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KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks.
Di Giammartino DC, Kloetgen A, Polyzos A, Liu Y, Kim D, Murphy D, Abuhashem A, Cavaliere P, Aronson B, Shah V, Dephoure N, Stadtfeld M, Tsirigos A, Apostolou E. Di Giammartino DC, et al. Among authors: murphy d. Nat Cell Biol. 2019 Oct;21(10):1179-1190. doi: 10.1038/s41556-019-0390-6. Epub 2019 Sep 23. Nat Cell Biol. 2019. PMID: 31548608 Free PMC article.
Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities.
Garg V, Yang Y, Nowotschin S, Setty M, Kuo YY, Sharma R, Polyzos A, Salataj E, Murphy D, Jang A, Pe'er D, Apostolou E, Hadjantonakis AK. Garg V, et al. Among authors: murphy d. bioRxiv [Preprint]. 2023 Mar 29:2023.03.28.534648. doi: 10.1101/2023.03.28.534648. bioRxiv. 2023. PMID: 37034770 Free PMC article. Preprint.
Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.
Luo R, Yan J, Oh JW, Xi W, Shigaki D, Wong W, Cho HS, Murphy D, Cutler R, Rosen BP, Pulecio J, Yang D, Glenn RA, Chen T, Li QV, Vierbuchen T, Sidoli S, Apostolou E, Huangfu D, Beer MA. Luo R, et al. Among authors: murphy d. Nat Genet. 2023 Aug;55(8):1336-1346. doi: 10.1038/s41588-023-01450-7. Epub 2023 Jul 24. Nat Genet. 2023. PMID: 37488417 Free PMC article.
Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expression.
Murphy D, Salataj E, Di Giammartino DC, Rodriguez-Hernaez J, Kloetgen A, Garg V, Char E, Uyehara CM, Ee LS, Lee U, Stadtfeld M, Hadjantonakis AK, Tsirigos A, Polyzos A, Apostolou E. Murphy D, et al. bioRxiv [Preprint]. 2023 Jul 19:2023.07.19.549714. doi: 10.1101/2023.07.19.549714. bioRxiv. 2023. PMID: 37577543 Free PMC article. Preprint.
3D Enhancer-promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages.
Murphy D, Salataj E, Di Giammartino DC, Rodriguez-Hernaez J, Kloetgen A, Garg V, Char E, Uyehara CM, Ee LS, Lee U, Stadtfeld M, Hadjantonakis AK, Tsirigos A, Polyzos A, Apostolou E. Murphy D, et al. Nat Struct Mol Biol. 2024 Jan;31(1):125-140. doi: 10.1038/s41594-023-01130-4. Epub 2023 Dec 5. Nat Struct Mol Biol. 2024. PMID: 38053013 Free PMC article.
Dynamic network-guided CRISPRi screen reveals CTCF loop-constrained nonlinear enhancer-gene regulatory activity in cell state transitions.
Luo R, Yan J, Oh JW, Xi W, Shigaki D, Wong W, Cho H, Murphy D, Cutler R, Rosen BP, Pulecio J, Yang D, Glenn R, Chen T, Li QV, Vierbuchen T, Sidoli S, Apostolou E, Huangfu D, Beer MA. Luo R, et al. Among authors: murphy d. bioRxiv [Preprint]. 2023 Mar 9:2023.03.07.531569. doi: 10.1101/2023.03.07.531569. bioRxiv. 2023. Update in: Nat Genet. 2023 Aug;55(8):1336-1346. doi: 10.1038/s41588-023-01450-7. PMID: 36945628 Free PMC article. Updated. Preprint.
Discovery of Competent Chromatin Regions in Human Embryonic Stem Cells.
Pulecio J, Tayyebi Z, Liu D, Wong W, Luo R, Damodaran JR, Kaplan S, Cho H, Yan J, Murphy D, Rickert RW, Shukla A, Zhong A, González F, Yang D, Li W, Zhou T, Apostolou E, Leslie CS, Huangfu D. Pulecio J, et al. Among authors: murphy d. bioRxiv [Preprint]. 2023 Jun 14:2023.06.14.544990. doi: 10.1101/2023.06.14.544990. bioRxiv. 2023. PMID: 37398096 Free PMC article. Preprint.
CRISPR Screening Uncovers a Long-Range Enhancer for ONECUT1 in Pancreatic Differentiation and Links a Diabetes Risk Variant.
Kaplan SJ, Wong W, Yan J, Pulecio J, Cho HS, Li Q, Zhao J, Leslie-Iyer J, Kazakov J, Murphy D, Luo R, Dey KK, Apostolou E, Leslie CS, Huangfu D. Kaplan SJ, et al. Among authors: murphy d. bioRxiv [Preprint]. 2024 Jun 28:2024.04.26.591412. doi: 10.1101/2024.04.26.591412. bioRxiv. 2024. Update in: Cell Rep. 2024 Aug 27;43(8):114640. doi: 10.1016/j.celrep.2024.114640. PMID: 38746154 Free PMC article. Updated. Preprint.
6,018 results