1. Kim YK, Heo I, Kim VN. (2010) Modifications of small RNAs and their associated proteins. Cell. 143:703-709.
2. Kim YK. (2015) Extracellular microRNAs as Biomarkers in Human Disease. Chonnam Med J. 51:51-57.
3. Kwon DH, Kim YK, Kook H. (2017) New Aspects of Vascular Calcification: Histone Deacetylases and Beyond. J Korean Med Sci. 32:1738-1748.
4. Kim YK, Nam KI, Song J. (2018) The Glymphatic System in Diabetes-Induced Dementia. Front Neurol. 9:867.
5. Kim YK, Song J. (2018) The Role of Long Noncoding RNAs in Diabetic Alzheimer's Disease. J Clin Med. 7:E461.
6. Kim YK, Kook H. (2019) Diverse roles of noncoding RNAs in vascular calcification. Arch Pharm Res. 42:244-251. (*co-corresponding authors)
7. Kwon DH, Ryu J, Kim YK*, Kook H*. (2020) Roles of Histone Acetylation Modifiers and Other Epigenetic Regulators in Vascular Calcification. Int J Mol Sci. 21:3246. (*co-corresponding authors)
8. Kim YK. (2020) RNA Therapy: Current Status and Future Potential. Chonnam Med J. 56:87-93.
9. Kim YK, Song J. (2020) Potential of Glucagon-Like Peptide 1 as a Regulator of Impaired Cholesterol Metabolism in the Brain. Adv Nutr. 11:1686-1695.
10. Kim YK, Kim OY, Song J. (2020) Alleviation of Depression by Glucagon-Like Peptide 1 Through the Regulation of Neuroinflammation, Neurotransmitters, Neurogenesis, and Synaptic Function. Front Pharmacol. 11:1270.
11. Ryu J, Ahn Y, Kook H, Kim YK. (2020) The roles of non-coding RNAs in vascular calcification and opportunities as therapeutic targets. Pharmacol Ther. 8:107675. (*co-corresponding authors)
12. Song J*, Kim YK*. (2021) Animal models for the study of depressive disorder. CNS Neurosci Ther. 27:633. (*co-corresponding authors)
13. Song J, Kim YK*. (2021) Targeting non-coding RNAs for the treatment of retinal diseases. Mol Ther Nucleic Acids. 24:284.
14. Kim YK, Song J*. (2021) Therapeutic applications of resveratrol in hepatic encephalopathy through its regulation of the microbiota, brain edema, and inflammation. J Clin Med. 10:3819.
15. Kim YK. (2022) RNA therapy: rich history, various applications and unlimited future prospects. Exp Mol Med. 54:455-465.
16. Kim YK. (2022) Circular RNAs as a promising biomarker for heart disease. Biomed. Pharmacother. 156:113935.
17. Lim YH, Kim YK*. (2023) Roles of non-coding RNAs in intercellular crosstalk in cardiovascular diseases. Korean J Physiol Pharmacol. 27:289.
18. Kim YK*. (2023) RNA therapy. Exp Mol Med. 55:1281.
19. Kim YK*, Han J. (2024) Nobel-winning microRNA, the micromaestro of gene silencing. Mol Cells. 47:100123.
20. Song J, Kim YK*. (2025) Regulatory Functions of Long Non-coding RNAs and Circular RNAs in the Molecular Pathogenesis of Autism Spectrum Disorder. Cell Mol Neurobiol. doi: 10.1007/s10571-025-01638-x.
1. Kim YK, Yeom S, Choi SY, Ryu Y, Jeong D, Jo D, Lee DH, Song J. (2025) The Change of Noncoding RNA Expression in Olfactory Bulb of Hepatic Encephalopathy Mouse Model: Transcriptomic Analysis and Cellular Analysis. CNS Neurosci Ther. 31(9):e70596.
2. Choe N, Jeong A, Joung H, Jeong D, Kim YK*, Kook H*, Kwon DH*. (2025) Circular RNA circAtxn10 regulates skeletal muscle cell differentiation by targeting miR-143-3p and Chrna1. Korean J Physiol Pharmacol. 29(5):637. (*co-corresponding authors)
3. Sun EG, Choi JN, Park MR, Kim DH, Sung M, Shim HJ, Hwang JE, Bae WK, Jung C, Kim YK*, Chung IJ*, Cho SH*. (2025) FGFR4 promotes CAF activation through the CXCL10-CXCR3 axis in colon cancer. Cell Death Dis. 16(1):424. (*co-corresponding authors)
4. Kim YK, Jo D, Choi S, Song J. (2025) High-fat diet triggers transcriptomic changes in the olfactory bulb. Heliyon. 11(3):e42196.
5. Yoon TM, Kim SA, Jung EK, Kim YK, Lee KH, Lim SC. (2025) MicroRNA-129-3p Suppresses Tumor Progression and Chemoradioresistance in Head and Neck Squamous Cell Carcinoma. Curr Oncol. 32(1):54.
6. Choe N, Shin S, Kim YK, Kook H, Kwon DH. (2024) CCAAT/Enhancer-Binding Protein beta (C/EBPbeta) Regulates Calcium Deposition in Smooth Muscle Cells. Int J Mol Sci. 25(24):13667.
7. Min KW, Choi KM, Mun H, Ko S, Lee JW, Sagum CA, Bedford MT, Kim YK, Delaney JR, Cho JH, Dawson TM, Dawson VL, Twal W, Kim DC, Panganiban CH, Lang H, Zhou X, Shin S, Hu J, Heise T, Kwon SH, Kim D, Kim YH, Kang SU, Kim K, Lewis S, Eroglu A, Ryu S, Kim D, Chang JH, Jung J, Yoon JH. (2024) Mature microRNA-binding protein QKI suppresses extracellular microRNA let-7b release. J Cell Sci. 137(21):jcs261575.
8. Bang HJ, Shim HJ, Park MR, Yoon S, Yoo KH, Kim YK, Lee H, Nam JS, Hwang JE, Bae WK, Chung IJ, Sun EG, Cho SH. (2024) NRXN1 as a Prognostic Biomarker: Linking Copy Number Variation to EMT and Survival in Colon Cancer. Int J Mol Sci. 25(21):11423.
9. Kwon DH, Shin S, Nam YS, Choe N, Lim Y, Jeong A, Lee YG, Kim YK, Kook H. (2024) CBL-b E3 ligase-mediated neddylation and activation of PARP-1 induce vascular calcification. Exp Mol Med. 56(10):2246-2259.
10. Mun H, Lee S, Choi S, Jeong JH, Ko S, Chun YL, Deaton B, Yeager CT, Boyette A, Palmera J, Newman L, Zhou P, Shin S, Kim DC, Sagum CA, Bedford MT, Kim YK, Kwon J, Jung J, Chang JH, Yoon JH. (2024) Targeting of CYP2E1 by miRNAs in alcohol-induced intestine injury. Mol Cells. 47:100074.
11. Kim YK, Jo D, Arjunan A, Ryu Y, Lim YH, Choi SY, Kim HK, Song J. (2024) Identification of IGF-1 Effects on White Adipose Tissue and Hippocampus in Alzheimer's Disease Mice via Transcriptomic and Cellular Analysis. Int J Mol Sci. 25:2567.
12. Lee JW, Mun H, Kim JH, Ko S, Kim YK, Shim MJ, Kim K, Ho CW, Park HB, Kim M, Lee C, Choi SH, Kim JW, Jeong JH, Yoon JH, Min KW*, Son TG*. (2023) Low-Dose Ionizing Radiation-Crosslinking Immunoprecipitation (LDIR-CLIP) Identified Irradiation-Sensitive RNAs for RNA-Binding Protein HuR-Mediated Decay. Biology (Basel). 12:1533.
13. Jeong A, Lim Y, Kook T, Kwon DH, Cho YK, Ryu J, Lee YG, Shin S, Choe N, Kim YS, Cho HJ, Kim JC, Choi Y, Lee SJ, Kim HS, Kee HJ, Nam KI, Ahn Y, Jeong MH, Park WJ, Kim YK*, Kook H*. (2023) Circular RNA circSMAD4 regulates cardiac fibrosis by targeting miR-671-5p and FGFR2 in cardiac fibroblasts. Mol Ther Nucleic Acids. 34:102071.
14. Lim YH, Yoon G, Ryu Y, Jeong D, Song J, KIM YS, Ahn Y, Kook H, Kim YK*. (2023) Human lncRNA SUGCT-AS1 regulates the proinflammatory response of macrophage. Int J Mol Sci. 24:13315.
15. Munkhzul C, Lee JM, Kim B, Nguyen TTM, Ginting RP, Jeong D, Kim YK, Lee MW, Lee M. (2023) H19X-encoded microRNAs induced by IL-4 in adipocyte precursors regulate proliferation to facilitate differentiation. Biol Direct. 18:32.
16. Jo D, Lim YH, Jung YS, Kim YK, Song J. (2023) Circular RNA Tmcc1 improves astrocytic glutamate metabolism and spatial memory via NF-κB and CREB signaling in a bile duct ligation mouse model: transcriptional and cellular analyses. J Neuroinflammation. 20:121.
17. Jo D, Yoon G, Lim YH, Kim YK*, Song J*. (2023) Profiling and Cellular Analyses of Obesity-Related circRNAs in Neurons and Glia under Obesity-like In Vitro Conditions. Int J Mol Sci. 24:6235. (*co-corresponding authors)
18. Kim YK, Jung YS, Song J. (2023) Transcriptome profile in the mouse brain of hepatic encephalopathy and Alzheimer’s disease. Int J Mol Sci. 24:675.
19. Nguyen MT, Lee MA, Kim YK, Kook H, Jeong D, Jang SP, Kwak TH, Park WJ. (2022) The matricellular protein CCN5 induces apoptosis in myofibroblasts through SMAD7-mediated inhibition of NFκB. PLoS One. 17:e0269735.
20. Kim YK*. (2022) Comparing the long non-coding RNA expression profiles of skeletal muscle and kidney tissues from patients with diabetes. PLoS One. 17:e0274794.
21. Jo D, Kim HK, Kim YK, Song J. (2022) Transcriptome profile of thyroid glands in bile duct ligation mouse model. Int J Mol Sci. 23:8244.
22. Cheon SY, Jo D, Kim YK*, Song J*. (2022) Long noncoding RNAs regulate hyperammonemia-induced neuronal damage in hepatic encephalopathy. Oxidative Med Cell Longev. 2022:7628522. (*co-corresponding authors)
23. Ryu J, Choe N, Kwon DH, Shin S, Lim YH, Yoon G, Kim JH, Kim HS, Lee IK, Ahn Y, Park WJ, Kook H*, Kim YK*. (2022) Circular RNA circSmoc1-2 regulates vascular calcification by acting as a miR-874-3p sponge in vascular smooth muscle cells. Mol Ther Nucleic Acids. 27:645. (*co-corresponding authors)
24. Kwon DH, Choe N, Shin S, Ryu J, Kim N, Eom GH, Nam KI, Kim HS, Ahn Y, Kim YK, Park WJ, Mendrysa SM, Kook H. (2021) Regulation of MDM2 E3 ligase-dependent vascular calcification by MSX1/2. Exp Mol Med. 53:1781.
25. Yoon G, Lim YH, Jo D, Ryu J, Song J*, Kim YK*. (2021) Obesity-linked circular RNA circTshz2-2 regulates the neuronal cell cycle and spatial memory in the brain. Mol Psychiatry. 26:6350. (*co-corresponding authors)
26. Lim Y, Jeong A, Kwon DH, Lee YU, Kim YK, Ahn Y, Kook T, Park WJ, Kook H. (2021) P300/CBP-associated factor activates cardiac fibroblasts by SMAD2 acetylation. Int J Mol Sci. 22:9944.
27. Kim S, Kim S, Chang HR, Kim D, Park J, Son N, Park J, Yoon M, Chae G, Kim YK, Kim VN, Kim YK, Nam JW, Shin C*, Baek D*. (2021) The regulatory impact of RNA-binding proteins on microRNA targeting. Nat Commun. 12:5057. (*co-corresponding authors)
28. Kwon DH, Kang JY, Joung H, Kim JY, Jeong A, Min HK, Shin S, Lee YG, Kim YK, Seo SB*, Kook H*. (2021) SRF is a nonhistone methylation target of KDM2B and SET7 in the regulation of skeletal muscle differentiation. Exp Mol Med. 53:250-263. (*co-corresponding authors)
29. Mun SK, Chae H, Piao XY, Lee HJ, Kim YK, Oh SH, Chang M*. (2021) MicroRNAs related to cognitive impairment after hearing loss. Clin Exp Otorhinolaryngol. 14:76.
30. Choe N, Kwon DH, Ryu J, Shin S, Cho HJ, Joung H, Eom GH, Ahn Y, Park WJ, Nam KI, Kim YK*, Kook H*. (2020) miR-27a-3p targets ATF3 to reduce calcium deposition in vascular smooth muscle cells. Mol Ther Nucleic Acids. 22:627-639. (*co-corresponding authors)
31. Lim YH, Ryu J, Kook H*, Kim YK*. (2020) Identification of long noncoding RNAs involved in differentiation and survival of vascular smooth muscle cells. Mol Ther Nucleic Acids. 22:209-221. (*co-corresponding authors)
32. Kim YK*, Kim YS, Kim S, Kim YJ, Ahn Y, Kook H. (2020) Comprehensive evaluation of differentially expressed non-coding RNAs identified during macrophage activation. Mol Immunol. 128:98-105. (*corresponding author)
33. Song J, Kim YK*. (2020) Discovery and functional prediction of long non-coding RNAs common to ischemic stroke and myocardial infarction. J Lipid Atheroscler. 9:e27.
34. Choe N, Shin S, Joung H, Ryu J, Kim YK, Ahn Y, Kook H*, Kwon DH*. (2020) The microRNA miR-134-5p induces calcium deposition by inhibiting histone deacetylase 5 in vascular smooth muscle cells. J Cell Mol Med. 24:10542-50. (*co-corresponding authors)
35. Nam KI, Yoon G, Kim YK* and Song J*. (2020) Transcriptome analysis of pineal glands in the mouse model of Alzheimer’s disease. Front Mol Neurosci. 12:318. (*co-corresponding authors)
36. Ryu J, Kwon DH, Choe N, Shin S, Jeong G, Lim YH, Kim J, Park WJ, Kook H*, Kim YK*. (2020) Characterization of circular RNAs in vascular smooth muscle cells with vascular calcification. Mol Ther Nucleic Acids. 19:31-41. (*co-corresponding authors)
37. Yoon G, Kim YK, Song J. (2020) Glucagon-like peptide-1 suppresses neuroinflammation and improves neural structure. Pharmacol Res. 24:104615.
38. Yoon S, Kim M, Min HK, Lee YU, Kwon DH, Lee M, Lee S, Kook T, Joung H, Nam KI, Ahn Y, Kim YK, Kim J, Park WJ, McMullen JR, Eom GH*, Kook H*. (2019) Inhibition of heat shock protein 70 blocks the development of cardiac hypertrophy by modulating the phosphorylation of histone deacetylase 2. Cardiovasc Res. 115:1850-1860. (*co-corresponding authors)
39. Kim YK*. (2019) Analysis of circular RNAs in the coronary arteries of patients with Kawasaki disease. J Lipid Atheroscler. 8:e1.
40. Jeong G, Kwon DH, Shin S, Choe N, Ryu J, Lim YH, Kim J, Park WJ, Kook H*, Kim YK*. (2019) Long noncoding RNAs in vascular smooth muscle cells regulate vascular calcification. Sci Rep. 9:5848. (*co-corresponding authors)
41. Yoon G, Cho KA, Song J*, Kim YK*. (2019) Transcriptomic analysis of high fat diet fed mouse brain cortex. Front Genet. 10:83. (*co-corresponding authors)
42. Ock S, Ahn J, Lee SH, Kim HM, Kang H, Kim YK, Kook H, Park WJ, Kim S, Kimura S, Jung CK, Shong M, Holzenberger M, Dale Abel E, Lee TJ, Cho BY, Kim HS, Kim J*. (2018) Thyrocyte-specific deletion of insulin and IGF-1 receptors induces papillary thyroid carcinoma-like lesions through EGFR pathway activation. Int J Cancer. 143:2458-2469.
43. Yoon S, Kook T, Min HK, Kwon DH, Cho YK, Kim M, Shin S, Joung H, Jeong SH, Lee S, Kang G, Park Y, Kim YS, Ahn Y, McMullen JR, Gergs U, Neumann J, Kim KK, Kim J, Nam KI, Kim YK, Kook H*, Eom GH*. (2018) PP2A negatively regulates the hypertrophic response by dephosphorylating HDAC2 S394 in the heart. Exp Mol Med. 50:83.
44. Ock S, Lee WS, Kim HM, Park KS, Kim YK, Kook H, Park WJ, Lee TJ, Abel ED, Kim J*. (2018) Connexin43 and zonula occludens-1 are targets of Akt in cardiomyocytes that correlate with cardiac contractile dysfunction in Akt deficient hearts. Biochim Biophys Acta Mol Basis Dis. 1864:1183-1191.
45. Lim YH, Kwon DH, Kim J, Park WJ, Kook H, Kim YK*. (2018) Identification of long noncoding RNAs involved in muscle differentiation. PLoS One. 13:e0193898.
46. Joung H, Kwon S, Kim KH, Lee YG, Shin S, Kwon DH, Lee YU, Kook T, Choe N, Kim JC, Kim YK, Eom GH*, Kook H*. (2018) Sumoylation of histone deacetylase 1 regulates MyoD signaling during myogenesis. Exp Mol Med. 50:e427.
47. Chang MY, Park S, Choi JJ, Kim YK, Suh MW, Lee JH, Oh SH, Park MK*. (2017) MicroRNAs 218a-5p, 219a-5p, and 221-3p regulate vestibular compensation. Sci Rep. 7:8701.
48. Song J, Kim YK*. (2017) Identification of the Role of miR-142-5p in Alzheimer’s Disease by Comparative Bioinformatics and Cellular Analysis. Front Mol Neurosci. 10:227.
49. Choe N, Kwon DH, Shin S, Kim YS, Kim YK, Kim J, Ahn Y, Eom GH*, Kook H*. (2017) The microRNA miR-124 inhibits vascular smooth muscle cell proliferation by targeting S100 calcium-binding protein A4 (S100A4). FEBS Lett. 591:1041-1052. (*co-corresponding authors)
50. Jeong G, Lim YH, Kim NJ, Wee G, Kim YK*. (2017) Knockout of miR-221 and miR-222 reveals common and specific targets for paralogous miRNAs. RNA Biol. 14:197-205.
51. Choi B, Yu J, Han TS, Kim YK, Hur K, Kang BC, Kim WH, Kim DY, Lee HJ, Kim VN, Yang HK*. (2017) Gastric Carcinogenesis in the miR-222/221 Transgenic Mouse Model. Cancer Res Treat. 49:150-160.
52. Jeong G, Lim YH, Kim YK*. (2016) Precise mapping of the transcription start sites of human microRNAs using DROSHA knockout cells. BMC Genomics. 17:908.
53. Choi J, Kim YK, Park K, Nah J, Yoon SS, Kim DW, Kim VN, Seong RH. (2016) MicroRNA-139-5p regulates proliferation of hematopoietic progenitors and is repressed during BCR-ABL-mediated leukemogenesis. Blood. 128:2117-2129.
54. Kim YK*, Kim B, Kim VN*. (2016) Re-evaluation of the roles of DROSHA, Exportin 5, and DICER in microRNA biogenesis. Proc Natl Acad Sci USA. 113:E1881-E1889. (*co-corresponding authors)
55. Kim YK*, Wee G*, Park J, Kim J, Baek D, Kim JS**, Kim VN**. (2013) TALEN-based knockout library for human microRNAs. Nat Struct Mol Biol. 20:1458-1464. (*equal contribution; **co-corresponding authors)
- Research Highlight: TALENs knock out human microRNAs (2014). Nat Meth. 11:10.
- Research Highlight: TALENs for microRNAs (2014). Nat Rev Genet. 15:2.
56. Kim YK, Yeo J, Kim B, Ha M, Kim VN*. (2012) Short Structured RNAs with Low GC Content Are Selectively Lost during Extraction from a Small Number of Cells. Molecular Cell. 46:893-895.
57. Kim WK, Park M, Kim YK, Tae YK, Yang HK, Lee JM, Kim H*. (2011) MicroRNA-494 downregulates KIT and inhibits gastrointestinal stromal tumor cell proliferation. Clin Cancer Res. 17:7584-7594.
58. Kim S, Lee S, Shin J, Kim Y, Evnouchidou I, Kim D, Kim YK, Kim YE, Ahn JH, Riddell SR, Stratikos E, Kim VN, Ahn K*. (2011) Human cytomegalovirus microRNA miR-US4-1 inhibits CD8(+) T cell responses by targeting the aminopeptidase ERAP1. Nat Immunol. 12:984-991.
59. Heo I*, Joo C*, Kim YK*, Ha M, Yoon MJ, Cho J, Yeom KH, Han J, Kim VN**. (2009) TUT4 in concert with Lin28 suppresses microRNA biogenesis through pre-microRNA uridylation. Cell. 138:696-708. (*equal contribution)
- Research Highlight: Small RNAs: Keeping let-7 young (2009). Nat Rev Mol Cell Biol. 10:652.
60. Kim YK*, Yu J*, Han TS, Park SY, Namkoong B, Kim DH, Hur K, Yoo MW, Lee HJ, Yang HK, Kim VN**. (2009) Functional links between clustered microRNAs: suppression of cell-cycle inhibitors by microRNA clusters in gastric cancer. Nucleic Acids Res. 37:1672-1681. (*equal contribution)
61. Han J, Pedersen JS*, Kwon SC*, Belair CD*, Kim YK, Yeom KH, Yang WY, Haussler D, Blelloch R, Kim VN*. (2009) Posttranscriptional crossregulation between Drosha and DGCR8. Cell. 136:75-84. (*equal contribution)
62. Oh M, Lee H, Kim YK, Nam JW, Rhee JK, Zhang BT, Kim VN, Lee I*. (2007) Identification and Characterization of Small RNAs from Vernalized Arabidopsis thaliana. J. Plant Biol. 50:562-572.
63. Kim YK, Kim VN*. (2007) Processing of intronic microRNAs. EMBO J. 26:775-783.
64. Lee Y*, Hur I*, Park SY*, Kim YK, Suh MR, Kim VN**. (2006) The role of PACT in the RNA silencing pathway. EMBO J. 25:522-532. (*equal contribution)
65. Nam S, Kim YK, Kim P, Kim VN, Shin S, Lee S*. (2005) Prediction of Mammalian MicroRNA Targets - Comparative Genomics Approach with Longer 3' UTR Databases. Genomics Inform. 3:53-62.
66. Han J*, Lee Y*, Yeom KH, Kim YK, Jin H, Kim VN**. (2004) The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev. 18:3016-3027. (*equal contribution)