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Manipulating the 3D organization of the largest synthetic yeast chromosome.
Zhang W, Lazar-Stefanita L, Yamashita H, Shen MJ, Mitchell LA, Kurasawa H, Lobzaev E, Fanfani V, Haase MAB, Sun X, Jiang Q, Goldberg GW, Ichikawa DM, Lauer SL, McCulloch LH, Easo N, Lin SJ, Camellato BR, Zhu Y, Cai J, Xu Z, Zhao Y, Sacasa M; Build-A-Genome Class; Noyes MB, Bader JS, Deutsch S, Stracquadanio G, Aizawa Y, Dai J, Boeke JD. Zhang W, et al. Among authors: boeke jd. Mol Cell. 2023 Dec 7;83(23):4424-4437.e5. doi: 10.1016/j.molcel.2023.10.015. Epub 2023 Nov 8. Mol Cell. 2023. PMID: 37944526 Free article.
Safety by design: Biosafety and biosecurity in the age of synthetic genomics.
Hoffmann SA, Diggans J, Densmore D, Dai J, Knight T, Leproust E, Boeke JD, Wheeler N, Cai Y. Hoffmann SA, et al. Among authors: boeke jd. iScience. 2023 Feb 10;26(3):106165. doi: 10.1016/j.isci.2023.106165. eCollection 2023 Mar 17. iScience. 2023. PMID: 36895643 Free PMC article. Review.
Synthetic regulatory genomics uncovers enhancer context dependence at the Sox2 locus.
Brosh R, Coelho C, Ribeiro-Dos-Santos AM, Ellis G, Hogan MS, Ashe HJ, Somogyi N, Ordoñez R, Luther RD, Huang E, Boeke JD, Maurano MT. Brosh R, et al. Among authors: boeke jd. Mol Cell. 2023 Apr 6;83(7):1140-1152.e7. doi: 10.1016/j.molcel.2023.02.027. Epub 2023 Mar 16. Mol Cell. 2023. PMID: 36931273 Free PMC article.
Genomic context sensitizes regulatory elements to genetic disruption.
Ordoñez R, Zhang W, Ellis G, Zhu Y, Ashe HJ, Ribeiro-Dos-Santos AM, Brosh R, Huang E, Hogan MS, Boeke JD, Maurano MT. Ordoñez R, et al. Among authors: boeke jd. bioRxiv [Preprint]. 2024 Mar 12:2023.07.02.547201. doi: 10.1101/2023.07.02.547201. bioRxiv. 2024. Update in: Mol Cell. 2024 May 16;84(10):1842-1854.e7. doi: 10.1016/j.molcel.2024.04.013 PMID: 37781588 Free PMC article. Updated. Preprint.
Engineered transcription-associated Cas9 targeting in eukaryotic cells.
Goldberg GW, Kogenaru M, Keegan S, Haase MAB, Kagermazova L, Arias MA, Onyebeke K, Adams S, Beyer DK, Fenyö D, Noyes MB, Boeke JD. Goldberg GW, et al. Among authors: boeke jd. bioRxiv [Preprint]. 2024 Aug 18:2023.09.18.558319. doi: 10.1101/2023.09.18.558319. bioRxiv. 2024. Update in: Nat Commun. 2024 Nov 27;15(1):10287. doi: 10.1038/s41467-024-54629-9 PMID: 37781609 Free PMC article. Updated. Preprint.
Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions.
Zhao Y, Coelho C, Hughes AL, Lazar-Stefanita L, Yang S, Brooks AN, Walker RSK, Zhang W, Lauer S, Hernandez C, Cai J, Mitchell LA, Agmon N, Shen Y, Sall J, Fanfani V, Jalan A, Rivera J, Liang FX, Bader JS, Stracquadanio G, Steinmetz LM, Cai Y, Boeke JD. Zhao Y, et al. Among authors: boeke jd. Cell. 2023 Nov 22;186(24):5220-5236.e16. doi: 10.1016/j.cell.2023.09.025. Epub 2023 Nov 8. Cell. 2023. PMID: 37944511 Free article.
Design, construction, and functional characterization of a tRNA neochromosome in yeast.
Schindler D, Walker RSK, Jiang S, Brooks AN, Wang Y, Müller CA, Cockram C, Luo Y, García A, Schraivogel D, Mozziconacci J, Pena N, Assari M, Sánchez Olmos MDC, Zhao Y, Ballerini A, Blount BA, Cai J, Ogunlana L, Liu W, Jönsson K, Abramczyk D, Garcia-Ruiz E, Turowski TW, Swidah R, Ellis T, Pan T, Antequera F, Shen Y, Nieduszynski CA, Koszul R, Dai J, Steinmetz LM, Boeke JD, Cai Y. Schindler D, et al. Among authors: boeke jd. Cell. 2023 Nov 22;186(24):5237-5253.e22. doi: 10.1016/j.cell.2023.10.015. Epub 2023 Nov 8. Cell. 2023. PMID: 37944512 Free article.
Synthetic chromosome fusion: Effects on mitotic and meiotic genome structure and function.
Luo J, Vale-Silva LA, Raghavan AR, Mercy G, Heldrich J, Sun X, Li MK, Zhang W, Agmon N, Yang K, Cai J, Stracquadanio G, Thierry A, Zhao Y, Coelho C, McCulloch LH, Lauer S; Build-A-Genome Class; Kaback DB, Bader JS, Mitchell LA, Mozziconacci J, Koszul R, Hochwagen A, Boeke JD. Luo J, et al. Among authors: boeke jd. Cell Genom. 2023 Nov 9;3(11):100439. doi: 10.1016/j.xgen.2023.100439. eCollection 2023 Nov 8. Cell Genom. 2023. PMID: 38020967 Free PMC article.
Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast.
Shen Y, Gao F, Wang Y, Wang Y, Zheng J, Gong J, Zhang J, Luo Z, Schindler D, Deng Y, Ding W, Lin T, Swidah R, Zhao H, Jiang S, Zeng C, Chen S, Chen T, Wang Y, Luo Y, Mitchell L, Bader JS, Zhang G, Shen X, Wang J, Fu X, Dai J, Boeke JD, Yang H, Xu X, Cai Y. Shen Y, et al. Among authors: boeke jd. Cell Genom. 2023 Nov 9;3(11):100364. doi: 10.1016/j.xgen.2023.100364. eCollection 2023 Nov 8. Cell Genom. 2023. PMID: 38020968 Free PMC article.
422 results