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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: shi h. Nucleic Acids Res. 2024 Jan 5;52(D1):D590-D596. doi: 10.1093/nar/gkad890. Nucleic Acids Res. 2024. PMID: 37889041 Free PMC article.
Improved genome editing by an engineered CRISPR-Cas12a.
Ma E, Chen K, Shi H, Stahl EC, Adler B, Trinidad M, Liu J, Zhou K, Ye J, Doudna JA. Ma E, et al. Among authors: shi h. Nucleic Acids Res. 2022 Dec 9;50(22):12689-12701. doi: 10.1093/nar/gkac1192. Nucleic Acids Res. 2022. PMID: 36537251 Free PMC article.
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. Among authors: shi h. 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: shi h. 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.
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. Among authors: shi h. 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: shi h. Nat Commun. 2024 Dec 5;15(1):10627. doi: 10.1038/s41467-024-54812-y. Nat Commun. 2024. PMID: 39638800 Free PMC article.
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