Publications

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

Papers (Most recent first)

2017

  1. 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).
  2. 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).
  3. C. Lester, C. Yates and R. E. Baker, (2017). “Efficient parameter sensitivity computation for spatially-extended reaction networks“.  J. Chem. Phys. 146(4).

    2016

  4. R.N. Kelsh, K. Camargo Sosa, J. Owen and C.A. Yates (2016). “Zebrafish adult pigment stem cells are multipotent and form pigment cells by a progressive fate restriction process“.  BioEssays 39(3).
  5. R.J.H. Ross, R.E. Baker and C.A. Yates (2016). “The effect of domain growth on spatial correlations“. Physica A 466 334-345.
  6. 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).
  7. J.U. Harrison and C.A. Yates (2016). “A hybrid algorithm for coupling PDE and compartment-based dynamics“. J. R. Soc. Int. 13(122).
  8. 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.
  9. 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).
  10. 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).
  11. 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 modelNat. Comms 7 10288. Supplementary material to accompany this paper can be found here.

    2015

  12. 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
  13. L. Dyson*, C.A. Yates*, J. Buhl A.J. McKane (2015). “Onset of collective motion in locusts is captured by a minimal modelPhys. Rev. E (PRE) 92(5) 052708. Supplementary material to accompany this paper can be found here.
  14. C.A. Yates, A. Parker and R.E. Baker (2015) “Incorporating pushing in exclusion process models of cell migrationPhys. Rev. E (PRE) 91(5) 052711.
  15. C.A. Yates and M.B. Flegg (2015) “The pseudo-compartment method for coupling PDE and compartment-based models of diffusionJournal of the Royal Society, Interface (JRSI) 12(106) 20150141. Supplementary material to accompany this paper can be found here.
  16. 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 domainsMathematical Biosciences 26(11) 108-118.
  17. B, Knapp, R. Bardenet, …, C.A. Yates, D. Gavaghan and C.M. Deane (2015). “Ten simple rules for a successful cross-disciplinary collaborationPLoS Computational Biology 11(4) e1004214.
  18. 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).
  19. P. Taylor, R.E. Baker and C.A. Yates (2015). “Deriving appropriate boundary conditions, and accelerating position-jump simulations, of diffusion using non-local jumpingPhysical Biology 12(1) 016006.
    Also appearing in Physical Biology highlights of 2015.
  20. C. Lester, C.A. Yates, M.B. Giles, and R.E. Baker (2015). “An adaptive multi-level simulation algorithm for stochastic biological systemsJournal of Chemical Physics 142(2) 024113.

    2014

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

    2013

  23. 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.
  24. 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 sphaeroidesPLoS Computational Biology 9(10) e1003276
  25. 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.
  26. C.A. Yates and G. Klingbeil (2013). “Recycling random numbers in the stochastic simulation algorithmJournal of Chemical Physics (JCP) 138(9) 094103.

    2012

  27. C.A. Yates, R.E. Baker R. Erban and P.K. Maini (2012). “Going from microscopic to macroscopic on nonuniform growing domainsPhysical Review E (PRE) 86 021921. Supplementary material to accompany this paper can be found here.
  28. C.A. Yates (2012) “Comparing stochastic discrete and deterministic continuum models of cell migration”. ESMTB Communications 1(15) 31-36.
  29. R. Thompson, C.A. Yates and R.E. Baker (2012). “Modelling cell migration and adhesion during developmentBulletin of Mathematical Biology 72(12) 2793-2809.
  30. 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

  31. 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.
  32. 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

  33. 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

  34. 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.
  35. 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.

Papers submitted and in preparation

  • C.A. Yates, M.J. Ford, R.L. Mort “A multi-stage representation of cell proliferation as a Markov Process” (under review at Bulletin of Mathematical Biology).
  • G. Chappelle, C.A. Yates “Incorporating pulling in on-lattice models of cell migration.” (In preparation).
  • E. Gavagnin, C.A. Yates “Modelling persistence in on-lattice models of cell migration.” (In preparation).
  • E. Gavagnin*, J. Owen*, C.A. Yates “Re-evaluating the on-lattice pair-correlation function.” (In preparation).
  • C. Smith, C.A. Yates “The auxiliary region method (ARM) for coupling PDE and Brownian dynamics” (In preparation).
  • C. Smith, C.A. Yates “Hybrid methodologies for reaction-diffusion mechanisms” (In preparation).
  • C. Smith, C.A. Yates “Implementing hybrid coupling methodologies on growing domains” (In preparation).
  • M. Malickova, C.A. Yates, K. Bodova (2016). A stochastic model of ant trail following with two pheromones” (under review at Journal of the Royal Society Interface (JRSI)).
  • M. Bentley, C.A. Yates, J. Hein, G. Preston, K. Foster (2016) “Molecular evolution of cooperative traits in bacteria” (In preparation).
  • M.C. Stoddard*, C.A. Yates* and Rick Prum (2016)”How the eggshell got its spots: a computational model of avian eggshell pigmentation patterns” (In preparation).

* Denotes joint first authorship.

Attempts to understand Biology through the lens of Mathematics