Phanstiel DH - Search Results

1

CTCF: an R/bioconductor data package of human and mouse CTCF binding sites.

Dozmorov MG, Mu W, Davis ES, Lee S, Triche TJ Jr, Phanstiel DH, Love MI. Dozmorov MG, et al. Among authors: phanstiel dh. Bioinform Adv. 2022 Dec 16;2(1):vbac097. doi: 10.1093/bioadv/vbac097. eCollection 2022. Bioinform Adv. 2022. PMID: 36699364 Free PMC article.

2

Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development.

Phanstiel DH, Van Bortle K, Spacek D, Hess GT, Shamim MS, Machol I, Love MI, Aiden EL, Bassik MC, Snyder MP. Phanstiel DH, et al. Mol Cell. 2017 Sep 21;67(6):1037-1048.e6. doi: 10.1016/j.molcel.2017.08.006. Epub 2017 Sep 7. Mol Cell. 2017. PMID: 28890333 Free PMC article.

3

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.

4

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.

5

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.

6

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.

7

A multi-omic dissection of super-enhancer driven oncogenic gene expression programs in ovarian cancer.

Kelly MR, Wisniewska K, Regner MJ, Lewis MW, Perreault AA, Davis ES, Phanstiel DH, Parker JS, Franco HL. Kelly MR, et al. Among authors: phanstiel dh. Nat Commun. 2022 Jul 22;13(1):4247. doi: 10.1038/s41467-022-31919-8. Nat Commun. 2022. PMID: 35869079 Free PMC article.

8

3D chromatin structure in chondrocytes identifies putative osteoarthritis risk genes.

Thulson E, Davis ES, D'Costa S, Coryell PR, Kramer NE, Mohlke KL, Loeser RF, Diekman BO, Phanstiel DH. Thulson E, et al. Among authors: phanstiel dh. Genetics. 2022 Nov 30;222(4):iyac141. doi: 10.1093/genetics/iyac141. Genetics. 2022. PMID: 36099032 Free PMC article.

9

Temporal analysis suggests a reciprocal relationship between 3D chromatin structure and transcription.

Reed KSM, Davis ES, Bond ML, Cabrera A, Thulson E, Quiroga IY, Cassel S, Woolery KT, Hilton I, Won H, Love MI, Phanstiel DH. Reed KSM, et al. Among authors: phanstiel dh. Cell Rep. 2022 Nov 1;41(5):111567. doi: 10.1016/j.celrep.2022.111567. Cell Rep. 2022. PMID: 36323252 Free PMC article.

10

Guiding the design of well-powered Hi-C experiments to detect differential loops.

Parker SM, Davis ES, Phanstiel DH. Parker SM, et al. Among authors: phanstiel dh. bioRxiv [Preprint]. 2023 Mar 16:2023.03.15.532762. doi: 10.1101/2023.03.15.532762. bioRxiv. 2023. Update in: Bioinform Adv. 2023 Oct 16;3(1):vbad152. doi: 10.1093/bioadv/vbad152. PMID: 36993250 Free PMC article. Updated. Preprint.

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