Publications

Preprints

  • F. R. Cooper, R. E. Baker and A. G. Fletcher (2017). Numerical analysis of the immersed boundary method for cell-based simulation. bioRxiv
  • D. J. Warne, R. E. Baker and M. J. Simpson (2017). Accelerating computational Bayesian inference for stochastic biochemical reaction network models using multi-level Monte Carlo sampling. bioRxiv
  • J. U. Harrison and R. E. Baker (2017). An automatic adaptive method to combine summary statistics in approximate Bayesian computation. arXiv
  • S. Engblom, D. B. Wilson and R. E. Baker (2017). Scalable population-level modeling of biological cells incorporating
    mechanics and kinetics in continuous time. arXiv

Articles

2017

  1. J. Kursawe, R. E. Baker and A. G. Fletcher (2017). Impact of implementation choices on quantitative predictions of cell-based computational models. To appear in J. Comp. Phys.  DOI
  2. O. M. Matsiaka, C. J. Penington, R. E. Baker and M. J. Simpson (2017). Continuum approximations for lattice-free multi-species models of collective cell migration. J. Theor. Biol. 7(422):1-11. DOI bioRxiv
  3. S. T. Johnston, D. L. S. McElwain, R. E. Baker and M. J. Simpson (2017). Co-operation, competition and crowding: a discrete framework linking Allee kinetics, nonlinear diffusion, shocks and sharp-fronted travelling waves. Sci. Rep. 7:42134. DOI
  4. R. J. H. Ross, R. E. Baker and C. A. Yates (2017). Variable species densities are induced by volume exclusion interactions upon domain growth. Phys. Rev. E 95:032416. DOI bioRxiv
  5. R. J. H. Ross, R. E. Baker, A. Parker, M. J. Ford, R. L. Mort and C. A. Yates (2017). Using approximate Bayesian computation to quantify cell–cell adhesion parameters in a cell migratory process. npj Sys. Biol. Appl. 3:9. DOI bioRxiv
  6. C. Lester, C. A. Yates and R. E. Baker (2017). Efficient parameter sensitivity computation for spatially-extended reaction networks. J. Chem. Phys. 146:044106. DOI arXiv
  7. A. G. Fletcher, F. Cooper and R. E. Baker (2017). Mechanocellular models of epithelial morphogenesis. Philos. Trans. R. Soc. Lond. B Biol. Sci.19(372):1720.  DOI
  8. S. T. Johnston, R. E. Baker and M. J. Simpson (2017). A new and accurate continuum description of moving fronts. New J. Phys. 19:033010. DOI bioRxiv

2016

  1. J. Kursawe, R. Bardenet, J. J. Zartman, R. E. Baker and A. G. Fletcher (2016). Robust cell tracking in epithelial tissues through identification of maximum common subgraphs. J. Roy. Soc. Interface. 13(124):20160725. DOI bioRxiv
  2. R. J. H. Ross, C. A. Yates and R. E. Baker (2016). The effect of domain growth on spatial correlations. Physica A 466:334-345. DOI bioRxiv
  3. A. J. Ellery, R. E. Baker and M. J. Simpson (2016). An analytical method for disentangling the roles of adhesion and crowding for random walk models on a crowded lattice. Phys. Biol. 13(5):05LT02. DOI
  4. C. J. Penington, R. E. Baker and M. J. Simpson (2016). Exits in order: how crowding affects particle lifetimes. J. Chem. Phys. 144:244107. DOI
  5. R. J. H. Ross, C. A. Yates and R. E. Baker (2016). How domain growth is implemented determines the long term behaviour of a cell population through its effect on spatial correlations. Phys. Rev. E 94:012408. DOI
  6. L. J. Schumacher, P. M. Kulesa, R. McLennan, R. E. Baker and P. K. Maini (2016). Multidisciplinary approaches to understanding collective cell migration in developmental biology. To appear in Open Biol. DOI
  7. P. R. Taylor, R. E. Baker, M. J. Simpson and C. A. Yates (2016). Coupling volume-excluding compartment-based models of diffusion at different scales: Voronoi and pseudo-compartment approaches. J. Roy. Soc. Interface 13(120). DOI 
  8. D. Wilson and R. E. Baker (2016). Multi-level methods and approximating distribution functions. AIP Adv. 6:075020. DOI 
  9. C. Lester, R. E. Baker, M. B. Giles and C. A. Yates (2016). Extending the multi-level method for the simulation of stochastic biological systems. Bull. Math. Biol. 78(8):1640-1677.  DOI
  10. A. N. Simonov, G. P. Morris, E. Mashkina, B. Braithwaite, K. Gillow, R. E. Baker, D. J. Gavaghan and A. M. Bond (2016). Multiparameter estimation in voltammetry when an electron transfer process is coupled to a chemical reaction. Anal. Chem. 88(9):4724-4732 DOI
  11. S. T. Johnston, R. E. Baker and M. J. Simpson (2016). Filling the gaps: A robust description of adhesive birth-death-movement processes. Phys. Rev. E 93(4):042413. DOI
  12. A. J. Ellery, R. E. Baker and M. J. Simpson (2016). Distinguishing between short-time non-Fickian diffusion and long-time Fickian diffusion for a random walk on a crowded lattice. J. Chem. Phys. (Communication) 144(17):171104. DOI
  13. A. J. Ellery, M. J. Simpson, S. W. McCue and R. E. Baker (2016). Modelling transport through an environment crowded by a mixture of obstacles of different shapes and sizes. Physica A 449:74-84. DOI
  14. R. L. Mort, R. J. H. Ross, K. J. Hainey, O. J. Harrison, M. A. Keighren, G. Landini, R. E. Baker, K. J. Painter, I. J. Jackson and C. A. Yates (2016). Reconciling diverse mammalian pigmentation patterns with a fundamental mathematical model. Nature Comm. 7:10288. DOI

2015

  1. P. K. Maini, R. E. Baker and S. Schnell (2015). Rethinking models of pattern formation in somitogenesis. Cell Sys. 1(4):248-249. DOI
  2. J. Kursawe, P. A. Brodskiy, J. J. Zartman, R. E. Baker and A. G. Fletcher (2015). Capabilities and limitations of tissue size control through passive mechanical forces. PLoS Comp. Biol. 11(12):e1004679. DOI
  3. R. McLennan, L. J. Schumacher, J. A. Morrison, J. M. Teddy, D. A. Ridenour, A. C. Box, C. L. Semerad, H. Li, W. McDowell, D. Kay, P. K. Maini, R. E. Baker and P. M. Kulesa (2015). VEGF signals induce trailblazer cell identity that drives neural crest migration. Dev. Biol. 407(1):12-25. DOI
  4. A. J. Ellery, R. E. Baker and M. J. Simpson (2015). Calculating the Fickian diffusivity for a lattice-based random walk with agents and obstacles of different shapes and sizes. Phys. Biol. 12(6):066010 DOI
  5. P. R. Taylor, C. A. Yates, M. J. Simpson and R. E. Baker (2015). Reconciling transport models across scales: the role of volume exclusion. Phys. Rev. E Rapid Communication 92:040701(R). DOI
  6. M. J. Simpson, J. A. Sharpe, L. C. Morrow and R. E. Baker (2015). Exact solutions of coupled multispecies linear reaction-diffusion equations on a uniformly growing domain. PLoS ONE 10(9): e0138894. DOI
  7. C. Narciso, Q. Wu, P. A. Brodskiy, G. Garston, R. E. Baker, A. G. Fletcher, J. J. Zartman (2015). Patterning of wound-induced intercellular calcium flashes in a developing epithelium. Phys. Biol. 12:056005. DOI
  8. M. J. Simpson and R. E. Baker (2015). Exact calculations of survival probability for diffusion on growing lines, disks and spheres: the role of dimension. J. Chem. Phys. 143:094109. DOI
  9. T. E. Woolley, E. A. Gaffney, J. M. Oliver, S. L. Waters, R. E. Baker and A. Goriely (2015). Global contraction or local growth: bleb shape depends on more than cell structure. J. Theor. Biol. 380:83-97. DOI
  10. L. Dyson and R. E. Baker (2015). The importance of volume exclusion in modelling cellular migration. J. Math. Biol. 71(3):691-711. DOI
  11. C. A. Yates, A. Parker and R. E. Baker (2015). Incorporating pushing in exclusion process models of cell migration. Phys. Rev. E 91:052711. DOI
  12. R. McLennan, L. J. Schumacher, J. A. Morrison, J. M. Teddy, D. A. Ridenour, A. C. Box, C. L. Semerad, H. Li, W. McDowell, D. Kay, P. K. Maini, R. E. Baker and P. M. Kulesa (2015). Neural crest migration is driven by a few trailblazer cells with a unique molecular signature narrowly confined to the invasive front. Development 142:2014-2025. DOI
  13. M. J. Simpson, J. A. Sharpe and R. E. Baker (2015). Survival probability for a diffusive process on a growing domain. Phys. Rev. E 91:042701. DOI
  14. R. 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. Math. Biosci. 264:108-118. DOI
  15. D. C. Markham, M. J. Simpson and R. E. Baker (2014). Choosing an appropriate modelling framework for analysing multispecies co-culture cell biology experiments. Bull. Math. Biol. 77(4):713-734. DOI
  16. G. Morris, R. E. Baker, K. Gillow, J. J. Davis, D. J. Gavaghan and A. M. Bond (2015). Theoretical analysis of the relative significance of thermodynamic and kinetic dispersion in the DC and AC voltammeter of surface-confined molecules. Langmuir 30(17):4996-5004. DOI
  17. S. T. Johnston, M. J. Simpson and R. E. Baker (2015). Modelling the movement of interacting cell populations: a moment dynamics approach. J. Theor. Biol. 370:81-92. DOI
  18. C. Lester, M. B. Giles, C. A. Yates and R. E. Baker (2015). An adaptive multi-level simulation algorithm for stochastic biological systems. J. Chem. Phys. 124:024113. DOI
  19. P. R. Taylor, R. E. Baker and C. A. Yates (2015). Deriving appropriate boundary conditions, and accelerating position-jump simulations, of diffusion using non-local jumping. Phys. Biol. 12(1):016006. DOI

2014

  1. P. K. Maini and R. E. Baker (2014). Modelling collective cell motion in biology. Springer Proc. Math. Stat. 87:1-11. DOI
  2. A. N. Simonov, G. P. Morris, E. A. Mashkina, B. Bethwaite, K. Gillow, R. E. Baker, D. J. Gavaghan and A. M. Bond (2014). Inappropriate use of the quasi-reversible electrode kinetic model in simulation-experiment comparisons of voltammetric processes that approach the reversible limit. Anal. Chem. 86(16): 8408-8417. DOI
  3. T. E. Woolley, E. A. Gaffney, J. M. Oliver, R. E. Baker, S. L. Waters and A. Goriely (2014). Three mechanical models of blebbing and multi-blebbing. IMA J. Appl. Math. 79(4):636-660. DOI
  4. D. C. Markham, R. E. Baker and P. K. Maini (2014). Modelling collective cell motion. Dis. Cont. Dyn. Sys. B 34(12):5123-5133. DOI
  5. K. K. Treloar, M. J. Simpson, B. J. Binder, D. L. S. McElwain and R. E. Baker (2014). Assessing the role of spatial correlations during collective cell spreading. Sci. Rep. 4:5713 DOI
  6. D. C. Markham, M. J. Simpson, P. K. Maini, E. A. Gaffney and R. E. Baker (2014). Comparing methods for modelling spreading cell fronts. J. Theor. Biol. 353:95-103. DOI
  7. G. Rosser, R. E. Baker, J. P. Armitage and A. G. Fletcher (2014). Modelling and analysis of bacterial tracks suggest an active reorientation mechanism in Rhodobacter spheroides. J. Roy. Soc. Interface 11(97):20140320.  DOI bioRxiv
  8. K. K. Treloar, M. J. Simpson, D. L. S. McElwain and R. E. Baker (2014). Are in vitro estimates of cell diffusivity and cell proliferation rate sensitive to assay geometry? J. Theor. Biol. 356:71-84. DOI
  9. A. G. Fletcher, M. Osterfield, R. E. Baker and S. Y. Shvartsman (2014). Vertex models of epithelial morphogenesis. Biophys. J. 106(11):2291-2304. DOI
  10. T. E. Woolley, E. A. Gaffney, J. M. Oliver, R. E. Baker, S. L. Waters and A. Goriely (2014). Cellular blebs: pressure-driven, axisymmetric, membrane protrusions. Biomech. Model Mechanobiol. 13(2):463-476. DOI
  11. A. J. Ellery, M. J. Simpson, S. W. McCue and R. E. Baker (2014). Characterizing transport through a crowded environment with different obstacle sizes. J. Chem. Phys. 140:054108. DOI
  12. T. E. Woolley, R. E. Baker, C. Tickle, P. K. Maini and M. Towers (2014). Mathematical modelling of digit specification by a sonic hedgehog gradient. Dev. Dyn. 243(2):290-208. DOI
  13. B. L. Vaughan, R. E. Baker, D. Kay and P. K. Maini (2014). A modified Oster-Murray-Harris mechanical model of morphogenesis. SIAM J. Appl. Math. 73(6):2124-2142. DOI
  14. M. J. Simpson, J. A. Sharp and R. E. Baker (2014). Distinguishing between mean-field, moment dynamics and stochastic descriptions of birth-death-movement processes. Physica A 395:236–246. DOI

2013

  1. K. K. Treloar, M. J. Simpson, P. Haridas, K. J. Manton, D. I. Leavesley, D. L. S. McElwain and R. E. Baker (2013). Multiple types of data are required to identify the mechanisms influencing the spatial expansion of melanoma cell colonies. BMC Sys. Biol. 7:137 DOI
  2. G. P. Morris, A. N. Simonov, E. A. Mashkina, R. Bordas, K. Gillow, R. E. Baker, D. J. Gavaghan and A. M. Bond (2013). A comparison of fully automated methods of data analysis and computer assisted heuristic methods in an electrode kinetic study of the pathologically variable [Fe(CN)6]3- /4- process by AC voltammetry. Anal. Chem. 85(24):11780–11787. DOI
  3. D. C. Markham, M. J. Simpson, P. K. Maini, E. A. Gaffney and R. E. Baker (2013). Incorporating spatial correlations into multispecies mean-field models. Phys. Rev. E 88(5):052713. DOI
  4. C. A. Yates and R. E. Baker (2013). Importance of the Voronoi domain partition for position-jump reaction-diffusion processes on nonuniform rectilinear lattices. Phys. Rev. E. 88(5):054701. DOI
  5. A. J. Ellery, M. J. Simpson, S. W. McCue and R. E. Baker (2012). Simplified approach for calculating moments of action for linear reaction-diffusion equations. Phys. Rev. E 88(5):054102. DOI
  6. S. S. Lee, R. E. Baker, E. A. Gaffney and S. M. White (2013). Optimal barrier zones for stopping the invasion of Aedes aegypti mosquitoes via transgenic or sterile insect techniques. Theor. Ecol. 6(4):427–442. DOI
  7. C. A. Yates and R. E. Baker (2013). Isotropic model for cluster growth on a regular lattice. Phys. Rev. E 88(2):023304. DOI
  8. L. G. Bowden, M. J. Simpson and R. E. Baker (2013). Design and interpretation of cell trajectory assays. J. Roy. Soc. Interface 10(88):20130630. DOI
  9. 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 Comput. Biol. 9(10):e1003276. DOI
  10. S. S. Lee, R. E. Baker, E. A. Gaffney and S. M. White (2013). Modelling Aedes aegypti mosquito control via transgenic and sterile insect techniques: endemics and emerging outbreaks. J. Theor. Biol. 331:78–90. DOI
  11. M. J. Simpson, B. J. Binder, P. Haridas, K. K. Treloar, D. L. S. McElwain and R. E. Baker (2013). Experimental and modelling investigation of monolayer development with clustering. Bull. Math. Biol. 75(5):871–889. DOI
  12. D. C. Markham, M. J. Simpson and R. E. Baker (2013). Simplified method for including spatial correlations in mean-field approximations. Phys. Rev. E 87(6):062702. DOI
  13. G. Rosser, A. G. Fletcher, P. K. Maini and R. E. Baker (2013). The effect of sampling rate on observed statistics in a correlated random walk. J. Roy. Soc. Interface 10(85):20130273. DOI
  14. L. J. Schumacher, T. E. Woolley and R. E. Baker (2013). Noise-induced temporal dynamics in Turing systems. Phys. Rev. E 87(4):042719. DOI
  15. M. J. Simpson, R. E. Baker, S. W. McCue and A. J. Ellery (2013). Critical time scales and critical time intervals for coupled linear processes. ANZIAM J. 54(3):127-142. DOI
  16. M. J. Simpson, K. K. Treloar, B. J. Binder, P. Haridas, K. J. Manton, D. I. Leavesley, D. L. S. McElwain and R. E. Baker (2013). Quantifying the roles of cell motility and cell proliferation in a circular barrier assay. J. Roy. Soc. Interface. 10(82):20130007. DOI
  17. G. P. Stevenson, R. E. Baker, A. M. Bond, S. W. Feldberg, D. J. Gavaghan and K. Gillow (2013). Access to enhanced differences in Marcus-Hush and Butler-Volmer electron transfer theories by systematic analysis of higher order AC harmonics. Phys. Chem. Chem. Phys. 15(6):2210-2221. DOI
  18. P. J. Murray, P. K. Maini and R. E. Baker (2013). Modelling oscillator synchronisation during vertebrate segmentation. To appear in Springer Proceedings in Mathematics: Pattern Formation in Morphogenesis Problems and Mathematical Issues 15:95–105. DOI
  19. P. J. Murray, P. K. Maini and R. E. Baker (2013). Modelling Delta-Notch perturbations during zebrafish somitogenesis. Dev. Biol. 373(2):407-421. DOI

2012

  1. R. E. Baker and P. J. Murray (2012). Understanding hair follicle cycling: a systems approach. Curr. Opin. Genet. Dev. 22(6):617-622. DOI
  2. P. J. Murray, M. V. Plikus, C.-M. Chuong, P. K. Maini and R. E. Baker (2012). Modelling hair growth dynamics using an excitable medium framework. PLoS Comput. Biol. 8(12):e1002804. DOI
  3. R. N. Thompson, C. A. Yates and R. E. Baker (2012). Modelling cell migration and adhesion during development. Bull. Math. Biol. 74(12):2793-809. DOI
  4. P. K. Maini, T. E. Woolley, R. E. Baker, E. A. Gaffney and S. S. Lee (2012). Turing’s model for biological pattern formation and the robustness problem. Interface Focus 2(4):487-496. DOI
  5. A. J. Ellery, M. J. Simpson, S. W. McCue and R. E. Baker (2012). Moments of action provide insight into critical times for advection-diffusion-reaction processes. Phys. Rev. E 83(3):031137. DOI
  6. E. A. Gaffney, N. A. M. Monk, R. E. Baker and S. S. Lee (2012). Reply to correspondence: no oscillations in real activator-inhibitor systems in accomplishing pattern formation. Bull. Math. Biol. 74(10):2268-2271. DOI
  7. L. Dyson, P. K. Maini and R. E. Baker (2012). Macroscopic limits of individual-based models for motile cell populations with volume exclusion. Phys. Rev. E 86(3):031903. DOI
  8. C. A. Yates, R. E. Baker, R. Erban and P. K. Maini (2012). Going from microscopic to macroscopic on nonuniform growing domains. Phys. Rev. E. 86(2):021921 DOI
  9. A. M. Smith, R. E. Baker, D. Kay and P. K. Maini (2012). Incorporating chemical signalling factors into cell-based models of growing epithelial tissues. J. Math. Biol. 65(3):441-463. DOI
  10. J. L. Aragon. R. A. Barrio, T. E. Woolley, R. E. Baker and P. K. Maini (2012). Nonlinear effects on Turing patterns: time oscillations and chaos. Phys. Rev. E 86(2):026201. DOI
  11. R. McLennan, L. Dyson, K. W. Prather, J. A Morrison, R. E. Baker, P. K. Maini and P. M. Kulesa (2012). Multiscale mechanisms of cell migration during development: theory and experiment. Development 139:2395-2944. DOI
  12. P. K. Maini, T. E. Woolley, R. E. Baker, E. A. Gaffney and S. Seirin Lee (2012). Turing’s model for biological pattern formation and the robustness problem. Roy. Soc. Interface Focus “Computability and the Turing Centenary” 2(4):487-496. DOI
  13. G. P. Stevenson, C.-Y. Lee, G. Kennedy, A. Parkin, R. E. Baker, K. Gillow, F. A. Armstrong, D. J. Gavaghan and A. M. Bond (2012). Theoretical analysis of the two-electron, surface-confined cytochrome c peroxidase transfer reaction, using large amplitude Fourier transformed ac voltammetry. Langmuir 28(25)9864-9877. DOI
  14. S. T. Johnston, M. J. Simpson and R. E. Baker (2012). Mean-field descriptions of collective migration with strong adhesion. Phys. Rev. E 85(5)051922. DOI
  15. H. Collins-Hooper, T. E. Woolley, L. Dyson, A. Patel, P. Potter, R. E. Baker, E. A. Gaffney, P. K. Maini, P. R. Dash and K. Patel (2012). Age related changes in speed and mechanism of adult skeletal muscle stem cell migration. Stem Cells 30(6):1182-1195. DOI
  16. T. E. Woolley, R. E. Baker, E. A. Gaffney, P. K. Maini and S. S. Lee (2012). Effects of intrinsic stochasticity on delayed reaction-diffusion patterning systems. Phys. Rev. E. 85(5):051914. DOI
  17. A. J. Ellery, M. J. Simpson, S. W. McCue and R. E. Baker (2012). Critical time scales for advection-diffusion-reaction processes. Phys. Rev. E 85(4):041135. DOI
  18. S. Shvartsman and R. E. Baker (2012). Mathematical models of morphogen gradients and their effects on gene expression. Wiley Interdisciplinary Reviews: Developmental Biology. DOI
  19. R. E. Baker and M. J. Simpson (2012). Models of collective cell motion for cell populations with different aspect ratio: diffusion, proliferation and travelling waves. Physica A 391(14):3729-3750. DOI
  20. V. Klika, R. E. Baker, D. Headon and E. A. Gaffney (2012).  The influence of receptor-mediated reactions on reaction-diffusion mechanisms of cellular self-organisation. Bull. Math. Biol. 74(4):935-957. DOI
  21. G. Trichas, A. M. Smith,  N. White, V. Wilkins,  T. Watanabe, A. Moore, B. Joyce, J. Sugnaseelan, T. A. Rodriguez, D. Kay, R. E. Baker, P. K. Maini and S. Srinivas (2012). Multicellular rosettes in the mouse visceral endoderm facilitate the ordered migration of AVE cells. PLoS Biol. 10(2):e1001256. DOI

2011

  1. S. Seirin Lee, E. A. Gaffney and R. E. Baker (2011). The dynamics of Turing patterns for morphogen-regulated growing domains with cellular response delays. Bull. Math. Biol. 73(11):2527-2551. DOI
  2. T. E. Woolley, R. E. Baker, E. A. Gaffney and P. K. Maini (2011). Stochastic reaction and diffusion on growing domains: understanding the breakdown of robust pattern formation. Phys. Rev. E. 84(4):046216. DOI
  3. T. E. Woolley, R. E. Baker, E. A. Gaffney and P. K. Maini (2011). The influence of stochastic domain growth on pattern nucleation for diffusive systems with internal noise. Phys. Rev. E 84(4):041095. DOI
  4. T. E. Woolley, R. E. Baker, E. A. Gaffney and P. K. Maini (2011). Power spectra methods for a stochastic description of diffusion on deterministically growing domains. Phys. Rev. E 84(2):021915. DOI
  5. S. MacNamara, R. E. Baker and P. K. Maini (2011). Distinguishing graded and ultrasensitive signalling cascade kinetics by the shape of morphogen gradients in Drosophila. J. Theor. Biol. 285(1):136-146. DOI
  6. P. J. Murray, P. K. Maini and R. E. Baker (2011). The clock and wavefront model revisited. J. Theor. Biol. 283(1)227-238. DOI
  7. M. J. Simpson and R. E Baker (2011). Correcting mean-field approximations for spatially-dependent advection-diffusion-reaction processes. Phys. Rev. E. 82(4):e041905. DOI
  8. M. V. Plikus, R. E. Baker, C. Fare, D. De La Cruz, P. K. Maini, R. Widelitz and C.-M. Chuong (2011). Self-organising and stochastic behaviours. Science 332(6069):586-589. DOI
  9. C.-Y. Lee, G. P Stevenson, A. M. Bond, A. Parkin, M. M. Roessler, R. E. Baker, K. Gillow, D. J. Gavaghan and F. A. Armstrong (2011). Theoretical and experimental investigation of surface-confined two-center metalloproteins by large-amplitude Fourier transformed ac voltammetry. J. Electroanal. Chem. 656(1-2):293-303. DOI
  10. S.-W. Cho, S. Kwak, T. E. Woolley, M.-J. Lee, E.-J. Kim, R. E. Baker, H.-J. Kim, J.-S. Shin, C. Tickle, P. K. Maini and H.-S. Jung (2011). Interactions between Shh, Sostdc1 and Wnt signalling and a new feedback look for spatial patterning of the teeth. Developmental 138(9):1807-1816. DOI
  11. M. J. Simpson, R. E. Baker and S. W. McCue (2011). Models of collective cell spreading with variable cell aspect ration: a motivation for degenerate diffusion models. Phys. Rev. E. 83(2):021901. DOI

2010

  1. C. A. Yates, R. E. Baker, R. Erban and P. K. Maini (2010). Refining self-propelled particle models for collective behaviour. Can. Appl. Math. Q. 18(3)299:350.
  2. T. E. Woolley, R. E. Baker, P. K. Maini, J. L. Aragon and R. Barrio (2010). Analysis of stationary droplets in a generic Turing reaction-diffusion system. Phys. Rev. E. 82(5):051929. DOI
  3. R. E. Baker and M. J. Simpson (2010). Correcting mean-field approximations for birth-death-movement processes. Phys. Rev. E. 82(4):e041905. DOI
  4. B. Benazeraf, P. Francois, R. E. Baker, C. D. Little and O. L. Pourquie (2010). A random cell motility gradient downstream of FGF controls elongation of amniote embryos. Nature 466(7303):248-252. DOI
  5. R. E. Baker, C. A. Yates and R. Erban (2010). From microscopic to macroscopic descriptions of cell migration on growing domains. Bull. Math. Biol. 72(3):719-762. DOI

2009

  1. C.-M. Lin, T.-X. Jiang, R. E. Baker,  P. K. Maini, R. B. Widelitz and C.-M. Chuong (2009). Spots and stripes: pleomorphic patterning of stem cells via p-ERK-dependent cell chemotaxis shown by feather morphogeneis and mathematical simulation. Dev. Biol. 334(2):369-382. DOI
  2. Y. Tan, G. P. Stevenson, R. E. Baker, D. Elton, K. Gillow, J. Zhang, A. M. Bond and D. J. Gavaghan (2009). Designer based Fourier transform voltammetry: a multi-frequency, variable amplitude, sinusoidal waveform. J. Electroanal. Chem. 634(1):11-21. DOI
  3. R. E. Baker and S. Schnell (2009). How can mathematics help us explore vertebrate segmentation? HFSP J. 1(3):1-5. DOI
  4. C. Chang, P. Wu, R. E. Baker, P. K. Maini, L. Alibardi and C.-M. Chuong (2009). The reptile scale paradigm: Evo-Devo, pattern formation and regeneration. Int. J. Dev. Biol. 53:813-826. DOI
  5. R. E. Baker, S. Schnell and P. K. Maini (2009). Waves and patterning in developmental biology: vertebrate segmentation and feather bud formation as case studies. Int. J. Dev. Biol. 53:783-794. DOI
  6. R. A. Barrio, R. E. Baker, B. Vaughan, K. Tribuzy, M. R. de Carvalho, R. Bassanezi and P. K. Maini (2009). Modelling the skin pattern of fishes. Phys. Rev. E 79(3):03198. DOI

2008

  1. R. E. Baker, E. A. Gaffney and P. K. Maini (2008). PDEs for self-organisation in cellular and developmental biology. Nonlinearity 21:R251-R290. DOI
  2. R. E. Baker, S. Schnell and P. K. Maini (2008). Mathematical models for somite formation. Curr. Top. Dev. Biol. 81:183-203. DOI
  3. M. V. Plikus, D. De La Cruz, J. Mayer, R. E. Baker, R. Maxon, P. K. Maini and C.-M. Chuong (2008). Cyclic dermal BMP signalling regulates stem cell activation during hair regeneration. Nature 451(7176)340-344. DOI

2007

  1. R. E. Baker and P. K. Maini (2007). Travelling gradients in interacting morphogen systems. Math. Biosci. 209(1):30-50. DOI
  2. P. M. Kulesa, S. Schnell, S. Rudloff, R. E. Baker and P. K. Maini (2007). From segment to somite: segmentation to epithelialisation analysed within quantitative frameworks. Dev. Dyn. 236(6):1392-1402. DOI
  3. N. V. Kotov, R. E. Baker, D. A. Dawidov, K. V. Platov, N. V. Valeyev, A. I. Skorinkin and P. K. Maini (2007). A study of the temperature dependence of bienzyme systems and enzymatic chains. Comp. Math. Meth. Med. 8(2):93-112. DOI
  4. H. Yamada, T. Nakagaki, R. E. Baker and P. K. Maini (2007). Dispersion relation in oscillatory reaction-diffusion systems with self-consistent flow in true slime mold. J. Math. Biol. 54(6):745-760. DOI
  5. R. E. Baker and P. K. Maini (2007). A mechanism for morphogen-controlled domain growth. J. Math. Biol. 54(5):597-622. DOI

2006

  1. P. K. Maini, R. E. Baker and C.-M. Chuong (2006). The Turing model comes of molecular age. Science 314:1397-1398. DOI
  2. R. B. Widelitz, R. E. Baker, M. Plikus, C.-M. Lin, P. K. Maini, R. Paus and C.-M. Chuong (2006). Distinct mechanisms underlie pattern formation in the skin and skin appendages. Birth Defects Res. Part C 78(3):280-291. DOI
  3. R. E. Baker, S. Schnell and P. K. Maini (2006). A mathematical investigation of a clock and wavefront model for somitogenesis. J. Math. Biol. 52(4):458-482. DOI
  4. R. E. Baker, S. Schnell and P. K. Maini (2006). A clock and wavefront mechanism for somite formation. Dev. Biol. 293(1):116-126. DOI

2004

  1. D. McInerney, S. Schnell, R. E. Baker and P. K. Maini (2004). A mathematical formulation for the cell cycle model in somitogenesis: analysis, parameter constraints and numerical solutions. Math. Med. Biol. 21(2):85-113. DOI

2003

  1. R. E. Baker, S. Schnell and P. K. Maini (2003). Formation of vertebral precursors: past models and future predictions. J. Theor. Med. 5(1):23-35. DOI

Special Issues

  1. M. J. Simpson and R. E. Baker (Eds.) (2015). Bulletin of Mathematical Biology – Special Issue “Spatial Moment Techniques for Modelling Biological Processes”. Volume 77. DOI
  2. S. Y. Shvartsman and R. E. Baker (Eds.) (2014). Seminars in Cell and Developmental Biology – Special Issue “Modelling Developmental Pathways”. Volume 35. DOI
  3. R. E. Baker and P. K. Maini (Eds.) (2009). Mathematical Modelling of Natural Phenomena – Special Issue “Morphogenesis”. Vol. 4 No. 4. DOI

Book Chapters

  1. T. E. Woolley, E. A. Gaffney, P. K. Maini and R. E. Baker (2017). Turing’s Theory of Developmental Pattern Formation. Chapter 9, The Once and Future Turing. ISBN 978-1-107-01083-3.
  2. T. E. Woolley, R. E. Baker and P. K. Maini (2016). Turing’s Theory of Morphogenesis. Chapter 34, The Turing Guide. ISBN 978-0-1987-4782-6.
  3. T. E. Woolley, R. E. Baker, E. A. Gaffney and P. K. Maini (2012). How long can we survive? Chapter 8, Mathematical Modelling of Zombies. ISBN 978-0-7766-2210-1.

Encyclopaedia

  1. R. E. Baker and P. K. Maini (2012). Springer Encyclopedia of Applied and Computational Mathematics – Pattern Formation and Development. ISBN 978-3-540-70528-4
  2. P. K. Maini and R. E. Baker (2012). Developmental Biology: Mathematical Modelling of Development. eLS. DOI

Other

  1. C.-M. Lin, T.-X. Jiang, R. E. Baker, P. K. Maini, M. Hughes, R. B. Widelitz and C.-M. Chuong (2008). Periodic patterning stem cells and induction of skin appendages: p-ERK-dependent mesenchymal condensation is coupled with Turing mechanism to convert stripes to spots. International Investigative Dermatology Meeting. J. Invest. Dermatol. 128:S156.
  2. M. V. Plikus, D. De La Cruz, J. Mayer, R. E. Baker, R. Maxon, P. K. Maini and C.-M. Chuong (2007). BMP activity defines refractory and competent hair follicle populations during the propagation of regenerative waves.
  3. N. Scheerlinck, C. Escudero, R. E. Baker and P. K. Maini (2007). Modelling spatio-temporal starch degradation patterns in apples during fruit growth. Proceedings of the 39th meeting of the Agricultural Research Modeller’s Group. J. Ag. Sci. 145(6):635-650.
  4. C.-M. Lin, T.-J. Jiang, R. Widelitz, R. E. Baker, P. K. Maini and C.-M. Chuong (2006). Embryonic patterning makes the feathers fly. American Society for Cell Biology Press Release.