Jonathan Cooper : Publications
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@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",
}
@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{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{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{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{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",
}
@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",
}
@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.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{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",
}