Dr Christian Yates


Papers, Talks and Conferences

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

Papers (Most recent first)

    2016

  1. 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).
  2. 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

  3. 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
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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).
  10. 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.
  11. 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.
  12. 2014

  13. C.A. Yates (2014). "Discrete and continuous models for tissue growth and shrinkage" Journal of Theoretical Biology (JTB) 350 37-48.
  14. 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.
  15. Supplementary material to accompany this paper can be found here.

    2013

  16. 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.
  17. Supplementary material to accompany this paper can be found here.
  18. 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
  19. 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.
  20. C.A. Yates and G. Klingbeil (2013). "Recycling random numbers in the stochastic simulation algorithm" Journal of Chemical Physics (JCP) 138(9) 094103.

    2012

  21. 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.
  22. C.A. Yates (2012) "Comparing stochastic discrete and deterministic continuum models of cell migration". ESMTB Communications 1(15) 31-36.
  23. 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.
  24. 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.
  25. 2011

  26. 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.
  27. 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).
  28. 2010

  29. 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.
  30. 2009

  31. 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.
  32. 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


* 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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