Publications

 Publications

2026

Yu, J.†, Park, J.-C.†, Uhm, H., Kim, Y.-W., Im, H. W., & Bae, S. Evolution of Prime Editing: Enhancing Efficiency and Expanding Capacity. Advanced Science, n/a(n/a), e21015. https://doi.org/10.1002/advs.202521015 

Choi, H., Lee, Y., Jin, H., Yu, J., Lee, H., Choi, D., & Lee, J. (2026). Antarctic moss fairy rings serve as reservoirs for plant growth-promoting bacteria. BMC Plant Biol. https://doi.org/10.1186/s12870-026-08127-3

2025

Jeong, Y. Y., Han, J. H., Yu, J., Bae, S., & Seo, P. J. (2025). Identification of optimal adenine and cytosine base editors for genome editing in Arabidopsis and soybean. BMB Rep, 58(7), 288-292. https://doi.org/10.5483/BMBRep.2024-0102 

Nam, Hye J.†, Han, Jun H.†, Yu, J.†, Cho, Chang S., Kim, D., Kim, Young E., Kim, Min J., Kim, Jeong H., Jo, Dong H., & Bae, S. (2025). Autophagy induction enhances homologous recombination-associated CRISPR–Cas9 gene editing. Nucleic Acids Research, 53(7). https://doi.org/10.1093/nar/gkaf258 

Choi, Y.-J., Nam, Y. A., Hyun, J. Y., Yu, J., Mun, Y., Yun, S. H., Lee, W., Park, C. J., Han, B. W., & Lee, B.-H. (2025). Impaired chaperone-mediated autophagy leads to abnormal SORT1 (sortilin 1) turnover and CES1-dependent triglyceride hydrolysis. Autophagy, 21(4), 827-839. https://doi.org/10.1080/15548627.2024.2435234 

2024

Yu, J., Lee, H., Cho, S.M., Lee, Y., Kim, D., Hong, S.G., Park, S.-J., Kim, S.-G., Jin, H., and Lee, J. (2024). Life under the snow: A year-round transcriptome analysis of Antarctic mosses in natural habitats provides insight into the molecular adaptation of plants under extreme environment. Plant, Cell & Environment 47, 976-991. https://doi.org/10.1111/pce.14793

Kim, H., Lee, Y., Yu, J., Park, J.-Y., Lee, J., Kim, S.-G., & Hyun, Y. (2024). Production of the antimalarial drug precursor amorphadiene by microbial terpene synthase-like from the moss Sanionia uncinata. Planta, 260(6), 145. https://doi.org/10.1007/s00425-024-04558-0 

2023

Kim, J. Y., Kim, J. H., Jang, Y. H., Yu, J., Bae, S., Kim, M.-S., Cho, Y.-G., Jung, Y. J., & Kang, K. K. (2023). Transcriptome and Metabolite Profiling of Tomato SGR-Knockout Null Lines Using the CRISPR/Cas9 System. International Journal of Molecular Sciences, 24(1), 109. https://www.mdpi.com/1422-0067/24/1/109

Kim, H. K., Kim, J. Y., Kim, J. H., Go, J. Y., Jung, Y.-S., Lee, H. J., Ahn, M.-J., Yu, J., Bae, S., Kim, H. S., Kwak, S.-S., Kim, M.-S., Cho, Y.-G., Jung, Y. J., & Kang, K. K. (2023). Biochemical Characterization of Orange-Colored Rice Calli Induced by Target Mutagenesis of OsOr Gene. Plants, 12(1), 56. https://www.mdpi.com/2223-7747/12/1/56 

Jin, H.†, Yu, J.†, Kaleku, J., Lee, Y., Park, E., Lee, H., Kim, H.-W., & Lee, J. (2023). High-Quality Genome Resource of a Novel Venturiaceae sp. KMAF11, Isolated from Diseased Colobanthus quitensis, an Antarctic Flowering Plant. Plant Disease, 107(3), 911-914. https://doi.org/10.1094/pdis-03-22-0706-a

Choi, Y.-J., Yun, S.H., Yu, J., Mun, Y., Lee, W., Park, C.J., Han, B.W., and Lee, B.-H. (2023). Chaperone-mediated autophagy dysregulation during aging impairs hepatic fatty acid oxidation via accumulation of NCoR1. Molecular Metabolism 76, 101784. https://doi.org/10.1016/j.molmet.2023.101784

2022

Kim, N.-S., Yu, J., Bae, S., Kim, H.S., Park, S., Lee, K., Lee, S.I., and Kim, J.A. (2022). Identification and Characterization of PSEUDO-RESPONSE REGULATOR (PRR) 1a and 1b Genes by CRISPR/Cas9-Targeted Mutagenesis in Chinese Cabbage (Brassica rapa L.). International Journal of Molecular Sciences 23(13), 6963. https://www.mdpi.com/1422-0067/23/13/6963

Kim, J.H., Yu, J., Kim, H.K., Kim, J.Y., Kim, M.-S., Cho, Y.-G., Bae, S., Kang, K.K., and Jung, Y.J. (2022). Genome Editing of Golden SNP-Carrying Lycopene Epsilon-Cyclase (LcyE) Gene Using the CRSPR-Cas9/HDR and Geminiviral Replicon System in Rice. International Journal of Molecular Sciences 23(18), 10383. https://www.mdpi.com/1422-0067/23/18/10383

Kim, E. J., Chae, H., Koo, M. H., Yu, J., Kim, H., Cho, S. M., Hong, K. W., Lee, J. Y., Youn, U. J., Kim, S., Choi, H.-G., & Han, S. J. (2022). Statistical optimization of phytol and polyunsaturated fatty acid production in the Antarctic microalga Micractinium variabile KSF0031. Algae, 37(2), 175-183. https://doi.org/10.4490/algae.2022.37.4.1

Hong, S.-A.†, Seo, J.H.†, Wi, S., Jung, E.S., Yu, J., Hwang, G.-H., Yu, J.H., Baek, A., Park, S., Bae, S., and Cho, S.-R. (2022). In vivo gene editing via homology-independent targeted integration for adrenoleukodystrophy treatment. Molecular Therapy 30(1), 119-129. https://doi.org/10.1016/j.ymthe.2021.05.022

2021

Yu, J.†, Tu, L.†, Subburaj, S.†, Bae, S., and Lee, G.-J. (2021). Simultaneous targeting of duplicated genes in Petunia protoplasts for flower color modification via CRISPR-Cas9 ribonucleoproteins. Plant Cell Reports 40(6), 1037-1045. https://doi.org/10.1007/s00299-020-02593-1

Song, B., Yang, S., Hwang, G.-H., Yu, J., and Bae, S. (2021). Analysis of NHEJ-Based DNA Repair after CRISPR-Mediated DNA Cleavage. International Journal of Molecular Sciences 22(12), 6397. https://www.mdpi.com/1422-0067/22/12/6397

Lee, K., Park, O.-S., Go, J.Y., Yu, J., Han, J.H., Kim, J., Bae, S., Jung, Y.J., and Seo, P.J. (2021). Arabidopsis ATXR2 represses de novo shoot organogenesis in the transition from callus to shoot formation. Cell Reports 37(6), 109980. https://doi.org/10.1016/j.celrep.2021.109980

Lee, H.G., Kim, D.H., Choi, Y.-R., Yu, J., Hong, S.-A., Seo, P.J., and Bae, S. (2021). Enhancing plant immunity by expression of pathogen-targeted CRISPR-Cas9 in plants. Gene and Genome Editing 1, 100001. https://doi.org/10.1016/j.ggedit.2021.100001

Kyung, J., Jeon, M., Jeong, G., Shin, Y., Seo, E., Yu, J., Kim, H., Park, C.-M., Hwang, D., and Lee, I. (2021). The two clock proteins CCA1 and LHY activate VIN3 transcription during vernalization through the vernalization-responsive cis-element. The Plant Cell 34(3), 1020-1037. https://doi.org/10.1093/plcell/koab304

Kim, Y.†, Hong, S.-A.†, Yu, J.†, Eom, J., Jang, K., Yoon, S., Hong, D. H., Seo, D., Lee, S.-N., Woo, J.-S., Jeong, J., Bae, S., & Choi, D. (2021). Adenine base editing and prime editing of chemically derived hepatic progenitors rescue genetic liver disease. Cell Stem Cell, 28(9), 1614-1624.e1615. https://doi.org/10.1016/j.stem.2021.04.010

Kim, E.J., Chae, H., Yu, J., Kim, H., Cho, S.M., Shin, S.C., Choi, H.-G., Kim, S., and Han, S.J. (2021). Mitochondrial genome of the Antarctic microalga Micractinium simplicissimum KSF0127 (Chlorellaceae, Trebouxiophyceae). Mitochondrial DNA Part B 6(3), 878-879. https://doi.org/10.1080/23802359.2021.1886010

Kim, C.†, Jeong, Y.K.†, Yu, J., Shin, H. J., Ku, K. B., Cha, H. J., Han, J. H., Hong, S.-A., Kim, B.-T., Kim, S.-J., Woo, J.-S., & Bae, S. (2021). Efficient Human Cell Coexpression System and Its Application to the Production of Multiple Coronavirus Antigens. Advanced Biology, 5(4), 2000154. https://doi.org/10.1002/adbi.202000154

Jung, Y.J., Lee, H.J., Yu, J., Bae, S., Cho, Y.-G., and Kang, K.K. (2021). Transcriptomic and physiological analysis of OsCAO1 knockout lines using the CRISPR/Cas9 system in rice. Plant cell reports 40(6), 1013-1024. https://doi.org/10.1007/s00299-020-02607-y

Jang, H.-K.†, Jo, D.H.†, Lee, S.-N., Cho, C.S., Jeong, Y.K., Jung, Y., Yu, J., Kim, J.H., Woo, J.-S., and Bae, S. (2021). High-purity production and precise editing of DNA base editing ribonucleoproteins. Science advances 7(35), eabg2661. https://doi.org/doi:10.1126/sciadv.abg2661

Hur, J.H., Kang, C.Y., Lee, S., Parveen, N., Yu, J., Shamim, A., Yoo, W., Ghosh, A., Bae, S., Park, C.-J., and Kim, Kyeong K. (2021). AC-motif: a DNA motif containing adenine and cytosine repeat plays a role in gene regulation. Nucleic Acids Research 49(17), 10150-10165. https://doi.org/10.1093/nar/gkab728

2020

Yun, Y., Hong, S.-A., Kim, K.-K., Baek, D., Lee, D., Londhe, A. M., Lee, M., Yu, J., McEachin, Z. T., Bassell, G. J., Bowser, R., Hales, C. M., Cho, S.-R., Kim, J., Pae, A. N., Cheong, E., Kim, S., Boulis, N. M., Bae, S., & Ha, Y. (2020). CRISPR-mediated gene correction links the ATP7A M1311V mutations with amyotrophic lateral sclerosis pathogenesis in one individual. Communications Biology, 3(1), 33. https://doi.org/10.1038/s42003-020-0755-1

Yu, J.†, Cho, E.†, Choi, Y.-G.†, Jeong, Y.K., Na, Y., Kim, J.-S., Cho, S.-R., Woo, J.-S., and Bae, S. (2020). Purification of an Intact Human Protein Overexpressed from Its Endogenous Locus via Direct Genome Engineering. ACS Synthetic Biology 9(7), 1591-1598. https://doi.org/10.1021/acssynbio.0c00090

Jung, Y.J., Kim, J.H., Lee, H.J., Kim, D.H., Yu, J., Bae, S., Cho, Y.-G., and Kang, K.K. (2020). Generation and Transcriptome Profiling of Slr1-d7 and Slr1-d8 Mutant Lines with a New Semi-Dominant Dwarf Allele of SLR1 Using the CRISPR/Cas9 System in Rice. International Journal of Molecular Sciences 21(15), 5492. https://www.mdpi.com/1422-0067/21/15/5492

Hwang, G.-H.†, Yu, J.†, Yang, S., Son, W.J., Lim, K., Kim, H.S., Kim, J.-S., and Bae, S. (2020). CRISPR-sub: Analysis of DNA substitution mutations caused by CRISPR-Cas9 in human cells. Computational and Structural Biotechnology Journal 18, 1686-1694. https://doi.org/https://doi.org/10.1016/j.csbj.2020.06.026

2019

Lee, C., Hyun Jo, D., Hwang, G.-H., Yu, J., Kim, J.H., Park, S.-e., Kim, J.-S., Kim, J.H., and Bae, S. (2019). CRISPR-Pass: Gene Rescue of Nonsense Mutations Using Adenine Base Editors. Molecular Therapy 27(8), 1364-1371. https://doi.org/10.1016/j.ymthe.2019.05.013

Kim, D.-H.†, Yu, J.†, Park, J.C., Jeong, C.-B., Bae, S., and Lee, J.-S. (2019). Targeted cytochrome P450 3045C1 (CYP3045C1) gene mutation via CRISPR-Cas9 ribonucleoproteins in the marine rotifer Brachionus koreanus. 844(1), 117-128. https://doi.org/10.1007/s10750-018-3854-y

Jeong, Y.K.†, Yu, J.†, and Bae, S. (2019). Construction of non-canonical PAM-targeting adenosine base editors by restriction enzyme-free DNA cloning using CRISPR-Cas9. Scientific Reports 9(1), 4939. https://doi.org/10.1038/s41598-019-41356-1

2018

Jeon, Y., Choi, Y.H., Jang, Y., Yu, J., Goo, J., Lee, G., Jeong, Y.K., Lee, S.H., Kim, I.-S., Kim, J.-S., et al. (2018). Direct observation of DNA target searching and cleavage by CRISPR-Cas12a. Nature Communications 9(1), 2777. https://doi.org/10.1038/s41467-018-05245-x

Hwang, G.-H., Park, J., Lim, K., Kim, S., Yu, J., Yu, E., Kim, S.-T., Eils, R., Kim, J.-S., and Bae, S. (2018). Web-based design and analysis tools for CRISPR base editing. BMC Bioinformatics 19(1), 542. https://doi.org/10.1186/s12859-018-2585-4

Baek, K., Yu, J., Jeong, J., Sim, S.J., Bae, S., and Jin, E. (2018). Photoautotrophic production of macular pigment in a Chlamydomonas reinhardtii strain generated by using DNA-free CRISPR-Cas9 RNP-mediated mutagenesis. Biotechnology and Bioengineering 115(3), 719-728. https://doi.org/https://doi.org/10.1002/bit.26499

2017

Yu, J.†, Baek, K.†, Jin, E., and Bae, S. (2017). DNA-free Genome Editing of Chlamydomonas reinhardtii Using CRISPR and Subsequent Mutant Analysis. Bio-protocol 7(11), e2352. https://doi.org/10.21769/BioProtoc.2352

Lee, S. H.†, Yu, J.†, Hwang, G. H., Kim, S., Kim, H. S., Ye, S., Kim, K., Park, J., Park, D. Y., Cho, Y. K., Kim, J. S., & Bae, S. (2017). CUT-PCR: CRISPR-mediated, ultrasensitive detection of target DNA using PCR. Oncogene, 36(49), 6823-6829. https://doi.org/10.1038/onc.2017.281

Lee, J.-H., Park, S.-J., Hariharasudhan, G., Kim, M.-J., Jung, S.M., Jeong, S.-Y., Chang, I.-Y., Kim, C., Kim, E., Yu, J., et al. (2017). ID3 regulates the MDC1-mediated DNA damage response in order to maintain genome stability. Nature Communications 8(1), 903. https://doi.org/10.1038/s41467-017-01051-z

Jeong, J.†, Baek, K.†, Yu, J.†, Kirst, H., Betterle, N., Shin, W., Bae, S., Melis, A., and Jin, E. (2017). Deletion of the chloroplast LTD protein impedes LHCI import and PSI–LHCI assembly in Chlamydomonas reinhardtii. Journal of Experimental Botany 69(5), 1147-1158. https://doi.org/10.1093/jxb/erx457

-2016

Seo, E., Yu, J., Ryu, K.H., Lee, M.M., and Lee, I. (2011). WEREWOLF, a Regulator of Root Hair Pattern Formation, Controls Flowering Time through the Regulation of FT mRNA Stability. Plant Physiology 156(4), 1867-1877. https://doi.org/10.1104/pp.111.176685

Hyun, Y., Choi, S., Hwang, H.-J., Yu, J., Nam, S.-J., Ko, J., Park, J.-Y., Seo, Y. S., Kim, E. Y., Ryu, S. B., Kim, W. T., Lee, Y.-H., Kang, H., & Lee, I. (2008). Cooperation and Functional Diversification of Two Closely Related Galactolipase Genes for Jasmonate Biosynthesis. Developmental Cell, 14(2), 183-192.  https://doi.org/10.1016/j.devcel.2007.11.010