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Papers, Talks and Conferences
ResearcherID: A-8863-2014
ORCID: 0000-0003-0461-7297
Papers (Most recent first)
2016
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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. (In press).
- 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) 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" The Journal of the Royal Society Interface (JRSI) 12(106) 20150141. Supplementary material to accompany this paper can be found here.
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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.
- 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.
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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.
- 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.
Papers submitted and in preparation
- 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. (accepted).
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J.U. Harrison and C.A. Yates (2016). "A hybrid algorithm for coupling PDE and compartment-based dynamics". J. R. Soc. Int. (submitted).
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R.J.H. Ross, C.A. Yates and R.E. Baker (2016). "Pattern formation and variable species densities are induced by domain growth". Phys. Rev. E (submitted).
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R.J.H. Ross, R.E. Baker and C.A. Yates (2016). "How domain growth is implemented determines the long term
behaviour of a cell population through its e?ect on spatial
correlations". Phys. Rev. E (under review).
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R.J.H. Ross, R.E. Baker and C.A. Yates (2016). "The effect of domain growth on spatial correlations". Journal of Theoretical biology (under review).
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R.J.H. Ross, R.E. Baker and C.A. Yates (2016). "Using aproximate Bayesian Computation to quantify cell-cell adhesion parameters in cell migratory processes". Nature publishing group Systems Biology and Applications (submitted).
- 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)).
- B. Franz, J. Taylor-King, C. Yates and R. Erban (2015). "Hard-sphere interactions in velocity jump models" (under review at Phys. Rev. E)
- 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.
Selected press coverage for "Ergodic directional switching in mobile insect groups"
Physical Review Focus
Science News
Selected press coverage for "Inherent noise can facilitate coherence in collective swarm motion"
Oxford Science Blog
Oxford Today
CSIC-Consejo Superior de Investigaciones Cientificas (Spain)
Talks
05-2016 Invited speaker at the Evolution group seminar series at the University of Bath Biology and Biochemistray Department. "Hybrid frameworks for modelling cell migration".
05-2016 Invited speaker at the Cell and Developmental Biology Seminar series at the University of Bath Biology and Biochemistray Department. "Hybrid frameworks for modelling cell migration".
05-2016 Invited speaker at the applied non-linar mathematics Seminar at the University of Bristol Engineering Department. "Hybrid frameworks for modelling cell migration".
04-2016 Invited speaker at the workshop on "fluctuation-driven phenomena in biological systems" at the University of Warwick Mathematics department. "Hybrid frameworks for modelling cell migration".
11-2015 Invited speaker at the University of Birmingham Applied Mathematics seminar, "A PDE/compartment-based hybrid method for simulating stochastic reaction-diffusion".
10-2015 Invited speaker at the Biomath seminar series, Chalmers University, Gothenburg, Sweden, "Developing PDE-compartment hybrid frameworks for modeling cell migration".
09-2015 Contributed talk at the IMA Conference on Numerical Methods for Simulation, University of Oxford, "The pseudo-compartment method for coupling PDE and compartment-based models of diffusion".
06-2015 Speaker, chair and organizer at SMB mini-symposium on “Multiscale hybrid modelling of stochastic reaction-diffusion systems”, Atlanta, Georgia, "The pseudo-compartment method for coupling PDE and compartment-based models of diffusion".
03-2015 Speaker at the SAMBa student seminar, University of Bath. "Developing biologically-inspired stochastic methodologies."
11-2014 Invited speaker at the BIRS workshop "Particle-Based Stochastic Reaction-Diffusion Models in Biology" in Banff, Canada. "A PDE/compartment-based hybrid method for simulating stochastic diffusion."
10-2014 Invited Speaker Imperial College London Biomathematics seminar. "Adaptive, discrete-state multi-level simulation for biochemical reaction networks."
06-2014 Organiser of and speaker at the mini-symposium "Position-jump models of biological processes on irregular lattices" at the 9th European Conference on Theoretical and Mathematical Biology at Chalmers University of Technology, Gothenberg. "Relevance of the Voronoi domain partition for position-jump reaction-diffusion processes on nonuniform rectilinear lattices."
06-2014 Invited Speaker at the mini-symposium "Collective motion of about 100 particles" at the 9th European Conference on Theoretical and Mathematical Biology at Chalmers University of Technology, Gothenberg. "Spatial "self-propelled particle" and non-spatial "reaction-network" models explain locust swarm cohesion."
05-2014 Invited speaker, CoMPLEX, University College London, “Modelling Melanocyte cell migration”.
03-2014 Invited speaker, School of Physics and Astronomy, University of Manchester. “Revisiting locust switching behaviour”.
11-2013 Invited speaker at the Department of Mathematical Sciences, University of Essex. “Modelling Melanocyte cell migration”.
10-2013 Invited speaker, School of Physics and Astronomy, University of Manchester. “Modelling Melanocyte cell migration”.
11-2012 Invited speaker at Herriot Watt University, Department of Mathematics in Edinburgh.
10-2012 Invited speaker at statistic workshop, University of Oxford. "From Antigenic variation to antZ".
07-2012 Invited speaker at the University of Hakodate, Japan.
06-2012 Invited speaker at statistic workshop, University of Oxford. "From Antigenic variation to antZ".
05-2012 2020 science seminar series. "From Antigenic variation to AntZ".
05-2012 Departmental research update Centre for Mathematical Biology, University of Oxford. "From Antigenic variation to AntZ".
03-2012 Invited speaker at the CoSy Lunch Seminar series, University of Uppsala, Sweden. "Modelling cell migration: from discrete to continuous".
02-2012 Invited speaker at the Computational biology group meeting , University of Oxford. "Stochastic modelling: From Locusts to Egg-shells".
10-2011 Invited speaker at the stochastic modelling discussion group series, University of Oxford. "Efficient and Accelerated Stochastic Simulation Algorithms".
06-2011 Invited speaker at the Doctoral Training Centre summer conference, University of Oxford. "Modelling cell migration: A D.Phil. in movies".
05-2012 Departmental research update Centre for Mathematical Biology, University of Oxford. "Modelling cell migration: A D.Phil. in movies".
04-2011 Invited speaker at the individual based modelling discussion group series, University of Oxford. "Return to Eden: How biologically relevant can on-lattice models really be?".
10-2010 Invited speaker at the Math-Bio-Medicine (MBM) seminars series, University of Leeds. "United by noise: Randomness helps swarms stay together".
09-2010 Invited speaker at Culham Science Centre (home of UK's fusion research programme, and JET). "United by noise: Randomness helps swarms stay together".
06-2010 Invited speaker at the Fourth annual Systems Biology Inter-DTC Conference (University of Warwick Systems Biology Centre) "A comparison of stochastic and analytical models for cell migration".
04-2010 Invited speaker at the Manchester SIAM student chapter conference "Comparing Stochastic and Continuum Models For Cell Migration".
11/2009 - Junior Applied Mathematics Seminar "A comparison of stochastic and analytical models for cell migration".
10/2009 - Departmental Transfer of Status talk "A comparison of stochastic and analytical models for cell migration".
06/2009 - Invited speaker at the third annual Systems Biology Inter-DTC Conference (University of Manchester Systems Biology Centre)
"A comparison of stochastic and analytical models for cell migration during early embryo somitogenesis.*"
05/2009 - Invited speaker at Princeton University Department of Engineering:
"United by noise: Randomness helps swarms stay together"*.
05/2009 - Mini-symposium speaker at the SIAM Conference on Applications of Dynamical Systems, Snowbird, Utah: "United by noise: Randomness helps swarms stay together"*.
02/2009 - Invited speaker at the 2nd Annual Oxford SIAM Student Chapter Conference: "United by noise: Randomness helps swarms stay together".
10/2008 - Junior Applied Mathematics Seminar "Locust Pocus: How Does Randomness Help Swarms Stay Together".
*These talks were created using LaTeX's presentation document class, beamer and contain movies. The movies cannot be played in Linux and require the correct media player on other operating systems
(although the rest of the talk will function perfectly well in Linux).
Peer Reviewing Duties
PLoS Computational Biology - Reviewer.
Physical Reveiw Letters (PRL) - Reviewer.
Physical Reveiw E (PRE) - Reviewer.
Journal of Theoretical Biology (JTB)- Reviewer.
Bulletin of Mathematical Biology (BMB) - Reviewer.
Physica A - Reviewer.
Journal of Mathematical Biology (JMB) - Reviewer.
AFOSR - Air Force Office of Scientific Research (AFOSR, USA) - Grant Reviewer.
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