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Super-resolution measurement of distance between transcription sites using RNA FISH with intronic probes.

Larkin JD, Cook PR.

Methods. 2015 Nov 9. pii: S1046-2023(15)30148-1. doi: 10.1016/j.ymeth.2015.11.009. [Epub ahead of print]


Why the activity of a gene depends on its neighbors.

Feuerborn A, Cook PR.

Trends Genet. 2015 Sep;31(9):483-90. doi: 10.1016/j.tig.2015.07.001. Epub 2015 Aug 7. Review.


Merging drops in a Teflon tube, and transferring fluid between them, illustrated by protein crystallization and drug screening.

Feuerborn A, Prastowo A, Cook PR, Walsh E.

Lab Chip. 2015 Sep 21;15(18):3766-75. doi: 10.1039/c5lc00726g.


Dissecting the nascent human transcriptome by analysing the RNA content of transcription factories.

Caudron-Herger M, Cook PR, Rippe K, Papantonis A.

Nucleic Acids Res. 2015 Aug 18;43(14):e95. doi: 10.1093/nar/gkv390. Epub 2015 Apr 20.


Splicing of many human genes involves sites embedded within introns.

Kelly S, Georgomanolis T, Zirkel A, Diermeier S, O'Reilly D, Murphy S, Längst G, Cook PR, Papantonis A.

Nucleic Acids Res. 2015 May 19;43(9):4721-32. doi: 10.1093/nar/gkv386. Epub 2015 Apr 20.


Phosphorylation of ORF1p is required for L1 retrotransposition.

Cook PR, Jones CE, Furano AV.

Proc Natl Acad Sci U S A. 2015 Apr 7;112(14):4298-303. doi: 10.1073/pnas.1416869112. Epub 2015 Mar 23.


Exon Skipping Is Correlated with Exon Circularization.

Kelly S, Greenman C, Cook PR, Papantonis A.

J Mol Biol. 2015 Jul 31;427(15):2414-7. doi: 10.1016/j.jmb.2015.02.018. Epub 2015 Feb 26.


TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning.

Diermeier S, Kolovos P, Heizinger L, Schwartz U, Georgomanolis T, Zirkel A, Wedemann G, Grosveld F, Knoch TA, Merkl R, Cook PR, Längst G, Papantonis A.

Genome Biol. 2014 Dec 3;15(12):536. doi: 10.1186/s13059-014-0536-6.


A simple model for DNA bridging proteins and bacterial or human genomes: bridging-induced attraction and genome compaction.

Johnson J, Brackley CA, Cook PR, Marenduzzo D.

J Phys Condens Matter. 2015 Feb 18;27(6):064119. doi: 10.1088/0953-8984/27/6/064119. Epub 2015 Jan 7.


"Dark matter" worlds of unstable RNA and protein.

Baboo S, Cook PR.

Nucleus. 2014 Jul-Aug;5(4):281-6. doi: 10.4161/nucl.29577.


Most human proteins made in both nucleus and cytoplasm turn over within minutes.

Baboo S, Bhushan B, Jiang H, Grovenor CR, Pierre P, Davis BG, Cook PR.

PLoS One. 2014 Jun 9;9(6):e99346. doi: 10.1371/journal.pone.0099346. eCollection 2014.


The HNF4A R76W mutation causes atypical dominant Fanconi syndrome in addition to a β cell phenotype.

Hamilton AJ, Bingham C, McDonald TJ, Cook PR, Caswell RC, Weedon MN, Oram RA, Shields BM, Shepherd M, Inward CD, Hamilton-Shield JP, Kohlhase J, Ellard S, Hattersley AT.

J Med Genet. 2014 Mar;51(3):165-9. doi: 10.1136/jmedgenet-2013-102066. Epub 2013 Nov 27.


Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization.

Brackley CA, Taylor S, Papantonis A, Cook PR, Marenduzzo D.

Proc Natl Acad Sci U S A. 2013 Sep 17;110(38):E3605-11. doi: 10.1073/pnas.1302950110. Epub 2013 Sep 3.


Multiscale spatial organization of RNA polymerase in Escherichia coli.

Endesfelder U, Finan K, Holden SJ, Cook PR, Kapanidis AN, Heilemann M.

Biophys J. 2013 Jul 2;105(1):172-81. doi: 10.1016/j.bpj.2013.05.048.


Transcription factories: genome organization and gene regulation.

Papantonis A, Cook PR.

Chem Rev. 2013 Nov 13;113(11):8683-705. doi: 10.1021/cr300513p. Epub 2013 Apr 18. Review. No abstract available.


Promoter type influences transcriptional topography by targeting genes to distinct nucleoplasmic sites.

Larkin JD, Papantonis A, Cook PR.

J Cell Sci. 2013 May 1;126(Pt 9):2052-9. doi: 10.1242/jcs.123653. Epub 2013 Feb 26.


Derivation of a new banded waveguide model topology for sound synthesis.

Fink AM, Spanias AS, Cook PR.

J Acoust Soc Am. 2013 Feb;133(2):EL76-81. doi: 10.1121/1.4773287.


Space exploration by the promoter of a long human gene during one transcription cycle.

Larkin JD, Papantonis A, Cook PR, Marenduzzo D.

Nucleic Acids Res. 2013 Feb 1;41(4):2216-27. doi: 10.1093/nar/gks1441. Epub 2013 Jan 8.


TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed.

Papantonis A, Kohro T, Baboo S, Larkin JD, Deng B, Short P, Tsutsumi S, Taylor S, Kanki Y, Kobayashi M, Li G, Poh HM, Ruan X, Aburatani H, Ruan Y, Kodama T, Wada Y, Cook PR.

EMBO J. 2012 Nov 28;31(23):4404-14. doi: 10.1038/emboj.2012.288. Epub 2012 Oct 26.


Maximum precision closed-form solution for localizing diffraction-limited spots in noisy images.

Larkin JD, Cook PR.

Opt Express. 2012 Jul 30;20(16):18478-93. doi: 10.1364/OE.20.018478.

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