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A universal deep-learning model for zinc finger design enables transcription factor reprogramming.
Ichikawa DM, Abdin O, Alerasool N, Kogenaru M, Mueller AL, Wen H, Giganti DO, Goldberg GW, Adams S, Spencer JM, Razavi R, Nim S, Zheng H, Gionco C, Clark FT, Strokach A, Hughes TR, Lionnet T, Taipale M, Kim PM, Noyes MB. Ichikawa DM, et al. Among authors: hughes tr. Nat Biotechnol. 2023 Aug;41(8):1117-1129. doi: 10.1038/s41587-022-01624-4. Epub 2023 Jan 26. Nat Biotechnol. 2023. PMID: 36702896 Free PMC article.
Evaluation of methods for modeling transcription factor sequence specificity.
Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S; DREAM5 Consortium; Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR. Weirauch MT, et al. Among authors: hughes tr. Nat Biotechnol. 2013 Feb;31(2):126-34. doi: 10.1038/nbt.2486. Epub 2013 Jan 27. Nat Biotechnol. 2013. PMID: 23354101 Free PMC article.
A compendium of RNA-binding motifs for decoding gene regulation.
Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X, Gueroussov S, Albu M, Zheng H, Yang A, Na H, Irimia M, Matzat LH, Dale RK, Smith SA, Yarosh CA, Kelly SM, Nabet B, Mecenas D, Li W, Laishram RS, Qiao M, Lipshitz HD, Piano F, Corbett AH, Carstens RP, Frey BJ, Anderson RA, Lynch KW, Penalva LO, Lei EP, Fraser AG, Blencowe BJ, Morris QD, Hughes TR. Ray D, et al. Among authors: hughes tr. Nature. 2013 Jul 11;499(7457):172-7. doi: 10.1038/nature12311. Nature. 2013. PMID: 23846655 Free PMC article.
C2H2 zinc finger proteins greatly expand the human regulatory lexicon.
Najafabadi HS, Mnaimneh S, Schmitges FW, Garton M, Lam KN, Yang A, Albu M, Weirauch MT, Radovani E, Kim PM, Greenblatt J, Frey BJ, Hughes TR. Najafabadi HS, et al. Among authors: hughes tr. Nat Biotechnol. 2015 May;33(5):555-62. doi: 10.1038/nbt.3128. Epub 2015 Feb 18. Nat Biotechnol. 2015. PMID: 25690854
282 results