Publications

Featured Publications

118. Park J-C, Uhm H, Kim Y-W, Oh YE, Lee JH, Yang J, Kim K and Bae S*, "AI-generated MLH1 small binder improves prime editing efficiency" Cell DOI: 10.1016/j.cell.2025.07.010 (2025).

113. Nam HJ*, Han JH, Yu J, Cho CS, Kim D, Kim YE, Kim M, Jo DH* and Bae S*, "Autophagy induction enhances homologous recombination-associated CRISPR-Cas9 gene editing" Nucleic Acids Research 53(7): gkaf258 (2025).

108. Hwang G-H, Lee S-H, Oh M, Kim S, Habib O, Jang H-K, Kim HS, Kim CH, Kim S and Bae S*, "Large DNA deletions occur during DNA repair at 20-fold lower frequency for base editors and prime editors than for Cas9 nucleases" Nature Biomedical Engineering 9(1), 79–92 (2025).

75. Habib O, Habib H, Hwang G-H and Bae S*, "Comprehensive analysis of prime editing outcomes in human embryonic stem cells" Nucleic Acids Research 50(2), 1187-1197 (2022).

69. Jang H-K, Jo DH, Lee S-N, Cho CS, Jeong YK, Jung Y, Yu J, Kim JH*, Woo J-S* and Bae S*, "High-purity production and precise editing of DNA base editing ribonucleoproteins" Science Advances 7(35), eabg2661 (2021).

66. Jeong YK, Lee S-H, Hwang G-H, Hong S-A, Park S-e, Kim J-S, Woo J-S* and Bae S*, "Adenine base editor engineering reduces editing of bystander cytosines" Nature Biotechnology 39(11), 1426-1433 (2021).

62. Kim Y, Hong S-A, Yu J, Eom J, Jang K, Yoon S, Hong DH, Seo D, Lee S-N, Woo J-S, Jeong J*, Bae S*,† and Choi D*, "Adenine base editing and prime editing of chemically derived hepatic progenitors rescue genetic liver disease" Cell Stem Cell 28(9), 1614-1624 (2021). (†Lead Contact) (Featured on the front cover)

61. Hwang G-H, Jeong YK, Habib O, Hong S-A, Lim K, Kim J-S and Bae S*, "PE-Designer and PE-Analyzer: Web-based design and analysis tools for CRISPR prime editing" Nucleic Acids Research 49(W1), W499–W504 (2021).

50. Jeong YK, Song B and Bae S*, "(Review) Current status and challenges of DNA base editing tools" Molecular Therapy 28(9), 1938-1952 (2020).

40. Kim HS, Jeong YK, Hur JK, Kim J-S* and Bae S*, "Adenine base editors catalyze cytosine conversions in human cells" Nature Biotechnology 37(10), 1145–1148 (2019).

33. Jeon Y, Choi YH, Jang Y, Yu J, Goo J, Lee G, Jeong YK, Lee SH, Kim I-S, Kim J-S, Jeong C*, Lee S* and Bae S*, "Direct observation of DNA target searching and cleavage by CRISPR-Cas12a" Nature Communications 9, 2777 (2018).

24. Park J, Childs L, Kim D, Hwang G-H, Kim S, Kim S-T, Kim J-S* and Bae S*, "Digenome-seq web tool for profiling CRISPR specificity" Nature Methods 14(6), 548–549 (2017).

19. Lim Y, Bak SY, Sung K, Jeong E, Lee SH, Kim J-S, Bae S* and Kim SK*, “Structural roles of guide RNAs in the nuclease activity of Cas9 endonuclease” Nature Communications 7, 13350 (2016).

7. Bae S*,†, Park J† and Kim J-S*, "Cas-OFFinder: A fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases" Bioinformatics 30(10), 1473-1475 (2014).

2025

@. Park J-C and Bae S*, "(Review) Therapeutic applications of genome editing tools for genetic diseases" Journal of Electrodiagnosis and Neuromuscular Diseases 27(1): 1-5 (2025).

@. 임현우, 배상수*, "유전자 편집을 위한 도구, 유전자가위의 모든 것" 한경 바이오 인사이트 (BIO Insight) 8월호, 26-29 (2025).

@. 김용우, 송용휘, 배상수*, "암과 CRISPR" 대한암학회 연구동향보고서 1-1 (2025).

@. 박주찬, 유지현, 엄희수, 배상수*, "고효율 프라임교정 기술 개발을 위한 다양한 전략들" 대한피부면역학회지 (2025).

126. Uhm H and Bae S*, "(News & Views) Expansion of Artificial Intelligence for Genome Editing: From Prediction to Design" Nature Structural & Molecular Biology (Submitted).

125. Jung H, Jeong B, Kim Y-W, Jung C, Uhm H, Kim H, Oh YE, Park Y, Lee Y and Bae S*, "Site-specific replacement of large-scale DNA fragments in human cells" (Submitted). bioRxiv Link (2025).

124. Im HW, Jeong B, Lee Y, Oh YE, Jung C, Kim Y-W, Uhm H and Bae S*, "Engineered ADARs enable single-nucleotide resolution DNA A-to-G editing without bystander effects" (Submitted). bioRxiv Link (2025).

123. Jerabek S, Kim J, Sung J, Jung C, Kulmann M R, Isado M, Jang H-S, Li M, Bhatele S, Kappy M, Xu S, Hwang G-H, Xu J, Marin D, Woo J-S, Bae S, Treff N, Egli D, "Efficient base editing and development in human embryos without chromosomal alterations" (Submitted).

122. Ko M, Ha J, Kwon S, Lee HE, Mun JY, Yoon D, Yoo J, Cho H, Lee M, Park SH, Choi J-H, Lee Y, Bae S, Lee JY, Kim JY, Shin SH, Moon MH, Kwon HJ, "ER Chaperone HYOU1 Couples MAM Remodeling to Autophagic Lipid Clearance in Atherosclerosis" (Submitted).

121. Lee S-H, Park J, Jung C and Bae S*, "Hijacking and recording intracellular RNAs in human cells using eukaryotic reprogrammed tracrRNAs" (Submitted). bioRxiv Link (2024).

120. Nam B-G, Seo JH, Hong S-A, Kim J-H, Kang M, Notario GR, Hong Y, Cho S, Bae S* and Cho S-R*, "In vivo adenine base editing of mutant GALC gene ameliorates Krabbe disease progression" (Submitted).

119. Lee SJ, Nam B-G, Hong S-A, Jo DH, Lee S-M*, Bae S* and Kim JH*, "Topical application of Cas9 ribonucleoproteins inhibits corneal neovascularization in a mouse model of alkali burn injury" (Submitted).

118. Park J-C, Uhm H, Kim Y-W, Oh YE, Lee JH, Yang J, Kim K and Bae S*, "AI-generated MLH1 small binder improves prime editing efficiency" Cell DOI: 10.1016/j.cell.2025.07.010 (2025). bioRxiv Link (2024).

- 생성형 AI를 통한 세계 최고 수준의 유전자 교정 효율 달성 (2025년 8월 6일) [브릭], [동아사이언스], [베리타스알파], [이코노미사이언스], [한국강사신문], [불교방송]

- 생성형 AI와 유전자 편집 기술의 융합, 새로운 연구 지평 열다 (병원신문, 2025.09.02)

- Research Highlight in Nature Methods, "Enhancing prime editing via AI-guided binder design" Nature Methods 22(10):2007 (2025).

117. Hu SW, Jeong S, Jiang L, Koo H, Wang Z, Choi WH, Zhu B, Seok H, Zhou Y, Kim MG, Mu D, Guo H, Zhou Z, Jung SH, Zhang Y, Chae HB, Chen L, Lee S-Y, Guo L, Suh M-W, Xiao Y, Park MK, Tang H, Song J-J, Chen X, Chen A, Lee JH, Bae S*, Lee S-Y* and Shu Y*, "PAM-flexible adenine base editing rescues hearing loss in a humanized MPZL2 mouse model harboring an East Asian founder mutation" Nature Communications 16, 7186 (2025). bioRxiv Link (2024).

- 난청 일으키는 돌연변이, '원샷' 유전자가위로 교정 (2025년 8월 25일) [동아사이언스], [의학신문], [헬스경향], [헤럴드경제], [디지털조선], [이데일리], [의사신문], [후생신보], [서울대학교병원]

116. Jeong YY, Han JH, Yu J, Bae S* and Seo PJ*, "Identification of optimal adenine and cytosine base editors for genome editing in Arabidopsis and soybean" BMB Reports 58(7), 288-292 (2025).

115. Jung Y, Seo E, Yang S, Bae S, Kim JH, Jang H-k, Jo DH, "Establishment and rescue of fibroblast cell lines carrying a nonsense mutation of RB1 by CRISPR-based base editing" Scientific Reports 15: 25074 (2025).

114. Sung K, Jung Y, Kim N, Kim Y-W, Kim HH*, Kim SK* and Bae S*, "A rational engineering strategy for structural dynamics modulation enables target specificity enhancement of the Cas9 nuclease" Nucleic Acids Research 53(12):gkaf535 (2025).

- 유전자가위 오작동 줄였다…배상수 서울대교수 연구팀, ‘Correct-Cas9’ 개발 (2025년 7월 2일) [동아사이언스], [베리타스알파], [브릭]

- 세포 내 청소 '자가포식'으로 유전자 교정 효율 극대화 (2025년 5월 25일) [동아사이언스], [헤럴드경제], [연합뉴스], [조선비즈], [디지털타임스], [전자신문], [뉴스1], [파이낸셜뉴스], [브릭]

112. Lee S-H, Wu J, Im D, Hwang G-H, Jeong YK, Jiang H, Lee SJ, Jo D, GoddardIII WA, Kim JH* and Bae S*, "Bystander editing by adenine base editors impairs vision restoration in a mouse model of Leber congenital amaurosis" Molecular Therapy — Methods & Clinical Development 33(2), 101461 (2025). bioRxiv Link (2024).

111. Lim J, Lee N, Ju S, Kim J, Mun S, Jeon M, Lee Y-k, Lee S-H, Ku J, Kim S, Bae S, Kim J-S and Kim Y, "Cellular dsRNA interactome captured by K1 antibody reveals the regulatory map of exogenous RNA sensing" Communications Biology 8(1):389 (2025).

110. Jang JW, Kim MJ, Cho CS, Han HJ, Bae S, Jeon H, Jo DH, Nam HJ, "Optimizing HDAC inhibitors to enhance HDR-associated CRISPR-Cas9 gene editing efficiency in vivo and in vitro" Heliyon 11(5): e42971 (2025).

109. Jeong YY, Hong C, Han JH, Bae S* and Seo PJ*, "Development of a prime editor with improved editing efficiency in Arabidopsis" BMB Reports 58(2): 70-74 (2025).

- 유전자 편집 과정에서 발생하는 긴 DNA 손실 발생원인 규명 (2024년 11월 7일) [브릭], [조선비즈], [베리타스알파]

2024

@. 박주찬, 배상수*, [뉴스포럼 25호] Focus on: "크리스퍼 유전자 편집 치료제 최신 동향" 대한진단유전학회 25, p2-7 (2024).

107. Kang J-H, Uddin N, Kim S, Zhao Y, Yoo K-C, Kim M-J, Bae S, Shin I, Jin YW, O’Hagan HM, Yi JM and Lee S-J, "Tumor-intrinsic role of ICAM-1 in driving metastatic progression of triple-negative breast cancer through direct interaction with EGFR" Molecular Cancer 23(1):230 (2024).

106. Song A, Hwang G-H, Kim S-E, Roh MR, Hong S-A, Bae S* and Lee SE*, "Revertant Mosaic Skin Punch Grafting in Recessive Dystrophic Epidermolysis Bullosa" JAMA dermatology 160(10): 1132-1135 (2024).

- 난치성 피부질환자 대상 '피부세포 이식 치료' 성과 국내 첫 보고 (2024년 10월 25일) [헬스조선], [연합뉴스], [의학신문], [메디컬헤럴드], [헬스오], [데일리메디]

105. Kim YR, Joo J, Lee HJ, Kim C, Park J-C, Yu YS, Kim CR, Lee DH, Cha J, Kwon H, Hanssen KM, Grünewald TGP, Choi M, Han I, Bae S, Jung I, Shin Y and Baek SH, "Prion-like domain mediated phase separation of ARID1A promotes oncogenic potential of Ewing’s sarcoma" Nature Communications 15(1): 6569 (2024).

104. Kim HS, Grimes SM, Chen T, Sathe A, Lau BT, Hwang G-H, Bae S and Ji HP, "Direct measurement of engineered cancer mutations and their transcriptional phenotypes in single cells" Nature Biotechnology 42(8), 1254-1262 (2024).

103. Song B* and Bae S*, "(Review) Genome editing using CRISPR, CAST, and Fanzor systems" Molecules and Cells 47(7): 100086 (2024).

102. Cha JH, Lee S-H, Yun Y, Choi WH, Koo H, Jung SH, Chae HB, Lee DH, Lee SJ, Jo DH, Kim JH, Song J-J, Chae J-H, Lee JH, Oh SH, Park J, Kang JY, Bae S* and Lee S-Y*, "Discovery of novel disease-causing mutation in SSBP1 and its correction using adenine base editor to improve mitochondrial function" Molecular Therapy — Nucleic Acids 35(3), 102257 (2024).

101. Park J-C, Kim Y-J, Hwang G-H, Kang CY, Bae S and Cha H-J, "Enhancing genome editing in hPSCs through dual inhibition of DNA damage response and repair pathways" Nature Communications 15(1): 4002 (2024).

100. Kim JH, Yu J, Kim JY, Park YJ, Bae S, Kang KK and Jung YJ, "Phenotypic characterization of pre-harvest sprouting resistance mutants generated by the CRISPR/Cas9-geminiviral replicon system in rice" BMB Reports 57(2): 79-85 (2024).

99. Hong C, Han JH, Hwang G-H, Bae S* and Seo PJ*, "Genome-wide In-Locus Epitope Tagging of Arabidopsis Proteins using Prime Editors" BMB Reports 57(1): 66-70 (2024).

98. Park J-C and Bae S*, "Current status of genome editing technologies: special issue of BMB Reports in 2024" BMB Reports 57(1): 1 (2024).

2023

@. Song B* and Bae S*, The Springer Book Series "Genome Editing Using CRISPR" Handbook of Chemical Biology of Nucleic Acids, 1-26 (2023).

@. Bae S* and Song B, The Springer Book Series "Base Editors (Methods and Protocols)" Methods in Molecular Biology (MIMB, volume 2606) (2023).

@. 정유경, 배상수*, "크리스퍼 유전자가위 기술이 가져온 '유전자 교정 시대'" 화학세계 3월호 9-15 (2023).

97. Lee ES, Heo J, Bang WY, Chougule KM, Waminal NE, Hong NT, Kim MJ, Beak HK, Kim YJ, Priatama RA, Jang JI, Cha KI, Son SH, Rajendran S, Choo YK, Bae JH, Kim CM, Lee YK, Bae S, Jones JDG, Sohn KH, Lee J, Kim HH, Hong JC, Ware D, Kim K and Park SJ, "Engineering homoeologs provide a fine scale for quantitative traits in polyploid" Plant Biotechnol J 21(12), 2458-2472 (2023).

96. Shim JA, Lee SM, Jeong JW, Kim H, Son WJ, Park JH, Song P, Im S-H, Bae S, Park J-H, Jo Y and Hong C, "NFAT1 and NFκB regulates expression of the common γ-chain cytokine receptor in activated T cells" Cell Communication and Signaling 21(1), 309 (2023).

95. Park J-C, Kim Y-J, Han JH, Kim D, Park MJ, Kim J, Jang H-K, Bae S and Cha H-J, "MutSα and MutSβ as size-dependent cellular determinants for prime editing in human 1 embryonic stem cells" Molecular Therapy — Nucleic Acids 32, 914-922 (2023).

94. Kim Y, Shin S, Kwon S, Moon K, Baek S-V, Jo A, Kim H-S, Hwang G-H, Bae S, Kim YH, Cho S-Y and Oh J-M, "METTL3 regulates alternative splicing of cell cycle-related genes via crosstalk between mRNA m6A modifications and splicing factors" Am J Cancer Res 13(4), 1443-1456 (2023).

93. Lah S, Kim S, Kang I, Kim H, Hupperetz C, Jung H, Choi HR, Lee Y-H, Jang H-K, Bae S and Kim CH, "Engineering second-generation TCR-T cells by site-specific integration of TRAF-binding motifs into the CD247 locus" J Immunother Cancer 11(4):e005519 (2023).

92. Jo DH, Bae S, Kim HH, Kim J-S and Kim JH, "In vivo application of base and prime editing to treat inherited retinal diseases" Progress in Retinal and Eye Research 94, 101132 (2023).

91. Jo DH, Jang H-K, Cho CS, Han JH, Ryu G, Jung Y, Bae S* and Kim JH*, "Visual function restoration in a mouse model of Leber congenital amaurosis via therapeutic base editing" Molecular Therapy — Nucleic Acids 31(3), 16-27 (2023). bioRxiv Link

90. Kim S, Jeong YK, Cho CS, Lee S-H, Sohn CH, Kim JH, Jeong Y, Jo DH*, Bae S* and Lee H*, "Enhancement of Gene Editing and Base Editing with Therapeutic Ribonucleoproteins through In Vivo Delivery Based on Absorptive Silica Nanoconstruct" Advanced Healthcare Materials 12(4):e2201825. (Featured on the front cover)

89. Kwon J, Kim M, Hwang W, Jo A, Hwang G-H, Jung M, Cui G, Kim H, Eom J-H, Hur JK, Lee J, Kim Y, Bae S and Lee JK, "Extru-seq: a method for predicting genome-wide Cas9 off-target sites with advantages of both cell-based and in vitro approaches" Genome Biology 24: 4 (2023).

88. Hwang G-H and Bae S*, "Web-Based Computational Tools for Base Editors" Methods in Molecular Biology 2606, 13-22 (2023).

87. Song B and Bae S*, "Introduction and Perspectives of DNA Base Editors" Methods in Molecular Biology 2606, 3-11 (2023).

2022

@. Hwang G-H and Bae S*, "(Invited) Chapter 5. Computational Tools for Target Design and Analysis" Genome Editing in Drug Discovery DOI: 10.1002/9781119671404.ch5 (2022).

86. Kim HK, Kim JY, Kim JH, Go JY, Jung Y-S, Lee HJ, Ahn M-J, Yu J, Bae S, Kim HS, Kwak S-S, Kim M-S, Cho Y-G, Jung YJ and Kang KK, "Biochemical Characterization of Orange-Colored Rice Calli Induced by Target Mutagenesis of OsOr Gene" Plants 12(1), 56 (2023).

85. Kim JY, Kim JH, Jang YH, Yu J, Bae S, Kim M-S, Cho Y-G, Jung YJ and Kang KK, "Transcriptome and Metabolite profiling of SGR-Knockout Null Lines by CRISPR-Cas9 in Tomato" International Journal of Molecular Sciences 24(1), 109 (2023).

84. Heo YB, Hwang G-H, Kang SW, Bae S* and Woo HM*, "High-Fidelity Cytosine Base Editing in a GC-Rich Corynebacterium glutamicum with Reduced DNA Off-Target Editing Effects" Microbiology Spectrum 10(6):e0376022 (2022).

83. Kim JH, Yu J, Kim HK, Kim JY, Kim M-S, Cho Y-G, Bae S, Kang KK and Jung YJ, "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(13), 10383 (2022).

82. Song B and Bae S*, "(News & Views) Voyage to minimal base editors" Nature Chemical Biology 18(9), 920-921 (2022).

81. Kim N-S, Yu J, Bae S, Kim HS, Park S, Lee K, Lee SI and Kim JA, "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 (2022).

80. Hong S-A, Kim S-E, Lee A-y, Hwang G-H, Kim JH, Iwata H, Kim S-C, Bae S* and Lee SE*, "Therapeutic base editing and prime editing of COL7A1 mutations in recessive dystrophic epidermolysis bullosa" Molecular Therapy 30(8), 2664-2679 (2022). bioRxiv Link. (Featured on the front cover)

- '괴로운 수포성 표피박리증, 유전자 치료 가능성 커졌다' (2022년 8월 3일) [매일경제], [경향신문], [세계일보], [동아사이언스], [한국일보], [중앙일보], [국민일보], [헬스조선], [연합뉴스], [한국경제]

79. Park J-C, Kim J, Jang H-K, Lee S-Y, Kim K-T, Park S, Park S-J, Moon S-H, Bae S and Cha H-J, "Multiple isogenic GNE-myopathy modeling with mutation specific phenotypes from human pluripotent stem cells by base editors" Biomaterials 282, 121419 (2022).

78. Son H, Park J, Choi YH, Jung Y, Lee J-W, Bae S and Lee S, "Exploring the dynamic nature of divalent metal ions involved in DNA cleavage by CRISPR-Cas12a" Chemical Communications 58(12), 1978-1981 (2022).

77. Park J-C, Jang H-K, Kim J, Han JH, Jung Y, Kim K, Bae S* and Cha H-J*, "High expression of uracil DNA glycosylase determines C to T substitution in human pluripotent stem cells" Molecular Therapy — Nucleic Acids 27, 175-183 (2022).

76. Byeon E, Kim M-S, Kim D-H, Lee Y, Jeong H, Lee J-S, Hong S-A, Park JC, Kang H-M, Sayed AE-DH, Kato Y, Bae S, Watanabe H, Lee YH and Lee J-S, "The freshwater water flea Daphnia magna NIES strain genome as a resource for CRISPR/Cas9 gene targeting: The glutathione S-transferase omega 2 gene" Aquatic Toxicology 242, 106021 (2022).

75. Habib O, Habib H, Hwang G-H and Bae S*, "Comprehensive analysis of prime editing outcomes in human embryonic stem cells" Nucleic Acids Research 50(2), 1187-1197 (2022).

74. Hong S-A, Seo JH, Wi S, Jung ES, Yu J, Hwang G-H, Yu JH, Baek A, Park S, Bae S* and Cho S-R*, "In vivo gene editing via homology-independent targeted integration for adrenoleukodystrophy treatment" Molecular Therapy 30(1), 119-129 (2022).

- '로렌조 오일병', 유전자 교정으로 치료 가능성 확인 (2021년 8월 31일) [연합뉴스], [의사신문], [사이언스타임즈], [헬스조선], [팜뉴스], [쿠키뉴스], [브릭]

2021

73. Son H, Park J, Hwang I, Jung Y, Bae S and Lee S, "Mg(2+)-dependent conformational rearrangements of CRISPR-Cas12a R-loop complex are mandatory for complete double-stranded DNA cleavage" Proceedings of the National Academy of Sciences USA 118(49), e2113747118 (2021).

72. Lee K, Park O-S, Go JY, Yu J, Han JH, Kim J, Bae S, Jung YJ and Seo PJ, "Arabidopsis ATXR2 represses de novo shoot organogenesis in the transition from callus to shoot formation" Cell Reports 37(6), 109980 (2021).

71. Son H, Bae S* and Lee S*, "A thermodynamic understanding of the salt-induced B-to-Z transition of DNA containing BZ junctions" Biochemical and Biophysical Research Communications 583, 142-145 (2021).

70. Bak SY, Jung Y, Park J, Sung K, Jang H-K, Bae S* and Kim SK*, "Quantitative assessment of engineered Cas9 variants for target specificity enhancement by single-molecule reaction pathway analysis" Nucleic Acids Research 49(19), 11312–11322 (2021).

- 부작용 없는 유전자가위 개발에 초석 다져...크리스퍼 유전자가위 대표 변이체 6종의 메커니즘 분석 (2021년 10월 7일) [브릭], [한국대학생신문], [교수신문], [베리타스알파]

- 선천망막질환, 바이러스 대신 단백질로 유전자 교정 (2021년 9월 9일) [매일경제], [MBN 뉴스], [후생신보], [뉴시스], [청년의사]

68. Hur JH, Kang CY, Lee S, Parveen N, Yu J, Shamim A, Ghosh A, Bae S*, Park C-J* and Kim KK*, "AC-motif: a DNA motif containing adenine and cytosine repeat plays a role in gene regulation" Nucleic Acids Research 49(17), 10150-10165 (2021).

- 이중나선과 다른 4중나선 DNA 구조 발견...발암유전자 발현 조절 (2021년 9월 5일) [동아사이언스], [이데일리], [디지털타임스], [헤럴드경제], [뉴스1], [아이뉴스24], [브릭]

67. Cecchin M, Jeong J, Son W, Kim M, Park S, Zuliani L, Cazzaniga S, Pompa A, Kang C, Bae S, Ballottari M and Jin ES, "LPA2 protein is involved in Photosystem II assembly in Chlamydomonas reinhardtii" The Plant Journal 107, 1648–1662 (2021).

- “디엔에이 이중나선 구조 첫 발견자도 이론물리학자였어요” (2021년 7월 6일) [한겨레], [전자신문], [한국대학신문], [베리타스알파], [테크월드뉴스], [교수신문], [브릭]

65. Song B, Yang S, Hwang G-H, Yu J and Bae S*, "(Invited) Analysis of NHEJ-based DNA repair after CRISPR-mediated DNA cleavage" International Journal of Molecular Sciences 22(12), 6397 (2021).

64. Song B*, Kang CY, Han JH, Kano M, Konnerth A and Bae S*, "In vivo genome editing in single mammalian brain neurons through CRISPR-Cas9 and cytosine base editors" Computational and Structural Biotechnology Journal 19, 2477–2485 (2021).

63. Hwang G-H, Song B and Bae S*, "(Invited) Current widely-used web-based tools for CRISPR nucleases, base editors, and prime editors" Gene and Genome Editing 1, 100004 (2021).

- 난치성 간질환, 체외 유전자교정 세포치료제 개발...Cell Stem Cell 9월호 표지 선정 (2021년 5월 13일) [브릭], [한국대학신문], [베리타스알파], [교수신문], [테크월드뉴스], [헬스조선]

- "한양대 배상수 교수 유전자 프라임교정 디자인·분석 도구 개발" (2021년 5월 14일) [베리타스알파], [교수신문], [테크월드뉴스], [브릭]

60. Lee HG, Kim DH, Choi Y-R, Yu J, Hong S-A, Seo PJ* and Bae S*, "Enhancing plant immunity by expression of pathogen-targeted CRISPR-Cas9 in plants" Gene and Genome Editing 1, 100001 (2021).

59. Kim C, Jeong YK, Yu J, Shin HJ, Ku KB, Cha HJ, Han JH, Hong S-A, Kim B-T, Kim S-J*, Woo J-S* and Bae S*, "Efficient Human Cell Coexpression System and Its Application to the Production of Multiple Coronavirus Antigens" Advanced Biology 5(4), e2000154 (2021). (Featured on the front cover)

58. Hwang G-H and Bae S*, "Web-based Base Editing toolkits: BE-Designer and BE-Analyzer" Methods in Molecular Biology 2189, 81-88 (2021).

57. Hwang G-H, Kim J-S* and Bae S*, "Web-based CRISPR toolkits: Cas-OFFinder, Cas-Designer, and Cas-Analyzer" Methods in Molecular Biology 2162, 22-33 (2021).

56. Yu J, Tu L, Subburaj S, Bae S* and Lee G-J*, "Simultaneous targeting of duplicated genes in Petunia protoplasts for flower color modification via CRISPR-Cas9 ribonucleoproteins" Plant Cell Reports 40(6), 1037–1045 (2021). Free Share Link.

55. Jung YJ, Lee HJ, Yu J, Bae S, Cho YG and Kang KK, "Transcriptomic and physiological analysis of OsCAO1 knockout lines using the CRISPR/Cas9 system in rice" Plant Cell Reports 40(6), 1013–1024 (2021).

54. Kim HS, Hwang G-H, Lee H, Bae T, Park S-H, Kim YJ, Lee S, Park J-H, Bae S* and Hur JK*, "CReVIS-seq: a highly accurate and multiplexable method for genome-wide mapping of lentiviral integration sites" Molecular Therapy — Methods & Clinical Development 20, 792-800 (2021).

2020

@. Vivien Marx, "Guide RNAs: it’s good to be choosy" Nature Methods 17, 1179–1182 (2020).

@. 배상수*, "2020 노벨화학상 – 유전자 혁명 가져온 크리스퍼" 한경 바이오 인사이트 (BIO Insight) 11월호, 118-121 (2020).

@. 배상수*, "2020 노벨화학상 - 크리스퍼 유전자가위의 개발" [과학과기술] 11월호, 56-58 (2020).

@. 정유경, 황규호, 배상수*, "프라임 에디팅 유전자 교정기술 소개와 전망" BioINpro (바이오인프로) 78호 2020 바이오미래유망기술(하) 1-17 (2020).

53. Jung YJ, Kim DH, Lee HJ, Nam KH, Bae S, Nou SI, Cho Y-G, Kim MK and Kang KK, "Knockout of SlMS10 Gene (Solyc02g079810) Encoding bHLH Transcription Factor using CRISPR/Cas9 System Confers Male Sterility Phenotype in Tomato" Plants 9, 1189 (2020).

52. Kim K-T, Park J-C, Jang H-K, Lee H, Park S-W, Kwon O-S, Go Y-H, Jin Y, Kim W, Lee J, Bae S and Cha H-J, "Safe Scarless Cassette-free Selection of Genome-edited Human Pluripotent Stem Cells Using Temporary Drug Resistance" Biomaterials 262, 120295 (2020).

51. Jung YJ, Lee HJ, Lee HJ, Kim DH, Yu J, Bae S, Cho Y‑G and Kang KK, "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 (2020).

50. Jeong YK, Song B and Bae S*, "(Invited) Current status and challenges of DNA base editing tools" Molecular Therapy 28(9), 1938-1952 (2020).

49. Yu J, Cho E, Choi Y-G, Jeong YK, Na Y, Kim J-S, Cho S-R*, Woo J-S* and Bae S*, "Purification of an intact human protein overexpressed from its endogenous locus via direct genome engineering" ACS Synthetic Biology 9(7), 1591–1598 (2020). (cover article)

48. Hwang G-H, Yu J, Yang S, Son WJ, Lim K, Kim HS, Kim J-S and Bae S*, "CRISPR-Sub: analysis of DNA substitution mutations caused by CRISPR-Cas9 in human cells" Computational and Structural Biotechnology Journal 18, 1686-1694 (2020).

47. Jang H-K, Song B, Hwang G-H and Bae S*, "(Review) Current trends in gene recovery mediated by the CRISPR-Cas system" Experimental & Molecular Medicine 52(7), 1016-1027 (2020).

46. Yoon J-K, Kim D-H, Kang M-L, Jang H-K, Park H-J, Lee JB, Yi SW, Kim H-S, Baek S, Park DB, You J, Lee S-D, Sei Y, Ahn SI, Shin YM, Kim CS, Bae S, Kim YT and Sung H-J, "Anti-Atherogenic Effect of Stem Cell Nanovesicles Targeting Disturbed Flow Sites" Small 16(16):e2000012 (2020).

45. Jeong C-B, Kang H-M, Hong S-A, Byeon E, Lee J-S, Lee YH, Choi I-Y, Bae S and Lee J-S, "Generation of albino via SLC45a2 gene targeting by CRISPR/Cas9 in the marine medaka Oryzias melastigma" Marine Pollution Bulletin 154, 111038 (2020).

44. Jang H-K and Bae S*, "(Commentary) i-Silence, Please! An Alternative for Gene Disruption via Adenine Base Editors" Molecular Therapy 28(2), 348-349 (2020).

43. Yun Y, Hong S-A, Kim K-K, Baek D, Lee D, Londhe AM, Lee M, Yu J, Mceachin ZT, Bassell GJ, Bowser R, Hales CM, Cho S-R, Kim J, Pae AN, Cheong E, Kim S, Boulis NM, Bae S* and Ha Y*, "CRISPR-mediated gene correction links the ATP7A M1311V mutations with amyotrophic lateral sclerosis pathogenesis in one individual" Communications Biology 3, 33 (2020).

2019

42. Jung YJ, Lee HJ, Kim JH, Kim DH, Kim HK, Cho Y‑G, Bae S* and Kang KK*, "CRISPR/Cas9-targeted mutagenesis of F3′H, DFR and LDOX, genes related to anthocyanin biosynthesis in black rice (Oryza sativa L.)" Plant Biotechnology Reports 13(5), 521–531 (2019).

41. Jung YJ, Lee HJ, Bae S, Kim JH, Kim DH, Kim HK, Nam KH, Nogoy FM, Cho Y‑G and Kang KK, "Acquisition of seed dormancy breaking in rice (Oryza sativa L.) via CRISPR/Cas9-targeted mutagenesis of OsVP1 gene" Plant Biotechnology Reports 13(5), 511–520 (2019).

40. Kim HS, Jeong YK, Hur JK, Kim J-S* and Bae S*, "Adenine base editors catalyze cytosine conversions in human cells" Nature Biotechnology 37(10), 1145–1148 (2019).

- "기존 염기교정 유전자가위에서 새 기능 확인" (2019년 9월 24일) [연합뉴스], [한국경제], [뉴스1], [뉴시스], [동아사이언스], [아주경제], [아시아경제], [뉴스윅스], [이데일리], [IT조선], [브릭]

- [BRIC] "생명과학부문 연구성과 2019 Top5"에 선정 (의생명과학분야 종사자 986명 온라인 투표 결과)

39. Lee C, Jo DH, Hwang G-H, Yu J, Kim JH, Park S-e, Kim J-S, Kim JH* and Bae S*, "CRISPR-Pass: Gene Rescue of Nonsense Mutations Using Adenine Base Editors" Molecular Therapy 27(8), 1364-1371 (2019). bioRxiv Link (2019).

- Commentary by David J. Segal, "The Right Tools for the Right Job: CRISPR-pass Could Offer Safe Gene Correction for Many Disorders" Molecular Therapy 27(8), 1346-1347 (2019).

38. Gruffaz M, Yuan H, Meng W, Liu H, Bae S, Kim J-S, Lu C, Huang Y and Gao S-J, "CRISPR-Cas9 Screening of Kaposi's Sarcoma-Associated Herpesvirus-Transformed Cells Identifies XPO1 as a Vulnerable Target of Cancer Cells" mBio 10(3): e00866-19 (2019).

37. Jeong YK, Yu J and Bae S*, "Construction of non-canonical PAM-targeting adenosine base editors by restriction enzyme-free DNA cloning using CRISPR-Cas9" Scientific Reports 9, 4939 (2019).

36. Kim D-H, Yu J, Park JC, Jeong C-B, Bae S* and Lee J-S*, "Targeted cytochrome P450 3045C1 (CYP3045C1) gene mutation via CRISPR-Cas9 ribonucleoproteins in the marine rotifer Brachionus koreanus" Hydrobiologia 844, 117-128 (2019).

2018

@. Jung YJ, Lee G-J, Bae S and Kang KK, "토마토 과실에서 CRSPR/Cas9 시스템 이용 LeMADS-RIN 유전자 편집에 의한 에틸렌 생산량 감소" Horticultural Science and Technology 36(3), 396-405 (2018).

@. 장현기, 배상수*, [뉴스포럼 1호] Focus on: "크리스퍼 유전자가위 소개- 발견부터 응용까지" 대한진단유전학회 1, p2-4 (2018).

35. Hwang G-H, Park J, Lim K, Kim S, Yu J, Kim S-T, Elis R, Kim J-S and Bae S*, "Web-based design and analysis tools for CRISPR base editing" BMC Bioinformatics 19, 542 (2018). bioRxiv Link (2018).

34. Bae S and Kim J-S*, "(News & Views) Machine learning finds Cas9-edited genotypes" Nature Biomedical Engineering 2, 892–893 (2018).

- 크리스퍼 유전자가위 핵심 단백질 표적 탐색·절단 메커니즘 규명 (2017년 7월 24일) [전자신문], [이데일리], [아시아경제]

32. Kim S-T, Park J, Kim D, Kim K, Bae S, Schlesner M and Kim J-S, "Response to “Unexpected mutations after CRISPR–Cas9 editing in vivo”" Nature Methods 15(4), 239-240 (2018). bioRxiv Link (2017).

31. Jeong J, Baek K, Yu J, Kirst H, Betterle N, Shin W, Bae S*, Melis A* and Jin ES*, "Deletion of the chloroplast LTD protein impedes LHCI import and PSI-LHCI assembly in Chlamydomonas reinhardtii" Journal of Experimental Botany 69(5), 1147-1158 (2018).

30. Park J and Bae S*, "Cpf1-Database: Web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cpf1" Bioinformatics 34(6), 1077-1079 (2018).

29. Baek K, Yu J, Jeong J, Sim SJ, Bae S and Jin ES, "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 (2018).

2017

@. 장현기, 배상수*, "유전체 교정 시대의 도래와 전망" 한국생물공학회 BT News 24, 2 (2017).

@. Yu J, Baek K, Jin ES* and Bae S*, "DNA-free Genome Editing of Chlamydomonas reinhardtii Using CRISPR and Subsequent Mutant Analysis" Bio-protocol 7(11): e2352 (2017).

@. Jung YJ, Bae S, Lee G-J, Seo PJ, Cho Y-G and Kang KK, "벼에서 CRISPR/Cas9 활용 고빈도 유전자 편집 방법" J. Plant Biotechnol. 44, 89–96 (2017).

28. Yu N-K, Uhm H, Shim J, Choi J-H, Bae S, Sacktor TC, Hohng S and Kaang B-K, "Increased PKMζ activity impedes lateral movement of GluA2-containing AMPA receptors" Molecular Brain 10, 56 (2017).

27. Lee J-H, Park S-J, Hariharasudhan G, Kim M-J, Jung SM, Jeong S-Y, Chang I-Y, Kim C, Kim E, Yu J, Bae S and You HJ, "ID3 regulates the MDC1-mediated DNA damage response in order to maintain genome stability" Nature Communications 8, 903 (2017).

26. Lee SH, Yu J, Hwang G-H, Kim S, Kim HS, Ye S, Kim K, Park J, Park DY, Cho Y-K, Kim J-S and Bae S*, "CUT-PCR: CRISPR-mediated, ultrasensitive detection of target DNA using PCR" Oncogene 36(49), 6823-6829 (2017).

25. Koo T, Yoon AR, Cho H-Y, Bae S, Yun C-O and Kim J-S, "Selective disruption of an oncogenic mutant allele by CRISPR/Cas9 induces efficient tumor regression" Nucleic Acids Research 45(13), 7897-7908 (2017).

24. Park J, Childs L, Kim D, Hwang G-H, Kim S, Kim S-T, Kim J-S* and Bae S*, "Digenome-seq web tool for profiling CRISPR specificity" Nature Methods 14(6), 548–549 (2017).

- 한양대 연구팀, '유전자가위' 정확도 분석 프로그램 개발 (2017년 5월 31일) [뉴스1], [연합뉴스], [전자신문], [대학저널], [베리타스알파], [매일경제], [브릭]

23. Kim HS, Lee KJ, Bae S, Park J, Lee C-K, Kim M, Kim E, Kim M, Kim S, Kim C and Kim J-S, "CRISPR/Cas9-mediated Gene-knockout Screens and Target Identification via Whole Genome Sequencing Uncover Host Genes Required for Picornavirus Infection" Journal of Biological Chemistry 292(25), 10664–10671 (2017).

22. Park J, Lim K, Kim J-S* and Bae S*, "Cas-Analyzer: an online tool for assessing genome editing results using NGS data" Bioinformatics 33(2), 286-288 (2017).

2016

@. CiRA-ISSCR meeting review, "Ten years of induced pluripotency: from basic mechanisms to therapeutic applications" Development 143(12), 2039-2043 (2016).

21. Subburaj S, Tu L, Jin Y-T, Bae S, Seo PJ, Jung YJ and Lee G-J, "(Review) Targeted Genome Editing, an Alternative Tool for Trait Improvement in Horticultural Crops" Horticulture, Environment, and Biotechnology 57(6), 531-543 (2016).

20. Kim S, Jeong S-N, Bae S, Chung H and Yoo SY, "Sensitive Surface Enhanced Raman Scattering-Based Detection of a BIGH3 Point Mutation Associated with Avellino Corneal Dystrophy" Analytical Chemistry 88(23), 11288-11292 (2016).

19. Lim Y, Bak SY, Sung K, Jeong E, Lee SH, Kim J-S, Bae S* and Kim SK*, “Structural roles of guide RNAs in the nuclease activity of Cas9 endonuclease” Nature Communications 7, 13350 (2016).

- 서울대·한양대 연구팀, 크리스퍼유전자가위 작동원리 첫 규명 (2016년 11월 2일) [연합뉴스], [KBS뉴스], [동아사이언스], [이데일리], [헤럴드경제], [국민일보]

- [BRIC] "응용기술부문 연구성과 2016 Top5"에 선정 (의생명과학분야 종사자 1,218명 온라인 투표 결과)

18. He M, Yuan H, Tan B, Bai R, Kim HS, Bae S, Che L, Kim J-S and Gao S-J, "SIRT1-mediated downregulation of p27Kip1 is essential for overcoming contact inhibition of Kaposi's sarcoma-associated herpesvirus transformed cells" Oncotarget 7(46), 75698-75711 (2016).

17. Baek K, Kim DH, Jeong J, Sim SJ, Melis A, Kim J-S*, Jin ES* and Bae S*, "DNA-free two-gene knockout in Chlamydomonas reinhardtii via CRISPR-Cas9 ribonucleoproteins" Scientific Reports 6, 30620 (2016).

16. Lee SH and Bae S*, "(Invited) Structural and dynamic views of the CRISPR-Cas system at the single-molecule level" BMB Reports 49(4), 201-207 (2016).

15. Park J, Kim J-S* and Bae S*, “Cas-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cas9" Bioinformatics 32(13), 2017-2023 (2016).

14. Uhm H, Bae S, Lee M and Hohng S, "Single-Molecule FRET Combined with Magnetic Tweezers at Low Force Regime" Bulletin of the Korean Chemical Society 37(3), 408-410 (2016).

13. Subburaj S, Chung SJ, Lee CI, Ryu S, Kim DH, Kim J-S, Bae S* and Lee G-J*, "Site-directed mutagenesis in Petunia × hybrida protoplast system using direct delivery of purified recombinant Cas9 ribonucleoproteins" Plant Cell Reports 35(7), 1535-1544 (2016).

2015

12. Park J, Bae S* and Kim J-S*, "Cas-Designer: A web-based tool for choice of CRISPR-Cas9 target sites" Bioinformatics 31(24), 4014-4016 (2015).

11. Park C-Y, Kim DH, Son JS, Sung JJ, Lee J, Bae S, Kim J-H, Kim D-W and Kim J-S, "Functional Correction of Large Factor VIII Gene Chromosomal Inversions in Hemophilia A Patient-Derived iPSCs Using CRISPR-Cas9" Cell Stem Cell 17(2), 213-220 (2015).

10. Kim D†, Bae S†, Park J, Kim E, Kim S, Yu HR, Hwang J, Kim J-I and Kim J-S, "Digenome seq: Genome-wide Profiling of CRISPR-Cas9 Off-target Effects in Human Cells" Nature Methods 12(3), 237-243 (2015).

Before 2015

@. 배상수, 김헌석, 김진수, "유전체교정 기법의 민주화: Cas9 RNA-guided engineered nuclease 의 작동원리와 응용 및 전망" KSBMB Webzine 6월호, 67-75 (2014).

9. Bae S, Kweon J, Kim HS and Kim J-S, "Microhomology-based choice of Cas9 nuclease target sites" Nature Methods 11(7), 705-706 (2014).

8. Kim D, Hur J, Park K, Bae S, Shin D, Ha SC, Hwang H-Y, Hohng S, Lee J-H, Lee S, Kim Y-G and Kim KK, "Distinct Z-DNA binding mode of a PKR-like protein kinase containing a Z-DNAbinding domain (PKZ)" Nucleic Acids Research 42(9), 5937-5948 (2014).

6. Cho SW, Kim S, Kim Y, Kweon J, Kim HS, Bae S and Kim J-S, "Analysis of off-target effects ofCRISPR/Cas-derived RNA-guided endonucleases and nickases" Genome Research 24(1), 132-141 (2014).

5. Bae S, Kim Y, Kim D, Kim KK, Kim Y-G and Hohng S, "Energetics of Z-DNA Binding Protein-Mediated Helicity Reversals in DNA, RNA, and DNA–RNA Duplexes" J. Phys. Chem. B 117(44), 13866–13871 (2013).

4. Ta HM, Bae S, Han S, Song J, Ahn TK, Hohng S, Lee S and Kim KK, "Structure-basedelucidation of the regulatory mechanism for aminopeptidase activity" Acta Crystallogr. D 69(9), 1738-1747 (2013).

3. Bae S, Son H, Kim Y-G and Hohng S, "Z-DNA stabilization is dominated by the Hofmeister effect" Phys. Chem. Chem. Phys. 15(38), 15829-15832 (2013).

2. Hwang W, Bae S and Hohng S, "Autofocusing system based on optical astigmatism analysis of single-molecule images" Opt. Express 20(28), 29353-29360 (2012).

1. Bae S, Kim D, Kim KK, Kim Y-G and Hohng S, "Intrinsic Z-DNA is stabilized by theconformational selection mechanism of Z-DNA binding protein" J. Am. Chem. Soc. 133(4), 668- 671 (2011).

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