Jonathan Whiteley: Publications

[1]

Chaste: Incorporating a Novel Multiscale Spatial and Temporal Algorithm into a Large Scale Open Source Library

Bernabeu MO, Bordas R, Pathmanathan P, Pitt-Francis J, Cooper J, Garny A, Gavaghan DJ, Rodriguez B, Southern JA, Whiteley JP

Phil Trans Roy Soc (A), Vol. 367, No. 1895, pages 1907-1930. May 2009.

Details | BibTeX | DOI (10.1098/rsta.2008.0309)

[2]

Chaste: A test-driven approach to software development for biological modelling

J Pitt-Francis, P Pathmanathan, MO Bernabeu, R Bordas, J Cooper, AG Fletcher, GR Mirams, P Murray, JM Osborne, A Walter, SJ Chapman, A Garny, I van Leeuwen, PK Maini, B RodrÃguez, SL Waters, JP Whiteley, HM Byrne, DJ Gavaghan

Computer Physics Communications, Vol. (in press). 2009.

Details | BibTeX

[3]	A Note on the Effect of the Choice of Weak Form on GMRES Convergence for Incompressible Nonlinear Elasticity Problems P Pathmanathan, JP Whiteley, SJ Chapman, DJ Gavaghan Journal of Applied Mechanics, Vol. (in press). 2009. Details \| BibTeX

[4]	A Numerical Method for Cardiac Mechanoelectric Simulations P. Pathmanathan, J.P. Whiteley Annals of Biomedical Engineering, Vol. 37(5), pages 860-873. 2009. Details \| BibTeX

[5]

An integrative computational model for intestinal tissue renewal

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

Cell Proliferation, 2009.

Details | BibTeX

[6]

Chaste: Using Agile Programming Techniques to Develop Computational Biology Software

J Pitt-Francis, MO Bernabeu, JC, A Garny, L Momtahan, J Osborne, P Pathmanathan, B Rodriguez, JP Whiteley, DJ Gavaghan

Philosophical Transactions of the Royal Society A, Vol. 366(1878), pages 3111-3136. 2008.

Details | BibTeX

[7]	Predicting tumor location by modeling the deformation of the breast P Pathmanathan, DJ Gavaghan, JP Whiteley, SJ Chapman, JM Brady IEEE Transactions on Biomedical Engineering, Vol. 55(10), pages 2471-2480. 2008. Details \| BibTeX

[8]	Multi-scale computational modelling in biology and physiology J.A. Southern, J.M. Pitt-Francis, J.P. Whiteley, D. Stokeley, H. Kobashi, R. Nobes, Y. Kadooka, D.J. Gavaghan 2008. Details \| BibTeX

[9]	Non—linear modelling of breast tissue J.P. Whiteley et al. Mathematical Medicine and Biology, Vol. 24, pages 327—345. 2007. Details \| BibTeX

[10]	Soft tissue modelling of cardiac fibres for use in coupled mechano—electric simulations J.P. Whiteley, M.J. Bishop and D.J. Gavaghan Bulletin of Mathematical Biology, Vol. 69, pages 2199—2225. 2007. Details \| BibTeX

[11]	Physiology driven adaptivity for the numerical solution of the bidomain equations J.P. Whiteley Annals of Biomedical Engineering, Vol. 35, pages 1510—1520. 2007. Details \| BibTeX

[12]	Synchronization between arterial blood pressure and cerebral oxyhaemoglobin concentration investigated by wavelet cross—correlation A.B. Rowley et al. Physiological Measurement, Vol. 28, pages 161—173. 2007. Details \| BibTeX

[13]	An efficient numerical technique for the solution of the monodomain and bidomain equations J.P. Whiteley IEEE Transactions on Biomedical Engineering, Vol. 53, pages 2139—2147. 2006. Details \| BibTeX

[14]	Some factors affecting pulmonary oxygen transport J.P. Whiteley Mathematical Biosciences, Vol. 202, pages 115—132. 2006. Details \| BibTeX

[15]	Synthesis of voltage—sensitive optical signals: application to panoramic optical mapping M.J. Bishop et al. Biophysical Journal, Vol. 90, pages 2938—2945. 2006. Details \| BibTeX

[16]	Oxygen transport to muscle tissue where regions of low oxygen tension exist J.P. Whiteley, D.J. Gavaghan and C.E.W. Hahn Mathematical and Computer Modelling, Vol. 42, pages 1113—1122. 2005. Details \| BibTeX

[17]	The solution of inverse non—linear elasticity problems that arise when locating breast tumours J.P. Whiteley Journal of Theoretical Medicine, Vol. 6, pages 143—149. 2005. Details \| BibTeX

[18]	Predicting tumour location by simulating large deformations of the breast using a 3D finite element model and nonlinear elasticity P. Pathmanathan et al. In Proceedings of MICCAI 2004 Vol. 3217 of Lecture Notes in Computer Science, pages 217—224. 2004. Details \| BibTeX

[19]	Periodic breathing induced by arterial oxygen partial pressure oscillations J.P. Whiteley, D.J. Gavaghan and C.E.W. Hahn Mathematical Medicine and Biology, Vol. 20, pages 205—224. 2003. Details \| BibTeX

[20]	Mathematical modelling of pulmonary gas transport J.P. Whiteley, D.J. Gavaghan and C.E.W. Hahn Journal of Mathematical Biology, Vol. 47, pages 79—99. 2003. Details \| BibTeX

[21]	The effect of diffusion in the respiratory tree on the alveolar amplitude response technique (AART) J.P. Whiteley, D.J. Gavaghan and C.E.W. Hahn Respiratory Physiology & Neurobiology, Vol. 137, pages 81—96. 2003. Details \| BibTeX

[22]	Efficient computations of gas transport in the respiratory tree J.P. Whiteley, D.J. Gavaghan Mathematical Medicine and Biology, Vol. 20, pages 91—104. 2003. Details \| BibTeX

[23]	A tidal ventilation model for oxygenation in respiratory failure J.P. Whiteley et al. Respiratory Physiology & Neurobiology, Vol. 136, pages 77—88. 2003. Details \| BibTeX

[24]	The effects of ventilation pattern on carbon dioxide transfer in three computer models of the airways J.P. Whiteley et al. Respiratory Physiology & Neurobiology, Vol. 131, pages 269—284. 2002. Details \| BibTeX

[25]	Mathematical modelling of oxygen transport to tissue J.P. Whiteley, D.J. Gavaghan and C.E.W. Hahn Journal of Mathematical Biology, Vol. 44, pages 503—522. 2002. Details \| BibTeX

[26]	Variation of venous admixture, SF_6 shunt, P\small a_O_2, and the P\footnotesize a_O_2/F\small I_O_2 ratio with F\footnotesize I_O_2 J.P. Whiteley, D.J. Gavaghan and C.E.W. Hahn British Journal of Anaesthesia, Vol. 88, pages 771—778. 2002. Details \| BibTeX

[27]	Some factors affecting oxygen uptake by red blood cells in the pulmonary capillaries J.P. Whiteley, D.J. Gavaghan and C.E.W. Hahn Mathematical Biosciences, Vol. 169, pages 153—172. 2001. Details \| BibTeX

[28]	Modelling inert gas exchange in tissue and mixed—venous blood return to the lungs J.P. Whiteley, D.J. Gavaghan and C.E.W. Hahn Journal of Theoretical Biology, Vol. 209, pages 431—443. 2001. Details \| BibTeX

[29]	A mathematical model of electron transfer within the mitochondrial respiratory cytochromes A.D. Farmery, J.P. Whiteley Journal of Theoretical Biology, Vol. 213, pages 197—207. 2001. Details \| BibTeX

[30]	A tidal breathing model of the inert gas sinewave technique for inhomogeneous lungs J.P. Whiteley, D.J. Gavaghan and C.E.W. Hahn Respiration Physiology, Vol. 124, pages 65—83. 2000. Details \| BibTeX

[31]	The effect of inspired oxygen concentration on the ventilation—perfusion distribution in inhomogeneous lungs J.P. Whiteley, D.J. Gavaghan and C.E.W. Hahn Journal of Theoretical Biology, Vol. 204, pages 575—585. 2000. Details \| BibTeX

[32]	Discovering the structure of partial differential equations from example behavior L. Todorovski et al. In Proceedings of the International Conference on Machine Learning, Stanford, USA pages 991—998. 2000. Details \| BibTeX

[33]	The effect of the width of the ventilation—perfusion distribution on arterial blood oxygen content J.P. Whiteley, D.J. Gavaghan and C.E.W. Hahn Journal of Theoretical Biology, Vol. 201, pages 271—279. 1999. Details \| BibTeX

[34]	A tidal breathing model for the multiple inert gas elimination technique J.P. Whiteley, D.J. Gavaghan and C.E.W. Hahn Journal of Applied Physiology, Vol. 87, pages 161—169. 1999. Details \| BibTeX

[35]	Pulmonary blood flow measured by inspiratory inert gas concentration forcing oscillations E.M. Williams et al. Respiration Physiology, Vol. 113, pages 47—56. 1998. Details \| BibTeX

[36]	A mathematical evaluation of the multiple breath nitrogen washout (MBNW) technique and the multiple inert gas elimination technique (MIGET) J.P. Whiteley, D.J. Gavaghan and C.E.W. Hahn Journal of Theoretical Biology, Vol. 194, pages 517—539. 1998. Details \| BibTeX