Jonathan Cooper : Publications
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[1] |
Chaste: an open source C++ library for computational physiology and biology 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 and D.J. Gavaghan In PLoS Computational Biology. Vol. 9. No. 3. Pages e1002970. 2013. Details | BibTeX | DOI (10.1371/journal.pcbi.1002970) | Link |
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[2] |
Computational assessment of drug−induced effects on the electrocardiogram: from ion channel block to body surface potentials N Zemzemi‚ MO Bernabeu‚ J Saiz‚ J Cooper‚ P Pathmanathan‚ GR Mirams‚ J Pitt−Francis and B Rodriguez In British Journal of Pharmacology. Vol. 168. No. 3. Pages 718−733. 2013. |
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[3] |
Considerations for the use of cellular electrophysiology models within cardiac tissue simulations D. Noble J. Cooper A. Corrias D. Gavaghan In Prog Biophys Mol Biol. Vol. 107. No. 1. Pages 74−80. 2011. Details | BibTeX | DOI (10.1016/j.pbiomolbio.2011.06.002) | Download (pdf) |
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[4] |
High−throughput functional curation of cellular electrophysiology models Niederer S.A. Cooper J. Mirams G.R. In Progress in Biophysics and Molecular Biology. Vol. 107. Pages 11 − 20. 2011. |
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[5] |
Simulation of multiple ion channel block provides improved early prediction of compounds' clinical torsadogenic risk G. R. Mirams‚ Y. Cui‚ A. Sher‚ M. Fink‚ J. Cooper‚ B. M. Heath‚ N. C. McMahon‚ D. J. Gavaghan and D. Noble In Cardiovascular Research. Vol. 91. No. 1. Pages 53–61. 2011. |
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[6] |
The Virtual Physiological Human ToolKit – Evolution and Sustainability Jonathan Cooper‚ John Fenner‚ Keith McCormack‚ David Gavaghan and Peter Coveney In Abstract booklet for VPH2010. Pages 39−41. September, 2010. |
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[7] |
Markup Languages for In Silico Oncology David Johnson‚ Jonathan Cooper and Steve McKeever In Georgios Stamatakos and Dimitra Dionysiou, editors, Proceedings of the 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation (4th IARWISOCI) – The ContraCancrum Workshop. Pages 108–110. September, 2010. Details | BibTeX | Download (pdf) | Link |
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[8] |
The Virtual Physiological Human ToolKit Jonathan Cooper‚ Frederic Cervenansky‚ Gianni De Fabritiis‚ John Fenner‚ Denis Friboulet‚ Toni Giorgino‚ Steven Manos‚ Yves Martelli‚ Jordi Villa−Freixa‚ Stefan Zasada‚ Sharon Lloyd‚ Keith McCormack and Peter V. Coveney In Phil Trans R Soc A. Vol. 368. No. 1925. Pages 3925−3936. August, 2010. |
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[9] |
A numerical guide to the solution of the bidomain equations of cardiac electrophysiology P. Pathmanathan‚ M.O. Bernabeu‚ R. Bordas‚ J. Cooper‚ A. Garny‚ J. Pitt−Francis‚ J.P. Whiteley and D.J. Gavaghan In Progress in Biophysics and Molecular Biology. Vol. 102. No. (2−3). Pages 136−155. 2010. |
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[10] |
Chaste: Incorporating a Novel Multiscale Spatial and Temporal Algorithm into a Large Scale Open Source Library M.O. Bernabeu‚ R. Bordas‚ P. Pathmanathan‚ J. Pitt−Francis‚ J. Cooper‚ A. Garny‚ D.J. Gavaghan‚ B. Rodriguez‚ J.A. Southern and J.P. Whiteley In Phil Trans Roy Soc (A). Vol. 367. No. 1895. Pages 1907−1930. May, 2009. |
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[11] |
Chaste: a test−driven approach to software development for biological modelling D.J. Gavaghan 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 In Computer Physics Communications. Vol. 180. No. 12. Pages 2452–2471. 2009. |
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[12] |
Toward a VPH/Physiome ToolKit Peter J. Hunter Alan Garny Jonathan Cooper In Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 2009. |
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[13] |
A computational study of discrete mechanical tissue models P Pathmanathan‚ J Cooper‚ A Fletcher‚ G Mirams‚ P Murray‚ J Osborne‚ J Pitt−Francis‚ A Walter and S J Chapman In Physical Biology. Vol. 6. No. 3. 2009. |
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[14] |
An integrative computational model for intestinal tissue renewal HM Byrne 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 In Cell Proliferation. Vol. 42. Pages 617−636. 2009. |
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[15] |
Automatic Validation and Optimisation of Biological Models Jonathan Cooper PhD Thesis 2009. |
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[16] |
Chaste: using agile programming techniques to develop computational biology software 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 In Philosophical Transactions of the Royal Society A: Mathematical‚ Physical and Engineering Sciences. Vol. 366. No. 1878. Pages 3111–3136. 2008. |
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[17] |
CellML and Associated Tools and Techniques Alan Garny‚ David Nickerson‚ Jonathan Cooper‚ Rodrigo Weber dos Santos‚ Steve McKeever‚ Poul Nielsen and Peter Hunter In Phil Trans Roy Soc A. Vol. 366. No. 1878. Pages 3017–3043. 2008. |
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[18] |
A model−driven approach to automatic conversion of physical units Jonathan Cooper and Steve McKeever In Softw. Pract. Exper.. Vol. 38. No. 4. Pages 337−359. 2008. |
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[19] |
Experience Report: A Haskell interpreter for CellML Jonathan Cooper and Steve McKeever Pages 247–250. New York‚ NY‚ USA. October, 2007. ACM Press. |
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[20] |
On the application of partial evaluation to the optimisation of cardiac electrophysiological simulations Jonathan Cooper‚ Steve McKeever and Alan Garny In PEPM '06: Proceedings of the 2006 ACM SIGPLAN Symposium on Partial Evaluation and Semantics−Based Program Manipulation. Pages 12–20. New York‚ NY‚ USA. 2006. ACM Press. |