Jonathan Cooper : Publications
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@article{CooperWebLab2016,
title = "The Cardiac Electrophysiology Web Lab",
author = "Cooper, Jonathan and Scharm, Martin and Mirams, Gary",
year = "2016",
journal = "Biophysical Journal",
number = "2",
pages = "292-300",
volume = "110",
doi = "10.1016/j.bpj.2015.12.012",
}
@article{cooper2015cce,
title = "Cellular cardiac electrophysiology modelling with Chaste and CellML",
author = "Jonathan Cooper and Raymond Spiteri and Gary Mirams",
year = "2015",
journal = "Frontiers in Physiology",
month = "January",
pages = "511",
url = "http://journal.frontiersin.org/Journal/10.3389/fphys.2014.00511",
volume = "5",
doi = "10.3389/fphys.2014.00511",
}
@article{Osborne2014TenSimple,
title = "Ten simple rules for effective computational research",
author = "Osborne, James M and Bernabeu, Miguel O and Bruna, Maria and Calderhead, Ben and Cooper, Jonathan and Dalchau, Neil and Dunn, Sara-Jane and Fletcher, Alexander G and Freeman, Robin and Groen, Derek and others",
year = "2014",
journal = "PLoS Computational Biology",
number = "3",
pages = "e1003506",
publisher = "Public Library of Science San Francisco, USA",
volume = "10",
doi = "10.1371/journal.pcbi.1003506",
}
@article{Cooper2013Connecting,
title = "Connecting models to data in multiscale multicellular tissue simulations",
author = "Cooper, J, Osborne, J.M.",
year = "2013",
journal = "Procedia Computer Science",
pages = "712-721",
volume = "18",
doi = "10.1016/j.procs.2013.05.235",
}
@article{MiramsChaste2013,
title = "Chaste: an open source C++ library for computational physiology and biology",
author = "Mirams, Gary R and Arthurs, Christopher J and Bernabeu, Miguel O and Bordas, Rafel and Cooper, Jonathan and Corrias, Alberto and Davit, Yohan and Dunn, Sara-Jane and Fletcher, Alexander G and Harvey, Daniel G and others",
year = "2013",
journal = "PLoS computational biology",
number = "3",
pages = "e1002970",
publisher = "Public Library of Science San Francisco, USA",
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",
}
@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, Pras and Bernabeu, Miguel O and Bordas, Rafel and Cooper, Jonathan and Garny, Alan and Pitt-Francis, Joe M and Whiteley, Jonathan P and Gavaghan, David J",
year = "2010",
journal = "Progress in biophysics and molecular biology",
number = "2-3",
pages = "136--155",
publisher = "Pergamon",
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 = "Pitt-Francis, Joe and Pathmanathan, Pras and Bernabeu, Miguel O and Bordas, Rafel and Cooper, Jonathan and Fletcher, Alexander G and Mirams, Gary R and Murray, Philip and Osborne, James M and Walter, Alex and others",
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",
}
@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 = "Van Leeuwen and Ingeborg MM and Mirams, GR and Walter, Alex and Fletcher, A and Murray, P and Osborne, J and Varma, S and Young, SJ and Cooper, J and Doyle, B and others",
year = "2009",
journal = "Cell proliferation",
number = "5",
pages = "617--636",
publisher = "Blackwell Publishing Ltd Oxford, UK",
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 = "Pitt-Francis, Joe and Bernabeu, Miguel O and Cooper, Jonathan and Garny, Alan and Momtahan, Lee and Osborne, James and Pathmanathan, Pras and Rodriguez, Blanca and Whiteley, Jonathan P and Gavaghan, David 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 London",
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",
}