Mathematical Biology › Publications › Recent Papers

Selected Recent Papers

2012

  • P. D. H. M. Verhaegen, J. Van Marle, A. Kuehne, H. J. Schouten, E. A. Gaffney, P. K. Maini, E. Middlekoop and P. P. M. Van Zuijlen (2012). Collagen bundle morphometry in skin & scar tissue: a novel distance mapping method provides superior measurements compared to Fourier analysis. J. Microsc. 245:82-89. (eprints)
  • M. J. Tindall, L. Dyson, K. Smallbone and P. K. Maini (2012). Modelling acidosis and the cell cycle in multicellular tumour spheroids. J. Theor. Biol. 298:107-115. (eprints)
  • S.-J. Dunn, A. G. Fletcher, S. J. Chapman, D.J. Gavaghan and J.M. Osborne (2012). Modelling the role of the basement membrane in the colonic epithelium. J. Theor. Biol. 298:82-91. (eprints)
  • A. G. Fletcher, C. J. W. Breward and S. J. Chapman (2012). Mathematical modelling of monoclonal conversion in the colonic crypt. J. Theor. Biol. 300:118-133. (eprints)
  • M. Flegg, S.J. Chapman and R. Erban (2012). The two-regime method for optimizing stochastic reaction–diffusion simulations. J. Roy. Soc. Interface 9:859-868.
  • D. Basanta, J. G. Scott, M. N. Fishman, G. E. Ayala, S. W. Hayward, and A. R. A. Anderson (2012) Investigating prostate cancer tumour-stroma interactions - clinical and biological insights from an evolutionary game. Brit. J. Cancer. 106(1):174-181. (eprints)
  • J. G. Scott (2012) Phase i trialist. Lancet. Oncol. 13(3):236. (eprints)
  • J. G. Scott, P. Kuhn, and A. R. A .Anderson (2012) Unifying metastasis--Integrating intravasation, circulation and end organ colonization.  Nat. Rev. Cancer. 12:445. (eprints)
  • G. Trichas, A. M. Smith, N. White, V. Wilkins, T. Watanbe, A. Moore, B. Joyce, J. Sugnaseelan, T. A. Rodrigues, D. Kay, R. E. Baker, P. K. Maini and S. Srinivas (2012). Multi-cellular rosettes in the mouse visceral endoderm facilitate the ordered migration of AVE cells. PLoS Biol. 10(2):e1001256. (eprints)
  • 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. (eprints)
  • S. Shvartsman and R. E. Baker (2012). Mathematical models of morphogen gradients and their effects on gene expression. WIREs Dev. Biol. doi:10.1002/wdev.55. (eprints)
  • 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 139:2935–2944. (eprints) 
  • 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. (eprints) 
  • A. A.  Al-Shammari,  E. A.  Gaffney and  S.  Egginton (2012).  Re-evaluating  the  use  of  voronoi  tessellations  in  the assessment of oxygen supply from capillaries in muscle. Bull. Math. Biol. 74(9): 2204-2231. (eprints)
  • G. R. Mirams, A. G. Fletcher, P. K. Maini and H.M. Byrne (2012). A theoretical investigation of the effect of proliferation and adhesion on monoclonal conversion in the colonic crypt. J. Theor. Biol. 74(9): 2204-2231. (eprints)
  • R. Dello Ioio, C. Galinha, A. G. Fletcher, S. P. Grigg, A. Molnar, S. Sabatini, D. Baulcombe, P. K. Maini and M. Tsiantis (2012). A PHABULOSA/cytokinin feedback loop controls root growth in Arabidopsis. Curr. Biol. 22:1699-1704. (eprints)

2011

  • S. W. Cho, S. W. 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 signaling and a new feedback loop for spatial patterning of the teeth. Development 138:1807-1816. (eprints)
  • E. A. Gaffney, H. Gadelha, D. J. Smith, J. R. Blake and J. C. Kirkman-Brown (2011). Mammalian sperm motility: observation and theory. Ann. Rev. Fluid Mech. 43:501-528. (eprints)
  • A. Hamadeh, M. A. J. Roberts, E. August, P. E. McSharry, P. K. Maini, J. P. Armitage and A. Papchristodoulou (2011). Feedback control architecture and the bacterial chemotaxis network. PLoS Comput. Biol. 7. (eprints)
  • G. Klingbeil, R. Erban, M Giles and P. K. Maini (2011). STOCHSIMGPU: Parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB. Bioinformatics 27:1170-1171. (eprints)
  • N. K. Martin, E. A. Gaffney, R. A. Gatenby, R. J. Gillies, I. F. Robey and P. K. Maini (2011). A mathematical model of tumour and blood pHe regulation: The HCO-3/CO2 buffering system. Math. Biosci. 230:1-11. (eprints)
  • P. J. Murray, A. Walter, A. G. Fletcher, C. M. Edwards, M. J. Tindall and P. K. Maini (2011). Comparing a discrete and continuum model of the intestinal crypt. Phys. Biol. 8:026011. (eprints)
  • H. Perfahl, H. M. Byrne, T. Chen, V. Estrella, T. Alarcon, A. Lapin, R. A. Gatenby, R. J. Gillies, M. C. Lloyd, P. K. Maini, M. Reuss and M. R. Owen (2011). Multiscale modelling of vascular tumour growth in 3D: the roles of domain size and boundary conditions. PLoS One 6. (eprints)
  • M. V. Plikus, R. E Baker, C. C. Chen, C. Fare, D. de la Cruz, T. Andl, P. K. Maini, S. E. Millar, R. Widelitz and C. M. Chuong (2011). Self-organizing and stochastic behaviors during the regeneration of hair stem cells. Science 332:586. (eprints)
  • J. W. Schofield, E. A. Gaffney, R. A. Gatenby and P. K. Maini (2011). Tumour angiogenesis: The gap between theory and experiments. J. Theor. Biol. 274:97-102. (eprints)
  • M. J. Simpson and R. E Baker (2011). Correcting mean-field approximations for spatially-dependent advection-diffusion-reaction processes. Phys. Rev. E 82:e041905. (eprints)
  • 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. (eprints)
  • 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 J. Chem. Phys. 134:084109. (eprints)
  • C.A. Yates, R. Baker, R. Erban and P.K. Maini (2011). Refining self-propelled particle models for collective behaviour. Can. Appl. Math. Q. 18:299-350.  (eprints)
  • S. Cotter, K. Zygalakis, I. Kevrekidis and R. Erban (2011). A constrained approach to multiscale stochastic simulation of chemically reacting systems.  J. Chem. Phys. 135(9):094102.
  • J. Lipkova, K. Zygalakis, J. Chapman and R. Erban (2011).  Analysis of brownian dynamics simulations of reversible bimolecular reactions. Siam J. Appl. Math. 71(3):714-730. (eprints)
  • C. Xue, H. Hwang, K. Painter and R. Erban (2011). Travelling waves in hyperbolic chemotaxis equations. B. Math. Biol. 73(8):1695-1733. (eprints)
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2010

  • F. Bai, R. W. Branch, D. V. Nicolau Jr, T. Pilizota, B. C. Steele, P. K. Maini and R. M. Berry (2010). Conformational spread as a mechanism for cooperativity in the bacterial flagellar switch. Science 327:685-689. (eprints)
  • R. E. Baker, C. A. Yates and R. Erban (2010). From microscopic to macroscopic descriptions of cell migration on growing domains. Bull. Math. Biol. 72:719-762. (eprints)
  • 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 466:248-252. (eprints)
  • O. Cominetti, A. Matzavinos, S. Samarasinghe, D. Kulasiri, S. Liu, P. K. Maini and R. Erban (2010). DifFUZZY: A fuzzy clustering algorithm for complex data sets. Int. J. of Comput. Intelligence in Bioinformatics and Systems Biology 1:402-417. (eprints)
  • S. Egginton and E. A. Gaffney (2010). Tissue capillary supply - it's quality not quantity that counts! Exp. Physiol. 95:971-979. (eprints)
  • C. Escudero, C. A. Yates, J. Buhl, I. D. Couzin, R. Erban, I. G. Kevrekidis and P. K. Maini (2010). Ergodic directional switching in mobile insect groups. Phys. Rev. E 82:011926. (eprints)
  • H. Gadelha, E. A. Gaffney,  D. J. Smith and J. C. Kirkman-Brown (2010). Nonlinear instability in flagellar dynamics: a novel modulation mechanism in sperm migration? J. Roy. Soc. Interface 7:1689-1697. (eprints)
  • E. A. Gaffney, J. M. Tiffany, N. Yokoi, A. J. Bron (2010). A mass and solute balance model for tear volume and osmolarity in the normal and the dry eye. Prog. Retin. Eye Res. 29:59-78. (eprints)
  • M. D. Johnston, P. K. Maini, S. J. Chapman, C. M. Edwards and W. F. Bodmer (2010). On the proportion of cancer stem cells in a tumour. J. Theor. Biol. 266:708-711. (eprints)
  • A. Madzvamuse, E. A. Gaffney and P. K. Maini (2010). Stability analysis of non-autonomous reaction-diffusion systems: the effects of growing domains. J. Math. Biol. 61:133-164. (eprints)
  • N. K. Martin, E. A. Gaffney, R. A. Gatenby and P. K. Maini (2010). Tumour-stromal interactions in acid-mediated invasion: a mathematical model. J. Theor. Biol. 267:461-470. (eprints)
  • N. K. Martin, E. A. Gaffney, R. A. Gatenby and P. K. Maini (2010). Leaky vessels as a potential source of stromal acidification in tumours. J. Theor. Biol. 267:454-460. (eprints)
  • P. J. Murray, J. W. Kang, G. R. Mirams, S. Y. Shin, H. M. Byrne, P. K. Maini and K. H. Cho (2010). Modelling spatially regulated β-catenin dynamics and invasion in intestinal crypts. Biophys. J. 99:716-725. (eprints)
  • J. M. Osborne, A. Walter, S. K. Kershaw, G. R. Mirams, A. G. Fletcher, P. Pathmanathan, D. Gavaghan, O. E. Jensen, P. K. Maini and H. M. Byrne (2010). A hybrid approach to multi-scale modelling of cancer. Phil. Trans. R. Soc. A. 368:5013-5028. (eprints)
  • S. Seirin Lee and E. A. Gaffney (2010). Aberrant behaviours of reaction diffusion self-organisation models on growing domains in the presence of gene expression time delays. Bull. Math. Biol. 72:2161-2179. (eprints)
  • S. Seirin Lee, E. A. Gaffney and N. A. M. Monk (2010). The influence of gene expression time delays on Gierer-Meinhardt pattern formation systems. Bull. Math. Biol. 72:2139-2160. (eprints)
  • H. Shum, E. A. Gaffney and D. J. Smith (2010). Modelling bacterial behaviour close to a no-slip plane boundary: the influence of bacterial geometry. Proc. Roy. Soc. A 466:1725-1748. (eprints)
  • K. Smallbone, P. K. Maini and R. A. Gatenby (2010). Episodic, transient systemic acidosis delays evolution of the malignant phenotype: possible mechanism for cancer prevention by increased physical activity. Biology Direct 5:22. (eprints)
  • 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. 82:051929. (eprints)
  • 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. 18:299-350. (eprints)

2009

  • C. A. Yates, R. Erban, C. Escudero, I. D. Couzin, J. Buhl, I. G. Kevrekidis, P. K. Maini, P. K. and D. J. T. Sumpter (2009). Inherent noise can facilitate coherence in collective swarm motion. Proc. Natl. Acad. Sci. USA 106:5464-5469. (eprints)
  • D. V. Nicolau Jr, J. P. Armitage and P. K. Maini (2009). Directional persistence and the optimality of run-and-tumble chemotaxis. Comput. Biol. Chem. 33:269-274. (eprints)
  • D. J. Smith, E. A. Gaffney, J. R. Blake and J. C. Kirkman-Brown (2009). Human sperm accumulation near surfaces: a simulation study. J. Fluid Mech. 621:289-320. (eprints)
  • R. Erban and S. J. Chapman (2009). Stochastic modelling of reaction-diffusion processes: algorithms for bimolecular reactions. Phys. Biol. 6:046001. (eprints)
  • H. C. Monro and E. A. Gaffney (2009). Modelling chemotherapy resistance in palliation and failed cure. J. Theor. Biol. 257:292-302. (eprints)
  • 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 79:03198. (eprints)
  • D. J. Smith, E. A. Gaffney, H. Gadelha, N. Kapur and J.C. Kirkman-Brown (2009). Bend propagation in the flagella of migrating human sperm, and its modulation by viscosity. Cell. Motil. Cytoskel. 66:220-336. (eprints)
  • R. Erban, S. J. Chapman, I. Kevrekidis and T. Vejchodsky (2009). Analysis of a stochastic chemical system close to a SNIPER bifurcation of its mean-field model. SIAM J. Appl. Math. 70:984-1016. (eprints)
  • I. M. M. van Leeuwen, G. R. Mirams, A. Walter, A. Fletcher, P. Murray, J. Osborne, S. Varma, S. J. Young, J. Cooper, B. Doyle, J. Pitt-Francis, L. Momtahan, P. Pathmanathan, J. P. Whiteley, S. J. Chapman, D. J. Gavaghan, O. E. Jensen, J. R. King, P. K. Maini, S. L. Waters, H. M. Byrne (2009). An integrative computational model for intestinal tissue renewal. Cell Prolif. 42:617-636. (eprints)
  • M. J. Tindall, S. L. Porter, G. H. Wadhams, P. K. Maini and J. P. Armitage (2009). Spatiotemporal modelling of CheY complexes in Escherichia coli chemotaxis. Prog. Biophys. Mol. Biol. 100:40-46. (eprints)

2008

  • K. Smallbone, R. A. Gatenby and P. K. Maini (2008). Mathematical modelling of tumour acidity. J. Theor. Biol. 255(1):106-112. (eprints)
  • 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 451:340-344. (eprints)
  • B. Addison-Smith, D. L. S. McElwain and P. K. Maini (2008). A simple mechanistic model of sprout spacing in tumour-associated angiogenesis. J. Theor. Biol. 250:1-15. (eprints)
  • D. J. Smith, E. A. Gaffney and J. R. Blake (2008). Fluid mechanics of nodal flow due to embryonic primary cilia. J. Roy. Soc. Interface 5:567-573. (eprints)
  • M. J. Tindall, S. L. Porter, P. K. Maini, G. Gaglia and J. P. Armitage (2008). Overview of mathematical approaches used to model bacterial chemotaxis I: the single cell, Bull. Math. Biol. 70:1525-1569. (eprints)
  • M. J. Tindall,  P. K. Maini,  S. L. Porter and J. P. Armitage (2008). Overview of mathematical approaches used to model bacterial chemotaxis II: bacterial populations. Bull. Math. Biol. 70:1570-1607. (eprints)
  • E. A. Gaffney, J. K. Heath and M. Z. Kwiatkowska (2008). A mass action model of a fibroblast growth factor signaling pathway and its simplification. Bull. Math. Biol. 68:99-130. (eprints)
  • R. E. Baker, E. A. Gaffney and P. K. Maini (2008). PDEs for self-organisation in cellular and developmental biology. Nonlinearity 21:R251-R290. (eprints)
  • D. V. Nicolau Jr, K. Burrage, D. V. Nicolau, and P. K. Maini (2008). 'Extremotaxis': Computing with a bacterial-inspired algorithm. Biosystems 94:47-54. (eprints)

2007

  • D. J. Smith, E. A. Gaffney and J. R. Blake (2007). A viscoelastic traction layer model of mucociliary flow. Bull. Math. Biol. 69:289-327. (eprints)
  • D. J. Smith, E. A. Gaffney and J. R. Blake (2007). Discrete cilia modelling with singularity distributions. Bull. Math. Biol. 69:1477-1510. (eprints)
  • M. D. Johnston, C. M. Edwards, W. F. Bodmer, P. K. Maini and S. J. Chapman (2007). Mathematical modeling of cell population dynamics in the colonic crypt and in colorectal cancer. Proc. Natl. Acad. Sci. USA 104:4008-4013. (eprints)
  • R. E. Baker and P. K. Maini  (2007) A mechanism for morphogen-controlled domain growth. J. Math. Biol. 54:597-622. (eprints)
  • R. Erban and S. J. Chapman (2007). Reactive boundary conditions for stochastic simulations of reaction-diffusion processes. Phys. Biol. 4:16-28. (eprints)
  • 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. 54:745-760. (eprints)
  • R. Erban and S. J. Chapman (2007). Time scale of random sequential adsorption. Phys. Rev. E 75:041116. (eprints)
  • M. D. Johnston, C. M. Edwards, W. F. Bodmer, P. K. Maini and S. J. Chapman (2007). Examples of mathematical modeling: tales from the crypt. Cell Cycle 6:2106-2112. (eprints)
  • K. M. Page, N. A. M. Monk and P. K. Maini (2007). Speed of reaction diffusion in embryogenesis. Phys. Rev. E 76:011902-1. (eprints)
  • M. J. Tindall and C. P. Please (2007). Modelling the cell cycle and cell movement in multicellular spheroids. Bull. Math. Biol. 69:1147-65.
  • A. Madzvamuse and P. K. Maini (2007). Velocity-induced numerical solutions of reaction-diffusion systems on continuously growing domains. J. Comput. Phys. 225:100-119. (eprints)

2006

  • P. K. Maini, L. Malaguti, C. Marcelli and S. Matucci (2006). Diffusion-aggregation processes with mono-stable reaction terms. Dis. Cont. Dyn. Sys. B 6:1175-1189. (eprints)
  • P. K. Maini, R. E. Baker and C. M. Chuong (2006). The Turing model comes of molecular age. Science 314:397-1398. (eprints)
  • Baker, Ruth E. and Schnell, S. and Maini, P. K. (2006). A clock and wavefront mechanism for somite formation. Dev. Biol. 293:116-126. (eprints)
  • R. E. Baker, S. Schnell and P. K. Maini (2006). A mathematical investigation of a new model for somitogenesis. J. Math. Biol. 52:458-482. (eprints)
  • Barrass, I. and Crampin, E. J. and Maini, P. K. (2006). Mode transitions in a model reaction-diffusion system driven by domain growth and noise. Bull. Math. Biol. 68:981-995. (eprints)
  • M. Meyer-Herrmann, P. K. Maini and D. Iber (2006). An analysis of B cell selection mechanisms in germinal centres. Math. Med. Biol. 23:255-277. (eprints)
  • T. Miura, K. Shiota, G. Morriss-Kay, G. and P. K. Maini (2006). Mixed mode pattern in Doublefoot mutant mouse limb - Turing reaction-diffusion model on a growing domain during limb development. J. Theor. Biol. 240:562 -573. (eprints)
  • E. A. Gaffney and N. A. M. Monk (2006). Gene expression time delays and Turing pattern formation systems. Bull. Math. Biol. 68:99-130. (eprints)
  • R. T. Liu, S. S. Liaw, S. S. and P. K. Maini (2006). Two-stage Turing model for generating pigment patterns on the leopard and the jaguar. Phys. Rev. E 74:011914. (eprints)

 

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