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", }