Research Area
Genome-wide nuclease libraries for disruption of coding and noncoding elements, genome editing tools for biomedical research and biotechnology, and potential therapeutic applications of CRISPR-Cas9 to genetic eye and liver diseases.
Team Description
Currently, we are trying to improve and/or develop genome-wide nuclease libraries for disruption of coding and noncoding elements. Other ongoing projects in the lab include potential therapeutic applications of CRISPR-Cas9 to genetic eye and liver diseases. We are also interested in high-throughput approaches for evaluating the activity of CRISPR-Cas9 based on target sequences. We will continue our research to improve or develop genome editing tools for biomedical research and biotechnology and apply these advanced genome editing methods as therapeutic modalities for various diseases.
Team Members
Team Show
Publications
1. Kim HK, Yu GS, Park JM, Min SW, Lee ST, Yoon SR, KimH+. (Corresponding author). Predicting the efficiency of prime editing guide RNAs in human cells. Nat. Biotechnol. 2020 Sep 21.doi:10.1038/s41587-020-0573-5.
2. Song MJ, Kim HK, Lee ST, Kim YG, Seo SY, Park JM, Choi JW, Jang HW, Shin JH, Min SW, Zhejiu Quan, Kim JH, Kang HC, Yoon S, KimH+. (Corresponding author). Sequence-specific prediction of the efficiencies of adenine and cytosine base editors.Nat. Biotechnol. 2020 ; doi: 10.1038/s41587-020-0573-5. Epub 2020 Jul 6.
3. Kim N, Kim HK, Lee ST, Seo JH, Choi JW, Park J, Min SW, Yoon S, Cho SR, KimH+. (Corresponding author). Prediction of the sequence-specific cleavage activity of Cas9 variants. Nat. Biotechnol. 2020; doi : 10.1038/s41587-020-0537-9. Epub 2020 Jun 8.
4. Kim HK, Lee S, Kim Y, Park J, Min S, Choi JW, Huang TP, Yoon S, Liu DR, KimH+ (+Corresponding author). High-throughput analysis of the activities of xCas9, SpCas9-NG and SpCas9 at matched and mismatched target sequences in human cells. Nat Biomed Eng. 2020 ;4(1):111-124., DOI: 10.1038 /s41551-019-0505-1
5. Kim HK, Kim Y, Lee S, Min S, Bae JY, Choi JW, Park J, Jung D, Yoon S, Kim H+ (+Corresponding author). SpCas9 activity prediction by DeepSpCas9, a deep learning – based model with high generalization performance. Sci. Adv. 2019; 5 (11): eaax9249, DOI: 10.1126/sciadv.aax9249
6. Kim HK, Min S, Song M, Jung S, Choi JW, Kim Y, Lee S, Yoon S+, Kim H+ (+Corresponding author). Deep learning improves prediction of CRISPR–Cpf1 guide RNA activity. Nat Biotechnol. Published online 29 January 2018. http://rdcu.be/FOM1
7. Kim W, Lee S, Kim HS, Song M, Cha YH, Kim YH, Shin J, Lee ES, Joo Y, Song JJ, Choi EJ, Choi JW, Lee J, Kang M, Yook JI, Lee MG, Kim YS, Paik S.Kim H+ (+Corresponding author). Targeting mutant KRAS with CRISPR-Cas9 controls tumor growth. Genome Res. 2018 Jan 11. pii: gr.223891.117. doi: 10.1101/gr.223891.117.
8. Gopalappa R, Suresh B, Ramakrishna S+, Kim H+ (+Corresponding authors). Paired D10A Cas9 nickases are sometimes more efficient than individual nucleases for gene disruption. Nucleic Acids Res. 2018.
9. Kim HK, Song M, Lee J, Menon AV, Jung S, Kang YM, Choi JW, Woo E, Koh HC, Nam JW, Kim H+ (+Corresponding author). In vivo high-throughput profiling of CRISPR-Cpf1 activity. Nat. Methods., 2017; 14: 153-159
10. Lim JS, Gopalappa R, Kim SH, Ramakrishna S, Lee M, Kim W, Kim J, Park SM, Lee J, Oh JH, Kim HD, Park CH, Lee JS, Kim S, Kim SD, Han JM, Kang HC+, Kim H+, Lee JH+ (+Corresponding authors). Somatic Mutations in TSC1 and TSC2 cause focal cortical dysplasia. Am J Hum Genet. 2017 ;100(3) :454-472
11. Kim YH, Kim HO, Baek EJ, Kurita R, Cha HJ, Nakamura Y, Kim H+ (+Corresponding author). Rh D blood group conversion using transcription activator-like effector nucleases. Nat. Commun., 2015 Jun 16; 6:7451.
12. Ramakrishna S, Dad A-B D, Beloor J, Gopalappa R, Lee S-K, Kim H+ (+Corresponding author). Gene disruption by cell-penetrating peptide-mediated delivery of Cas9 protein and guide RNA. Genome Res., 2014 June. 24: 1020-1027 (Featured on the cover; http://genome.cshlp.org/content/24/6.cover-expansion).
13. Kim H, Kim JS. A guide to genome engineering with programmable nucleases. Nat. Rev. Genet., 2014 May;15(5):321-34.
14. Ramakrishna S, Cho SW, Kim S, Song M, Gopalappa R, Kim JS+, Kim H+ (+Corresponding authors). Surrogate reporter-based enrichment of cells containing RNA-guided Cas9 nuclease-induced mutations. Nat. Commun., 2014 Feb 26; 5: 3378.
15. Kim H, Um E, Cho SR, Jung C, Kim H+, and Kim JS+ (+Corresponding authors). Surrogate reporters for enrichment of cells with nuclease-induced mutations. Nat. Methods, 2011 Oct 9;8:941-3.