@book{Book2012,
  title = "Guide to Scientific Computing in C++",
  author = "Joe Pitt-Francis and Jonathan Whiteley",
  year = "2012",
  booktitle = "Guide to Scientific Computing in C++",
  isbn = "978-1-4471-2735-2",
  issn = "1863-7310",
  lccn = "2012931858",
  publisher = "Springer",
  series = "Undergraduate Topics in Computer Science",
  url = "http://www.springer.com/computer/swe/book/978-1-4471-2735-2?changeHeader",
  doi = "10.1007/978-1-4471-2736-9",
}
@article{2011Multiphysics,
  title = "Error bounds on block Gauss--Seidel solutions of coupled multiphysics problems",
  author = "J.P.\ Whiteley, K.\ Gillow, S.J.\ Tavener and A.C.\ Walter",
  year = "2011",
  journal = "International Journal for Numerical Methods in Engineering",
  pages = "1219-1237",
  volume = "88",
  doi = "10.1002/nme.3217",
}
@article{IJNMBE2011a,
  title = "The significant effect of the choice of ionic current integration method in cardiac electrophysiological simulations",
  author = "P.\ Pathmanathan, G.R.\ Mirams, J.A.\ Southern, and J.P.\ Whiteley",
  year = "2011",
  journal = "International Journal for Numerical Methods in Biomedical Engineering",
  pages = "1751--1770",
  volume = "27",
  doi = "10.1002/cnm.1438",
}
@article{3940,
  title = "A numerical guide to the solution of the bidomain equations of cardiac electrophysiology",
  author = "Pathmanathan, P. and Bernabeu, M.O. and Bordas, R. and Cooper, J. and Garny, A. and Pitt-Francis, J. and Whiteley, J.P. and Gavaghan, D.J.",
  year = "2010",
  journal = "Progress in Biophysics and Molecular Biology",
  number = "(2-3)",
  pages = "136-155",
  volume = "102",
  doi = "10.1016/j.pbiomolbio.2010.05.006",
}
@article{Whiteley 2010i,
  title = "A numerical method for the multiphase viscous flow equations",
  author = "J.M. Osborne, J.P. Whiteley",
  year = "2010",
  journal = "Computer Methods in Applied Mechanics and Engineering",
  pages = "3402-3417",
  volume = "199",
  doi = "10.1016/j.cma.2010.07.011",
}
@article{Whiteley 2010h,
  title = "Non-local models for the formation of hepatocyte-stellate cell aggregates",
  author = "J.E.F. Green, S.L. Waters, J.P. Whiteley, L. Edelstein-Keshet, K.M. Shakesheff, H.M. Byrne",
  year = "2010",
  journal = "Journal of Theoretical Biology",
  pages = "106-120",
  volume = "267",
  doi = "10.1016/j.jtbi.2010.08.013",
}
@article{Whiteley 2010g,
  title = "Cardiac electromechanics: the effect of contraction model on the mathematical problem and accuracy of the numerical scheme",
  author = "P. Pathmanathan, S.J. Chapman, D.J. Gavaghan, J.P. Whiteley",
  year = "2010",
  journal = "Quarterly Journal of Mechanics and Applied Mathematics",
  number = "3",
  pages = "375-399",
  volume = "63",
  doi = "10.1093/qjmam/hbq014",
}
@article{Whiteley 2010e,
  title = "A posteriori error analysis for the use of lookup tables in cardiac electrophysiology simulations",
  author = "J. Cooper, J.P. Whiteley, D.J. Gavaghan",
  year = "2010",
  journal = "SIAM Journal on Scientific Computing",
  number = "4",
  pages = "2167-2189",
  volume = "32",
  doi = "10.1137/090773064",
}
@article{Whiteley 2010d,
  title = "Modeling alveolar volume changes during periodic breathing in heterogeneously ventilated lungs",
  author = "S.-J. Dunn, J.P. Whiteley",
  year = "2010",
  journal = "Annals of Biomedical Engineering",
  number = "9",
  pages = "2988-2999",
  volume = "38",
  doi = "10.1007/s10439-010-0034-2",
}
@article{Whiteley 2010c,
  title = "Model reduction using a posteriori analysis",
  author = "J.P. Whiteley",
  year = "2010",
  journal = "Mathematical Biosciences",
  pages = "44-52",
  volume = "225",
  doi = "10.1016/j.mbs.2010.01.008",
}
@article{Whiteley 2010b,
  title = "Computational and Numerical Methods for the Accurate and Efficient Solution of the Bidomain Equations",
  author = "J.P. Whiteley",
  year = "2010",
  journal = "Mathematics In Industry",
  pages = "377-382",
  volume = "15",
  doi = "10.1007/978-3-642-12110-4_57",
}
@article{OzzyLongWavelength,
  title = "The Influence of Bioreactor Geometry and the Mechanical Environment on Engineered Tissues",
  author = "J. M. Osborne and R. D. O'Dea and J. P. Whiteley and H. M. Byrne and S. L. Waters",
  year = "2010",
  journal = "Journal of Biomechanical Engineering",
  month = "May",
  number = "5",
  pages = "051006",
  volume = "132",
  doi = "10.1115/1.4001160",
}
@article{Whiteley 2010a,
  title = "A Note on the Effect of the Choice of Weak Form on GMRES Convergence for Incompressible Nonlinear Elasticity Problems",
  author = "P Pathmanathan, JP Whiteley, SJ Chapman and DJ Gavaghan",
  year = "2010",
  journal = "Journal of Applied Mechanics",
  pages = "034501",
  volume = "77",
  doi = "10.1115/1.4000414",
}
@article{ChasteCPC09,
  title = "Chaste: A test-driven approach to software development for biological modelling",
  author = "J. Pitt-Francis and P. Pathmanathan and M.O. Bernabeu and R. Bordas and J. Cooper and A.G. Fletcher and G.R. Mirams and P. Murray and J.M. Osborne and A. Walter and S.J. Chapman and A. Garny and I.M.M. van Leeuwen and P.K. Maini and B. Rodriguez and S.L. Waters and J.P. Whiteley and H.M. Byrne and D.J. Gavaghan",
  year = "2009",
  journal = "Computer Physics Communications",
  number = "12",
  pages = "2452-2471",
  volume = "180",
  doi = "10.1016/j.cpc.2009.07.019",
}
@article{Whiteley2009d,
  title = "Solving the Coupled System Improves Computational Efficiency of the Bidomain Equations",
  author = "J.A. Southern, G. Plank, E.J. Vigmond, J.P. Whiteley",
  year = "2009",
  journal = "IEEE Transactions on Biomedical Engineering",
  number = "10",
  pages = "2404-2412",
  volume = "56",
  doi = "10.1109/TBME.2009.2022548",
}
@article{Whiteley2009c,
  title = "A Comparison of Numerical Methods used for Finite Element Modelling of Soft Tissue Deformation",
  author = "P. Pathmanathan, D.J. Gavaghan, J.P. Whiteley",
  year = "2009",
  journal = "Journal of Strain Analysis",
  pages = "391-406",
  volume = "44",
  doi = "10.1243/03093247JSA482",
}
@article{Whiteley2009a,
  title = "Discontinuous Galerkin Finite Element Methods for Incompressible Non-linear Elasticity",
  author = "J.P. Whiteley",
  year = "2009",
  journal = "Computer Methods in Applied Mechanics and Engineering",
  pages = "3464-3478",
  volume = "198",
  doi = "10.1016/j.cma.2009.07.002",
}
@article{3269,
  title = "A Numerical Method for Cardiac Mechanoelectric Simulations",
  author = "P. Pathmanathan and J.P. Whiteley",
  year = "2009",
  journal = "Annals of Biomedical Engineering",
  pages = "860-873",
  volume = "37(5)",
  doi = "10.1007/s10439-009-9663-8",
}
@article{cancerchaste1,
  title = "An integrative computational model for intestinal tissue renewal",
  author = "IMM van Leeuwen, GR Mirams, A Walter, A Fletcher, P Murray, J Osborne, S Varma, SJ Young, J Cooper, B Doyle, J Pitt-Francis, L Momtahan, P Pathmanathan, JP Whiteley, SJ Chapman, DJ Gavaghan, OE Jensen, JR King, PK Maini, SL Waters, HM Byrne",
  year = "2009",
  journal = "Cell Proliferation",
  keywords = "Wnt signalling, Crypt dynamics, Cell cycle, Colorectal cancer, Stem cells",
  pages = "617-636",
  volume = "42",
  doi = "10.1111/j.1365-2184.2009.00627.x",
}
@article{Chaste2,
  title = "Chaste: Incorporating a Novel Multiscale Spatial and Temporal Algorithm into a Large Scale Open Source Library",
  author = "Bernabeu, M.O. and Bordas, R. and Pathmanathan, P. and Pitt-Francis, J. and Cooper, J. and Garny, A. and Gavaghan, D.J. and Rodriguez, B. and Southern, J.A. and Whiteley, J.P.",
  year = "2009",
  journal = "Phil Trans Roy Soc (A)",
  month = "May",
  number = "1895",
  pages = "1907-1930",
  volume = "367",
  doi = "10.1098/rsta.2008.0309",
}
@article{Whiteley2008d,
  title = "An Efficient Technique for the Numerical Solution of the Bidomain equations",
  author = "J.P. Whiteley",
  year = "2008",
  journal = "Annals of Biomedical Engineering",
  number = "8",
  pages = "1398-1408",
  volume = "36",
  doi = "10.1007/s10439-008-9513-0",
}
@article{Chaste.08:Chaste,
  title = "Chaste: Using Agile Programming Techniques to Develop Computational Biology Software",
  author = "Joe Pitt-Francis and Miguel O. Bernabeu and Jonathan Cooper and Alan Garny and Lee Momtahan and James Osborne and Pras Pathmanathan and Blanca Rodriguez and Jonathan P. Whiteley and David J. Gavaghan",
  year = "2008",
  journal = "Philosophical Transactions of the Royal Society A",
  number = "1878",
  pages = "3111-3136",
  volume = "366",
  doi = "10.1098/rsta.2008.0096",
}
@article{3270,
  title = "Predicting tumor location by modeling the deformation of the breast",
  author = "P Pathmanathan, DJ Gavaghan, JP Whiteley, SJ Chapman and JM Brady",
  year = "2008",
  journal = "IEEE Transactions on Biomedical Engineering",
  pages = "2471-2480",
  volume = "55(10)",
  doi = "10.1109/TBME.2008.925714",
}
@article{2008a,
  title = "Multi-scale computational modelling in biology and physiology",
  author = "J.A. Southern, J.M. Pitt-Francis, J.P. Whiteley, D. Stokeley, H. Kobashi, R. Nobes, Y. Kadooka, D.J. Gavaghan",
  year = "2008",
  journal = "Progress in Biophysics and Molecular Biology",
  pages = "60-89",
  volume = "96",
  doi = "10.1016/j.pbiomolbio.2007.07.019",
}
@article{2007_4,
  title = "Non--linear modelling of breast tissue",
  author = "J.P.\ Whiteley and D.J.\ Gavaghan and S.J.\ Chapman and J.M.\ Brady",
  year = "2007",
  journal = "Mathematical Medicine and Biology",
  pages = "327--345",
  volume = "24",
  doi = "10.1093/imammb/dqm006",
}
@article{2007_2,
  title = "Soft tissue modelling of cardiac fibres for use in coupled mechano--electric simulations",
  author = "J.P.\ Whiteley and M.J.\ Bishop and D.J.\ Gavaghan",
  year = "2007",
  journal = "Bulletin of Mathematical Biology",
  pages = "2199--2225",
  volume = "69",
  doi = "10.1007/s11538-007-9213-1",
}
@article{2007_3,
  title = "Physiology driven adaptivity for the numerical solution of the bidomain equations",
  author = "J.P.\ Whiteley",
  year = "2007",
  journal = "Annals of Biomedical Engineering",
  pages = "1510--1520",
  volume = "35",
  doi = "10.1007/s10439-007-9337-3",
}
@article{2007_1,
  title = "Synchronization between arterial blood pressure and cerebral oxyhaemoglobin concentration investigated by wavelet cross--correlation",
  author = "A.B.\ Rowley and S.J.\ Payne and I.\ Tachtsidis and M.J.\ Ebden and J.P.\ Whiteley and D.J.\ Gavaghan and L.\ Tarassenko and M.\ Smith and C.E.\ Elwell and D.T.\ Delpy",
  year = "2007",
  journal = "Physiological Measurement",
  pages = "161--173",
  volume = "28",
  doi = "10.1088/0967-3334/28/2/005",
}
@article{2006_3,
  title = "An efficient numerical technique for the solution of the monodomain and bidomain equations",
  author = "J.P.\ Whiteley",
  year = "2006",
  journal = "IEEE Transactions on Biomedical Engineering",
  pages = "2139--2147",
  volume = "53",
  doi = "10.1109/TBME.2006.879425",
}
@article{2006_2,
  title = "Some factors affecting pulmonary oxygen transport",
  author = "J.P.\ Whiteley",
  year = "2006",
  journal = "Mathematical Biosciences",
  pages = "115--132",
  volume = "202",
  doi = "10.1016/j.mbs.2006.03.014",
}
@article{2006_1,
  title = "Synthesis of voltage--sensitive optical signals: application to panoramic optical mapping",
  author = "M.J.\ Bishop and B.\ Rodriguez and J.\ Eason and J.P.\ Whiteley and N.A.\ Trayanova and D.J.\ Gavaghan",
  year = "2006",
  journal = "Biophysical Journal",
  pages = "2938--2945",
  volume = "90",
  doi = "10.1529/biophysj.105.076505",
}
@article{2005_1,
  title = "Oxygen transport to muscle tissue where regions of low oxygen tension exist",
  author = "J.P.\ Whiteley and D.J.\ Gavaghan and C.E.W.\ Hahn",
  year = "2005",
  journal = "Mathematical and Computer Modelling",
  pages = "1113--1122",
  volume = "42",
  doi = "10.1016/j.mcm.2004.09.009",
}
@article{2005_2,
  title = "The solution of inverse non--linear elasticity problems that arise when locating breast tumours",
  author = "J.P.\ Whiteley",
  year = "2005",
  journal = "Journal of Theoretical Medicine",
  pages = "143--149",
  volume = "6",
  doi = "10.1080/10273660500148606",
}
@inproceedings{2004_1,
  title = "Predicting tumour location by simulating large deformations of the breast using a 3D finite element model and nonlinear elasticity",
  author = "P. Pathmanathan and D.J. Gavaghan and J.P. Whiteley and J.M. Brady and M.P. Nash and P.F. Nielsen and V. Rajagopal",
  year = "2004",
  booktitle = "Proceedings of MICCAI 2004",
  pages = "217--224",
  series = "Lecture Notes in Computer Science",
  volume = "3217",
}
@article{2003_5,
  title = "Periodic breathing induced by arterial oxygen partial pressure oscillations",
  author = "J.P.\ Whiteley and D.J.\ Gavaghan and C.E.W.\ Hahn",
  year = "2003",
  journal = "Mathematical Medicine and Biology",
  pages = "205--224",
  volume = "20",
}
@article{2003_4,
  title = "Mathematical modelling of pulmonary gas transport",
  author = "J.P.\ Whiteley and D.J.\ Gavaghan and C.E.W.\ Hahn",
  year = "2003",
  journal = "Journal of Mathematical Biology",
  pages = "79--99",
  volume = "47",
  doi = "10.1007/s00285-003-0196-8",
}
@article{2003_2,
  title = "The effect of diffusion in the respiratory tree on the alveolar amplitude response technique ({AART})",
  author = "J.P.\ Whiteley and D.J.\ Gavaghan and C.E.W.\ Hahn",
  year = "2003",
  journal = "Respiratory Physiology \& Neurobiology",
  pages = "81--96",
  volume = "137",
  doi = "10.1016/S1569-9048(03)00124-1",
}
@article{2003_3,
  title = "Efficient computations of gas transport in the respiratory tree",
  author = "J.P.\ Whiteley and D.J.\ Gavaghan",
  year = "2003",
  journal = "Mathematical Medicine and Biology",
  pages = "91--104",
  volume = "20",
}
@article{2003_1,
  title = "A tidal ventilation model for oxygenation in respiratory failure",
  author = "J.P.\ Whiteley and A.D.\ Farmery and D.J.\ Gavaghan and C.E.W.\ Hahn",
  year = "2003",
  journal = "Respiratory Physiology \& Neurobiology",
  pages = "77--88",
  volume = "136",
  doi = "10.1016/S1569-9048(03)00066-1",
}
@article{2002_2,
  title = "The effects of ventilation pattern on carbon dioxide transfer in three computer models of the airways",
  author = "J.P.\ Whiteley and M.J.\ Turner and A.B.\ Baker and D.J.\ Gavaghan and C.E.W.\ Hahn",
  year = "2002",
  journal = "Respiratory Physiology \& Neurobiology",
  pages = "269--284",
  volume = "131",
}
@article{2002_3,
  title = "Mathematical modelling of oxygen transport to tissue",
  author = "J.P.\ Whiteley and D.J.\ Gavaghan and C.E.W.\ Hahn",
  year = "2002",
  journal = "Journal of Mathematical Biology",
  pages = "503--522",
  volume = "44",
  doi = "10.1007/s002850200135",
}
@article{2002_1,
  title = "Variation of venous admixture, {SF}$_{6}$ shunt, {P}{\small a}$_{\text{O}_{2}}$, and the {P}{\footnotesize a}$_{\text{O}_{2}}/${F{\small I}}$_{\text{O}_{2}}$ ratio with {F{\footnotesize I}}$_{\text{O}_{2}}$",
  author = "J.P.\ Whiteley and D.J.\ Gavaghan and C.E.W.\ Hahn",
  year = "2002",
  journal = "British Journal of Anaesthesia",
  pages = "771--778",
  volume = "88",
}
@article{2001_3,
  title = "Some factors affecting oxygen uptake by red blood cells in the pulmonary capillaries",
  author = "J.P.\ Whiteley and D.J.\ Gavaghan and C.E.W.\ Hahn",
  year = "2001",
  journal = "Mathematical Biosciences",
  pages = "153--172",
  volume = "169",
}
@article{2001_1,
  title = "Modelling inert gas exchange in tissue and mixed--venous blood return to the lungs",
  author = "J.P.\ Whiteley and D.J.\ Gavaghan and C.E.W.\ Hahn",
  year = "2001",
  journal = "Journal of Theoretical Biology",
  pages = "431--443",
  volume = "209",
  doi = "10.1006/jtbi.2001.2278",
}
@article{2001_2,
  title = "A mathematical model of electron transfer within the mitochondrial respiratory cytochromes",
  author = "A.D.\ Farmery and J.P.\ Whiteley",
  year = "2001",
  journal = "Journal of Theoretical Biology",
  pages = "197--207",
  volume = "213",
  doi = "10.1006/jtbi.2001.2411",
}
@article{2000_2,
  title = "A tidal breathing model of the inert gas sinewave technique for inhomogeneous lungs",
  author = "J.P.\ Whiteley and D.J.\ Gavaghan and C.E.W.\ Hahn",
  year = "2000",
  journal = "Respiration Physiology",
  pages = "65--83",
  volume = "124",
}
@article{2000_1,
  title = "The effect of inspired oxygen concentration on the ventilation--perfusion distribution in inhomogeneous lungs",
  author = "J.P.\ Whiteley and D.J.\ Gavaghan and C.E.W.\ Hahn",
  year = "2000",
  journal = "Journal of Theoretical Biology",
  pages = "575--585",
  volume = "204",
  doi = "10.1006/jtbi.2000.2036",
}
@inproceedings{2000_3,
  title = "Discovering the structure of partial differential equations from example behavior",
  author = "L.\ Todorovski and S.\ Dzeroski and A.\ Srinivasan and J.P.\ Whiteley and D.J.\ Gavaghan",
  year = "2000",
  booktitle = "Proceedings of the International Conference on Machine Learning, Stanford, USA",
  pages = "991--998",
}
@article{1999_2,
  title = "The effect of the width of the ventilation--perfusion distribution on arterial blood oxygen content",
  author = "J.P.\ Whiteley and D.J.\ Gavaghan and C.E.W.\ Hahn",
  year = "1999",
  journal = "Journal of Theoretical Biology",
  pages = "271--279",
  volume = "201",
}
@article{1999_1,
  title = "A tidal breathing model for the multiple inert gas elimination technique",
  author = "J.P.\ Whiteley and D.J.\ Gavaghan and C.E.W.\ Hahn",
  year = "1999",
  journal = "Journal of Applied Physiology",
  pages = "161--169",
  volume = "87",
}
@article{1998_1,
  title = "Pulmonary blood flow measured by inspiratory inert gas concentration forcing oscillations",
  author = "E.M.\ Williams and M.C.\ Sainsbury and L.\ Sutton and L.\ Xiong and A.M.S.\ Black and J.P.\ Whiteley and D.J.\ Gavaghan and C.E.W.\ Hahn",
  year = "1998",
  journal = "Respiration Physiology",
  pages = "47--56",
  volume = "113",
}
@article{1998_2,
  title = "A mathematical evaluation of the multiple breath nitrogen washout ({MBNW}) technique and the multiple inert gas elimination technique ({MIGET})",
  author = "J.P.\ Whiteley and D.J.\ Gavaghan and C.E.W.\ Hahn",
  year = "1998",
  journal = "Journal of Theoretical Biology",
  pages = "517--539",
  volume = "194",
}