2025

Wu, J., Jang, H., Kwak, H., Son, M., Jiang, W., Hwang, H.Y., Jo, D.H., Kim, D., Kim, H.H. and Kim, J.H. (2025) Engineered virus-like particle-assembled Vegfa-targeting Cas9 ribonucleoprotein treatment alleviates neovascularization in wet age-related macular degeneration. Genome Biol, 26, 346.

 

Shrestha, M., Kim, Y., Park, S., Jiang, H.L., Lee, J.Y., Kim, D. and Jeong, J.H. (2025) eVLP-Mediated Cas9 Delivery for Preventing IBMIR in Islet Transplantation. Small, e08128.

 

Oh, J., Hwang, Y.H., Lee, J., Seok, C., Oh, S., Kim, H.Y., Mariam, N., Ahn, J., Yu, G., Park, J. et al. (2025) AIM2 drives inflammatory cell death and monkeypox pathogenesis. Cell Mol Immunol, 22, 1615-1628.

 

Kweon, J., Park, S., Jeon, M.Y., Lim, K., Jang, G., Jang, A.H., Lee, M., Seok, C., Lee, C., Park, S. et al. (2025) High-efficiency base editing for nuclear and mitochondrial DNA with an optimized DYW-like deaminase. Mol Ther, 33, 5611-5623.

 

Kim, B.S., Hwang, I., Ko, H.R., Kim, Y.K., Kim, H.J., Seo, S.W., Choi, Y., Lim, S., Kim, Y.K., Nie, S. et al. (2025) EBP1 potentiates amyloid beta pathology by regulating gamma-secretase. Nat Aging, 5, 486-503.

 

Hwang, H.Y., Lee, M., Yi, H., Seok, C., Lim, K., Na, Y.R., Kang, J.S., Park, J.H. and Kim, D. (2025) Engineered Sdd7 cytosine base editors with enhanced specificity. Nat Commun, 16, 5881.

 

Hong, J.K., Yeom, M., Hwang, H.Y., Mun, E., Woo, J.H., Kim, Y., Shin, J.H., Lee, Y., Kim, D., Peter Guengerich, F. and Choi, J.Y. (2025) Four germline POLH variants, including two found in skin tumors, impair DNA polymerase eta function and cellular tolerance to UV radiation and cisplatin. Chem Biol Interact, 416, 111551.

 

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2024

Gopalappa, R., Lee, M., Kim, G., Jung, E.S., Lee, H., Hwang, H.Y., Lee, J.G., Kim, S.J., Yoo, H.J., Sung, Y.H. et al. (2024) In vivo adenine base editing rescues adrenoleukodystrophy in a humanized mouse model. Mol Ther, 32, 2190-2206.

 

Yi, H., Yun, Y., Choi, W.H., Hwang, H.Y., Cha, J.H., Seok, H., Song, J.J., Lee, J.H., Lee, S.Y. and Kim, D. (2024) CRISPR-based editing strategies to rectify EYA1 complex genomic rearrangement linked to haploinsufficiency. Mol Ther Nucleic Acids, 35, 102199.

 

Hwang, H.Y., Gim, D., Yi, H., Jung, H., Lee, J. and Kim, D. (2024) Precise editing of pathogenic nucleotide repeat expansions in iPSCs using paired prime editor. Nucleic Acids Res.

 

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2023

Seo, J.H., Shin, J.H., Lee, J., Kim, D., Hwang, H.Y., Nam, B.G., Lee, J., Kim, H.H. and Cho, S.R. (2023) DNA double-strand break-free CRISPR interference delays Huntington's disease progression in mice. Commun Biol, 6, 466.

   

Oh, S., Lee, J., Oh, J., Yu, G., Ryu, H., Kim, D. and Lee, S. (2023) Integrated NLRP3, AIM2, NLRC4, Pyrin inflammasome activation and assembly drive PANoptosis. Cell Mol Immunol, 20, 1513-1526.

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Kweon, J., Hwang, H.Y., Ryu, H., Jang, A.H., Kim, D. and Kim, Y. (2023) Targeted genomic translocations and inversions generated using a paired prime editing strategy. Mol Ther, 31, 249-259.

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Kim, M.J., Kim, J.Y., Shin, J.H., Kang, Y., Lee, J.S., Son, J., Jeong, S.K., Kim, D., Kim, D.H., Chun, E. and Lee, K.Y. (2023) FFAR2 antagonizes TLR2- and TLR3-induced lung cancer progression via the inhibition of AMPK-TAK1 signaling axis for the activation of NF-kappaB. Cell Biosci, 13, 102.

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Kim, J.Y., Shin, J.H., Kim, M.J., Kang, Y., Lee, J.S., Son, J., Jeong, S.K., Kim, D., Kim, D.H., Chun, E. and Lee, K.Y. (2023) beta-arrestin 2 negatively regulates lung cancer progression by inhibiting the TRAF6 signaling axis for NF-kappaB activation and autophagy induced by TLR3 and TLR4. Cell Death Dis, 14, 422.

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2022

Kim, D.Y., Lee, J.M., Moon, S.B., Chin, H.J., Park, S., Lim, Y., Kim, D., Koo, T., Ko, J.H. and Kim, Y.S. (2022) Efficient CRISPR editing with a hypercompact Cas12f1 and engineered guide RNAs delivered by adeno-associated virus. Nat Biotechnol, 40, 94-102.

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Jang, H., Jo, D.H., Cho, C.S., Shin, J.H., Seo, J.H., Yu, G., Gopalappa, R., Kim, D., Cho, S.R., Kim, J.H. and Kim, H.H. (2022) Application of prime editing to the correction of mutations and phenotypes in adult mice with liver and eye diseases. Nat Biomed Eng, 6, 181-194.

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Choi, E., Hwang, H.Y., Kwon, E., Kim, D. and Koo, T. (2022) Expanded targeting scope of LbCas12a variants allows editing of multiple oncogenic mutations. Mol Ther Nucleic Acids, 30, 131-142.

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2021

Na, Y.R., Jung, D., Stakenborg, M., Jang, H., Gu, G.J., Jeong, M.R., Suh, S.Y., Kim, H.J., Kwon, Y.H., Sung, T.S. et al. (2021) Prostaglandin E(2) receptor PTGER4-expressing macrophages promote intestinal epithelial barrier regeneration upon inflammation. Gut, 70, 2249-2260.

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Kim, D., Kang, B.C. and Kim, J.S. (2021) Identifying genome-wide off-target sites of CRISPR RNA-guided nucleases and deaminases with Digenome-seq. Nat Protoc, 16, 1170-1192.

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2020

Na, Y.R., Kwon, J.W., Kim, D.Y., Chung, H., Song, J., Jung, D., Quan, H., Kim, D., Kim, J.S., Ju, Y.W. et al. (2020) Protein Kinase A Catalytic Subunit Is a Molecular Switch that Promotes the Pro-tumoral Function of Macrophages. Cell Rep, 31, 107643.

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Lee, J.S., Lee, J.Y., Song, D.W., Bae, H.S., Doo, H.M., Yu, H.S., Lee, K.J., Kim, H.K., Hwang, H., Kwak, G. et al. (2020) Targeted PMP22 TATA-box editing by CRISPR/Cas9 reduces demyelinating neuropathy of Charcot-Marie-Tooth disease type 1A in mice. Nucleic Acids Res, 48, 130-140.

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Kim, D.Y., Moon, S.B., Ko, J.H., Kim, Y.S. and Kim, D. (2020) Unbiased investigation of specificities of prime editing systems in human cells. Nucleic Acids Res, 48, 10576-10589.

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Kim, D., Lim, K., Kim, D.E. and Kim, J.S. (2020) Genome-wide specificity of dCpf1 cytidine base editors. Nat Commun, 11, 4072.

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Ha, D.I., Lee, J.M., Lee, N.E., Kim, D., Ko, J.H. and Kim, Y.S. (2020) Highly efficient and safe genome editing by CRISPR-Cas12a using CRISPR RNA with a ribosyl-2'-O-methylated uridinylate-rich 3'-overhang in mouse zygotes. Exp Mol Med, 52, 1823-1830.

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2019

Kim, D., Luk, K., Wolfe, S.A. and Kim, J.S. (2019) Evaluating and Enhancing Target Specificity of Gene-Editing Nucleases and Deaminases. Annu Rev Biochem, 88, 191-220.

 

Kim, D., Kim, D.E., Lee, G., Cho, S.I. and Kim, J.S. (2019) Genome-wide target specificity of CRISPR RNA-guided adenine base editors. Nat Biotechnol, 37, 430-435.

  

Jo, D.H., Song, D.W., Cho, C.S., Kim, U.G., Lee, K.J., Lee, K., Park, S.W., Kim, D., Kim, J.H., Kim, J.S. et al. (2019) CRISPR-Cas9-mediated therapeutic editing of Rpe65 ameliorates the disease phenotypes in a mouse model of Leber congenital amaurosis. Sci Adv, 5, eaax1210.

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2018

Lee, J.K., Jeong, E., Lee, J., Jung, M., Shin, E., Kim, Y.H., Lee, K., Jung, I., Kim, D., Kim, S. and Kim, J.S. (2018) Directed evolution of CRISPR-Cas9 to increase its specificity. Nat Commun, 9, 3048.

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Koo, T., Park, S.W., Jo, D.H., Kim, D., Kim, J.H., Cho, H.Y., Kim, J., Kim, J.H. and Kim, J.S. (2018) CRISPR-LbCpf1 prevents choroidal neovascularization in a mouse model of age-related macular degeneration. Nat Commun, 9, 1855.

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Koo, T., Lu-Nguyen, N.B., Malerba, A., Kim, E., Kim, D., Cappellari, O., Cho, H.Y., Dickson, G., Popplewell, L. and Kim, J.S. (2018) Functional Rescue of Dystrophin Deficiency in Mice Caused by Frameshift Mutations Using Campylobacter jejuni Cas9. Mol Ther, 26, 1529-1538.

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Kim, S.T., Park, J., Kim, D., Kim, K., Bae, S., Schlesner, M. and Kim, J.S. (2018) Response to "Unexpected mutations after CRISPR-Cas9 editing in vivo". Nat Methods, 15, 239-240.

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Kim, D. and Kim, J.S. (2018) DIG-seq: a genome-wide CRISPR off-target profiling method using chromatin DNA. Genome Res, 28, 1894-1900.

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Georgiadis, C., Preece, R., Nickolay, L., Etuk, A., Petrova, A., Ladon, D., Danyi, A., Humphryes-Kirilov, N., Ajetunmobi, A., Kim, D. et al. (2018) Long Terminal Repeat CRISPR-CAR-Coupled "Universal" T Cells Mediate Potent Anti-leukemic Effects. Mol Ther, 26, 1215-1227.

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Bin Moon, S., Lee, J.M., Kang, J.G., Lee, N.E., Ha, D.I., Kim, D.Y., Kim, S.H., Yoo, K., Kim, D., Ko, J.H. and Kim, Y.S. (2018) Highly efficient genome editing by CRISPR-Cpf1 using CRISPR RNA with a uridinylate-rich 3'-overhang. Nat Commun, 9, 3651.

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2017

Park, J., Childs, L., Kim, D., Hwang, G.H., Kim, S., Kim, S.T., Kim, J.S. and Bae, S. (2017) Digenome-seq web tool for profiling CRISPR specificity. Nat Methods, 14, 548-549.

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Ma, H., Marti-Gutierrez, N., Park, S.W., Wu, J., Lee, Y., Suzuki, K., Koski, A., Ji, D., Hayama, T., Ahmed, R. et al. (2017) Correction of a pathogenic gene mutation in human embryos. Nature, 548, 413-419.

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Kim, K., Ryu, S.M., Kim, S.T., Baek, G., Kim, D., Lim, K., Chung, E., Kim, S. and Kim, J.S. (2017) Highly efficient RNA-guided base editing in mouse embryos. Nat Biotechnol, 35, 435-437.

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Kim, K., Park, S.W., Kim, J.H., Lee, S.H., Kim, D., Koo, T., Kim, K.E., Kim, J.H. and Kim, J.S. (2017) Genome surgery using Cas9 ribonucleoproteins for the treatment of age-related macular degeneration. Genome Res, 27, 419-426.

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Kim, E., Koo, T., Park, S.W., Kim, D., Kim, K., Cho, H.Y., Song, D.W., Lee, K.J., Jung, M.H., Kim, S. et al. (2017) In vivo genome editing with a small Cas9 orthologue derived from Campylobacter jejuni. Nat Commun, 8, 14500.

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Kim, D., Lim, K., Kim, S.T., Yoon, S.H., Kim, K., Ryu, S.M. and Kim, J.S. (2017) Genome-wide target specificities of CRISPR RNA-guided programmable deaminases. Nat Biotechnol, 35, 475-480.

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Fogarty, N.M.E., McCarthy, A., Snijders, K.E., Powell, B.E., Kubikova, N., Blakeley, P., Lea, R., Elder, K., Wamaitha, S.E., Kim, D. et al. (2017) Genome editing reveals a role for OCT4 in human embryogenesis. Nature, 550, 67-73.

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2016

Kim, D., Kim, S., Kim, S., Park, J. and Kim, J.S. (2016) Genome-wide target specificities of CRISPR-Cas9 nucleases revealed by multiplex Digenome-seq. Genome Res, 26, 406-415.

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Kim, D., Kim, J., Hur, J.K., Been, K.W., Yoon, S.H. and Kim, J.S. (2016) Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells. Nat Biotechnol, 34, 863-868.

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2015

Kim, D., Bae, S., Park, J., Kim, E., Kim, S., Yu, H.R., Hwang, J., Kim, J.I. and Kim, J.S. (2015) Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells. Nat Methods, 12, 237-243, 231 p following 243.

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2014

Kim, S., Kim, D., Cho, S.W., Kim, J. and Kim, J.S. (2014) Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins. Genome Res, 24, 1012-1019.

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Kim, J.M., Kim, D., Kim, S. and Kim, J.S. (2014) Genotyping with CRISPR-Cas-derived RNA-guided endonucleases. Nat Commun, 5, 3157.