@article{MiramsChaste2013,
  title = "Chaste: an open source C++ library for computational physiology and biology",
  author = "G.R. Mirams and C.J. Arthurs and M.O. Bernabeu and R. Bordas and J. Cooper and A. Corrias and Y. Davit and S-J. Dunn and A.G. Fletcher and D.G. Harvey and M.E. Marsh and J. M. Osborne and P. Pathmanathan and J. Pitt-Francis and J. Southern and N. Zemzemi and D.J. Gavaghan",
  year = "2013",
  journal = "PLoS Computational Biology",
  number = "3",
  pages = "e1002970",
  url = "http://dx.plos.org/10.1371/journal.pcbi.1002970",
  volume = "9",
  doi = "10.1371/journal.pcbi.1002970",
}
@article{Zemzemi2012,
  title = "Computational assessment of drug-induced effects on the electrocardiogram: from ion channel block to body surface potentials",
  author = "N Zemzemi and MO Bernabeu and J Saiz and J Cooper and P Pathmanathan and GR Mirams and J Pitt-Francis and B Rodriguez",
  year = "2013",
  journal = "British Journal of Pharmacology",
  number = "3",
  pages = "718-733",
  volume = "168",
  doi = "10.1111/j.1476-5381.2012.02200.x",
}
@article{5993,
  title = "Considerations for the use of cellular electrophysiology models within cardiac tissue simulations",
  author = "J. Cooper, A. Corrias, D. Gavaghan, D. Noble",
  year = "2011",
  journal = "Prog Biophys Mol Biol",
  number = "1",
  pages = "74-80",
  url = "http://www.cs.ox.ac.uk/chaste/publications/2011-Cooper-Model%20Interfaces.pdf",
  volume = "107",
  doi = "10.1016/j.pbiomolbio.2011.06.002",
}
@article{CooperMiramsNiederer2011,
  title = "High-throughput functional curation of cellular electrophysiology models",
  author = "Cooper J., Mirams G.R., Niederer S.A.",
  year = "2011",
  editor = "Denis Noble",
  journal = "Progress in Biophysics and Molecular Biology",
  pages = "11 - 20",
  volume = "107",
  doi = "10.1016/j.pbiomolbio.2011.06.003",
}
@article{f20eb73a440003b,
  title = "Simulation of multiple ion channel block provides improved early prediction of compounds' clinical torsadogenic risk",
  author = "Mirams, G. R. and Cui, Y. and Sher, A. and Fink, M. and Cooper, J. and Heath, B. M. and McMahon, N. C. and Gavaghan, D. J. and Noble, D.",
  year = "2011",
  issn = "00086363",
  journal = "Cardiovascular Research",
  number = "1",
  pages = "53--61",
  url = "http://dx.doi.org/10.1093/cvr/cvr044",
  volume = "91",
  doi = "10.1093/cvr/cvr044",
}
@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",
}
@inproceedings{3941,
  title = "The Virtual Physiological Human ToolKit – Evolution and Sustainability",
  author = "Jonathan Cooper and John Fenner and Keith McCormack and David Gavaghan and Peter Coveney",
  year = "2010",
  booktitle = "Abstract booklet for VPH2010",
  howpublished = "Online",
  location = "Brussels",
  month = "September",
  pages = "39-41",
  url = "http://www.vph-noe.eu/vph-repository/doc_download/204-book-of-abstracts-for-vph2010",
}
@inproceedings{iarwisoci:oxford,
  title = "Markup Languages for In Silico Oncology",
  author = "David Johnson and Jonathan Cooper and Steve McKeever",
  year = "2010",
  booktitle = "Proceedings of the 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation (4th IARWISOCI) – The ContraCancrum Workshop",
  editor = "Georgios Stamatakos and Dimitra Dionysiou",
  howpublished = "Online",
  location = "Athens, Greece",
  month = "September",
  pages = "108--110",
  url = "http://www.4th-iarwisoci.iccs.ntua.gr/",
}
@article{3656,
  title = "The Virtual Physiological Human ToolKit",
  author = "Jonathan Cooper and Frederic Cervenansky and Gianni De Fabritiis and John Fenner and Denis Friboulet and Toni Giorgino and Steven Manos and Yves Martelli and Jordi Villa-Freixa and Stefan Zasada and Sharon Lloyd and Keith McCormack and Peter V. Coveney",
  year = "2010",
  journal = "Phil Trans R Soc A",
  month = "August",
  number = "1925",
  pages = "3925-3936",
  volume = "368",
  doi = "10.1098/rsta.2010.0144",
}
@article{ChasteCPC09,
  title = "Chaste: a test-driven approach to software development for biological modelling",
  author = "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",
  year = "2009",
  journal = "Computer Physics Communications",
  number = "12",
  pages = "2452--2471",
  publisher = "North-Holland",
  volume = "180",
  doi = "10.1016/j.cpc.2009.07.019",
}
@article{3383,
  title = "Toward a VPH/Physiome ToolKit",
  author = "Alan Garny, Jonathan Cooper, Peter J. Hunter",
  year = "2009",
  journal = "Wiley Interdisciplinary Reviews: Systems Biology and Medicine",
  publisher = "John Wiley & Sons, Inc.",
  doi = "10.1002/wsbm.63",
}
@phdthesis{jonathan_cooper_thesis,
  title = "Automatic Validation and Optimisation of Biological Models",
  author = "Jonathan Cooper",
  year = "2009",
  institution = "University of Oxford",
  url = "http://ora.ouls.ox.ac.uk/objects/uuid:24b96d62-b47c-458d-9dff-79b27dbdc9f2",
}
@article{chaste_dtm,
  title = "A computational study of discrete mechanical tissue models",
  author = "P Pathmanathan and J Cooper and A Fletcher and G Mirams and P Murray and J Osborne and J Pitt-Francis and A Walter and S J Chapman",
  year = "2009",
  journal = "Physical Biology",
  number = "3",
  volume = "6",
  doi = "10.1088/1478-3975/6/3/036001",
}
@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{Chaste.08:Chaste,
  title = "Chaste: using agile programming techniques to develop computational biology software",
  author = "Pitt-Francis, J. and Bernabeu, M.O. and Cooper, J. and Garny, A. and Momtahan, L. and Osborne, J. and Pathmanathan, P. and Rodriguez, B. and Whiteley, J.P. and Gavaghan, D.J.",
  year = "2008",
  journal = "Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences",
  number = "1878",
  pages = "3111--3136",
  publisher = "The Royal Society",
  volume = "366",
  doi = "10.1098/rsta.2008.0096",
}
@article{CellML_tools_08,
  title = "CellML and Associated Tools and Techniques",
  author = "Alan Garny and David Nickerson and Jonathan Cooper and Rodrigo Weber dos Santos and Steve McKeever and Poul Nielsen and Peter Hunter",
  year = "2008",
  journal = "Phil Trans Roy Soc A",
  number = "1878",
  pages = "3017--3043",
  volume = "366",
  doi = "10.1098/rsta.2008.0094",
}
@article{key1,
  title = "A model-driven approach to automatic conversion of physical units",
  author = "Jonathan Cooper and Steve McKeever",
  year = "2008",
  issn = "0038-0644",
  journal = "Softw. Pract. Exper.",
  number = "4",
  pages = "337-359",
  publisher = "Wiley",
  volume = "38",
  doi = "10.1002/spe.828",
}
@inproceedings{key2,
  title = "Experience Report: A Haskell interpreter for CellML",
  author = "Jonathan Cooper and Steve McKeever",
  year = "2007",
  address = "New York, NY, USA",
  isbn = "978-1-59593-815-2",
  journal = "ICFP '07: Proceedings of the 2007 ACM SIGPLAN international conference on Functional programming",
  location = "Freiburg, Germany",
  month = "October",
  pages = "247--250",
  publisher = "ACM Press",
  doi = "10.1145/1291151.1291190",
}
@inproceedings{Cooper.06,
  title = "On the application of partial evaluation to the optimisation of cardiac electrophysiological simulations",
  author = "Jonathan Cooper and Steve McKeever and Alan Garny",
  year = "2006",
  address = "New York, NY, USA",
  booktitle = "PEPM '06: Proceedings of the 2006 ACM SIGPLAN Symposium on Partial Evaluation and Semantics-Based Program Manipulation",
  isbn = "1-59593-196-1",
  location = "Charleston, South Carolina",
  pages = "12--20",
  publisher = "ACM Press",
  doi = "10.1145/1111542.1111546",
}