Brackley CA - Search Results

1

Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers.

Mikulasova A, Kent D, Trevisan-Herraz M, Karataraki N, Fung KTM, Ashby C, Cieslak A, Yaccoby S, van Rhee F, Zangari M, Thanendrarajan S, Schinke C, Morgan GJ, Asnafi V, Spicuglia S, Brackley CA, Corcoran AE, Hambleton S, Walker BA, Rico D, Russell LJ. Mikulasova A, et al. Among authors: brackley ca. Genome Res. 2022 Jul;32(7):1343-1354. doi: 10.1101/gr.276042.121. Epub 2021 Dec 21. Genome Res. 2022. PMID: 34933939 Free PMC article.

2

High-resolution simulations of chromatin folding at genomic rearrangements in malignant B cells provide mechanistic insights into proto-oncogene deregulation.

Rico D, Kent D, Karataraki N, Mikulasova A, Berlinguer-Palmini R, Walker BA, Javierre BM, Russell LJ, Brackley CA. Rico D, et al. Among authors: brackley ca. Genome Res. 2022 Jul 27;32(7):1355-1366. doi: 10.1101/gr.276028.121. Genome Res. 2022. PMID: 35863900 Free PMC article.

3

Evolutionarily conserved enhancer-associated features within the MYEOV locus suggest a regulatory role for this non-coding DNA region in cancer.

Davidson BSA, Arcila-Galvis JE, Trevisan-Herraz M, Mikulasova A, Brackley CA, Russell LJ, Rico D. Davidson BSA, et al. Among authors: brackley ca. Front Cell Dev Biol. 2024 Jul 30;12:1294510. doi: 10.3389/fcell.2024.1294510. eCollection 2024. Front Cell Dev Biol. 2024. PMID: 39139450 Free PMC article.

4

Nucleosome positions alone can be used to predict domains in yeast chromosomes.

Wiese O, Marenduzzo D, Brackley CA. Wiese O, et al. Among authors: brackley ca. Proc Natl Acad Sci U S A. 2019 Aug 27;116(35):17307-17315. doi: 10.1073/pnas.1817829116. Epub 2019 Aug 15. Proc Natl Acad Sci U S A. 2019. PMID: 31416914 Free PMC article.

5

Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models.

Brackley CA, Brown JM, Waithe D, Babbs C, Davies J, Hughes JR, Buckle VJ, Marenduzzo D. Brackley CA, et al. Genome Biol. 2016 Mar 31;17:59. doi: 10.1186/s13059-016-0909-0. Genome Biol. 2016. PMID: 27036497 Free PMC article.

6

capC-MAP: software for analysis of Capture-C data.

Buckle A, Gilbert N, Marenduzzo D, Brackley CA. Buckle A, et al. Among authors: brackley ca. Bioinformatics. 2019 Nov 1;35(22):4773-4775. doi: 10.1093/bioinformatics/btz480. Bioinformatics. 2019. PMID: 31173058

7

Topological constraints strongly affect chromatin reconstitution in silico.

Brackley CA, Allan J, Keszenman-Pereyra D, Marenduzzo D. Brackley CA, et al. Nucleic Acids Res. 2015 Jan;43(1):63-73. doi: 10.1093/nar/gku1085. Epub 2014 Nov 28. Nucleic Acids Res. 2015. PMID: 25432958 Free PMC article.

8

Simulating the chromatin-mediated phase separation of model proteins with multiple domains.

Ancona M, Brackley CA. Ancona M, et al. Among authors: brackley ca. Biophys J. 2022 Jul 5;121(13):2600-2612. doi: 10.1016/j.bpj.2022.05.039. Epub 2022 May 28. Biophys J. 2022. PMID: 35643628 Free PMC article.

9

Facilitated diffusion on mobile DNA: configurational traps and sequence heterogeneity.

Brackley CA, Cates ME, Marenduzzo D. Brackley CA, et al. Phys Rev Lett. 2012 Oct 19;109(16):168103. doi: 10.1103/PhysRevLett.109.168103. Epub 2012 Oct 17. Phys Rev Lett. 2012. PMID: 23215135

10

Effect of DNA conformation on facilitated diffusion.

Brackley CA, Cates ME, Marenduzzo D. Brackley CA, et al. Biochem Soc Trans. 2013 Apr;41(2):582-8. doi: 10.1042/BST20120234. Biochem Soc Trans. 2013. PMID: 23514158 Review.

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