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

### Papers (Most recent first)

## 2020

**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” (Accepted at*Journal of the Royal Society Interface*).- J. Owen, R. Kelsh and
**C.A.****Yates**, (2020) “A quantitative modelling approach to zebrafish pigment pattern formation”*E-life 9*. - 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

- 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*. - 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) .* - G. Chappelle,
**C.A. Yates,**(2019) “Pulling in on-lattice models of cell migration”*Physical Review E 99 (6)*. - C. Smith, C. Mailler,
**C.A. Yates**, (2019) “Unbiased on-lattice domain growth”*Physical Review E 100(6)*.

## 2018

- C. Smith and
**C.A. Yates,**(2018) “The auxiliary region method (ARM) for coupling PDE and Brownian dynamics”*Royal Society Open Science 5(8)*. - 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*. - 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. - K. Minors, T. Rogers and
**C.A. Yates**, (2018) “Noise-driven bias in the non-local voter model”*Europhysics Letters*. - 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)*. - C. Smith and
**C.A. Yates**, (2018) “Spatially extended hybrid methods: a review”*Journal of the Royal Society Interface**15(139)*. - E. Gavagnin*, J. Owen*,
**C.A. Yates**, (2018) “Pair correlation functions for identifying spatial correlation in discrete domains”*Physical Review E 97(6)*.

## 2017

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

- 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)*. - J.U. Harrison and
**C.A. Yates**(2016). “A hybrid algorithm for coupling PDE and compartment-based dynamics“.*J. R. Soc. Int. 13(122).* - 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. - 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).* - 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)*. - 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

- 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 - 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. **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.**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.- 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. - 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. - 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*). - 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*. - 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

**C.A. Yates**(2014). “**Discrete and continuous models for tissue growth and shrinkage**”*Journal of Theoretical Biology (JTB)*350 37-48.- 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

**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.- 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 **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.**C.A. Yates**and G. Klingbeil (2013). “**Recycling random numbers in the stochastic simulation algorithm**”*Journal of Chemical Physics (JCP)*138(9) 094103.

## 2012

**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.**C.A. Yates**(2012) “Comparing stochastic discrete and deterministic continuum models of cell migration”.*ESMTB Communications*1(15) 31-36.- 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. - 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

**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.**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

- 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

- 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. **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

- E. Gavagnin, S.T. Vitadello, G. Guansingh, N.K. Haass, M.J. Simpson, T.C. Rogers and
**C.A. Yates**“Synchronous oscillations in growing cell populations are explained by demographic noise”. (In preparation). - C. Smith,
**C.A. Yates**“Challenges associated with 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**” (*In preparation*). - M. Bentley, J. Hein, G. Preston, K. Foster,
**C.A. Yates**(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.