Eric Charles Dykeman

Search results

• 2024

  Design of a self‐regulating mRNA gene circuit

  Dykeman, E. C., 21 Aug 2024, In: Scientific Reports. 14, 12 p., 19421.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• 2023

  Modelling ribosome kinetics and translational control on dynamic mRNA

  Dykeman, E. C., 23 Jan 2023, In: PLoS Computational Biology. 19, 1, 20 p., e1010870.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• 2022

  Genome-regulated Assembly of a ssRNA Virus May Also Prepare It for Infection

  Chandler-Bostock, R., Bingham, R. J., Clark, S., Scott, A. J. P., Wroblewski, E., Barker, A., White, S. J., Dykeman, E. C., Mata, C. P., Bohon, J., Farquhar, E., Twarock, R. & Stockley, P. G., 30 Oct 2022, In: Journal of Molecular Biology. 434, 20, 18 p., 167797.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• 2021

  Comparing antiviral strategies against COVID-19 via multiscale within-host modelling

  Fatehi Chenar, F., Bingham, R. J., Dykeman, E. C., Stockley, P. G. & Twarock, R., 11 Aug 2021, In: Royal Society Open Science. 8, 8, 17 p., 210082.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• The impact of local assembly rules on RNA packaging in a T = 1 satellite plant virus

  Dykeman, E. C., Twarock, R. & Hill, S., 24 Aug 2021, In: PLoS Computational Biology. 17, 8, 18 p., e1009306.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• 2020

  An Intracellular Model of Hepatitis B Viral Infection: An In Silico Platform for Comparing Therapeutic Strategies

  Fatehi Chenar, F., Bingham, R. J., Dykeman, E. C., Patel, N., Stockley, P. G. & Twarock, R., 23 Dec 2020, (E-pub ahead of print) In: Viruses. 13(1), 11

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• A stochastic model for simulating ribosome kinetics in vivo

  Dykeman, E. C., 12 Feb 2020, In: PLoS Computational Biology. 20 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• 2019

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

  Bayfield, O. W., Klimuk, E., Winkler, D. C., Hesketh, E. L., Chechik, M., Cheng, N., Dykeman, E. C., Minakhin, L., Ranson, N. A., Severinov, K., Steven, A. C. & Antson, A. A., 26 Feb 2019, In: Proceedings of the National Academy of Sciences of the United States of America. 116, 9, p. 3556-3561 6 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• 2018

  A modelling paradigm for RNA virus assembly

  Twarock, R., Bingham, R. J., Dykeman, E. C. & Stockley, P. G., Aug 2018, In: Current Opinion in Virology. 31, p. 74-81

  Research output: Contribution to journal › Article › peer-review

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• 2017

  A model for viral assembly around an explicit RNA sequence generates an Implicit fitness landscape

  Dykeman, E. C., 8 Aug 2017, In: Biophysical Journal. 113, 3, p. 506-516 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• Genomic RNA folding mediates assembly of human parechovirus

  Twarock, R., Dykeman, E. C., Shakeel, S., White, S., Ora, A., Cockburn, J., Butcher, S. & Stockley, P., 23 Feb 2017, In: Nature Communications. 8, 11 p., 5.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• HBV RNA pre-genome encodes specific motifs that mediate interactions with the viral core protein that promote nucleocapsid assembly

  Dykeman, E. C., Bingham, R. J., Weiss, E. U. & Twarock, R., 19 Jun 2017, In: Nature reviews. Microbiology. 2, 10 p., 17098.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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

  Dykeman, E. C. & Borodavka, A., 18 Sept 2017, In: eLife. 6, 22 p., e27453.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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

  Twarock, R., Bingham, R. J. & Dykeman, E. C., 17 Nov 2017, In: Viruses. 9, 347, 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• 2016

  Bacteriophage MS2 Genomic RNA Encodes an Assembly Instruction Manual for Its Capsid

  Stockley, P. G., White, S. J., Dykeman, E. C., Rolfsson, Ó., Patel, N., Bingham, R. J., Iain, M., Amy, B., Emma, W., Rebecca, C.-B., Weiss, E. U., Ranson, N. A., Tuma, R. & Twarock, R., 2 Mar 2016, (E-pub ahead of print) In: Bacteriophage. 6, 1, 8 p., e1157666.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• Direct Evidence for Packaging Signal-Mediated Assembly of Bacteriophage MS2

  Rolfsson, Ó., Middleton, S., Manfield, I. W., White, S. J., Fan, B., Vaughan, R., Ranson, N. A., Dykeman, E., Twarock, R., Ford, J., Cheng Kao, C. & Stockley, P. G., 29 Jan 2016, In: Journal of Molecular Biology. 428, 2, p. 431-448 18 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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

  Stewart, H., Bingham, R. J., White, S. J., Dykeman, E. C., Zothner, C., Tuplin, A. K., Stockley, P. G., Twarock, R. & Harris, M., 14 Mar 2016, In: Scientific Reports. 6, 22952.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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• 2015

  Asymmetric Genome Organization in an RNA Virus Revealed via Graph-Theoretical Analysis of Tomographic Data

  Geraets, J. A., Dykeman, E. C., Stockley, P. G., Ranson, N. A. & Twarock, R., 20 Mar 2015, In: PLoS Computational Biology. 11, 3, p. 1-16 16 p., e1004146.

  Research output: Contribution to journal › Article › peer-review

• Revealing the density of encoded functions in a viral RNA

  Patel, N., Dykeman, E. C., Coutts, R. H. A., Lomonossoff, G. P., Rowlands, D. J., Phillips, S. E. V., Ranson, N., Twarock, R., Tuma, R., Stockley, P. G. & Johnson, J. E. (Editor), 17 Feb 2015, In: Proceedings of the National Academy of Sciences of the United States of America. 112, 7, p. 2227-2232 6 p.

  Research output: Contribution to journal › Article › peer-review
• 2014

  On the subgroup structure of the hyperoctahedral group in six dimensions

  Zappa, E., Dykeman, E. C. & Twarock, R., Sept 2014, In: Acta crystallographica. Section A, Foundations and advances. 70, 5, p. 417-428 12 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

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

  Dykeman, E. C., Stockley, P. G. & Twarock, R., 8 Apr 2014, In: Proceedings of the National Academy of Sciences of the United States of America. 111, 14, p. 5361-5366

  Research output: Contribution to journal › Article › peer-review
• 2013

  Building a viral capsid in the presence of genomic RNA

  Dykeman, E. C., Stockley, P. G. & Twarock, R., 25 Feb 2013, In: Physical Review E. 87, 2, p. 1-12 12 p., 022717.

  Research output: Contribution to journal › Article › peer-review

• Packaging signals in single-stranded RNA viruses: Nature's alternative to a purely electrostatic assembly mechanism

  Stockley, P. G., Twarock, R., Bakker, S. E., Barker, A. M., Borodavka, A., Dykeman, E., Ford, R. J., Pearson, A. R., Phillips, S. E. V., Ranson, N. A. & Tuma, R., 1 Mar 2013, In: Journal of Biological Physics. 39, 2, p. 277-287 11 p.

  Research output: Contribution to journal › Article › peer-review

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

  Dykeman, E. C., Stockley, P. G. & Twarock, R., 9 Sept 2013, In: Journal of Molecular Biology. 425, 17, p. 3235-3249 15 p.

  Research output: Contribution to journal › Article › peer-review
• 2012

  Structural basis for DNA recognition and loading into a viral packaging motor

  Buettner, C. R., Chechik, M., Ortiz-Lombardia, M., Smits, C., Ebong, I.-O., Chechik, V., Jeschke, G., Dykeman, E., Benini, S., Robinson, C. V., Alonso, J. C. & Antson, A. A., 17 Jan 2012, In: Proceedings of the National Academy of Sciences of the United States of America. 109, 3, p. 811-816 6 p.

  Research output: Contribution to journal › Article › peer-review
• 2011

  Degenerate RNA Packaging Signals in the Genome of Satellite Tobacco Necrosis Virus: Implications for the Assembly of a T=1 Capsid

  Bunka, D. H. J., Lane, S. W., Lane, C. L., Dykeman, E. C., Ford, R. J., Barker, A. M., Twarock, R., Phillips, S. E. V. & Stockley, P. G., 14 Oct 2011, In: Journal of Molecular Biology. 413, 1, p. 51-65 15 p.

  Research output: Contribution to journal › Article › peer-review

• Simple Rules for Efficient Assembly Predict the Layout of a Packaged Viral RNA

  Dykeman, E. C., Grayson, N. E., Toropova, K., Twarock, R., Ranson, N. A. & Stockley, P. G., 6 May 2011, In: Journal of Molecular Biology. 408, 3, p. 399-407 9 p.

  Research output: Contribution to journal › Article › peer-review
• 2010

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

  Dykeman, E. C. & Twarock, R., 10 Mar 2010, In: Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 81, 3, 10 p., 031908.

  Research output: Contribution to journal › Article › peer-review

• Dynamic Allostery Controls Coat Protein Conformer Switching during MS2 Phage Assembly

  Dykeman, E. C., Stockley, P. G. & Twarock, R., 5 Feb 2010, In: Journal of Molecular Biology. 395, 5, p. 916-923 8 p.

  Research output: Contribution to journal › Article › peer-review

• The impact of viral RNA on assembly pathway selection

  Morton, V. L., Dykeman, E. C., Stonehouse, N. J., Ashcroft, A. E., Twarock, R. & Stockley, P. G., Aug 2010, In: Journal of Molecular Biology. 401, 2, p. 298-308 11 p.

  Research output: Contribution to journal › Article › peer-review
• 2009

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

  Dykeman, E. C. & Sankey, O. F., 16 Dec 2009, In: Journal of physics : Condensed matter. 21, 50, p. - 6 p., 505102.

  Research output: Contribution to journal › Article › peer-review