, Wu X, Shao C, Peng L, Paré PW, Zhang H * (2022) Bacterial diacetyl suppresses abiotic stress-induced senescence in Arabidopsis. J Integr Plant Biol. 64: 1135-1139.

69. Singh SK, Wu, X, Shao, C, Zhang H* (2022) Microbial enhancement of plant nutrient acquisition. Stress Bio. 2:3.

68. Zhang H*, Zhu J, Gong Z, Zhu JK* (2022) Abiotic stress responses in plants. Nat Rev Genet. 23(2):104-119.

67. Huang WC, Liu ZJ, Jiang K, Luo YB, Jin XH, Zhang Z, Xu RH, Muchuku JK, Musungwa SS, Yukawa T, Wang W, Zeng XH, Zhang H, Cai YM, Hu C, Lan SR. (2022) Phylogenetic analysis and character evolution of tribe Arethuseae (Orchidaceae) reveal a new genus Mengzia. Mol Phylogenet Evol. 167:107362.

66. Morcillo RJL., Vílchez JI., Zhang S, Kaushal R, He D, Zi H, Liu R, Niehaus K, Handa AK, Zhang H* (2021) Plant Transcriptome Reprograming and Bacterial Extracellular Metabolites Underlying Tomato Drought Resistance Triggered by a Beneficial Soil Bacteria. Metabolites. 11: 369.

65. Feng Z, Zhan X, Pang J, Liu X, Zhang H, Lang Z, Zhu JK. (2021) Genetic analysis implicates a molecular chaperone complex in regulating epigenetic silencing of methylated genomic regions. J Integr Plant Biol. 63: 1451-1461.

64. Niu Q, Song Z, Tang K, Chen L, Wang L, Ban T, Guo Z, Kim C, Zhang H, Duan CG, Zhang H, Zhu JK, Du J, Lang Z. (2021) A histone H3K4me1-specific binding protein is required for siRNA accumulation and DNA methylation at a subset of loci targeted by RNA-directed DNA methylation. Nat Commun. 12: 3367.

63. Vilchez JI, Yang Y, Yi D, Zhang H* (2021) Measurements of root colonized bacteria species. Bio Protoc. 11: e3976.

62. Tang K*, Zhang H* (2021) Editorial: The interplay between epigenetic regulation and other cellular processes. Front. Genet. 12: 691202.

61. Kaushal R, Peng L, Singh SK, Zhang M, Zhang X, Vilchez JI, Wang Z, He D, Yang Y, Lv S, Xu Z, Morcillo RJ L, Wang W, Huang W, Pare PW, Song C-P, Zhu J-K, Liu R, Zhong W, Ma P, Zhang H * (2021) Dicer-like proteins influence Arabidopsis root microbiota independent of RNA-directed DNA methylation. Microbiome. 9: 57.

60. H Zhang, R Kaushal, SK Singh, PW Paré (2020) Bacterial Volatile-Mediated Plant Abiotic Stress Tolerance. In CM Ryu, L Weisskopf, and B Piechulla (eds.) Bacterial Volatile Compounds as Mediators of Airborne Interactions (pp 187-200), Springer Singapore.

59. Zeng W, Huang H, Lin X, Zhu C, Kosami KI, Huang C, Zhang H, Duan CG, Zhu JK, Miki (2020) Roles of DEMETER in regulating DNA methylation in vegetative tissues and pathogen resistance. J Integr Plant Biol. 63: 691-706.

58. Vílchez JI, Yang Y, He D, Zi H, Peng L, Lv S, Kaushal R, Wang W, Huang W, Liu R, Lang Z, Miki D, Tang K, Paré PW, Song CP, Zhu JK, Zhang H * (2020) DNA demethylases are required for myo-inositol-mediated mutualism between plants and beneficial rhizobacteria. Nat Plants. 6: 983-995.

57. Morcillo RJL, Singh SK, He D, Vílchez JI, Kaushal R, Wang W, Huang W, Paré PW, Zhang H * (2020) Bacteria-derived diacetyl enhances Arabidopsis phosphate starvation responses partially through the DELLA-dependent gibberellin signaling pathway. Plant Signal Behav. 17:1740872.

56. Chang YN, Zhu C, Jiang J, Zhang H, Zhu JK, Duan CG (2019) Epigenetic regulation in plant abiotic stress responses. J Integr Plant Biol. doi: 10.1111/jipb.12901.

55. Morcillo RJL, Singh SK, An G, He D, Vílchez JL, Tang K, Yuan F, Sun Y, Shao C, Zhang S, Yang Y, Wang W, Gao J, Huang W, Lei M, Zhu J-K, Macho AP, Paré PW, Zhang H * (2020) Rhizobacterium-derived diacetyl modulates plant immunity in a phosphate-dependent manner. EMBO J. 39 (2): e102602.

54. Dong J, Ma G, Sui L, Wei M, Satheesh V, Zhang R, Ge S, Li J, Zhang TE, Wittwer C, Jessen HJ, Zhang H, An GY, Chao DY, Liu D, Lei M. (2019) Inositol Pyrophosphate InsP8 Acts as an Intracellular Phosphate Signal in Arabidopsis. Mol Plant. pii: S1674-2052(19)30263-1.

53. Zhang H *, Zhang K, Zhu JK *. (2019) A model for the aberrant DNA methylomes in aging cells and cancer cells. Biochem Soc Trans. 47: 997-1003.

52. Wang W, Singh SK, Li X, Sun H, Yang Y, Jiang M, Zi H, Liu R, Zhang H, Chu Z. (2019) Partial defoliation of Brachypodium distachyon plants grown in petri dishes under low light increases P and other nutrient levels concomitantly with transcriptional changes in the roots. Peer J. 7:e7102

51. Nie WF, Lei M, Zhang M, Tang K, Huang H, Zhang C, Miki D, Liu P, Yang Y, Wang X, Zhang H, Lang Z, Liu N, Xu X, Yelagandula R, Zhang H, Wang Z, Chai X, Andreucci A, Yu JQ, Berger F, Lozano-Duran R, Zhu JK. (2019) Histone acetylation recruits the SWR1 complex to regulate active DNA demethylation in Arabidopsis. Proc Natl Acad Sci U S A. 116: 16641-16650.

50. Yang Y, Tang K, Datsenka TU, Liu W, Lv S, Lang Z, Wang X, Gao J, Wang W, Nie W, Chu Z, Zhang H, Handa AK, Zhu J-K, Zhang H * (2019) Critical function of DNA methyltransferase 1 in tomato development and regulation of the DNA methylome and transcriptome. J Integr Plant Biol. 61: 1224-1242.

49. Vílchez JI, Tang Q, Kaushal R, Wang W, Lv S, He D, Chu Z, Zhang H, Liu R, Zhang H * (2018) Complete Genome Sequence of Bacillus megaterium Strain TG1-E1, a Plant Drought Tolerance-Enhancing Bacterium. Microbiol Resour Announc. 7 (12): e00842-18.

48. Yang DL, Zhang G, Wang L, Li J, Xu D, Di C, Tang K, Yang L, Zeng L, Miki D, Duan CG, Zhang H, Zhu JK (2018) Four putative SWI2/SNF2 chromatin remodelers have dual roles in regulating DNA methylation in Arabidopsis. Cell Discov. 4: 55.

47. Vílchez JI, Tang Q, Kaushal R, Wang W, Lv S, He D, Chu Z, Zhang H, Liu R, Zhang H * (2018) Genome Sequence of Bacillus megaterium Strain YC4-R4, a Plant Growth-Promoting Rhizobacterium isolated from high salinity environment. Genome Announc. 6: e00527-18.

46. Zhang H*, Lang Z, Zhu JK* (2018) Dynamics and function of DNA methylation in Plants. Nat Rev Mol Cell Biol. 19: 489-506.

45. Vílchez JI, Tang Q, Kaushal R, Chen S, Liu R *, Zhang H * (2018) Genome Sequence of Bacillus cereus Strain TG1-6, a Plant Beneficial Rhizobacteria that is Highly Salt-Tolerant. Genome Announc. 6: e00351-18.

44. He L, Wu W, Zinta G, Yang L, Wang D, Liu R, Zhang H, Zheng Z, Huang H, Zhang Q, Zhu JK. (2018) A naturally occurring epiallele associates with leaf senescence and local climate adaptation in Arabidopsis accessions. Nat Commun. 9: 460.

43. Yang Y, Wang W, Chu Z, Zhu JK, Zhang H* (2017) Roles of Nuclear Pores and Nucleo-cytoplasmic Trafficking in Plant Stress Responses. Front Plant Sci. 8:574.

42. Zhang H*, Zhu JK*. (2017) New Discoveries Generate New Questions about RNA-directed DNA methylation in Arabidopsis. Natl. Sci. Rev. 4 (1): 10-15.

41. Miki D, Zhu P, Zhang W, Mao Y, Feng Z, Huang H, Zhang H, Li Y, Liu R, Zhang H, Qi Y, Zhu JK. (2017) Efficient Generation of diRNAs Requires Components in the Posttranscriptional Gene Silencing Pathway. Sci Rep. 7: 301.

40. Yang Y, La H, Tang K, Miki D, Yang L, Wang B, Duan CG, Nie W, Wang X, Wang S, Pan Y, Tran EJ, An L, Zhang H*, Zhu JK*. (2017) SAC3B, a central component of the mRNA export complex TREX-2, is required for prevention of epigenetic gene silencing in Arabidopsis. Nucleic Acids Res. 45: 181-197.

39. Tang K, Duan CG, Zhang H, Zhu JK. (2017) Computational Analysis of Genome-Wide ARGONAUTE-Dependent DNA Methylation in Plants. Methods Mol Biol. 1640: 219-225

38. Zhang Q, Wang D, Lang Z, He L, Yang L, Zeng L, Li Y, Zhao C, Huang H, Zhang H, Zhang H, Zhu JK.　(2016) Methylation interactions in Arabidopsis hybrids require RNA-directed DNA methylation and are influenced by genetic variation.　Proc Natl Acad Sci U S A. 113: E4248-56.

37. Liu XM, Zhang H. * (2015) The effects of bacterial volatile emissions on plant abiotic stress tolerance. Front. Plant Sci. 6:774.

36. Duan CG, Wang X, Tang K, Zhang H, Mangrauthia SK, Lei M, Hsu CC, Hou YJ, Wang C, Li Y, Tao WA, Zhu JK. (2015) MET18 Connects the Cytosolic Iron-Sulfur Cluster Assembly Pathway to Active DNA Demethylation in Arabidopsis. PLoS Genet. 11: e1005559.

35. Freitas, M., Medeiros, F., Carvalho, S., Guilherme, L., Teixeira, W., Zhang, H., Paré, P. (2015) Augmenting Iron Accumulation in Cassava by the Beneficial Soil Bacterium Bacillus subtilis (GB03). Front. Plant Sci. 6: 596.

34. Lei, M., Zhang, H., Julian, R., Tang, K., Xie, S., Zhu, J-K (2015) Regulatory link between DNA methylation and active demethylation in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 112: 3553-3557.

33. Wang, B., Duan, C., Wang, X., Hou, Y., Yan, J., Gao, C., Kim, J., Zhang, H., Zhu, J-K (2015) HOS1 Regulates Argonaute1 by Promoting the Transcription of the MicroRNA Gene MIR168b in Arabidopsis. Plant J. 81: 861-870.

32. Lang, Z., Lei, M., Wang, X., Tang, K., Miki, D., Zhang H., Mangrauthia S.K., Liu, W., Nie, W., Ma, G., Yan, J., Duan C., Hsu, C., Wang, C., Tao, A., Gong, Z., Zhu, J-K (2015) The methyl-CpG-binding protein MBD7 facilitates active DNA demethylation to limit DNA hypermethylation and transcriptional gene silencing. Mol. Cell 57(6)：971-983.

31. Duan, C. #, Zhang, H. #, Tang, K. #, Wang, B., Lang, Z., Zhou, J., Zhu, J.-K. (2015) Specific but interdependent functions for Arabidopsis AGO4 and AGO6 in RNA-directed DNA methylation. EMBO J. 34(5):581-592. # Co-first author

30. Li, Y., Córdoba-Ca?ero, D., Qian, W., Zhu, X., Tang, K., Zhang, H., Ariza, R., Roldán-Arjon, T., Zhu, J.-K. (2015) An AP endonuclease functions in active DNA demethylation and gene imprinting in Arabidopsis. PLoS Genet. 11(1):e1004905.

29. Zhang, H.*, Zhu, J.-K. (2014) Emerging roles of RNA processing factors in regulating long non-coding RNAs. RNA Biol. 11(7):793-7.

28. Zhang, H.*, Tang K., Wang, B., Lang, Z., Zhu, J.-K.* (2014) Protocol: a beginner's guide to the analysis of RNA-directed DNA methylation in plants. Plant Methods 10:18.

27. Zhang, H.*, Tang K, Qian, W., Zhang, H., Wang, P.C., Wang, B., Duan, C., Lang, Z., Yang, Y., Zhu, J.-K.* (2014) An Rrp6-like Protein Positively Regulates Non-coding RNA Levels and DNA Methylation in Arabidopsis. Mol Cell 54: 418-430.

26. Qian,W., Miki, D., Lei, M., Zhu, X., Zhang, H., Liu, Y., Li, Y., Zhao, Y., Lang, Z., Wang, J., Tang, K., Liu, R., Gong, Z., Zhu, J.-K. (2014) Regulation of Active DNA Demethylation by An α-Crystallin Domain Protein in Arabidopsis. Mol Cell 55: 361-371.

25. Hsu, Y.F., Hsiao, Y.C., Wang, C.S., Zhan, X., Zhang, H., Wang, C.S. (2014) AtRRP6L1, a homologue of conserved yeast exosomal Rrp6p, plays an important role in transcriptional gene silencing in Arabidopsis. Mol Plant 7: 1490-1493.

24. Wang, X., Duan, C.,Tang, K., Wang, B., Zhang, H., Lei, M., Lu, K., Mangrauthia, S.K., Wang, P., Zhu, G., Zhao, Y., Zhu, J.-K. (2013) RNA-binding protein regulates plant DNA methylation by controlling mRNA processing at the intronic heterochromatin-containing gene IBM1. Proc. Natl. Acad. Sci. U.S.A. 110: 15467-15472.

23. Zhang, H., Wang, B., Duan C-G, Zhu, J-K. (2013) Chemical probes in plant epigenetics studies. Plant Signal Behav. 8(9). pii: e25364.

22. Farag, M.A., Zhang H., Ryu C.M. (2013) Dynamic chemical crosstalk between plants and bacteria through airborne signals. J. Chem. Ecol. 39: 1007-1018.

21. Zhang, X., Li, Y., Wu, Z., Polishka, A., Zhang, H., Chinnusamy, V., Lonardi, S., Zhu, J.-K, Liu, R., Jin, H. (2013) Mechanisms of small RNA generation from cis-NATs in response to environmental and developmental cues. Mol. Plant 6: 704-715.

20. Wang, P., Xue, L., Batelli, G., Lee, S., Hou, Y., Oosten V., Zhang, H., Tao, W., Zhu, J.-K. (2013) Quantitative phosphoproteomics identifies SnRK2 protein kinase substrates and reveals the effectors of abscisic acid action. Proc. Natl. Acad. Sci. U.S.A. 110: 11205-11210.

19. Zhang, H., Zhu, J.-K. (2012) Active DNA demethylation in plants and animals. Cold Spring Harb Symp Quant Biol. 77: 161-173.

18. Zhang, H., Deng, X., Miki, D., Culter, S., Oh, J., Zhu, J-K. (2012) Sulfamethazine suppresses epigenetic silencing in Arabidopsis by impairing folate synthesis. Plant Cell 24: 1230-1241.

17. Soon, F-F, Ng, L-M, Zhou, X.E., West, G.M., Kovach, A., Tan, M.H.E.,Suino-Powell, K.M., He,Y., Xu,Y., Chalmers, M.J., Brunzelle, J.S., Zhang, H., Yang, H., Jiang, H., Li, J., Yong, E.-.L, Cutler, S., Zhu, J.-K., Griffin, P.R., Melcher, K., Xu, H.E. (2012) Molecular mimicry regulates ABA signaling by SnRK2 Kinases and PP2C Phosphatases. Science 335: 85-88.

16. Zhang, H., Zhu, J.-K. (2012) Seeing the forest for the trees: a wide perspective of RNA-directed DNA methylation. Genes Dev. 26: 1769-1773.

15. Zhang, X, Xia, J, Li, YE, Barrera-Figueroa, BE, Zhou, X, Gao, S, Lu, L, Niu, D, Chen, Z, Leung, C, Wong, T, Zhang, H, Guo, J, Li, Y, Liu, R, Liang, W, Zhu, J-K, Zhang, W, Jin, H. (2012) Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function. Genome Biol. 13: R20.

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13. Zhang, H., Zhu, J.-K. (2011) RNA-directed DNA methylation. Curr. Opin. Plant Biol. 14: 142-147.

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11. Zhang, H., Murzello, C., Sun, Y., Kim, M.S., Xie, X., Jeter, R.M., Zak, J.C., Dowd, S.E., Paré, P.W. (2010) Choline and Osmotic-Stress Tolerance Induced in Arabidopsis by the Soil Microbe Bacillus subtilis (GB03). Mol. Plant Microbe Interact. 23: 1097–1104.

10. Zhang, H., Sun, Y., Xie, X., Kim, M.S., Dowd, S.E., Paré, P.W. (2009) A soil bacteria regulates plant acquisition of iron via deficiency-inducible mechanisms. Plant J. 58: 568-577.

9. Banchio, E., Xie, X., Zhang, H., Pare?, P.W. (2009) Soil bacteria elevate essential oil accumulation and emissions in Sweet Basil. J. Agric. Food Chem. 57: 653-657.

8. Xie, X., Zhang, H., Paré, P.W. (2009) Sustained growth promotion in Arabidopsis with long-term exposure to the beneficial soil bacterium Bacillus subtilis (GB03). Plant Signal. Behav. 4: 948-953.

7. Medeiros, F.C.L., Resende, M.L.V., Medeiros, F.H.V., Zhang, H., Paré, P.W. (2009) Defense gene expression induced by a coffee-leaf extract formulation in tomato. Physiol. Mol. Plant. Path. 74: 175-183.

6. Zhang, H., Xie, X., Kim, M.S., Kornyeyev, D.A., Holaday, S., Paré, P.W. (2008) Soil bacteria augment Arabidopsis photosynthesis by decreasing glucose sensing and abscisic acid levels in planta. Plant J. 56: 264-273.

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