50．Hong, W. J‡., Moon, H.‡, Shin, C.*, & Jung, K. H.* (2024) CAFRI-Arabidopsis: An Intuitive Web-Based Functional Redundancy Inspector in Arabidopsis. Journal of Plant Biology 67, 99-108. ‡ Equal contributors, * Corresponding authors
49．Park, M.‡, Shin, S.‡, Moon, H., Choi, W., & Shin, C.* (2024) Analysis of the global transcriptome and miRNAome associated with seed dormancy during seed maturation in rice (Oryza sativa L. cv. Nipponbare). BMC Plant Biology 24, 215. ‡ Equal contributors, * Corresponding authors
48．Lee, H.‡, Park, M.‡, Kweon, Y., Lee, D., & Shin, C.* (2024) Targeted dsRNA-mediated suppression of Phytophthora infestans infection via Avr3a. Applied Biological Chemistry 67, 97. ‡ Equal contributors, * Corresponding authors
47．Kakumani, P. K., Ko, Y., Ramakrishna, S., Christopher, G., Dodgson, M., Shrinet, J., Harvey L. M., Shin, C., Simard, M. J. (2023) CSDE1 promotes miR-451 biogenesis. Nucleic Acids Research 51, 9385-9396.
46．Lee, J.‡, Lee, S‡., Park, K., Shin, S., Frost, J. M‡., Hsieh, P. H.‡, Shin, C., Fischer, F. R., Hsieh, T.F., Choi, Y.* (2023) Distinct regulatory pathways contribute to dynamic CHH methylation patterns in transposable elements throughout Arabidopsis embryogenesis. Frontiers in Plant Science 14, 1204279. ‡ Equal contributors, * Corresponding authors
45．Park, M.‡, Kweon, Y.‡, Eom, J., Oh, M., & Shin, C.* (2023) Development of multi-target dsRNAs targeting PcNLP gene family to suppress Phytophthora capsici infection in Nicotiana benthamiana. Applied Biological Chemistry 66, 69. ‡ Equal contributors, * Corresponding authors
44．Park, M.‡, Kweon, Y.‡, Lee, D., Shin, C.* (2023) Suppression of Phytophthora capsici using double-stranded RNAs targeting NLP effector genes in Nicotiana benthamiana. Applied Biological Chemistry 66, 5. ‡ Equal contributors, * Corresponding authors
43．Lee, J.‡, Shin, S.‡, Lee, S. K., Park, K., Gill, H., Hyun, Y., Jeong, C., Jeon, J. S., Shin, C.*, Choi, Y.* (2023) Contribution of RdDM to the ecotype-specific differential methylation on conserved as well as highly variable regions between Arabidopsis ecotypes. BMC Genomics 24, 36. ‡ Equal contributors, * Corresponding authors
42．Park, M., Um, T. Y., Jang, G., Choi, Y. D., Shin, C.* (2022) Targeted gene suppression through double-stranded RNA application using easy-to-use methods in Arabidopsis thaliana. Applied Biological Chemistry 65, 4. * Corresponding authors
41．Kweon, Y.‡, Fang, M‡, Shin, S.‡, Lee, D., Kim, K. H.*, Shin, C.* (2022) Sequence optimization and multiple gene-targeting improve the inhibitory efficacy of exogenous double-stranded RNA against pepper mottle virus in Nicotiana benthamiana. Applied Biological Chemistry 65, 87. * Corresponding authors
40．Kim, S.‡, Kim, S.‡, Chang, H.R.‡, Kim, D.‡, Park, J., Son, N., Park, J., Yoon, M., Chae, G., Kim., Y.K., Kim., V.N., Nam, J.-W., Shin, C.*, Baek, D.* (2021) The regulatory impac of RNA-binding proteins on microRNA targeting. Nature Communications. 12, 5057 ‡ Equal contributors,* Corresponding authors
39．Paul, P., Chhapekar, S.S., Rameneni, J.J., Oh, S.H., Dhandapani, V., Subburaj, S., Shin, S., Ramchiary, N., Shin, C., Choi, S.R., Lim, Y.P. (2021) MiR1885 Regulates Disease Tolerance Genes in Brassica rapa during Early Infection with Plasmodiophora brassicae. Int. J. Mol. Sci. 22, 9433.
38．Park, M., Choi, W., Shin, S., Moon, H., Lee, D., Gho, Y.S., Jung, K.H., Jeon, J.S., Shin, C. (2021) Identification of Genes and MicroRNAs Affecting Pre-harvest Sprouting in Rice (Oryza sativa L.) by Transcriptome and Small RNAome Analyses. Frontiers in Plant Science. 12, 727302
37．Park, S., Kang, I., Shin, C. (2021) MicroRNA clustering on the biogenesis of suboptimal microRNAs. Applied Biological Chemistry 64, 51
36．Kang, I., Kim, W., Lim, J.Y., Lee, Y., Shin, C. (2021) Organ-specific transcriptome analysis reveals differential gene expression in different castes under natural conditions in Apis cerana. Scientific Reports. 11, 11267.
35．Yoon, J.‡, Fang, M.‡, Lee, D., Park, M., Kim, K.H.*, Shin, C.* (2021) Double-stranded RNA confers resistance to pepper mottle virus in Nicotiana benthamiana. Applied Biological Chemistry 64, 1-8. ‡ Equal contributors,* Corresponding authors
34．Lee, D.‡, Park, D.‡, Park, J.H., Kim, J.H.*, Shin, C.* (2019) Poly(A)-specific ribonuclease sculpts the 3' ends of microRNAs. RNA. 25, 388-405. ‡ Equal contributors, * Corresponding authors
33．Seo, E.‡, Kim, T.‡, Park, J. H., Yeom, S., Kim, S., Seo, M., Shin, C.*, Choi, D.* (2018) Genome-wide comparative analysis in Solanaceous species, reveals evolution of microRNAs targeting defense genes in Capsicum spp., DNA Research. 25, 561-575. ‡ Equal contributors, * Corresponding authors
32．Shin, S., Jeong, J. S., Lim, J.Y., Kim, T., Park, J. H., Kim, J., Shin, C. (2018) Transcriptomic analyses of rice (Oryza sativa) genes and non-coding RNAs under nitrogen starvation using multiple omics technologies. BMC Genomics. 19, 532.
31．Kang, I., Choi, Y., Jung, S., Lim, J. Y., Lee, D., Gupta, S., Moon, W., Shin, C. (2018) Identification of target genes regulated by the Drosophila histone methyltransferase Eggless reveals a role of Decapentaplegic in apoptotic signaling. Scientific Reports. 8, 7123.
30．Kim, Y., Kang, Y. G., Choe, J. Y., Lee, D., Shin, C., Hong, S. W., Lee, D. K. (2018) RNA interference-mediated gene silencing by branched tripodal RNAs does not require dicer processing. Nucleic Acid Therapeutics. 28, 44-49.
29．Lee, D. and Shin, C. (2018) Emerging roles of DROSHA beyond primary microRNA processing. RNA Biology. 15, 186-193.
28．Kim, H., Han, Y., Na, H., Kim, J., Kim, T., Kim, H., Shin, C., Lee, J. W., Lee, M. (2017) Liver-specific deletion of RORα aggravates diet-induced nonalcoholic steatohepatitis by inducing mitochondrial dysfunction. Scientific Reports. 7, 16041.
27．Kim, T., Park, J. H., Lee, S., Kim, S., Kim, J., Lee, J., and Shin, C. (2017) Small RNA transcriptome of Hibiscus syriacus provides insights into the potential influence of microRNAs in flower development and terpene synthesis. Mol. Cells. 40, 587-597.
26．Lee, D., Nam, J., Shin, C. (2017) Drosha targets its own transcript to modulate alternative splicing. RNA. 23, 1035-1047.
25．Park, J. H. and Shin, C. (2017) Non-canonical targets play an important role in microRNA stability control mechanisms. BMB Rep. 50, 158-159.
24．Park, J. H., Shin, S., and Shin, C. (2017) Non-canonical targets destabilize microRNAs in human Argonautes. Nucleic Acids Res. 45, 1569-1583. *Selected as a NAR Breakthrough paper.
23．Son, H., Park, A. R., Lim, J. Y., Shin, C., Lee, Y. W. (2017) Genome-wide exonic small interfering RNA-mediated gene silencing regulates sexual reproduction in the homothallic fungus Fusarium graminearum. PLoS Genet. 13, e1006595.
22．Zhang, F., Wang, L., Lim, J. Y., Kim, T., Pyo, Y., Sung, S., Shin, C., and Qiao, H. (2016) Phosphorylation of CBP20 Links MicroRNA to Root Growth in the Ethylene Response. PLoS
Genet. 12, e1006437.
21．Kim, S., Lee, J. H., Kang, I., Hyun, S., Yu, J., and Shin, C. (2016) An Amphiphilic Peptide Induces Apoptosis Through the miR29b-p53 Pathway in Cancer Cells. Mol Ther Nucleic Acids. 5, e330.
20．Shin, S. and Shin, C. (2016) Regulatory non-coding RNAs in plants: potential gene resources for the improvement of agricultural traits. Plant Biotechnol. Rep. 10, 35-47.
19．Park, J. H. and Shin, C. (2015) Slicer-independent mechanism drives small-RNA strand separation during human RISC assembly. Nucleic Acids Res. 43, 9418-9433.
18．Jayakodi, M., Jung, J. W., Park, D. R., Ahn, Y. J., Lee, S. C., Shin, S., Shin, C., Yang, T. J., and Kwon, H. W. (2015) Genome-wide characterization of long intergenic non-coding RNAs (lincRNAs) provides new insight into viral diseases in honey bees Apis cerana and Apis mellifecra. BMC Genomics. 16, 680.
17．Park, J. H. and Shin, C. (2015) The role of plant small RNAs in NB-LRR regulation. Brief Funct Genomics. 14, 268-274.
16．Lee, H. J., Park, Y. J., Kwak, K. J., Kim, D. H., Park, J. H., Lim, J.Y., Shin, C., Yang, K. Y., Kang, H. (2015) MicroRNA844-guided Downregulation of Cytidinephosphate Diacylglycerol Synthase3 (CDS3) mRNA Affects the Response of Arabidopsis thaliana to Bacteria and Fungi. Mol Plant Microbe Interact. 28, 892-900.
15．Eichhorn, S. W., Guo, H., McGeary, S. E., Rodriguez-Mias, R.A., Shin, C., Baek, D., Hsu, S. H., Ghoshal, K., Villén, J., and Bartel, D.P. (2014) mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues. Mol Cell. 56, 104-115.
14．Park, J. H.‡, Hong, S. W.‡, Yun, S., Lee, D. K.*, and Shin, C.* (2014) Effect of siRNA with an asymmetric RNA/dTdT overhang on RNA interference activity. Nuclei Acid Ther. 24, 364-371. ‡ Equal contributors, * Corresponding authors
13．Park, J. H. and Shin, C. (2014) MicroRNA-directed cleavage of targets: mechanism and experimental approaches. BMB Rep. 47, 417-423.
12．Hong, S. W.‡, Park, J. H.‡, Yun, S., Lee, C. H., Shin, C.*, and Lee, D.K.* (2014) Effect of the guide strand 3'-end structure on the gene-silencing potency of asymmetric siRNA. Biochem J. 461, 427-434. ‡ Equal contributors, * Corresponding authors
11．Kim, S., Park, M., Yeom, S., Kim, Y., Lee, J. M., Lee, H., Seo, E., Choi, J., Cheong, K., Kim, K., Jung, K., Lee, G., Oh, K., Bae, D., Kim, S., Lee, H., Kim, S., Kim, M., Kang, B., Jo, Y. D., Yang, H., Jeong, H., Kang, W., Kwon, J., Shin, C., Lim, J. Y., Park, J. H., et. al. Lee, Y., and Doil Choi. (2014) Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat. Genet. 46, 270-278.
10．Hwang, D. G.‡, Park, J. H.‡, Lim, J. Y.‡, Kim, D., Choi, Y., Kim, S., Reeves, G., Yeom, S. I., Lee, J. S., Park, M., Kim, S., Choi, I. Y., Choi, D., and Shin, C. (2013) The hot pepper (Capsicum annuum) microRNA transcriptome reveals novel and conserved targets: a foundation for understanding MicroRNA functional roles in hot pepper. PLoS One 8, e64238.
‡ Equal contributors
09．Lee, J.‡, Kim, D. I.‡, Park, J. H.‡, Choi, I. Y., and Shin, C. (2013) MiRAuto: an automated user-friendly microRNA prediction tool utilizing plant small RNA sequencing data. Mol. Cells 35, 342-347. ‡ Equal contributors
08．Lee, T. Y., Chang, C. I., Lee, D., Hong, S. W., Shin, C., Li, C. J., Kim, S., Haussecker, D., and Lee, D. K. (2013) RNA interference-mediated simultaneous silencing of four genes using cross-shaped RNA. Mol. Cells 35, 320-326.
07．Park, J. H., Ahn, S., Kim, S., Lee, J., Nam, J. W.*, and Shin, C.* (2013) Degradome sequencing reveals an endogenous microRNA target in C. elegans. FEBS Lett. 587, 964-969. * Corresponding authors
06．Kim, J.‡, Park, J. H.‡, Lim, C. J., Lim, J. Y., Ryu, J. Y., Lee, B. W., Choi, J. P., Kim, W. B., Lee, H. Y., Choi, Y., Kim, D., Hur, C. G., Kim, S., Noh, Y. S., Shin, C.*, and Kwon, S. Y.* (2012) Small RNA and transcriptome deep sequencing proffers insight into floral gene regulation in Rosa cultivars. BMC Genomics 13, 657. ‡ Equal contributors, * Corresponding authors
05．Lim, J. S., Choi, B. S., Lee, J. S., Shin, C., Yang, T. J., Rhee, J. S., Lee, J. S., and Choi, I. Y. (2012) Survey of the application of NGS to whole-genome sequencing and expression profiling. Genomics Inform. 10, 1-8.
04．Lee, D. and Shin, C. (2012) MicroRNA-target interactions: new insights from genome-wide approaches. Ann. N. Y. Acad. Sci. 1271, 118-128.
03．Garcia, D. M., Baek, D., Shin, C., Bell, G. W., Grimson, A., and Bartel, D. P. (2011) Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat. Struct. Mol. Biol. 18, 1139-1146.
02．Flygare, J., Rayon Estrada, V., Shin, C., Gupta, S., and Lodish, H. F. (2011) HIF1alpha synergizes with glucocorticoids to promote BFU-E progenitor self-renewal. Blood 117, 3435-3444.
01．Shin, C., Nam, J. -W., Farh, K. K. -H., Chiang, H. R., Shkumatava, A., and Bartel, D. P. (2010) Expanding the microRNA targeting code: functional sites with centered pairing. Mol. Cell 38, 789-802.