Self-introduction
I received my graduate and postdoctoral training during an era in which the applications of “Next-Generation Sequencing” (NGS) have grown tremendously. I have applied these techniques to diverse biological questions, driving discovery across the field of plant epigenetics and genomics. My Ph.D. degree in Plant Biology and Master’s degree in Genetics have required extensive training in experimental or “wet lab” approaches; in addition, I earned two other Master’s degrees, one in Statistics and one in Bioinformatics, which greatly facilitated the development of my own “data-driven, hypothesis-generating” style of research.

Research Interests
The application of high-throughput techniques to the study of plant epigenetics has been the primary focus of my research for the past ten years, a field that is the nexus of non-coding RNA, DNA methylation and chromatin modifications. Equipped with a interdisciplinary background that integrates both “wet lab” and “dry lab” techniques, and having worked in three leading academic laboratories, I am able to collaborate effectively and communicate smoothly with experts from different areas, and to incorporate into my work insights from multiple fields. Together with our group members, we are poised to offer our own unique perspective in addressing important biological questions in the big-data era.

Professional Experience
2024 ~ present Professor, Southern University of Science and Technology of China

2016 ~ 2024 Associate Professor, Southern University of Science and Technology of China
2013 ~ 2016 Postdoctoral Researcher ，University of California, Los Angeles, USA. Advisor: Dr. Steven E. Jacobsen

Educational Background
2008 ~ 2013 Ph.D. in Plant Biology and Genomics ,University of Delaware, USA. Advisor: Dr. Blake C. Meyers
2011 ~ 2013 M.S. in Bioinformatics & Computational Biology,University of Delaware, USA
2009 ~ 2011 M.S. in Statistics,University of Delaware, USA
2005 ~ 2008 M.S. in Genetics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, China. Advisor: Dr. Xiaofeng Cao
2001 ~ 2005 B.S. in Biology, University of Science and Technology of China (USTC), China

Honors & Awards
2014 Life Science Research Foundation Postdoctoral Fellowship
2012 W. J. Benton Graduate Student Award, University of Delaware
2007 Academy Scholarship for Outstanding Master Student, Chinese Academy of Sciences
2004 Outstanding Student Scholarship, USTC

Selected Publication

(*co-first authors, #corresponding author)

At SUSTech

1. Liu Z*, Yang j*, Long Y*, Zhang C*, Wang D, Zhang X, Dong W, Zhao L, Liu C, Zhai J#, Wang E#. (2023) Single-nucleus transcriptomes reveal spatiotemporal symbiotic perception and early response in Medicago. Nature Plants. 10.1038/s41477-023-01524-8.

2. Zhang K*, Zhao X*, Zhao Y*, Zhang Z*, Liu Z, Liu Z, Yu Y, Li J, Ma Y, Dong Y, Pang X, Jin X, Li N, Liu B,  Wendel JF, Zhai J, Long Y#, Wang T#, Gong L#. (2023) Cell type–specific cytonuclear coevolution in three allopolyploid plant species. PNAS. 120 (40) e2310881120.

3. Mo W*, Shu Y*, Liu B, Long Y, Li T, Cao X, Deng X#, Zhai J#. (2023) Single-molecule targeted accessibility and methylation sequencing of centromeres, telomeres and rDNAs in Arabidopsis. Nature Plants. 10.1038/s41477-023-01498-7.

4. Liu Z*, Kong X*, Long Y*, Liu S, Zhang H, Jia J, Cui W, Zhang Z, Song X, Qiu L, Zhai J#, Yan Z#. (2023) Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation. Nature Plants. 10.1038/s41477-023-01387-z.

5. Tian S#, Li G, Ning D, Jing K, Xu Y, Yang Y, Fullwood MJ, Yin P, Huang G, Plewczynski D, Wang W, Zhai J, Wang Z, Dai Z, Lin Y, Chen W#, Zheng M#. (2022) MCIBox: A Toolkit for Single-molecule Multi-way Chromatin Interaction Visualization and Micro-Domains Identification. Briefings in Bioinformatics.23(6):bbac380.

6. Zhang H*, Jia J, Zhai J#. (2022) Plant Intron-Splicing Efficiency Database (PISE): exploringsplicing of ~1,650,000 introns in Arabidopsis, maize, riceandsoybean from ~57,000 public RNA-seq libraries. Science China Life Sciences.10.1007/s11427-022-2193-3.

7. Jiang K*#, Guo H, Zhai J#. (2022) Interplay of phytohormones and epigenetic regulation: a recipe for plant development and plasticity. Journal of Integrative Plant Biology. 65(2):381-398.

8. Qin Y, Long Y, Zhai J#. (2022) Genome-wide characterization of nascent RNA processing in plants. Current Opinion in Plant Biology. 69:102294.

9. Jia J*, Lu W*, Liu B, Fang H, Yu Y, Mo W, Zhang H, Jin X, Shu Y, Long Y, Pei Y, Zhai J#. (2022) An atlas of plant full-length RNA reveals tissue-specific and monocots–dicots conserved regulation of poly(A) tail length. Nature Plants. 8(9):1118-1126.

10. Lu D*, feng L*, Zhai J, Li B#, Xi M# (2022) Safeguard DCL2-Dependent 22-nt siRNA generation by DCL1. Biochemical and Biophysical Research Communications. 605, 97-103.

11. Li Z*, Long Y*, Yu Y, Zhang F, Zhang H, Liu Z, Jia J, Mo W, Tian SZ, Zheng M, Zhai J# (2022) Pore-C Simultaneously Captures Genome-wide Multi-way Chromatin Interaction and Associated DNA Methylation Status in Arabidopsis. Plant Biotechnol Journal. 20(6):1009-1011.

12. Yu Y*, Zhang H*, Long Y, Shu Y, Zhai J# (2022) Plant Public RNA-seq Database: a comprehensive online database for expression analysis of ~45 000 plant public RNA-Seq libraries. Plant Biotechnol Journal. 20, 806-808.

13. Lu D, Zhai J#, Xi M# (2022) Regulation of DNA Methylation During Plant Endosperm Development. Frontiers in Genetics. 13:760690.

14. Mo W*, Liu B*, Zhang H, Jin X, Lu D, Yu Y, Liu Y, Jia J, Long Y, Deng X, Cao X, Guo H, Zhai J# (2021) Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing. Genome Biology. 22(1):322.

15. Zhang Y*, Waseem M*, Zeng Z, Xu J, Chen C, Liu Y, Zhai J, Xia R#. (2021) MicroRNA482/2118, a miRNA superfamily essential for both disease resistance and plant development. New Phytologist. doi: 10.1111/nph.17853.

16. Wang Q*, Xue Y*, Zhang L*, Zhong Z, Feng S, Wang S, Xiao L, Yang Z, Harris CJ, Wu Z, Zhai J, Yang M, Li S#, Jacobsen SE#, Du J#. (2021) Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation. Science. 374(6571):1152-1157.

17. Long Y*, Jia J*, Mo W, Jin X, Zhai J#. (2021) FLEP-seq: simultaneous detection of RNA polymerase II position, splicing status, polyadenylation site and poly(A) tail length at genome-wide scale by single-molecule nascent RNA sequencing. Nature Protocols. 16:4355–4381.

18. Hu D*, Yu Y*, Wang C*, Long Y, Liu Y, Feng L, Lu D, Liu B, Jia J, Xia R, Du J, Zhong X, Gong L, Wang K#, Zhai J#. (2021) Multiplex CRISPR-Cas9 editing of DNA methyltransferases in rice uncovers a class of non-CG methylation specific for GC-rich regions. Plant Cell. 33(9):2950-2964.

19. Fang J*, Leichter SM*, Jiang J*, Biswal M, Lu J, Zhang Z, Ren W, Zhai J, Cui Q, Zhong X#, Song J#. (2021) Substrate deformation regulates DRM2-mediated DNA methylation in plants. Science Advances. 7(23):eabd9224.

20. Qiao Y*#, Xia R, Zhai J, Hou Y, Feng L, Zhai Y, Ma W#. (2021) Small RNAs in Plant Immunity and Virulence of Filamentous Pathogens. Annual Review of Phytopathology. doi.org/10.1146/annurev-phyto-121520-023514.

21. Chen C*, Li J*, Feng J, Liu B, Feng L, Yu X, Li G, Zhai J, Meyers BC, Xia R#. (2021) sRNAanno—a database repository of uniformly annotated small RNAs in plants. Horticulture Research. 8:45.

22. Long Y*, Liu Z*, Jia J*, Mo W, Fang L, Lu D, Liu B, Zhang H, Chen W, Zhai J#. (2021) FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants. Genome Biology. doi.org/10.1186/s13059-021-02288-0.

23. Yu Y, Zhai J#. (2020) The chromatin will never forget. Nature Plants. doi.org/10.1038/s41477-020-00803-y.

24. Wang C*, Ji W*, Liu Y, Zhou P, Meng Y, Zhang P, Wen J, Mysore KS, Zhai J, Young ND, Tian Z, Niu L, Lin H#. (2020) The antagonistic MYB paralogs RH1 and RH2 govern anthocyanin leaf markings in Medicago truncatula. New Phytologist. doi.org/10.1111/nph.17097.

25. Jia J*, Ji R*, Li Z, Yu Y, Nakano M, Long Y, Feng L, Qin C, Lu D, Zhan J, Xia R, Meyers BC, Liu B#, Zhai J#. (2020) Soybean Dicer-Like 2 Regulates Seed Coat Color via Production of Primary 22-nt Small Interfering RNAs from Long Inverted Repeats. Plant Cell. doi:10.1105/tpc.20.00562.

26. Zhang H*, Zhang F*, Yu Y*, Feng L, Jia J, Liu B, Li B, Guo H, Zhai J#.(2020) A comprehensive online database for exploring ∼20,000 public Arabidopsis RNA-Seq libraries. Molecular Plant. 13(9):1231-1233.

27. Jia J*, Long Y*, Zhang H, Li Z, Liu Z, Zhao Y, Lu D, Jin X, Deng X, Xia R, Cao X, Zhai J#. (2020) Post-transcriptional splicing of nascent RNA contributes to widespread intron retention in plants. Nature Plant. 6(7):780-788.

28. Liu Q*#, Bischof S*, Harris CJ Zhong Z, Zhan L, Nguyen C, Rashoff A, Barshop WD, Sun F, Feng S, Potok M, Gallego-Bartolome J, Zhai J, Wohlschlegel JA, Carey MF, Long JA, Jacobsen SE#. (2020) The characterization of Mediator 12 and 13 as conditional positive gene regulators in Arabidopsis. Nature Communications. 11(1):2798.

29. Wu H*, Li B*, Iwakawa HO, Pan Y, Tang X, Ling-Hu Q, Liu Y, Sheng S, Feng L, Zhang H, Zhang X, Tang Z, Xia X, Zhai J, Guo H#. (2020) Plant 22-nt siRNAs mediate translational repression and stress adaptation. Nature. 581(7806):89-93.

30. Bailey-Serres J, Zhai J, Seki M (2020) The Dynamic Kaleidoscope of RNA Biology in Plants. Plant Physiology. 182(1):1-9.

31. Feng L*, Zhang F*, Zhang H, Zhao Y, Meyers BC, Zhai J# (2020) An online database for exploring over 2,000 Arabidopsis small RNA libraries. Plant Physiology. 182(2):685-691.

32. Ricci W A, Lu Z, Ji L, Marand AP, Ethridge CL, Murphy NG, Noshay JM, Galli M, Guerra MKM, Tatché MC, Johannes F, Rowley MJ, Corce VG, Zhai J, Scanlon MJ, Buckler ES, Gallavotti A, Springer NM, Schmitz RJ, Zhang X (2019). Widespread long-range cis-regulatory elements in the maize genome. Nature Plants, 1-13

33. Hou Y, Zhai Y, Feng L, Karimi HZ, Rutter BD, Zeng L, Choi DS, Zhang B, Gu W, Chen X, Ye W, Innes RW, Zhai J, Ma W (2019) Cis-directed cleavage and nonstoichiometric abundances of 21-nt reproductive phasiRNAs in grasses. Cell Host Microbe 25(1):153-165

34. Tamim S, Cai Z, Mathioni S, Zhai J, Teng C, Zhang Q, Meyers BC (2018) Cis-directed cleavage and nonstoichiometric abundances of 21-nt reproductive phasiRNAs in grasses. New Phytologist 220(3):865-877

35. Liu W, Duttke SH, Hetzel J, Groth M, Feng S, Gallego-Bartolome J, Zhong Z, Kuo HY, Wang Z, Zhai J, Chory J, Jacobsen SE (2018) RNA-directed DNA methylation involves co-transcriptional small-RNA-guided slicing of polymerase V transcripts in Arabidopsis. Nature Plants. 4(3):181-188

36. Zhang Y*, Harris CJ*, Liu Q*, Liu W, Ausin I, Long Y, Xiao L, Feng L, Chen X, Xie Y, Chen X, Zhan L, Feng S, Li JJ, Wang H#, Zhai J#, Jacobsen SE# (2018) Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis. PNAS. 115(5) :E1069-E1074  

37. Fang H, Liu Z, Long Y, Liang Y, Jin Z, Zhang L, Liu D, Li H, Zhai J#, Pei Y# (2017) The Ca2+/CaM2 binding transcription factor TGA3 elevates LCD expression and H2S production to bolster Cr6+ tolerance in Arabidopsis. The Plant Journal 91(6):1038-1050

38. Kuo HY, Jacobsen E, Long Y, Chen X, Zhai J# (2017) Characteristics and processing of Pol IV transcripts in Arabidopsis. Journal of Genetics and Genomics 44(1):3-6.

39. Nan GL, Zhai J, Arikit S, Morrow D, Fernandes J, Mai L, Nguyen N, Meyers BC, Walbot V (2016), a master basic helix-loop-helix factor, regulates the specification and development of tapetum in maize Development dev.140673

40. Ausin I, Feng S, Yu C, Liu W, Kuo HY, Jacobsen EL, Zhai J, Gallego-Bartolome J, Wang L, Egertsdotter U, Street NR, Jacobsen SE, Wang H (2016) DNA methylome of the 20-gigabase Norway spruce genome. PNAS 113(50):E8106-13

At previous institutions

First author research papers:

41. Zhai J*, Bischof S*, Wang H, Feng S, Lee T, Teng C, Chen X, Park SY, Liu L, Gallego-Bartolome J, Liu W, Henderson I, Meyers BC, Ausin I, Jacobsen SE (2015) A ‘One precursor, One siRNA’ model for Pol IV-dependent siRNA Biogenesis. Cell 163, 445–455

42. Zhai J*, Zhang H*, Arikit S, Huang K, Nan G, Walbot V, Meyers BC (2015) Spatiotemporal and cell-type dependent phasiRNA biogenesis in maize male reproduction. PNAS 112(10): 3146-51

43. Zhai J, Zhao Y, Simon SA, Huang S, Petsch K, Arikit S, Pillay L, Ji L, et al. (2013) Plant microRNAs display differential 3’-truncation and tailing, modifications which are ARGONAUTE1-dependent and conserved across species. The Plant Cell 25(7):2417-28

44. Zhai J, Jeong D-H, Paoli ED, Park S, Rosen BD, Li Y, González AJ, Yan Z, et al. (2011) MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. Genes & Development 25(23):2540-53. 

45. Zhai J, Liu J, Liu B, Li P, Meyers BC, Chen X, Cao X. (2008) Small RNA-directed epigenetic natural variation in Arabidopsis thaliana. PLoS Genetics 4, e1000056.

46. Song X*, Li P*, Zhai J*, Zhou M, Ma L, Liu B, Jeong DH, Cao S, Cui X et al. (2011) Roles of DCL4 and DCL3b in rice phased small RNA biogenesis. The Plant Journal 69, 462-474.

47. Zhai J, Arikit S, Simon SA, Kingham B, Meyers BC (2013) Rapid Construction of Parallel Analysis of RNA End (PARE) Library for Illumina Hi-Seq sequencing. Methods S1046-2023(13)00237-5

48. Zhai J and Meyers BC (2013). Deep Sequencing from hen1 Mutants to Identify Small RNA 3' Modifications. Cold Spring Harb Symp Quant Biol 1943-4456

Co-authored papers (in reverse-chronological order):

49. Yu Y, Ji L, Le B, Zhai J, Chen J, Luscher E, Gao L, Liu C, Cao X, Mo B, Ma J, Meyers BC, Chen X (2017) ARGONAUTE10 promotes the degradation of miR165/6 through the SDN1 and SDN2 exonucleases in Arabidopsis. PLoS Biology. 15(2): e2001272.

50. Groth M, Moissiard G, Wirtz M, Wang H, GarciaSalinas G, Ramos-Parra PA, Bischof S, Feng S, Cokus SJ, John A, Smith DC, Zhai J, Hale CJ, Long JA, Hell R, Garza RID, Jacobsen SE (2016) MTHFD1 controls DNA methylation in Arabidopsis. Nature Communication 2016 Jun 13;7:11640

51. Wang H, Beyene G, Zhai J, Feng S, Fahlgren N, Taylor N, Bart R, Carrington JC, Jacobsen SE, Ausin I (2015) CG gene body DNA methylation changes and evolution of duplicated genes in cassava. PNAS 112(44):13729-34

52. Yan Z, Hossain MS, Valdés-López O, Hoang NT, Zhai J, Wang J, Libault M, Joshi T, Brechenmacher L, Findley S, Qiu L, Sherrier DJ, Meyers BC, Xu D, Stacey G (2015) Identification and functional characterization of soybean root hair microRNAs expressed in response to Bradyrhizobium japonicum infection. Plant Biotechnology Journal 10.1111/pbi.12387

53. Tu B, Xu C, Liu L, Zhai J, Li S, Lopez MA, Zhao Y, Yu Y, Ren G, Yu B, Li S, Meyers BC, Mo B, Chen X (2015) Distinct and cooperative activities of HESO1 and URT1 nucleotidyl transferases in microRNA turnover in Arabidopsis. PLoS Genetics 11(4): e1005119

54. Yan Z, Hossain MS, Arikit S, Valdé O, Zhai J, Wang J, Libault M, Ji T, Qiu L, Meyers BC, Stacey G (2015) Identification of MicroRNAs and their mRNA targets during soybean nodule development: Functional analysis of the role of miR393* in soybean nodulation. New Phytologist 10.1111/nph.13365

55. Zhao M, Cai C, Zhai J, Lin F, Li L, Shreve J, Thimmapuram J, Hughes TJ, Meyers BC, Ma J (2015) Coordination of MicroRNAs, PhasiRNAs, and NB-LRR Genes in Immune Responses: Insights from Analyses of Soybean Rps Gene Near-Isogenic Lines. The Plant Genome 10.3835

56. Cantó-Pastor A, Mollá-Morales A, Ernst E, Dahl W, Zhai J, Yan Y, Meyers BC, Shanklin J, Martienssen RA (2015) Efficient transformation and artificial miRNA gene silencing in Lemna minor. Plant Biology 10.1111/plb.12215

57. Arikit S, Xia R, Kakrana A, Huang K, Zhai J, Yan Z, Valdés-López O, Prince S, Musket TA, Nguyen HT, Stacey G, Meyers BC (2014) An atlas of soybean small RNAs demonstrates regulation by phased siRNAs of hundreds of coding genes. The Plant Cell 26: 4584-4601

58. Feng S, Cokus SJ, Schubert V, Zhai J, Pellegrini M, Jacobsen SE (2014) Genome-wide Hi-C analyses in wild type and mutants reveal high-resolution chromatin interactions in Arabidopsis. Molecular Cell 55(5):694-707

59. Wong J, Gao L, Yang Y, Zhai J, Arikit S, Yu Y, Duan S, Xiong Q, Yan J, Li S, Liu R, Wang Y, Tang G, Meyers BC, Chen X, Ma W (2014) Roles of Small RNAs in Soybean Defense against Phytophthora sojae Infection. The Plant Journal 10.1111/tpj.12590

60. Schapire AL*, Bologna NG*, Moro B, Zhai J, Meyers BC, Palatnik JF#. (2014) Reprint of: Construction of Specific Parallel Amplification of RNA Ends (SPARE) libraries for the systematic identification of plant microRNA processing intermediates. Methods. 67(1):36-44

61. Creasey KM, Zhai J, Borges F, Van EF, Meyers BC, Martienssen RA (2014) miRNAs trigger widespread epigenetically-activated siRNAs from transposons in Arabidopsis. Nature 508 (7496):411-5

62. Wei L, Gu L, Song X, Cui X, Lua Z, Zhou M, Wang L, Hu F, Zhai J, Meyers BC, Cao X (2014) Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice. PNAS 111(10):3877-82

63. Schapire A, Bologna NG, Moro B, Zhai J, Meyers BC, Palatnik JF (2013) Construction of Specific Parallel Amplification of RNA Ends (SPARE) libraries for the systematic identification of plant microRNA processing intermediates. Methods doi:10.1016/j.ymeth.2013.08.032

64. Jeong DH, Schmidt SA, Rymarquis LA, Park S, Ganssmann M, German MA, Accerbi M, Zhai J, Paoli ED, Fahlgren N, Fox SE, Garvin DF, Mockler TC, Carrington JC, Meyers BC, and Green PJ (2013) Parallel Analysis of RNA Ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon. Genome Biology 14(12):R145

65. Amborella Genome Project. (2013) The Amborella Genome and the Evolution of Flowering Plants. Science 342(6165):1241089

66. Jeong DH, Thatcher SR, Brown RS, Zhai J, Park S, Meyers BC, Green PJ (2013) Comprehensive investigation of miRNAs enhanced by analysis of sequence variants, expression patterns, AGO loading and target cleavage. Plant Physiology 162(3):1225

67. Raman V, Simon SA, Romag A, Demirci F, Mathioni SM, Zhai J, Meyers BC, Donofrio NM (2013) Physiological stressors and invasive plant infections alter the small RNA transcriptome of the rice blast fungus Magnaporthe oryzae. BMC Genomics 14:326

68. Bologna NG, Schapire AL, Zhai J, Chorostecki U, Boisbouvier J, Meyers BC, Palatnik J (2013) Multiple RNA recognition patterns during microRNA biogenesis in plants. Genome Research (10):1675-89

69. Arikit S, Zhai J, Meyers BC (2013) Biogenesis and function of rice small RNAs from non-coding RNA precursors. Current Opinion in Plant Biology 16(2):170-9. 

70. Lee TF, Gurazada SG, Zhai J, Li S, Simon SA, Matzke MA, Chen X, Meyers BC (2012) RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats. Epigenetics 7(7):781-95

71. Zhao Y, Yu Y, Zhai J, Ramachandran V, Dinh T, Meyers BC, Mo B, Chen X (2012) HESO1, a nucleotidyl transferase in Arabidopsis, uridylates unmethylated miRNAs and siRNAs to trigger their degradation. Current Biology 22(8):689-94

72. The_International_Medicago_Initiative (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480, 520-524

73. Jeong D-H, Park S, Zhai J, Gurazada SGR, Paoli ED, Meyers BC, Green PJ. (2011) Massive analysis of rice small RNAs: Mechanistic implications of regulated miRNAs and variants for differential target RNA cleavage. The Plant Cell 23(12):4185-207.

74. Yu B, Bi L, Zhai J, Agarwal M, Li S, Wu Q, Ding SW, Meyers BC, Vaucheret H, Chen X. (2010) siRNAs compete with miRNAs for methylation by HEN1 in Arabidopsis. Nucleic Acids Research 38(17):5844-5850.

75. The International Brachypodium Initiative. (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463(7282):763-768.

76. Meyers BC, Simon SA, Zhai J. (2010) MicroRNA processing: battle of the bulge. Current Biology 20(2):R68-70. (review)

77. Lee TF, Zhai J, Meyers BC. (2010) Conservation and divergence in eukaryotic DNA methylation. PNAS 107(20):9027-9028. (review)

78. Simon SA, Zhai J, Nandety RS, McCormick KP, Zeng J, Mejia D, Meyers BC. (2009) Short-read sequencing technologies for transcriptional analyses. Annual Review Plant Biology 60:305-333. (review)

79. Park W, Zhai J, Lee JY. (2009) Highly efficient gene silencing using perfect complementary artificial miRNA targeting AP1 or heteromeric artificial miRNA targeting AP1 and CAL genes. Plant Cell Rep 28(3):469-480.

80. De Paoli E, Dorantes-Acosta A, Zhai J, Accerbi M, Jeong DH, Park S, Meyers BC, Jorgensen RA, Green PJ. (2009) Distinct extremely abundant siRNAs associated with cosuppression in petunia. RNA 15(11):1965-1970.

81. Simon SA, Zhai J, Zeng J, Meyers BC. (2008) The cornucopia of small RNAs in plant genomes. Rice 1(1):52-62. (review)

82. Pei Y, Niu L, Lu F, Liu C, Zhai J, Kong X, Cao X. (2007) Mutations in the Type II protein arginine methyltransferase AtPRMT5 result in pleiotropic developmental defects in Arabidopsis. Plant Physiology 144, 1913-1923.

83. Ding Y, Wang X, Su L, Zhai J, Cao S, Zhang D, Liu C, Bi Y, Qian Q, Cheng Z, et al. (2007) SDG714, a histone H3K9 methyltransferase, is involved in Tos17 DNA methylation and transposition in rice. The Plant Cell 19, 9-22.

84. Xia R, Wang J, Liu C, Wang Y, Zhai J, Liu J, Hong X, Cao X, Zhu JK, Gong Z. (2006) ROR1/RPA2A, a putative replication protein A2, functions in epigenetic gene silencing and in regulation of meristem development in Arabidopsis. The Plant Cell 18, 85-103. 1(1):52-62.

Patents

1. Meyers BC, Zhai J, Sherrier J. Use of phased small RNAs for suppression of plant defense and other plant genes. US Patent 20140356961

2. Meyers BC, Zhai J, Walbot V. Regulatory non-coding RNAs as determinants of male sterility in grasses and other monocotyledonous plants. PCT/US2014/060081

3. Zhai J, Long Y, Xiao L, Zhang F, Lu D, Liu Z. A new library construction method for single-cell genome sequencing. ZL201911311804.2

4. Zhai J, Xiao L, Mo W, Long Y. The method for barcoded gel beads preparation and its application. 202010047034.1

5. Zhai J, Long Y, Jia J, Wen J, Lu D. The Preparation Methods and Applications of Novel Coronavirus-Like Particles. 202110333400.4