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Page 1
CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes.
Adler BA, Trinidad MI, Bellieny-Rabelo D, Zhang E, Karp HM, Skopintsev P, Thornton BW, Weissman RF, Yoon PH, Chen L, Hessler T, Eggers AR, Colognori D, Boger R, Doherty EE, Tsuchida CA, Tran RV, Hofman L, Shi H, Wasko KM, Zhou Z, Xia C, Al-Shimary MJ, Patel JR, Thomas VCJX, Pattali R, Kan MJ, Vardapetyan A, Yang A, Lahiri A, Maxwell MF, Murdock AG, Ramit GC, Henderson HR, Calvert RW, Bamert RS, Knott GJ, Lapinaite A, Pausch P, Cofsky JC, Sontheimer EJ, Wiedenheft B, Fineran PC, Brouns SJJ, Sashital DG, Thomas BC, Brown CT, Goltsman DSA, Barrangou R, Siksnys V, Banfield JF, Savage DF, Doudna JA. Adler BA, et al. Among authors: yoon ph. Nucleic Acids Res. 2024 Jan 5;52(D1):D590-D596. doi: 10.1093/nar/gkad890. Nucleic Acids Res. 2024. PMID: 37889041 Free PMC article.
To TnpB or not TnpB? Cas12 is the answer.
Yoon PH, Adler BA, Doudna JA. Yoon PH, et al. Nat Chem Biol. 2023 Mar;19(3):263-264. doi: 10.1038/s41589-022-01243-9. Epub 2023 Feb 16. Nat Chem Biol. 2023. PMID: 36797405 No abstract available.
Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes.
Yoon PH, Skopintsev P, Shi H, Chen LX, Adler BA, Al-Shimary M, Craig RJ, Li Z, Amerasekera J, Trinidad M, Nisonoff H, Chen K, Lahiri A, Boger R, Jacobsen S, Banfield JF, Doudna JA. Yoon PH, et al. bioRxiv [Preprint]. 2023 Aug 10:2023.08.09.552727. doi: 10.1101/2023.08.09.552727. bioRxiv. 2023. Update in: Nucleic Acids Res. 2023 Dec 11;51(22):12414-12427. doi: 10.1093/nar/gkad1053 PMID: 37609353 Free PMC article. Updated. Preprint.
Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes.
Yoon PH, Skopintsev P, Shi H, Chen L, Adler BA, Al-Shimary M, Craig RJ, Loi KJ, DeTurk EC, Li Z, Amerasekera J, Trinidad M, Nisonoff H, Chen K, Lahiri A, Boger R, Jacobsen S, Banfield JF, Doudna JA. Yoon PH, et al. Nucleic Acids Res. 2023 Dec 11;51(22):12414-12427. doi: 10.1093/nar/gkad1053. Nucleic Acids Res. 2023. PMID: 37971304 Free PMC article.
RNA language models predict mutations that improve RNA function.
Shulgina Y, Trinidad MI, Langeberg CJ, Nisonoff H, Chithrananda S, Skopintsev P, Nissley AJ, Patel J, Boger RS, Shi H, Yoon PH, Doherty EE, Pande T, Iyer AM, Doudna JA, Cate JHD. Shulgina Y, et al. Among authors: yoon ph. bioRxiv [Preprint]. 2024 Sep 16:2024.04.05.588317. doi: 10.1101/2024.04.05.588317. bioRxiv. 2024. Update in: Nat Commun. 2024 Dec 5;15(1):10627. doi: 10.1038/s41467-024-54812-y PMID: 38617247 Free PMC article. Updated. Preprint.
Rapid DNA unwinding accelerates genome editing by engineered CRISPR-Cas9.
Eggers AR, Chen K, Soczek KM, Tuck OT, Doherty EE, Xu B, Trinidad MI, Thornton BW, Yoon PH, Doudna JA. Eggers AR, et al. Among authors: yoon ph. Cell. 2024 Jun 20;187(13):3249-3261.e14. doi: 10.1016/j.cell.2024.04.031. Epub 2024 May 22. Cell. 2024. PMID: 38781968 Free PMC article.
Structure-guided discovery of ancestral CRISPR-Cas13 ribonucleases.
Yoon PH, Zhang Z, Loi KJ, Adler BA, Lahiri A, Vohra K, Shi H, Rabelo DB, Trinidad M, Boger RS, Al-Shimary MJ, Doudna JA. Yoon PH, et al. Science. 2024 Aug 2;385(6708):538-543. doi: 10.1126/science.adq0553. Epub 2024 Jul 18. Science. 2024. PMID: 39024377
RNA language models predict mutations that improve RNA function.
Shulgina Y, Trinidad MI, Langeberg CJ, Nisonoff H, Chithrananda S, Skopintsev P, Nissley AJ, Patel J, Boger RS, Shi H, Yoon PH, Doherty EE, Pande T, Iyer AM, Doudna JA, Cate JHD. Shulgina Y, et al. Among authors: yoon ph. Nat Commun. 2024 Dec 5;15(1):10627. doi: 10.1038/s41467-024-54812-y. Nat Commun. 2024. PMID: 39638800 Free PMC article.
Functional protein mining with conformal guarantees.
Boger RS, Chithrananda S, Angelopoulos AN, Yoon PH, Jordan MI, Doudna JA. Boger RS, et al. Among authors: yoon ph. Nat Commun. 2025 Jan 2;16(1):85. doi: 10.1038/s41467-024-55676-y. Nat Commun. 2025. PMID: 39747192 Free PMC article.
The extracellular matrix integrates mitochondrial homeostasis.
Zhang H, Tsui CK, Garcia G, Joe LK, Wu H, Maruichi A, Fan W, Pandovski S, Yoon PH, Webster BM, Durieux J, Frankino PA, Higuchi-Sanabria R, Dillin A. Zhang H, et al. Among authors: yoon ph. Cell. 2024 Aug 8;187(16):4289-4304.e26. doi: 10.1016/j.cell.2024.05.057. Epub 2024 Jun 27. Cell. 2024. PMID: 38942015
72 results