Chaste: Publications
Click here to download all publications in a single bibtex file
@article{Johnstone2016,
title = "Hierarchical Bayesian inference for ion channel screening dose-response data",
author = "RH Johnstone and R Bardenet and DJ Gavaghan and GR Mirams",
year = "2016",
journal = "Wellcome Open Research",
pages = "6",
publisher = "Wellcome Trust",
url = "https://wellcomeopenresearch.org/articles/1-6/v1",
volume = "1",
doi = "10.12688/wellcomeopenres.9945.1",
}
@article{Mirams2016,
title = "White Paper: Uncertainty and variability in computational and mathematical models of cardiac physiology",
author = "GR Mirams and P Pathmanathan and RA Gray and P Challenor and RH Clayton",
year = "2016",
journal = "Journal of Physiology",
doi = "10.1113/JP271671",
}
@article{Mahoney2016,
title = "Connexin 43 contributes to electrotonic conduction across scar tissue in the intact heart",
author = "VM Mahoney and V Mezzano and GR Mirams and K Maass and Z Li and M Cerrone and C Vasquez and A Bapat and M Delmar and GE Morley",
year = "2016",
journal = "Scientific Reports",
pages = "26744",
publisher = "Nature Publishing Group",
volume = "6",
doi = "10.1038/srep26744",
}
@article{Hill2016,
title = "White Paper: Computational Cardiology and Risk Stratification for Sudden Cardiac Death: One of the Grand Challenges for Cardiology in the 21st Century.",
author = "AP Hill and MD Perry and N Abi-Gerges and J-P Couderc and B Fermini and JC Hancox and BC Knollmann and GR Mirams and J Skinner and W Zareba and JI Vandenberg",
year = "2016",
journal = "Journal of Physiology",
doi = "10.1113/JP272015",
}
@article{Davies2016,
title = "Recent developments in using mechanistic cardiac modelling for drug safety evaluation",
author = "MR Davies and K Wang and GR Mirams and A Caruso and D Noble and A Walz and T Lavé and F Schuler and T Singer and L Polonchuk",
year = "2016",
journal = "Drug Discovery Today",
number = "6",
pages = "924–938",
volume = "21",
doi = "10.1016/j.drudis.2016.02.003",
}
@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{Johnstone2016,
title = "Uncertainty and variability in models of the cardiac action potential: can we build trustworthy models?",
author = "RH Johnstone and ET Chang and R Bardenet and TP de Boer and DJ Gavaghan and P Pathmanathan and RH Clayton and GR Mirams",
year = "2016",
journal = "Journal of Molecular and Cellular Cardiology",
pages = "49-62",
volume = "96",
doi = "10.1016/j.yjmcc.2015.11.018",
}
@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{Samanta2015,
title = "Ca2+ Channel Re-localization to Plasma-Membrane Microdomains Strengthens Activation of Ca2+-Dependent Nuclear Gene Expression",
author = "Krishna Samanta and Pulak Kar and Gary R. Mirams and Anant B. Parekh",
year = "2015",
journal = "Cell Reports",
number = "2",
pages = "203-216",
url = "http://dx.doi.org/10.1016/j.celrep.2015.06.018",
volume = "12",
doi = "10.1016/j.celrep.2015.06.018",
}
@article{williams2015,
title = "A web portal for in-silico action potential predictions",
author = "Geoff Williams and Gary Mirams",
year = "2015",
journal = "Journal of Pharmacological and Toxicological Methods",
pages = "10-16",
url = "http://dx.doi.org/10.1016/j.vascn.2015.05.002",
volume = "75",
doi = "10.1016/j.vascn.2015.05.002",
}
@article{Mirams2014,
title = "Prediction of Thorough QT study results using action potential simulations based on ion channel screens",
author = "GR Mirams and MR Davies and SJ Brough and MH Bridgland-Taylor and Y Cui and DJ Gavaghan and N Abi-Gerges",
year = "2014",
journal = "Journal of Pharmacological & Toxicological Methods",
number = "3",
pages = "246-254",
volume = "70",
doi = "10.1016/j.vascn.2014.07.002",
}
@article{Beattie2013,
title = "Evaluation of an In Silico Cardiac Safety Assay: Using Ion Channel Screening Data to Predict QT Interval Changes in the Rabbit Ventricular Wedge",
author = "Kylie A. Beattie and Chris Luscombe and Geoff Williams and Jordi Munoz-Muriedas and David J. Gavaghan and Yi Cui and Gary R. Mirams",
year = "2013",
journal = "Journal of Pharmacological and Toxicological Methods",
number = "1",
pages = "88-96",
url = "http://www.sciencedirect.com/science/article/pii/S105687191300244X",
volume = "68",
doi = "10.1016/j.vascn.2013.04.004",
}
@article{Elkins2013,
title = "Variability in high-throughput ion channel screening data and consequences for cardiac safety assessment",
author = "Ryan C. Elkins and Mark R. Davies and Stephen J. Brough and David J. Gavaghan and Yi Cui and Najah Abi-Gerges and Gary R. Mirams",
year = "2013",
journal = "Journal of Pharmacological and Toxicological Methods",
keywords = "high-throughput, compound screening, variability, uncertainty, cardiac safety, action potential, mathematical model",
number = "1",
pages = "112-122",
volume = "68",
doi = "10.1016/j.vascn.2013.04.007",
}
@article{BrittonPNAS2013,
title = "Experimentally-calibrated population of models predicts and explains inter-subject variability in cardiac cellular electrophysiology",
author = "Britton, O. and Bueno-Orovio, A. and Van Ammel, K. and Lu, HR. and Towart, R. and Gallacher, DJ. and Rodriguez, B.",
year = "2013",
journal = "Proceedings of the National Academy of Sciences",
doi = "10.1073/pnas.1304382110",
}
@article{Walmsley2013,
title = "mRNA expression levels in failing human hearts predict cellular electrophysiological remodelling: A population-based simulation study",
author = "Walmsley, J. and Rodriguez, J.F. and Mirams, G.R. and Burrage, K. and Efimov, I.R. and Rodriguez, B.",
year = "2013",
journal = "PLoS ONE",
number = "2",
pages = "e56359",
volume = "8",
doi = "10.1371/journal.pone.0056359",
}
@article{Figueredo2013,
title = "On-Lattice Agent-based Simulation of Populations of Cells within the Open-Source Chaste Framework.",
author = "Figueredo, G.P., Joshi, T.V., Osborne, J.M., Helen M. Byrne, H.M., and Owen, M.R.",
year = "2013",
journal = "Interface Focus",
volume = "3(2)",
doi = "10.1098/rsfs.2012.0081",
}
@article{6572,
title = "Computationally efficient simulation of electrical activity at cell membranes interacting with self-generated and externally imposed electric fields",
author = "Andres Agudelo-Toro and Andreas Neef",
year = "2013",
journal = "Journal of Neural Engineering",
number = "2",
pages = "026019",
url = "http://stacks.iop.org/1741-2552/10/i=2/a=026019",
volume = "10",
doi = "10.1088/1741-2560/10/2/026019",
}
@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",
}
@inproceedings{Walmsley2013b,
title = "Estimation of conductivity tensors from human ventricular optical mapping recordings",
author = "J. Walmsley and G.R. Mirams and I.R. Efimov and K. Burrage and B. Rodriguez",
year = "2013",
booktitle = "Functional Imaging and Modeling of the Heart",
journal = "Lecture Notes in Computer Science",
pages = "224--231",
volume = "7495",
}
@inproceedings{Mirams2013SPS,
title = "Evaluation of computational modelling as a preclinical proarrhythmic safety assay",
author = "G Mirams and K Beattie and Y Cui and C Luscombe and G Williams and D Gavaghan and N McMahon",
year = "2013",
journal = "Journal of Pharamcological and Toxicological Methods",
number = "1",
pages = "e21",
volume = "86",
doi = "10.1016/j.vascn.2013.01.081",
}
@article{BordasSiam,
title = "A bidomain model of the cardiac specialized conduction system of the heart.",
author = "Bordas, R. and Gillow, K. and Gavaghan, D. and Rodriguez, B. and Kay, D.",
year = "2012",
journal = "SIAM Journal on Applied Mathematics",
}
@article{wallman2012comparative,
title = "A Comparative Study of Graph-Based, Eikonal, and Monodomain Simulations for the Estimation of Cardiac Activation Times",
author = "Wallman, M. and Smith, N.P. and Rodriguez, B.",
year = "2012",
journal = "IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING",
number = "6",
pages = "1739",
volume = "59",
}
@article{Dunn12Modelling,
title = "Modelling the role of the basement membrane in the colonic epithelium",
author = "S.-J. Dunn, and A.G. Fletcher, and S.J. Chapman, and D.J. Gavaghan, and J.M. Osborne",
year = "2012",
journal = "J. Theor. Biol.",
number = "298",
pages = "82-91",
doi = "10.1016/j.jtbi.2011.12.013",
}
@article{Dunn12TwoDimensional,
title = "A two-dimensional model of the colonic crypt accounting for the role of the basement membrane and pericryptal fibroblast sheath",
author = "S.-J. Dunn, and P.L. Appleton, and S.A. Nelson, and I.S. Näthke, and D.J. Gavaghan, and J.M. Osborne",
year = "2012",
edition = "8",
journal = "Plos Computational Biology",
number = "5",
pages = "e1002515",
doi = "10.1371/journal.pcbi.1002515",
}
@article{Slaymaker12,
title = "On an infrastructure to support sharing and aggregating pre- and post-publication systems biology research data",
author = "Mark Slaymaker and James Osborne and Andrew Simpson and David Gavaghan",
year = "2012",
journal = "Systems and Synthetic Biology",
number = "1--2",
pages = "35--49",
volume = "6",
doi = "10.1007/s11693-012-9095-x",
}
@article{Mirams2012,
title = "Application of cardiac electrophysiology simulations to pro-arrhythmic safety testing",
author = "Mirams, Gary R. and Davies, Mark R. and Cui, Yi and Kohl, Peter and Noble, Denis",
year = "2012",
journal = "British Journal of Pharmacology",
number = "5",
pages = "932-945",
volume = "167",
doi = "10.1111/j.1476-5381.2012.02020.x",
}
@article{Pras_2011_1,
title = "Computational modelling of cardiac electro-physiology: explanation of the variability of results from different numerical solvers",
author = "P. Pathmanathan and M. Bernabeu and S. Niederer and D. Gavaghan and D. Kay",
year = "2012",
journal = "Int. J. Numerical Methods in Biomedical Engineering",
number = "8",
pages = "890-903",
volume = "28",
doi = "10.1002/cnm.2467",
}
@article{PUeyoBJ2011,
title = "A multi-scale investigation of repolarization variability and its role in cardiac arrhythmogenesis",
author = "Pueyo, E. and Corrias, A. and Virag, L. and Jost, N. and Szel, T. and Varro, A. and Szentandrassy, N. and Nanasi, P. and Burrage, K. and Rodriguez, B.",
year = "2011",
journal = "Biophysical journal",
}
@article{bordas2011rabbit,
title = "Rabbit-specific ventricular model of cardiac electrophysiological function including specialized conduction system",
author = "Bordas, R. and Gillow, K. and Lou, Q. and Efimov, IR and Gavaghan, D. and Kohl, P. and Grau, V. and Rodriguez, B.",
year = "2011",
journal = "Progress in biophysics and molecular biology",
publisher = "Pergamon",
}
@article{corrias2011ionic,
title = "Ionic mechanisms of electrophysiological properties and repolarization abnormalities in rabbit Purkinje fibers",
author = "Corrias, A. and Giles, W. and Rodriguez, B.",
year = "2011",
journal = "American Journal of Physiology-Heart and Circulatory Physiology",
number = "5",
pages = "H1806--H1813",
publisher = "Am Physiological Soc",
volume = "300",
}
@article{wallman2011estimation,
title = "Estimation of activation times in cardiac tissue using graph based methods",
author = "Wallman, M. and Smith, N. and Rodriguez, B.",
year = "2011",
journal = "Functional Imaging and Modeling of the Heart",
pages = "71--79",
publisher = "Springer",
}
@article{zemzemi2011simulating,
title = "Simulating Drug-Induced Effects on the Heart: From Ion Channel to Body Surface Electrocardiogram",
author = "Zemzemi, N. and Bernabeu, M. and Saiz, J. and Rodriguez, B.",
year = "2011",
journal = "Functional Imaging and Modeling of the Heart",
pages = "259--266",
publisher = "Springer",
}
@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{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{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{f20ea8a70f839df,
title = "A hybrid approach to multi-scale modelling of cancer",
author = "Osborne, J. M. and Walter, A. and Kershaw, S. K. and Mirams, G. R. and Fletcher, A. G. and Pathmanathan, P. and Gavaghan, D. and Jensen, O. E. and Maini, P. K. and Byrne, H. M.",
year = "2010",
journal = "Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences",
month = "Nov",
number = "1930",
pages = "5013--5028",
volume = "368",
doi = "10.1098/rsta.2010.0173",
}
@article{f20eabee9adffc7,
title = "Integrated approach for the study of anatomical variability in the cardiac Purkinje system: From high resolution MRI to electrophysiology simulation",
author = "Bordas, R. and Grau, V. and Burton, R. B. and Hales, P. and Schneider, J. E. and Gavaghan, DJ and Kohl, P. and Rodriguez, B.",
year = "2010",
journal = "Conf Proc IEEE Eng Med Biol Soc ",
pages = "6793--6",
volume = "1",
}
@article{PhilTrans2010,
title = "Arrhythmic risk biomarkers for the assessment of drug cardiotoxicity: from experiments to computer simulations",
author = "Corrias A, Jie A, Romero L, Bishop MJ, Bernabeu MO, Pueyo E, Rodriguez B",
year = "2010",
journal = "Phil Trans Roy Soc A",
}
@article{rodriguez2010systems,
title = "The systems biology approach to drug development: application to toxicity assessment of cardiac drugs",
author = "Rodriguez, B. and Burrage, K. and Gavaghan, D. and Grau, V. and Kohl, P. and Noble, D.",
year = "2010",
journal = "Clinical Pharmacology \& Therapeutics",
number = "1",
pages = "130--134",
publisher = "Nature Publishing Group",
volume = "88",
}
@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",
}
@inproceedings{corrias2010novel,
title = "A novel biophysically-detailed mathematical model of rabbit Purkinje cell electrophysiology",
author = "Corrias, A. and Rodriguez, B.",
year = "2010",
booktitle = "Engineering in Medicine and Biology Society (EMBC), 2010 Annual International Conference of the IEEE",
organization = "IEEE",
pages = "2658--2661",
}
@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{Niederer:2009b,
title = "The Role of the Frank-Starling Law in the Transduction of Cellular Work to Whole Organ Pump Function: A Computational Modeling Analysis",
author = "S. A. Niederer and N. P. Smith",
year = "2009",
journal = "PLoS computational biology",
pages = "e1000371",
url = "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2668184/",
volume = "5(4)",
}
@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",
}