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Chromatin alternates between A and B compartments at kilobase scale for subgenic organization.
Harris HL, Gu H, Olshansky M, Wang A, Farabella I, Eliaz Y, Kalluchi A, Krishna A, Jacobs M, Cauer G, Pham M, Rao SSP, Dudchenko O, Omer A, Mohajeri K, Kim S, Nichols MH, Davis ES, Gkountaroulis D, Udupa D, Aiden AP, Corces VG, Phanstiel DH, Noble WS, Nir G, Di Pierro M, Seo JS, Talkowski ME, Aiden EL, Rowley MJ. Harris HL, et al. Among authors: phanstiel dh. Nat Commun. 2023 Jun 6;14(1):3303. doi: 10.1038/s41467-023-38429-1. Nat Commun. 2023. PMID: 37280210 Free PMC article.
Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements.
Tycko J, Wainberg M, Marinov GK, Ursu O, Hess GT, Ego BK, Aradhana, Li A, Truong A, Trevino AE, Spees K, Yao D, Kaplow IM, Greenside PG, Morgens DW, Phanstiel DH, Snyder MP, Bintu L, Greenleaf WJ, Kundaje A, Bassik MC. Tycko J, et al. Among authors: phanstiel dh. Nat Commun. 2019 Sep 6;10(1):4063. doi: 10.1038/s41467-019-11955-7. Nat Commun. 2019. PMID: 31492858 Free PMC article.
CoralP: Flexible visualization of the human phosphatome.
Min A, Deoudes E, Bond ML, Davis ES, Phanstiel DH. Min A, et al. Among authors: phanstiel dh. J Open Source Softw. 2019;4(44):1837. doi: 10.21105/joss.01837. Epub 2019 Dec 3. J Open Source Softw. 2019. PMID: 31903446 Free PMC article.
Bedtoolsr: An R package for genomic data analysis and manipulation.
Patwardhan MN, Wenger CD, Davis ES, Phanstiel DH. Patwardhan MN, et al. Among authors: phanstiel dh. J Open Source Softw. 2019;4(44):1742. doi: 10.21105/joss.01742. Epub 2019 Dec 6. J Open Source Softw. 2019. PMID: 31903447 Free PMC article.
Phase separation drives aberrant chromatin looping and cancer development.
Ahn JH, Davis ES, Daugird TA, Zhao S, Quiroga IY, Uryu H, Li J, Storey AJ, Tsai YH, Keeley DP, Mackintosh SG, Edmondson RD, Byrum SD, Cai L, Tackett AJ, Zheng D, Legant WR, Phanstiel DH, Wang GG. Ahn JH, et al. Among authors: phanstiel dh. Nature. 2021 Jul;595(7868):591-595. doi: 10.1038/s41586-021-03662-5. Epub 2021 Jun 23. Nature. 2021. PMID: 34163069 Free PMC article.
Plotgardener: cultivating precise multi-panel figures in R.
Kramer NE, Davis ES, Wenger CD, Deoudes EM, Parker SM, Love MI, Phanstiel DH. Kramer NE, et al. Among authors: phanstiel dh. Bioinformatics. 2022 Mar 28;38(7):2042-2045. doi: 10.1093/bioinformatics/btac057. Bioinformatics. 2022. PMID: 35134826 Free PMC article.
42 results