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Items: 1 to 50 of 234

1.

Raising fluid walls around living cells.

Soitu C, Feuerborn A, Deroy C, Castrejón-Pita AA, Cook PR, Walsh EJ.

Sci Adv. 2019 Jun 5;5(6):eaav8002. doi: 10.1126/sciadv.aav8002. eCollection 2019 Jun.

2.
3.

Microfluidic chambers using fluid walls for cell biology.

Soitu C, Feuerborn A, Tan AN, Walker H, Walsh PA, Castrejón-Pita AA, Cook PR, Walsh EJ.

Proc Natl Acad Sci U S A. 2018 Jun 26;115(26):E5926-E5933. doi: 10.1073/pnas.1805449115. Epub 2018 Jun 12.

4.

Nonequilibrium Chromosome Looping via Molecular Slip Links.

Brackley CA, Johnson J, Michieletto D, Morozov AN, Nicodemi M, Cook PR, Marenduzzo D.

Phys Rev Lett. 2017 Sep 29;119(13):138101. doi: 10.1103/PhysRevLett.119.138101. Epub 2017 Sep 26.

PMID:
29341686
5.

Extrusion without a motor: a new take on the loop extrusion model of genome organization.

Brackley CA, Johnson J, Michieletto D, Morozov AN, Nicodemi M, Cook PR, Marenduzzo D.

Nucleus. 2018 Jan 1;9(1):95-103. doi: 10.1080/19491034.2017.1421825.

6.

Shaping epigenetic memory via genomic bookmarking.

Michieletto D, Chiang M, Colì D, Papantonis A, Orlandini E, Cook PR, Marenduzzo D.

Nucleic Acids Res. 2018 Jan 9;46(1):83-93. doi: 10.1093/nar/gkx1200.

7.

Microfluidics with fluid walls.

Walsh EJ, Feuerborn A, Wheeler JHR, Tan AN, Durham WM, Foster KR, Cook PR.

Nat Commun. 2017 Oct 10;8(1):816. doi: 10.1038/s41467-017-00846-4. Review.

8.

Ephemeral Protein Binding to DNA Shapes Stable Nuclear Bodies and Chromatin Domains.

Brackley CA, Liebchen B, Michieletto D, Mouvet F, Cook PR, Marenduzzo D.

Biophys J. 2017 Mar 28;112(6):1085-1093. doi: 10.1016/j.bpj.2017.01.025.

9.

Biocompatibility of fluids for multiphase drops-in-drops microfluidics.

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

Biomed Microdevices. 2016 Dec;18(6):114.

11.

Simulating topological domains in human chromosomes with a fitting-free model.

Brackley CA, Michieletto D, Mouvet F, Johnson J, Kelly S, Cook PR, Marenduzzo D.

Nucleus. 2016 Sep 2;7(5):453-461.

12.

Binding of nuclear factor κB to noncanonical consensus sites reveals its multimodal role during the early inflammatory response.

Kolovos P, Georgomanolis T, Koeferle A, Larkin JD, Brant L, Nikolicć M, Gusmao EG, Zirkel A, Knoch TA, van Ijcken WF, Cook PR, Costa IG, Grosveld FG, Papantonis A.

Genome Res. 2016 Nov;26(11):1478-1489. Epub 2016 Sep 15.

13.

Tibioperoneal Occlusive Disease: A Review of below the Knee Endovascular Therapy in Patients with Critical Limb Ischemia.

Muir KB, Cook PR, Sirkin MR, Aidinian G.

Ann Vasc Surg. 2017 Jan;38:64-71. doi: 10.1016/j.avsg.2016.09.008. Epub 2016 Oct 25.

PMID:
27793622
14.

Formation of droplet interface bilayers in a Teflon tube.

Walsh E, Feuerborn A, Cook PR.

Sci Rep. 2016 Sep 29;6:34355. doi: 10.1038/srep34355.

15.

The challenge of ORF1p phosphorylation: Effects on L1 activity and its host.

Furano AV, Cook PR.

Mob Genet Elements. 2015 Dec 4;6(1):e1119927. eCollection 2016 Jan-Feb.

16.

Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains.

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

Nucleic Acids Res. 2016 May 5;44(8):3503-12. doi: 10.1093/nar/gkw135. Epub 2016 Apr 8.

17.

Isolation of the protein and RNA content of active sites of transcription from mammalian cells.

Melnik S, Caudron-Herger M, Brant L, Carr IM, Rippe K, Cook PR, Papantonis A.

Nat Protoc. 2016 Mar;11(3):553-65. doi: 10.1038/nprot.2016.032. Epub 2016 Feb 25.

18.

L1 retrotransposition requires rapid ORF1p oligomerization, a novel coiled coil-dependent property conserved despite extensive remodeling.

Naufer MN, Callahan KE, Cook PR, Perez-Gonzalez CE, Williams MC, Furano AV.

Nucleic Acids Res. 2016 Jan 8;44(1):281-93. doi: 10.1093/nar/gkv1342. Epub 2015 Dec 15.

19.

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

Larkin JD, Cook PR.

Methods. 2016 Apr 1;98:150-157. doi: 10.1016/j.ymeth.2015.11.009. Epub 2015 Nov 11.

20.

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.

PMID:
26259670
21.

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;15(18):3766-75. doi: 10.1039/c5lc00726g.

PMID:
26246015
22.

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.

23.

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.

24.

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.

25.

Exon Skipping Is Correlated with Exon Circularization.

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

J Mol Biol. 2015 Jul 31;427(15):2414-2417. doi: 10.1016/j.jmb.2015.02.018. Epub 2015 Feb 26.

PMID:
25728652
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.

27.

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.

PMID:
25563801
28.

"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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

PMID:
23597155
34.

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.

35.

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.

PMID:
23363197
36.

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.

37.

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.

38.

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.

39.

T7 RNA polymerase functions in vitro without clustering.

Finan K, Torella JP, Kapanidis AN, Cook PR.

PLoS One. 2012;7(7):e40207. doi: 10.1371/journal.pone.0040207. Epub 2012 Jul 2.

40.

Dynamic reconfiguration of long human genes during one transcription cycle.

Larkin JD, Cook PR, Papantonis A.

Mol Cell Biol. 2012 Jul;32(14):2738-47. doi: 10.1128/MCB.00179-12. Epub 2012 May 14.

41.

Genetic susceptibility to experimental autoimmune glomerulonephritis in the Wistar Kyoto rat.

Reynolds J, Cook PR, Behmoaras J, Smith J, Bhangal G, Tadros S, Tee J, Salama AD, Evans DJ, Aitman TJ, Cook HT, Pusey CD.

Am J Pathol. 2012 May;180(5):1843-51. doi: 10.1016/j.ajpath.2012.01.029. Epub 2012 Mar 22.

42.

Transcription factories, chromatin loops, and the dysregulation of gene expression in malignancy.

Deng B, Melnik S, Cook PR.

Semin Cancer Biol. 2013 Apr;23(2):65-71. doi: 10.1016/j.semcancer.2012.01.003. Epub 2012 Jan 20. Review.

PMID:
22285981
43.

Enhancers and silencers: an integrated and simple model for their function.

Kolovos P, Knoch TA, Grosveld FG, Cook PR, Papantonis A.

Epigenetics Chromatin. 2012 Jan 9;5(1):1. doi: 10.1186/1756-8935-5-1.

44.

The proteomes of transcription factories containing RNA polymerases I, II or III.

Melnik S, Deng B, Papantonis A, Baboo S, Carr IM, Cook PR.

Nat Methods. 2011 Sep 25;8(11):963-8. doi: 10.1038/nmeth.1705.

45.

HTLV-1 HBZ protein deregulates interactions between cellular factors and the KIX domain of p300/CBP.

Cook PR, Polakowski N, Lemasson I.

J Mol Biol. 2011 Jun 10;409(3):384-98. doi: 10.1016/j.jmb.2011.04.003. Epub 2011 Apr 8.

46.

Only a patent right external carotid and left vertebral artery in a neurologically asymptomatic patient.

Hofmann LJ, Cook PR, Weber MA, Aidinian G.

J Vasc Surg. 2012 Mar;55(3):847. doi: 10.1016/j.jvs.2010.12.065. Epub 2011 Mar 31. No abstract available.

47.

Fixing the model for transcription: the DNA moves, not the polymerase.

Papantonis A, Cook PR.

Transcription. 2011 Jan-Feb;2(1):41-4. doi: 10.4161/trns.2.1.14275. Review.

48.

Endovascular repair of an abdominal aortic aneurysm in a patient with stenosis of bilateral common iliac artery stents.

Daab LJ, Aidinian G, Weber MA, Kembro RJ, Cook PR.

Ann Vasc Surg. 2011 Jan;25(1):133.e9-12. doi: 10.1016/j.avsg.2010.07.002.

PMID:
20889292
49.

Non-specific (entropic) forces as major determinants of the structure of mammalian chromosomes.

Finan K, Cook PR, Marenduzzo D.

Chromosome Res. 2011 Jan;19(1):53-61. doi: 10.1007/s10577-010-9150-y. Review.

PMID:
20714801
50.

Active RNA polymerases: mobile or immobile molecular machines?

Papantonis A, Larkin JD, Wada Y, Ohta Y, Ihara S, Kodama T, Cook PR.

PLoS Biol. 2010 Jul 13;8(7):e1000419. doi: 10.1371/journal.pbio.1000419.

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