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Items: 29

1.

Cryo-EM structure and in vitro DNA packaging of a thermophilic virus with supersized T=7 capsids.

Bayfield OW, Klimuk E, Winkler DC, Hesketh EL, Chechik M, Cheng N, Dykeman EC, Minakhin L, Ranson NA, Severinov K, Steven AC, Antson AA.

Proc Natl Acad Sci U S A. 2019 Feb 26;116(9):3556-3561. doi: 10.1073/pnas.1813204116. Epub 2019 Feb 8.

2.

A modelling paradigm for RNA virus assembly.

Twarock R, Bingham RJ, Dykeman EC, Stockley PG.

Curr Opin Virol. 2018 Aug;31:74-81. doi: 10.1016/j.coviro.2018.07.003. Epub 2018 Aug 2. Review.

3.

RNA Virus Evolution via a Quasispecies-Based Model Reveals a Drug Target with a High Barrier to Resistance.

Bingham RJ, Dykeman EC, Twarock R.

Viruses. 2017 Nov 17;9(11). pii: E347. doi: 10.3390/v9110347.

4.

Protein-mediated RNA folding governs sequence-specific interactions between rotavirus genome segments.

Borodavka A, Dykeman EC, Schrimpf W, Lamb DC.

Elife. 2017 Sep 18;6. pii: e27453. doi: 10.7554/eLife.27453.

5.

A Model for Viral Assembly around an Explicit RNA Sequence Generates an Implicit Fitness Landscape.

Dykeman EC.

Biophys J. 2017 Aug 8;113(3):506-516. doi: 10.1016/j.bpj.2017.06.037.

6.

Erratum: Genomic RNA folding mediates assembly of human parechovirus.

Shakeel S, Dykeman EC, White SJ, Ora A, Cockburn JJB, Butcher SJ, Stockley PG, Twarock R.

Nat Commun. 2017 Jul 14;8(1):83. doi: 10.1038/s41467-017-00026-4.

7.

Genomic RNA folding mediates assembly of human parechovirus.

Shakeel S, Dykeman EC, White SJ, Ora A, Cockburn JJB, Butcher SJ, Stockley PG, Twarock R.

Nat Commun. 2017 Feb 23;8(1):5. doi: 10.1038/s41467-016-0011-z. Erratum in: Nat Commun. 2017 Jul 14;8(1):83.

8.

Identification of novel RNA secondary structures within the hepatitis C virus genome reveals a cooperative involvement in genome packaging.

Stewart H, Bingham RJ, White SJ, Dykeman EC, Zothner C, Tuplin AK, Stockley PG, Twarock R, Harris M.

Sci Rep. 2016 Mar 14;6:22952. doi: 10.1038/srep22952.

9.

An implementation of the Gillespie algorithm for RNA kinetics with logarithmic time update.

Dykeman EC.

Nucleic Acids Res. 2015 Jul 13;43(12):5708-15. doi: 10.1093/nar/gkv480. Epub 2015 May 18.

10.

Asymmetric genome organization in an RNA virus revealed via graph-theoretical analysis of tomographic data.

Geraets JA, Dykeman EC, Stockley PG, Ranson NA, Twarock R.

PLoS Comput Biol. 2015 Mar 20;11(3):e1004146. doi: 10.1371/journal.pcbi.1004146. eCollection 2015 Mar.

11.

Revealing the density of encoded functions in a viral RNA.

Patel N, Dykeman EC, Coutts RH, Lomonossoff GP, Rowlands DJ, Phillips SE, Ranson N, Twarock R, Tuma R, Stockley PG.

Proc Natl Acad Sci U S A. 2015 Feb 17;112(7):2227-32. doi: 10.1073/pnas.1420812112. Epub 2015 Feb 2.

12.

On the subgroup structure of the hyperoctahedral group in six dimensions.

Zappa E, Dykeman EC, Twarock R.

Acta Crystallogr A Found Adv. 2014 Sep;70(Pt 5):417-28. doi: 10.1107/S2053273314007712. Epub 2014 Jul 10.

13.

Solving a Levinthal's paradox for virus assembly identifies a unique antiviral strategy.

Dykeman EC, Stockley PG, Twarock R.

Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):5361-6. doi: 10.1073/pnas.1319479111. Epub 2014 Mar 24.

14.

Packaging signals in two single-stranded RNA viruses imply a conserved assembly mechanism and geometry of the packaged genome.

Dykeman EC, Stockley PG, Twarock R.

J Mol Biol. 2013 Sep 9;425(17):3235-49. doi: 10.1016/j.jmb.2013.06.005. Epub 2013 Jun 11.

PMID:
23763992
15.

Building a viral capsid in the presence of genomic RNA.

Dykeman EC, Stockley PG, Twarock R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Feb;87(2):022717. Epub 2013 Feb 25.

PMID:
23496558
16.

Degenerate RNA packaging signals in the genome of Satellite Tobacco Necrosis Virus: implications for the assembly of a T=1 capsid.

Bunka DH, Lane SW, Lane CL, Dykeman EC, Ford RJ, Barker AM, Twarock R, Phillips SE, Stockley PG.

J Mol Biol. 2011 Oct 14;413(1):51-65. doi: 10.1016/j.jmb.2011.07.063. Epub 2011 Aug 3.

PMID:
21839093
17.

Normal mode analysis and applications in biological physics.

Dykeman EC, Sankey OF.

J Phys Condens Matter. 2010 Oct 27;22(42):423202. doi: 10.1088/0953-8984/22/42/423202. Epub 2010 Oct 7. Review.

PMID:
21403307
18.

Simple rules for efficient assembly predict the layout of a packaged viral RNA.

Dykeman EC, Grayson NE, Toropova K, Ranson NA, Stockley PG, Twarock R.

J Mol Biol. 2011 May 6;408(3):399-407. doi: 10.1016/j.jmb.2011.02.039. Epub 2011 Feb 25. Review.

PMID:
21354423
19.

The impact of viral RNA on assembly pathway selection.

Morton VL, Dykeman EC, Stonehouse NJ, Ashcroft AE, Twarock R, Stockley PG.

J Mol Biol. 2010 Aug 13;401(2):298-308. doi: 10.1016/j.jmb.2010.05.059. Epub 2010 Jun 1.

PMID:
20621589
20.

All-atom normal-mode analysis reveals an RNA-induced allostery in a bacteriophage coat protein.

Dykeman EC, Twarock R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Mar;81(3 Pt 1):031908. Epub 2010 Mar 10.

PMID:
20365771
21.

Atomistic modeling of the low-frequency mechanical modes and Raman spectra of icosahedral virus capsids.

Dykeman EC, Sankey OF.

Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Feb;81(2 Pt 1):021918. Epub 2010 Feb 19.

PMID:
20365606
22.

Vibrational energy funneling in viruses-simulations of impulsive stimulated Raman scattering in M13 bacteriophage.

Dykeman EC, Sankey OF.

J Phys Condens Matter. 2009 Dec 16;21(50):505102. doi: 10.1088/0953-8984/21/50/505102. Epub 2009 Nov 13.

PMID:
21836224
23.

Dynamic allostery controls coat protein conformer switching during MS2 phage assembly.

Dykeman EC, Stockley PG, Twarock R.

J Mol Biol. 2010 Feb 5;395(5):916-23. doi: 10.1016/j.jmb.2009.11.016. Epub 2009 Nov 12.

PMID:
19913554
24.

Simulations of impulsive laser scattering of biological protein assemblies: application to M13 bacteriophage.

Dykeman EC, Benson D, Tsen KT, Sankey OF.

Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Oct;80(4 Pt 1):041909. Epub 2009 Oct 7.

PMID:
19905344
25.

Theory of the low frequency mechanical modes and Raman spectra of the M13 bacteriophage capsid with atomic detail.

Dykeman EC, Sankey OF.

J Phys Condens Matter. 2009 Jan 21;21(3):035116. doi: 10.1088/0953-8984/21/3/035116. Epub 2008 Dec 15.

PMID:
21817274
26.

Low frequency mechanical modes of viral capsids: an atomistic approach.

Dykeman EC, Sankey OF.

Phys Rev Lett. 2008 Jan 18;100(2):028101. Epub 2008 Jan 14.

PMID:
18232930
27.

Raman intensity and spectra predictions for cylindrical viruses.

Dykeman EC, Sankey OF, Tsen KT.

Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Jul;76(1 Pt 1):011906. Epub 2007 Jul 11.

PMID:
17677493
28.

Probing the low-frequency vibrational modes of viruses with Raman scattering--bacteriophage M13 in water.

Tsen KT, Dykeman EC, Sankey OF, Tsen SW, Lin NT, Kiang JG.

J Biomed Opt. 2007 Mar-Apr;12(2):024009.

29.

Observation of the low frequency vibrational modes of bacteriophage M13 in water by Raman spectroscopy.

Tsen KT, Dykeman EC, Sankey OF, Lin NT, Tsen SW, Kiang JG.

Virol J. 2006 Sep 22;3:79.

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