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Affinity-optimizing enhancer variants disrupt development.
Lim F, Solvason JJ, Ryan GE, Le SH, Jindal GA, Steffen P, Jandu SK, Farley EK. Lim F, et al. Nature. 2024 Feb;626(7997):151-159. doi: 10.1038/s41586-023-06922-8. Epub 2024 Jan 17. Nature. 2024. PMID: 38233525 Free PMC article.
Conserved enhancers control notochord expression of vertebrate Brachyury.
Kemmler CL, Smolikova J, Moran HR, Mannion BJ, Knapp D, Lim F, Czarkwiani A, Hermosilla Aguayo V, Rapp V, Fitch OE, Bötschi S, Selleri L, Farley E, Braasch I, Yun M, Visel A, Osterwalder M, Mosimann C, Kozmik Z, Burger A. Kemmler CL, et al. Nat Commun. 2023 Oct 18;14(1):6594. doi: 10.1038/s41467-023-42151-3. Nat Commun. 2023. PMID: 37852970 Free PMC article.
3D genomics across the tree of life reveals condensin II as a determinant of architecture type.
Hoencamp C, Dudchenko O, Elbatsh AMO, Brahmachari S, Raaijmakers JA, van Schaik T, Sedeño Cacciatore Á, Contessoto VG, van Heesbeen RGHP, van den Broek B, Mhaskar AN, Teunissen H, St Hilaire BG, Weisz D, Omer AD, Pham M, Colaric Z, Yang Z, Rao SSP, Mitra N, Lui C, Yao W, Khan R, Moroz LL, Kohn A, St Leger J, Mena A, Holcroft K, Gambetta MC, Lim F, Farley E, Stein N, Haddad A, Chauss D, Mutlu AS, Wang MC, Young ND, Hildebrandt E, Cheng HH, Knight CJ, Burnham TLU, Hovel KA, Beel AJ, Mattei PJ, Kornberg RD, Warren WC, Cary G, Gómez-Skarmeta JL, Hinman V, Lindblad-Toh K, Di Palma F, Maeshima K, Multani AS, Pathak S, Nel-Themaat L, Behringer RR, Kaur P, Medema RH, van Steensel B, de Wit E, Onuchic JN, Di Pierro M, Lieberman Aiden E, Rowland BD. Hoencamp C, et al. Science. 2021 May 28;372(6545):984-989. doi: 10.1126/science.abe2218. Science. 2021. PMID: 34045355 Free PMC article.
Diverse logics and grammar encode notochord enhancers.
Song BP, Ragsac MF, Tellez K, Jindal GA, Grudzien JL, Le SH, Farley EK. Song BP, et al. Cell Rep. 2023 Feb 28;42(2):112052. doi: 10.1016/j.celrep.2023.112052. Epub 2023 Jan 31. Cell Rep. 2023. PMID: 36729834 Free PMC article.
Predictive analyses of regulatory sequences with EUGENe.
Klie A, Laub D, Talwar JV, Stites H, Jores T, Solvason JJ, Farley EK, Carter H. Klie A, et al. Nat Comput Sci. 2023 Nov;3(11):946-956. doi: 10.1038/s43588-023-00544-w. Epub 2023 Nov 16. Nat Comput Sci. 2023. PMID: 38177592 Free PMC article.
Conserved enhancer logic controls the notochord expression of vertebrate Brachyury.
Kemmler CL, Smolikova J, Moran HR, Mannion BJ, Knapp D, Lim F, Czarkwiani A, Hermosilla Aguayo V, Rapp V, Fitch OE, Bötschi S, Selleri L, Farley E, Braasch I, Yun M, Visel A, Osterwalder M, Mosimann C, Kozmik Z, Burger A. Kemmler CL, et al. bioRxiv [Preprint]. 2023 Apr 20:2023.04.20.536761. doi: 10.1101/2023.04.20.536761. bioRxiv. 2023. Update in: Nat Commun. 2023 Oct 18;14(1):6594. doi: 10.1038/s41467-023-42151-3 PMID: 37131681 Free PMC article. Updated. Preprint.
12 results