Chaste publications
Main publications
If you want a single citation for Chaste, please use one of these, especially if you publish a paper using Chaste!-
F.R. Cooper, R.E Baker, M.O. Bernabeu, R. Bordas, L. Bowler,
A. Bueno-Orovio, H.M. Byrne, V. Carapella, L. Cardone-Noott,
J. Cooper, S. Dutta, B.D. Evans, A.G. Fletcher, J.A. Grogan,
W. Guo, D.G. Harvey, M. Hendrix, D. Kay, J. Kursawe, P.K. Maini,
B. McMillan,G.R. Mirams, J.M. Osborne, P. Pathmanathan,
J.M. Pitt-Francis, M. Robinson, B. Rodriguez, R.J. Spiteri,
D.J. Gavaghan
Chaste: Cancer, Heart and Soft Tissue Environment
J. Open Source Softw. 5(47):1848, 2020. doi: 10.21105/joss.01848. -
G.R. Mirams, C.J. Arthurs, M.O. Bernabeu, R. Bordas, J. Cooper, A. Corrias, Y. Davit, S.-J. Dunn, A.G. Fletcher, D.G. Harvey, M.E. Marsh, J.M. Osborne, P. Pathmanathan, J. Pitt-Francis, J. Southern, N. Zemzemi, D.J. Gavaghan.
Chaste: An open source C++ library for computational physiology and biology.
PLoS Comput. Biol. 9(3):e1002970, 2013. doi: 10.1371/journal.pcbi.1002970. -
J. Pitt-Francis, P. Pathmanathan, M.O. Bernabeu, R. Bordas, J. Cooper, A.G. Fletcher, G.R. Mirams, P. Murray, J.M. Osborne, A. Walter, S.J. Chapman, A. Garny, I.M.M. van Leeuwen, P.K. Maini, B. Rodriguez, S.L. Waters, J.P. Whiteley, H.M. Byrne, D.J. Gavaghan.
Chaste: a test-driven approach to software development for biological modelling.
Comput. Phys. Commun. 180(12):2452-2471, 2009. doi: 10.1016/j.cpc.2009.07.019.
View all publications related to Chaste in the department's database.
Key publications about Chaste
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P. Pathmanathan, R. Gray.
Verification of computational models of cardiac electro-physiology.
Int. J. Numer. Methods Biomed. Eng. 30(5):525-544, 2014. doi: 10.1002/cnm.2615. -
P. Pathmanathan, M. Bernabeu, S. Niederer, D. Gavaghan, D. Kay.
Computational modelling of cardiac electro-physiology: explanation of the variability of results from different numerical solvers.
Int. J. Numer. Methods Biomed. Eng. 28(8):890-903, 2012. doi: 10.1002/cnm.2467. (Local pre-print) -
J. Cooper, A. Corrias, D. Gavaghan, D. Noble.
Considerations for the use of cellular electrophysiology models within cardiac tissue simulations.
Prog. Biophys. Mol. Biol. 107(1):74-80, 2011. doi: 10.1016/j.pbiomolbio.2011.06.002. (Local pre-print) -
J. Cooper, G. Mirams, S. Niederer.
High throughput functional curation of cellular electrophysiology models.
Prog. Biophys. Mol. Biol. 107(1):11-20, 2011. doi: 10.1016/j.pbiomolbio.2011.06.003. (Local pre-print) -
S.A. Niederer, E. Kerfoot, A.P. Benson, M.O. Bernabeu, O. Bernus, C. Bradley, E.M. Cherry, R. Clayton, F.H. Fenton, A. Garny, E. Heidenreich, S. Land, M. Maleckar, P. Pathmanathan, G. Plank, J.F. Rodriguez, I. Roy, F.B. Sachse, G. Seemann, O. Skavhaug, N.P. Smith.
Verification of cardiac tissue electrophysiology simulators using an N-version benchmark.
Phil. Trans. R. Soc. A 369(1954):4331-4351, 2011. doi: 10.1098/rsta.2011.0139. [Note: this paper compares the accuracy of various cardiac electro-physiology solvers, including Chaste]. -
P. Pathmanathan, G.R. Mirams, J. Southern, J.P. Whiteley.
The significant effect of the choice of ionic current integration method in cardiac electro-physiological simulations.
Int. J. Numer. Methods Biomed. Eng. 27(11):1751-1770, 2011. doi: 10.1002/cnm.1438 -
P. Pathmanathan, M.O. Bernabeu, R. Bordas, J. Cooper, A. Garny, J.M. Pitt-Francis, J.P. Whiteley and D.J. Gavaghan.
A numerical guide to the solution of the bidomain equations of cardiac electrophysiology.
Prog. Biophys. Mol. Biol. 102(2-3):136-155, 2010. doi: 10.1016/j.pbiomolbio.2010.05.006 -
P. Pathmanathan, J. Cooper, A. Fletcher, G. Mirams, P. Murray, J. Osborne, J. Pitt-Francis, A. Walter, S.J. Chapman.
A computational study of discrete mechanical tissue models.
Phys. Biol. 6:036001, 2009. doi: 10.1088/1478-3975/6/3/036001. -
I.M.M. van Leeuwen, G.R. Mirams, A. Walter, A. Fletcher, P. Murray, J. Osborne, S. Varma, S.J. Young, J. Cooper, 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.
An integrative computational model for intestinal tissue renewal.
Cell Prolif. 42:617-636, 2009. doi: 10.1111/j.1365-2184.2009.00627.x. -
J. Pitt-Francis, M.O. Bernabeu, J. Cooper, A. Garny, L. Momtahan, J. Osborne, P. Pathmanathan, B. Rodriguez, J.P. Whiteley and D.J. Gavaghan.
Chaste: Using agile programming techniques to develop computational biology software.
Phil. Trans. R. Soc. A 366(1878):3111-3136, 2008. doi: 10.1098/rsta.2008.0096.
We are in the process of moving our publications list to the departmental database. Until this is complete, a manual list is reproduced below.
Cardiac publications
Electrophysiology
2014
Verification of computational models of cardiac electro-physiology.
Int. J. Numer. Methods Biomed. Eng. 30(5):525-544, 2014. doi: 10.1002/cnm.2615.
2012
- P. Pathmanathan, M. Bernabeu, S. Niederer, D. Gavaghan, D. Kay. Computational modelling of cardiac electro-physiology: explanation of the variability of results from different numerical solvers. Int. J. Numer. Methods Biomed. Eng. 28(8):890-903, 2012. doi: 10.1002/cnm.2467. (Local pre-print)
- C. Sanchez, A. Corrias, A. Bueno-Orovio, M. Davies, J. Swinton, I. Jacobson, P. Laguna, E. Pueyo, B. Rodriguez. The Na+/K+ pump is an important modulator of refractoriness and rotor dynamics in human atrial tissue. Am. J. Physiol. Heart. Circ. Physiol. 302(5):H1146-H1159, 2012. doi: 10.1152/ajpheart.00668.2011.
- M. Wallman, N.P. Smith, B. Rodriguez. A comparative study of graph-based, eikonal, and monodomain simulations for the estimation of cardiac activation times. IEEE Trans. Biomed. Eng. 59(6):1739-1748, 2012. doi: 10.1109/TBME.2012.2193398
2011
- R. Bordas, K. Gillow, Q. Lou, I.R. Efimov, D. Gavaghan, P. Kohl, V. Grau, B. Rodriguez. Rabbit-specific ventricular model of cardiac electrophysiological function including specialized conduction system. Prog. Biophys. Mol. Biol. 107(1):90-100, 2011. doi: 10.1016/j.pbiomolbio.2011.05.002
- J. Cooper, G. Mirams, S. Niederer. High throughput functional curation of cellular electrophysiology models. Prog. Biophys. Mol. Biol. 107(1):11-20, 2011. doi: 10.1016/j.pbiomolbio.2011.06.003. (Local pre-print)
- A. Corrias, W. Giles, B. Rodriguez. Ionic mechanisms of electrophysiological properties and repolarization abnormalities in rabbit Purkinje fibers. Am. J. Physiol. Heart. Circ. Physiol. 300(5):H1806-H1813, 2011. doi: 10.1152/ajpheart.01170.2010.
- S. Dutta, M. Bishop, P. Pathmanathan, P. Lee, P. Kohl, T. Quinn, B. Rodriguez. Interpreting optical mapping recordings in the ischemic heart: a combined experimental and computational investigation. Functional Imaging and Modeling of the Heart 6666:20-27, 2011. doi: 10.1007/978-3-642-21028-0_3.
- G.R. Mirams, Y. Cui, A. Sher, M. Fink, J. Cooper, B.M. Heath, N.C. McMahon, D.J. Gavaghan, D. Noble. Simulation of multiple ion channel block provides improved early prediction of compounds' clinical torsadogenic risk. Cardiovasc. Res. 91(1):53-61, 2011. doi: 10.1093/cvr/CVR044.
- S.A. Niederer, E. Kerfoot, A.P. Benson, M.O. Bernabeu, O. Bernus, C. Bradley, E.M. Cherry, R. Clayton, F.H. Fenton, A. Garny, E. Heidenreich, S. Land, M. Maleckar, P. Pathmanathan, G. Plank, J.F. Rodriguez, I. Roy, F.B. Sachse, G. Seemann, O. Skavhaug, N.P. Smith. Verification of cardiac tissue electrophysiology simulators using an N-version benchmark. Phil. Trans. R. Soc. A 369(1954):4331-4351, 2011. doi: 10.1098/rsta.2011.0139. [Note: this paper compares the accuracy of various cardiac electro-physiology solvers, including Chaste].
- P. Pathmanathan, G.R. Mirams, J. Southern, J.P. Whiteley. The significant effect of the choice of ionic current integration method in cardiac electro-physiological simulations. Int. J. Numer. Methods Biomed. Eng. 27(11):1751-1770, 2011. doi: 10.1002/cnm.1438
- E. Pueyo, A. Corrias, L. Virag, N. Jost, T. Szel, A. Varro, N. Szentandrassy, P.P. Nanasi, K. Burrage, B. Rodriguez. A multiscale investigation of repolarization variability and its role in cardiac arrhythmogenesis. Biophys. J. 101(12):2892-2902, 2011. doi: 10.1016/j.bpj.2011.09.060.
- M. Wallman, N. Smith, B. Rodriguez. Estimation of activation times in cardiac tissue using graph based methods. Functional Imaging and Modeling of the Heart 6666:71-79, 2011. doi: 10.1007/978-3-642-21028-0_9.
- N. Zemzemi, M. Bernabeu, J. Saiz, B. Rodriguez. Simulating drug-induced effects on the heart: from ion channel to body surface electrocardiogram. Functional Imaging and Modeling of the Heart 6666:259-266, 2011. doi: 10.1007/978-3-642-21028-0_32.
2010
- D. Abramson, M.O. Bernabeu, B. Bethwaite, K. Burrage, A. Corrias, C. Enticott, S. Garic, D. Gavaghan, T. Peachey, J. Pitt-Francis, E. Pueyo, B. Rodriguez, A. Sher and J. Tan. High-throughput cardiac science on the Grid. Phil. Trans. R. Soc. A 368(1925):3907-3923, 2010. doi: 10.1098/rsta.2010.0170.
- M.O. Bernabeu, P. Pathmanathan, J.M. Pitt-Francis, D. Kay. Stimulus protocol determines the most computationally-efficient preconditioner for the bidomain equations. IEEE Trans. Biomed. Eng. 57(12):2806-2815, 2010. doi: 10.1109/TBME.2010.2078817
- M.O. Bernabeu, M. Wallman, B. Rodriguez. Shock-induced arrhythmogenesis in the human heart: a computational modelling study. In Engineering in Medicine and Biology Society (EMBC, 2010 Annual International Conference of the IEEE) 760-763, 2010.
- R. Bordas, V. Grau, R.A.B. Burton, P. Hales, J.E. Schneider, D. Gavaghan, P. Kohl, B. Rodriguez. Integrated approach for the study of anatomical variability in the cardiac purkinje system: from high resolution MRI to electrophysiology simulation. In Engineering in Medicine and Biology Society (EMBC), 2010 Annual International Conference of the IEEE, pp6793-6796, 2010.
- A. Corrias, E. Pueyo, K. Burrage, B. Rodriguez. Causes of variability in ventricular repolarization: from isolated cells to ECG. Heart Rhythm, 2010. (Abstract)
- A. Corrias, X. Jie, L. Romero, M.J. Bishop, M. Bernabeu, E. Pueyo, B. Rodriguez. Arrhythmic risk biomarkers for the assessment of drug cardiotoxicity: from experiments to computer simulations. Phil. Trans. R. Soc. A 368(1921):3001-3025, 2010. doi: 10.1098/rsta.2010.0083,
- P. Pathmanathan, M.O. Bernabeu, R. Bordas, J. Cooper, A. Garny, J.M. Pitt-Francis, J.P. Whiteley and D.J. Gavaghan. A numerical guide to the solution of the bidomain equations of cardiac electrophysiology. Prog. Biophys. Mol. Biol. 102(2-3):136-155, 2010. doi: 10.1016/j.pbiomolbio.2010.05.006
- B. Rodriguez, K. Burrage, D. Gavaghan, V. Grau, P. Kohl, D. Noble. The systems biology approach to drug development: application to toxicity assessment of cardiac drugs. Clin. Pharmacol. Ther. 88(1):130-134, 2010. doi: 10.1038/clpt.2010.95.
- B. Rodriguez. Multiscale modelling and simulation investigation of variability and abnormalities in repolarization: application to drug cardiotoxicity. In Computers in Cardiology, 37:257-260, 2010.
- C. Sanchez, A. Corrias, P. Laguna, E. Pueyo, B. Rodriguez. Sensitivity of atrial fibrillation related biomarkers to changes in ionic current properties. Heart Rhythm, 2010. (Abstract)
- C. Sanchez, A. Corrias, P. Laguna, M. Davies, J. Swinton, I. Jacobson, E. Pueyo, and B. Rodriguez. Potential pharmacological therapies for atrial fibrillation. A computational study. In Computers in Cardiology, 37:413-416, 2010.
- J. Southern, G.J. Gorman, M.D. Piggott, P.E. Farrell, M.O. Bernabeu and J. Pitt-Francis. Simulating cardiac electrophysiology using anisotropic mesh adaptivity. J. Comput. Sci. 1(2):82-88, 2010. doi: 10.1016/j.jocs.2010.03.010.
2009
- M.O. Bernabeu, R. Bordas, P. Pathmanathan, J. Pitt-Francis, J. Cooper, A. Garny, D.J. Gavaghan, B. Rodriguez, J.A. Southern, J.P. Whiteley. Chaste: Incorporating a novel multi-scale spatial and temporal algorithm into a large-scale open-source library. Phil. Trans. R. Soc. A 367(1895):1907-1930, 2009. doi: 10.1098/rsta.2008.0309.
- M.O. Bernabeu, A. Corrias, J. Pitt-Francis, B. Rodriguez, B. Bethwaite, C. Enticott, S. Garic, T. Peachey, J. Tan, D. Abramson, D. Gavaghan. Grid computing simulations of ion channel block effects on the ECG using 3D anatomically-based models. Computers in Cardiology, 36:213-216, 2009. PDF.
2008
- M.O. Bernabeu, M.J. Bishop, J. Pitt-Francis, D.J. Gavaghan, V. Grau and B. Rodriguez. High performance computer study of biological function in 3D heart models incorporating fibre orientation and realistic geometry at para-cellular resolution. Computers in Cardiology, 35:721-724, 2008 doi: 10.1109/CIC.2008.4749143.
- J. Pitt-Francis, M.O. Bernabeu, J. Cooper, A. Garny, L. Momtahan, J. Osborne, P. Pathmanathan, B. Rodriguez, J.P. Whiteley and D.J. Gavaghan. Chaste: Using agile programming techniques to develop computational biology software. Phil. Trans. R. Soc. A 366(1878):3111-3136, 2008. doi: 10.1098/rsta.2008.0096.
Electromechanics
- P. Pathmanathan, S.J. Chapman, D.J. Gavaghan and J.P. Whiteley. Cardiac electromechanics: the effect of contraction model on the mathematical problem and accuracy of the numerical scheme. Q. J. Mech. Appl. Math. 63(3):375-399, 2010. doi: 10.1093/qjmam/hbq014.
- P. Pathmanathan and J.P. Whiteley. A numerical method for cardiac mechanoelectric simulations. Ann. Biomed. Eng. 37(5):860-873, 2009. doi: 10.1007/s10439-009-9663-8.
PyCml
- J. Cooper, A. Corrias, D. Gavaghan, D. Noble. Considerations for the use of cellular electrophysiology models within cardiac tissue simulations. Prog. Biophys. Mol. Biol. 107(1):74-80, 2011. doi: 10.1016/j.pbiomolbio.2011.06.002. (Local pre-print)
- J. Cooper. Automatic Validation and Optimisation of Biological Models. D.Phil. Thesis, University of Oxford, 2009. ORA record. (Local copy)
- J. Cooper, S. McKeever. A model-driven approach to automatic conversion of physical units. Softw. Pract. Exper. 38(4):337-359, 2008. doi: 10.1002/spe.828.
- J. Cooper, S. McKeever, A.Garny. On the application of partial evaluation to the optimisation of cardiac electrophysiological simulations. In PEPM '06: Proceedings of the 2006 ACM SIGPLAN symposium on Partial evaluation and semantics-based program manipulation 12-20, 2006. doi: 10.1145/1111542.1111546.
Cell-based publications
2013
- S.-J. Dunn, I.S. Näthke, J.M. Osborne. Computational models reveal a passive mechanism for cell migration in the crypt. PLOS ONE 8:e80516, 2013. doi: 10.1371/journal.pone.0080516.
- A.G. Fletcher, J.M. Osborne, P.K. Maini, D.J. Gavaghan. Implementing vertex dynamics models of cell populations in biology within a consistent computational framework. Prog. Biophys. Mol. Biol. 113:299-326, 2013. doi: 10.1016/j.pbiomolbio.2013.09.003.
- Y. Davit, J.M. Osborne, H.M. Byrne, D.J. Gavaghan, J.M. Pitt-Francis. Validity of the Cauchy-Born rule applied to discrete cellular-scale models of biological tissues. Phys. Rev. E 87(4):042724, 2013. doi: 10.1103/PhysRevE.87.042724.
- G.P. Figueredo, T.V. Joshi, J.M. Osborne, H.M. Byrne, M.R. Owen. On-lattice agent-based simulation of populations of cells within the open-source Chaste framework. Interface Focus 3(2):20120081, 2013. doi: 10.1098/rsfs.2012.0081.
2012
- S.-J. Dunn, A.G. Fletcher, S.J. Chapman, D.J. Gavaghan, J.M. Osborne. Modelling the role of the basement membrane in the colonic epithelium. J. Theor. Biol. 298:82-91, 2012. doi: 10.1016/j.jtbi.2011.12.013.
- S.-J. Dunn, P.L. Appleton, S.A. Nelson, I.S. Näthke, D.J. Gavaghan, J.M. Osborne. A two-dimensional model of the colonic crypt accounting for the role of the basement membrane and pericryptal fibroblast sheath. PLoS Comput. Biol. 8(5): e1002515, 2012. doi: 10.1371/journal.pcbi.1002515.
- A.G. Fletcher, C.J. Breward, S.J. Chapman. Mathematical modelling of monoclonal conversion in the colonic crypt. J. Theor. Biol. 300:118-133, 2012. doi: 10.1016/j.jtbi.2012.01.021.
- G.R. Mirams, A.G. Fletcher, P.K. Maini, H.M. Byrne. A theoretical investigation of the effect of proliferation and adhesion on monoclonal conversion in the colonic crypt. J. Theor. Biol., 312:143-156, 2012. doi: 10.1016/j.jtbi.2012.08.002.
- M.A. Slaymaker, J.M. Osborne, A.C. Simpson, D.J. Gavaghan. On an infrastructure to support sharing and aggregating pre- and post-publication systems biology research data. Syst. Synth. Biol. 6:35-49, 2012. doi: 10.1007/s11693-012-9095-x.
2011
- P.J. Murray, A. Walter, A.G. Fletcher, C.M. Edwards, M.J. Tindall, P.K. Maini. Comparing a discrete and continuum model of the intestinal crypt. Phys. Biol. 8:026011, 2011. doi: 10.1088/1478-3975/8/2/026011.
2010
- A.G. Fletcher, G.R. Mirams, P.J. Murray, A. Walter, J.-W. Kang, K.-H. Cho, P.K. Maini, H.M. Byrne. Multiscale modeling of colonic crypts and early colorectal cancer. In T.S. Deisboeck and G. Stamatakos (eds) Multiscale Cancer Modeling 111-134, CRC Press, 2010. ISBN: 9781439814406.
- P. J. Murray, J. W. Kang, G. R. Mirams, S. Y. Shin, H. M. Byrne, P. K. Maini, and K. H. Cho. Modelling spatially regulated -catenin dynamics and invasion in intestinal crypts. Biophys. J. 99(3):716-725, 2010. doi: 10.1016/j.bpj.2010.05.016.
- J.M. Osborne, A. Walter, S.K. Kershaw, G.R. Mirams, A.G. Fletcher, P. Pathmanathan, D.J. Gavaghan, O.E. Jensen, P.K. Maini, H.M. Byrne. A hybrid approach to multiscale modelling of cancer. Phil. Trans. R. Soc. A 368:5013-5028, 2010. doi: 10.1098/rsta.2010.0173.
2009
- P. Pathmanathan, J. Cooper, A. Fletcher, G. Mirams, P. Murray, J. Osborne, J. Pitt-Francis, A. Walter, S.J. Chapman. A computational study of discrete mechanical tissue models. Phys. Biol. 6:036001, 2009. doi: 10.1088/1478-3975/6/3/036001.
- I.M.M. van Leeuwen, G.R. Mirams, A. Walter, A. Fletcher, P. Murray, J. Osborne, S. Varma, S.J. Young, J. Cooper, 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. An integrative computational model for intestinal tissue renewal. Cell Prolif. 42:617-636, 2009. doi: 10.1111/j.1365-2184.2009.00627.x.