Nuclear Structure and Function Research Group

Finan, K., Cook, P.R., and Marenduzzo, D. (2011). Non-specific (entropic) forces as major determinants of the structure of mammalian chromosomes. Chromosome Res. 19, 53-61. [PubMed] [pdf]

Papantonis, A., and Cook, P.R. (2011). Fixing the model for transcription: the DNA moves, not the polymerase. Transcription 2, 41-44. [PubMed] [pdf]

Melnik, S., Deng, B., Papantonis, A., Baboo, S., Carr, I.M., and Cook, P.R. (2011). Proteomes of factories containing RNA polymerases I, II, or III. Nature Methods 8, 962-968. [PubMed] [Supporting information] [pdf]

Finan, K., and Cook, P.R. (2012). Transcriptional initiation: frequency, bursting, and transcription factories. In: Rippe, K., editor. Genome organization and function in the cell nucleus, Wiley-VCH Verlag GmbH & Co, KGaA, pp 235-254. [pdf]

Kolovos, P., Knoch, T.A., Grosveld, F.G., Cook, P.R., and Papantonis, A. (2012). Enhancers and silencers: an integrated and simple model for their function. Epigenetics Chromatin 5, 1. [PubMed] [pdf]

Finan, K., Torella, J.P., Kapanidis, A.N., and Cook, P.R. (2012). T7 RNA polymerase functions in vitro without clustering. PLoS One 7, e40207. [PubMed] [pdf]

Larkin, J.D., Cook, P.R., and Papantonis, A. (2012). Dynamic reconfiguration of long human genes during one transcription cycle. Mol. Cell. Biol. 32, 2738-2747. [PubMed] [pdf]

Larkin, J.D., and Cook, P.R. (2012). A maximum precision closed-form solution for localizing diffraction-limited spots in noisy images. Optics Express 20, 18478-18493. [PubMed] [pdf]

Papantonis. A., Kohro, T., Baboo, S., Larkin, J., Deng, B., Short, P., Tsutsumi, T., Taylor, S., Kanki, Y., Kobayashi, M., Li, G., Poh, H.-M., Ruan, X., Aburatani, H., Ruan, Y., Kodama, T., Wada, Y., and Cook, P.R. (2012). TNFa signals through specialized factories where responsive coding and micro-RNA genes are transcribed. EMBO J. 31, 4404-4414. [PubMed] [pdf]

Larkin, J.D., Papantonis, A., Cook, P.R., and Marenduzzo, D. (2013). Space exploration by the promoter of a long human gene during one transcription cycle. Nucl. Acids Res. 41, 2216-2227. [PubMed] [pdf]

Deng, B., Melnik, S., and Cook, P.R. (2013). Transcription factories, chromatin loops, and the dysregulation of gene expression in malignancy. Semin. Cancer Biol. 23, 65-71. [PubMed] [pdf]

Larkin, J.D., Papantonis, A., and Cook, P.R. (2013). Promoter type influences transcriptional topography by targeting genes to distinct nucleoplasmic sites. J. Cell Sci. 126, 2052-2059. [PubMed] [pdf]

Endesfelder, U., Finan, K., Holden, S.J., Cook, P.R., Kapanidis, A.N., and Heilemann, M. (2013). Multiscale spatial organization of RNA polymerase in Escherichia coli. Biophys. J. 105, 172-181. [PubMed] [pdf]

Brackley, C.A., Taylor, S., Papantonis, A., Cook, P.R., and Marenduzzo, D. (2013). Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization. Proc. Natl. Acad. Sci. USA 110, E3605-3611. [PubMed] [pdf]

Papantonis, A., and Cook, P.R. (2013). Transcription factories; genome organization and gene regulation. Chem. Rev. 113, 8683-8705. [PubMed] [pdf]

Baboo, S., Bhushan, B., Jiang, H., Grovenor, C.R.M., Pierre, P., Davis, B.G., and Cook, P.R. (2014). Most human proteins made in both nucleus and cytoplasm turn over within minutes. PLoS One 9, e99346. [PubMed] [pdf]

Baboo, S., and Cook, P.R. (2014). ‘Dark matter' worlds of unstable RNA and protein. Nucleus 5, 281-286. [PubMed][pdf]

Diermeier, S., Kolovos, P., Heizinger, L., Schwartz, U., Georgomanolis, T., Zirkel, A., Wedemann, G., Grosveld, G., Knoch, T.A., Merkl, R., Cook, P.R., Längst, G., and Papantonis, A. (2014). TNFa signalling primes chromatin for NF-kB binding and induces rapid and widespread nucleosome repositioning. Genome Biol. 15, 536. [PubMed] [pdf]

Johnson, J., Brackley, C.A., Cook, P.R., and Marenduzzo, D. (2015). A simple model for DNA bridging proteins and bacterial or human genomes: bridging-induced attraction and genome compaction. J. Phys. Condens. Matter 27, 064119. [PubMed] [pdf]

Kelly, S., Greenman, C., Cook, P.R., and Papantonis, A. (2015). Exon skipping is correlated with exon circularization. J. Mol. Biol. 427, 2414-2417. [PubMed] [pdf]

Caudron-Herger, M., Cook, P.R., Rippe, K., and Papantonis, A. (2015). Dissecting the nascent human transcriptome by analyzing the RNA content of transcription factories. Nucleic Acids Res. 43, e95. [PubMed] [pdf]

Kelly, S., Georgomanolis, T., Zirkel, A., Diermeier, S., O'Reilly, D., Murphy, S., Längst, G., Cook, P.R., Papantonis, A. (2015). Splicing of many human genes involves sites embedded within introns. Nucleic Acids Res. 43, 4721-4732. [PubMed] [pdf]

Feuerborn, A., Prastowo, A., Cook, P.R., and Walsh, E. (2015). Merging drops in a Teflon tube, and transferring fluid between them, illustrated by protein crystallization and drug screening. Lab Chip 15, 3766-3775. [PubMed] [pdf]

Feuerborn, A., and Cook, P.R. (2015). Why the activity of a gene depends on its neighbors. Trends Genet. 91, 483-490. [PubMed] [pdf]

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