Publications

ResearcherID: A-8863-2014 ORCID: 0000-0003-0461-7297

Papers (Most recent first)

2023

  1. J.W.G. Doran, R.N. Thompson, C.A. Yates and R. Bowness, “Mathematical methods for scaling from within-host to population-scale in infectious disease systems” (2023) Epidemics. 45 (10).
  2. A. Sontag, T. Rogers, and C. A. Yates, “Dynamics of Information Networks”. (2023) Journal of Applied Probability.
  3. J. Riddell, S. Raja Noureen, L. Sedda, J. D. Glover, W. K. W. Ho, C. A. Bain, A. Berbeglia, H. Brown, C. Anderson, Y. Chen, M. L. Crichton, C.A. Yates, R. L. Mort and D. J. Headon, “Rapid mechanosensitive migration and dispersal of newly divided mesenchymal cells aid their recruitment into dermal condensates”. (2023) PLOS Biology 21(9), e3002316.
  4. J. C. Kynaston, C. A. Yates, A.V.F. Hekkink and C. Guiver, “The regime-conversion method: a hybrid technique for simulating well-mixed chemical reaction networks”. (2023) Frontiers in Applied Mathematics and Statistics. 9(17), 1107441.
  5. S. Raja Noureen, J. P. Owen, R. L. Mort, and C. A. Yates, “Swapping in lattice-based cell migration models”.  (2023), Physical Review E. 107(4), 044402.
  6. A. Sontag, T. Rogers and C. A. Yates, “Stochastic drift in discrete waves of nonlocally interacting particles“, (2023). Physical Review E. 107(1), 014128.

    2022

  7. C. Pagel  and C.A. Yates,  “Role of mathematical modelling in future pandemic response policy” (2022)British Medical Journal. 378, e070615.
  8. D. Gurdasani, C. Pagel, M. McKee, S. Michie, T. Greenhalgh, C.A. Yates, G. Scally, and H. Ziauddeen. “Covid-19 in the UK: policy on children and schools” (2022) British Medical Journal. 378, e071234.
  9. M.A. Bentley, C.A. Yates, J. Hein, G. M. Preston and K.R. Foster” Pleiotropic constraints promote the evolution of cooperation in cellular groups” (2022) PLoS Biology. 20(6), e3001626.
  10. J.C. Kynaston, C. Guiver, and C.A. Yates “An equivalence framework for an age-structured multi-stage representation of the cell cycle” (2022) Physical Review E. 105(6), 064411
  11. C. Smith, C.A. Yates and B. Ashby “Critical weaknesses in shielding strategies for COVID-19” (2022) PLoS Global Public Health 2(4), e0000298.
  12. M. McKee, D. Altmann, A. Costello, K. Friston, Z. Haque, K. Khunti, S. Michie, T. Oni, C. Pagel, D. Pillay, S. Reicher, H. Salisbury, G. Scally, K. Yates, L. Bauld, L. Bear, J. Drury, M. Parker, A. Phoenix, E. Stokoe, and R. West “Open science communication: The first year of the UK’s Independent Scientific Advisory Group for Emergencies” (2022) Health Policy 126(3).
  13. A. Sontag, T. Rogers and C.A. Yates, “Misinformation can prevent the suppression of epidemics” (2022) Journal of The Royal Society Interface. 19(188).
  14. K. Yates “Was lockdown necessary?” (2022) British Medical Journal 376.
  15. K. Yates “Closing our eyes to covid won’t make it go away” (2022) British Medical Journal 376.
  16.  D. Gurdasani, A. Akrami, V. C. Bradley, A. Costello, T. Greenhalgh, S. Flaxman, M. McKee, S. Michie, C. Pagel, S. Rasmussen, G. Scally, C. Yates, H. Ziauddeen “Long COVID in children” (2022), The Lancet Child and Adolescent Health. 6(1).
  17. T. Greenhalgh, S. Griffin, D. Gurdasani, A. Hamdy, A. Katzourakis, M. McKee, S. Michie, C. Pagel,  A. Roberts, and K. Yates “Covid-19: An urgent call for global ‘vaccines-plus’ action” (2022) British Medical Journal 376 – Opinion Piece

    2021

  18. D. Gurdasani, S. Bhatt, A. Costello, S.C. Denaxas, S. Flaxman, T. Greenhalgh, S. Griffin, Z. Hyde, A. Katzourakis, M. McKee, S.  Michie, O. Ratmann, S. Reicher, G. Scally, C. Tomlinson, K. Yates, H. Ziauddeen, and C. Pagel, “Vaccinating adolescents against SARS-CoV-2 in England: a risk-benefit analysis” (2021) Journal of the Royal Society of Medicine (JRSM). 114(11).
  19.  C. Pagel, and C. A. Yates, “Tackling the pandemic with (biased) data” (2021) Science. 374, 6566.
  20.  D. Gurdasani, J. Drury, T. Greenhalgh, S. Griffin, Z. Haque, Z. Hyde, A. Katzourakis, M. McKee, S. Michie, C. Pagel, S. D. Reicher, A. Roberts, R. West, K. Yates and H. Ziauddeen, “Mass infection is not an option: We must do more to protect our young” (2021) The Lancet. 398, 10297
  21. K. Yates “(How) can we reach herd immunity?” (2021) British Medical Journal – Opinion Piece
  22. C. Pagel, J. Drury, T. Greenhalgh, S. Griffin, D. Gurdasani, Z. Haque, A. Katzourakis, M. McKee, S. Michie, G. Scally, R. West, K. Yates and H. Ziauddeen “Government’s plan recklessly exposes millions in the UK to infection when they could be vaccinated” (2021) British Medical Journal – Opinion Piece
  23. K. Yates “The dangers of allowing exponential growth” (2021) The British Medical Journal. 374(1770) – Opinion Piece
  24.  J. Owen, C. Yates and Kelsh, R. N., “Pigment patterning in teleosts” (2021) Pigments, Pigment Cells and Pigment Patterns. H. Hashimoto, M. Goda, R. Futuhashi, R. N. Kelsh and T. Akiyama, (eds.). 1 ed. Springer Nature Singapore Pte Ltd, p. 247-292.
  25. D. Pimenta, C.A. Yates, C. Pagel, D. Gurdasani “Delaying the second dose of covid-19 vaccines” (2021) British Medical Journal 372(710).
  26. C.A. Smith and C.A. Yates “Incorporating domain growth into hybrid methods for reaction-diffusion systems” (2021) Journal of the Royal Society Interface 18 177.
  27. E. Gavagnin, S.T. Vittadello, G. Gunasingh, N.K. Haass, M.J. Simpson, T. Rogers and C.A. Yates “Synchronised oscillations in growing cell populations are explained by demographic noise” (2021) Biophysical Journal 120(8).

    2020

  28. D. Gurdasani, L. Bear, … C.A. Yates, (2020) “The UK needs a sustainable strategy for COVID-19” The Lancet 396 (10265).
  29. C.A. Yates, A. George, A. Jordana, C.A. Smith, A.B. Duncan, Konstantinos C. Zygalakis, (2020) “The blending region hybrid framework for the simulation of stochastic reaction-diffusion processes” (Journal of the Royal Society Interface).
  30. J. Owen, R. Kelsh and C.A. Yates, (2020) “A quantitative modelling approach to zebrafish pigment pattern formation” E-life 9.
  31. W. Hart, P.K. Maini, C.A. Yates and R.N. Thompson, (2020) “A theoretical framework for transitioning from patient-level to population-scale epidemiological dynamics: influenza A as a case study” Journal of the Royal Society Interface 17(166).

    2019

  32. E. Gavagnin, M.J. Ford, R.L. Mort, T. Rogers, and C.A. Yates, (2019) “The invasion speed of cell migration models with realistic cell cycle time distributions” Journal of Theoretical Biology 418.
  33. Correction to: C.A. Yates, M.J. Ford  and R.L. Mort, (2017). “A multi-stage representation of cell proliferation as a Markov process” Bull. Math. Biol. 79(12) .
  34. G. Chappelle, C.A. Yates, (2019) “Pulling in on-lattice models of cell migration” Physical Review E 99 (6).
  35. C. Smith, C. Mailler, C.A. Yates, (2019) “Unbiased on-lattice domain growth” Physical Review E 100(6) .

    2018

  36. C. Smith and C.A. Yates, (2018) “The auxiliary region method (ARM) for coupling PDE and Brownian dynamics” Royal Society Open Science 5(8).
  37. C. Lester, C.A. Yates, R.E. Baker, (2018) “Robustly simulating biochemical reaction kinetics using multi-level Monte Carlo approaches” Journal of Computational Physics 375.
  38. E. Gavagnin and C.A. Yates, (2018) “Stochastic and deterministic models of cell migration.” Chapter in Handbook of Statistics: Integrated Population Biology and Modeling. Elsevier.
  39. K. Minors, T. Rogers and C.A. Yates, (2018) “Noise-driven bias in the non-local voter model” Europhysics Letters.
  40. E. Gavagnin and C.A. Yates, (2018) “Modelling persistence of motion in a crowded environment: the diffusive limit of excluding velocity-jump processes” Physical Review E 97(3).
  41. C. Smith and C.A. Yates, (2018) “Spatially extended hybrid methods: a review” Journal of the Royal Society Interface 15(139).
  42. E. Gavagnin*, J. Owen*, C.A. Yates, (2018) “Pair correlation functions for identifying spatial correlation in discrete domains” Physical Review E 97(6).

    2017

  43. C.A. Yates, M.J. Ford and R.L. Mort, (2017). “A multi-stage representation of cell proliferation as a Markov process“. Bull. Math. Biol. 79(12).
  44. R.J.H. Ross, C.A. Yates and R.E. Baker, (2017). “Variable species densities are induced by volume exclusion interactions upon domain growth“. Phys. Rev. E 95(3).
  45. R.J.H. Ross, R.E. Baker, A. Parker, M. Ford, R. Mort and C.A. Yates (2017). “Using approximate Bayesian computation to quantify cell-cell adhesion parameters in a cell migratory process“. npj Systems Biology and applications 3(1).
  46. C. Lester, C. Yates and R. E. Baker, (2017). “Efficient parameter sensitivity computation for spatially-extended reaction networks“.  J. Chem. Phys. 146(4).
  47. R.N. Kelsh, K. Camargo Sosa, J. Owen and C.A. Yates (2017). “Zebrafish adult pigment stem cells are multipotent and form pigment cells by a progressive fate restriction process“.  BioEssays 39(3).
  48. R.J.H. Ross, R.E. Baker and C.A. Yates (2017). “The effect of domain growth on spatial correlations“. Physica A 466 334-345.

    2016

  49. B. Franz, J.P. Taylor-King, C.A. Yates, R. Erban (2016). “Hard-sphere interactions in velocity jump models“. Phys. Rev. E (PRE) 94(1).
  50. J.U. Harrison and C.A. Yates (2016). “A hybrid algorithm for coupling PDE and compartment-based dynamics“. J. R. Soc. Int. 13(122).
  51. R.J.H. Ross, R.E. Baker, C.A. Yates (2016) “How domain growth is implemented determines the long-term behavior of a cell population through its effect on spatial correlations“. Phys. Rev. E (PRE) 94 012408.
  52. P.R. Taylor, M.J. Simpson, R.E. Baker and C.A. Yates, (2016) “Coupling volume-excluding compartment-based models of diffusion at different scales: Voronoi and pseudo-compartment approaches“. J. R. Soc. Int. 13(120).
  53. C. Lester, R.E. Baker, M.B. Giles and C. Yates (2016). “Extending the multi-level method for the simulation of stochastic biological systems“. Bull. Math. Bio. 78(8).
  54. R.L. Mort*, R.J.H. Ross*, K.J. Hainey, O. Harrison, M.A. Keighren, G. Landini, R.E. Baker, K.J. Painter, I.J. Jackson, C.A. Yates (2016). “Reconciling diverse mammalian pigmentation patterns with a fundamental mathematical model” Nat. Comms 7 10288. Supplementary material to accompany this paper can be found here.

    2015

  55. P.R. Taylor, C.A. Yates, M.J. Simpson, R.E. Baker (2015) “ Reconciling transport models across scales: The role of volume exclusion“. Phys. Rev. E (PRE) – Rapid Communication 92(4) 040701
  56. L. Dyson*, C.A. Yates*, J. Buhl A.J. McKane (2015). “Onset of collective motion in locusts is captured by a minimal model” Phys. Rev. E (PRE) 92(5) 052708. Supplementary material to accompany this paper can be found here.
  57. C.A. Yates, A. Parker and R.E. Baker (2015) “Incorporating pushing in exclusion process models of cell migration” Phys. Rev. E (PRE) 91(5) 052711.
  58. C.A. Yates and M.B. Flegg (2015) “The pseudo-compartment method for coupling PDE and compartment-based models of diffusion” Journal of the Royal Society, Interface (JRSI) 12(106) 20150141. Supplementary material to accompany this paper can be found here.
  59. R.J.H. Ross, C.A. Yates and R.E. Baker (2015). “Inference of cell-cell interactions from population density characteristics and cell trajectories on static and growing domains” Mathematical Biosciences 26(11) 108-118.
  60. B, Knapp, R. Bardenet, …, C.A. Yates, D. Gavaghan and C.M. Deane (2015). “Ten simple rules for a successful cross-disciplinary collaboration” PLoS Computational Biology 11(4) e1004214.
  61. J. P. Taylor-King, B. Franz, C.A. Yates and R. Erban (2015). “Mathematical Modelling of Turning Delays in Swarm Robotics” (Accepted for IMA Journal of Applied Mathematics).
  62. P. Taylor, R.E. Baker and C.A. Yates (2015). “Deriving appropriate boundary conditions, and accelerating position-jump simulations, of diffusion using non-local jumping” Physical Biology 12(1) 016006.
    Also appearing in Physical Biology highlights of 2015.
  63. C. Lester, C.A. Yates, M.B. Giles, and R.E. Baker (2015). “An adaptive multi-level simulation algorithm for stochastic biological systems” Journal of Chemical Physics 142(2) 024113.

    2014

  64. C.A. Yates (2014). “Discrete and continuous models for tissue growth and shrinkage” Journal of Theoretical Biology (JTB) 350 37-48.
  65. J.M. Osborne, M.O. Bernabeu … C.A. Yates et al. (2014) “Ten Simple Rules for Effective Computational Research” PLoS Computational Biology 10(3) e1003506. Supplementary material to accompany this paper can be found here.

    2013

  66. C.A. Yates and R.E. Baker (2013). “The importance of the Voronoi domain partition for position-jump reaction-diffusion processes on non-uniform rectilinear lattices.” Physical Review E (PRE) 88(5) 054701. Supplementary material to accompany this paper can be found here.
  67. G. Rosser, A.G. Fletcher, D.A. Wilkinson, J.A. de Beyer, C.A. Yates, J.P. Armitage, P.K. Maini and R.E. Baker (2013). “ Novel methods for analysing bacterial tracks reveal persistence in Rhodobacter sphaeroides” PLoS Computational Biology 9(10) e1003276
  68. C.A. Yates and R.E. Baker (2013). “Isotropic model for cluster growth on a regular lattice“. Physical Review E (PRE) 88(2) 023304. Supplementary material to accompany this paper can be found here.
  69. C.A. Yates and G. Klingbeil (2013). “Recycling random numbers in the stochastic simulation algorithm” Journal of Chemical Physics (JCP) 138(9) 094103.

    2012

  70. C.A. Yates, R.E. Baker R. Erban and P.K. Maini (2012). “Going from microscopic to macroscopic on nonuniform growing domains” Physical Review E (PRE) 86 021921. Supplementary material to accompany this paper can be found here.
  71. C.A. Yates (2012) “Comparing stochastic discrete and deterministic continuum models of cell migration”. ESMTB Communications 1(15) 31-36.
  72. R. Thompson, C.A. Yates and R.E. Baker (2012). “Modelling cell migration and adhesion during development” Bulletin of Mathematical Biology 72(12) 2793-2809.
  73. T. Wood, C.A. Yates, D. Wilkinson and G. Rosser (2012). “Simplified multitarget tracking using the PHD filter for microscopic video data“. IEEE Transactions on Circuits and Systems for Video Technology (IEEE. T. Circ. Syst. Vid.) 22(5) 702-713.

    2011

  74. C.A. Yates and K. Burrage (2011). “Look before you leap: A confidence-based method for selecting species criticality whilst avoiding negative populations in τ-leaping“. Journal of Chemical Physics (JCP) 134, 084109.
    Also appearing in JCP Biochemical Physics highlights journal.
  75. C.A. Yates, R. Baker, R. Erban and P.K. Maini (2011). “Refining self-propelled particle models for collective behaviour“. Canadian Applied Math Quarterly (CAMQ) 18(3).

    2010

  76. C. Escudero, C.A. Yates, J. Buhl, I.D. Couzin, R. Erban, I.G. Kevrekidis (2010). “Ergodic directional switching in mobile insect groups“. Physical Review E (PRE)) 82(1) 11926.

    2009

  77. R.E. Baker, C.A. Yates and R. Erban (2009). “From Microscopic to Macroscopic Descriptions of Cell Migration on Growing Domains“. Bulletin of Mathematical Biology 72(3) 719-762.
  78. C.A. Yates, R. Erban, C. Escudero, I. Couzin, J. Buhl, I. Kevrekidis, P. Maini and D. Sumpter, (2009). “Inherent noise can facilitate coherence in collective swarm motion“. Proceedings of the National Academy of Sciences (PNAS) 106(14) 5464-5469. Supplementary material to accompany this paper can be found here.

Submitted and in preparation

  • M. Malickova, C.A. Yates, K. Bodova (2022). A stochastic model of ant trail following with two pheromones” (In preparation).
  • M. Bentley, J. Hein, G. Preston, K. Foster, C.A. Yates (2022) “Molecular evolution of cooperative traits in bacteria” (In preparation).
  • M.C. Stoddard*, C.A. Yates* and Rick Prum (2022)”How the eggshell got its spots: a computational model of avian eggshell pigmentation patterns” (In preparation).

* Denotes joint first authorship.

Seeing the world through a mathematical lens