All Outputs (117)

Minimum Information about a Cardiac Electrophysiology Experiment (MICEE): Standardised reporting for model reproducibility, interoperability, and data sharing (2011)
Journal Article
Quinn, T. A., Granite, S., Allessie, M. A., Antzelevitch, C., Bollensdorff, C., Bub, G., …Kohl, P. (2011). Minimum Information about a Cardiac Electrophysiology Experiment (MICEE): Standardised reporting for model reproducibility, interoperability, and data sharing. Progress in Biophysics and Molecular Biology, 107(1), 4-10. https://doi.org/10.1016/j.pbiomolbio.2011.07.001

Cardiac experimental electrophysiology is in need of a well-defined Minimum Information Standard for recording, annotating, and reporting experimental data. As a step towards establishing this, we present a draft standard, called Minimum Information... Read More about Minimum Information about a Cardiac Electrophysiology Experiment (MICEE): Standardised reporting for model reproducibility, interoperability, and data sharing.

Novel approaches to assessing cardiac safety - Proceedings of a workshop: Regulators, industry and academia discuss the future of in silico cardiac modelling to predict the proarrhythmic safety of drugs (2011)
Journal Article
Fletcher, K., Shah, R. R., Thomas, A., Tobin, F., Rodriguez, B., Mirams, G. R., Saiz, J., & Noble, D. (2011). Novel approaches to assessing cardiac safety - Proceedings of a workshop: Regulators, industry and academia discuss the future of in silico cardiac modelling to predict the proarrhythmic safety of drugs. Drug Safety, 34(5), 439-443. https://doi.org/10.2165/11591950-000000000-00000

The significant effect of the choice of ionic current integration method in cardiac electro-physiological simulations (2011)
Journal Article
Pathmanathan, P., Mirams, G. R., Southern, J., & Whiteley, J. P. (2011). The significant effect of the choice of ionic current integration method in cardiac electro-physiological simulations. International Journal for Numerical Methods in Biomedical Engineering, 27(11), 1751-1770. https://doi.org/10.1002/cnm.1438

Finite element (FE) cardiac electro-physiology solvers commonly have ionic current determined at mesh nodes but required element interiors. We consider two interpolation approaches: (i) ionic current interpolation (ICI), where nodal ionic currents ar... Read More about The significant effect of the choice of ionic current integration method in cardiac electro-physiological simulations.

Simulation of multiple ion channel block provides improved prediction of compounds’ clinical torsadogenic risk (2011)
Journal Article
Mirams, G. R., Cui, Y., Sher, A., Fink, M., Cooper, J., Heath, B. M., …Noble, D. (2011). Simulation of multiple ion channel block provides improved prediction of compounds’ clinical torsadogenic risk. Cardiovascular Research, 91(1), 53-61. https://doi.org/10.1093/cvr/cvr044

© 2011 The Author. Aims The level of inhibition of the human Ether - go-go-related gene (hERG) channel is one of the earliest preclinical markers used to predict the risk of a compound causing Torsade-de-Pointes (TdP) arrhythmias. While avoiding the... Read More about Simulation of multiple ion channel block provides improved prediction of compounds’ clinical torsadogenic risk.

A hybrid approach to multi-scale modelling of cancer (2010)
Journal Article
Osborne, J. M., Walter, A., Kershaw, S. K., Mirams, G. R., Fletcher, A. G., Pathmanathan, P., …Byrne, H. M. (2010). A hybrid approach to multi-scale modelling of cancer. Philosophical Transactions A: Mathematical, Physical and Engineering Sciences, 368(1930), 5013-5028. https://doi.org/10.1098/rsta.2010.0173

In this paper, we review multi-scale models of solid tumour growth and discuss a middleout framework that tracks individual cells. By focusing on the cellular dynamics of a healthy colorectal crypt and its invasion by mutant, cancerous cells, we comp... Read More about A hybrid approach to multi-scale modelling of cancer.

Modelling spatially regulated β-catenin dynamics and invasion in intestinal crypts (2010)
Journal Article
Murray, P. J., Kang, J. W., Mirams, G. R., Shin, S. Y., Byrne, H. M., Maini, P. K., & Cho, K. H. (2010). Modelling spatially regulated β-catenin dynamics and invasion in intestinal crypts. Biophysical Journal, 99(3), 716-725. https://doi.org/10.1016/j.bpj.2010.05.016

Experimental data (e.g., genetic lineage and cell population studies) on intestinal crypts reveal that regulatory features of crypt behavior, such as control via morphogen gradients, are remarkably well conserved among numerous organisms (e.g., from... Read More about Modelling spatially regulated β-catenin dynamics and invasion in intestinal crypts.

Multiscale modeling of colonic crypts and early colorectal cancer (2010)
Book Chapter
Fletcher, A. G., Mirams, G. R., Murray, P. J., Walter, A., Kang, J. W., Cho, K. H., …Byrne, H. M. (2010). Multiscale modeling of colonic crypts and early colorectal cancer. In T. S. Deisboeck, & G. Stamatakos (Eds.), Multiscale Cancer Modeling (111-131). CRC Press. https://doi.org/10.1201/b10407

© 2011 by Taylor & Francis Group, LLC. Colorectal cancer accounts for 13% of all cancers in the United Kingdom, with around 35,300 new diagnoses and 16,000 deaths occurring each year (http://info.cancerresearchuk.org). Colorectal cancer is predomin... Read More about Multiscale modeling of colonic crypts and early colorectal cancer.

An integrative computational model for intestinal tissue renewal (2009)
Journal Article
Van Leeuwen, I. M., Mirams, G. R., Walter, A., Fletcher, A., Murray, P., Osborne, J., …Byrne, H. M. (2009). An integrative computational model for intestinal tissue renewal. Cell Proliferation, 42(5), 617-636. https://doi.org/10.1111/j.1365-2184.2009.00627.x

Objectives: The luminal surface of the gut is lined with a monolayer of epithelial cells that acts as a nutrient absorptive engine and protective barrier. To maintain its integrity and functionality, the epithelium is renewed every few days. Theoreti... Read More about An integrative computational model for intestinal tissue renewal.

Chaste: A test-driven approach to software development for biological modelling (2009)
Journal Article
Pitt-Francis, J., Pathmanathan, P., Bernabeu, M. O., Bordas, R., Cooper, J., Fletcher, A. G., …Gavaghan, D. J. (2009). Chaste: A test-driven approach to software development for biological modelling. Computer Physics Communications, 180(12), 2452-2471. https://doi.org/10.1016/j.cpc.2009.07.019

Chaste ('Cancer, heart and soft-tissue environment') is a software library and a set of test suites for computational simulations in the domain of biology. Current functionality has arisen from modelling in the fields of cancer, cardiac physiology an... Read More about Chaste: A test-driven approach to software development for biological modelling.

A multiple timescale analysis of a mathematical model of the Wnt/β-catenin signalling pathway (2009)
Journal Article
Mirams, G. R., Byrne, H. M., & King, J. R. (2010). A multiple timescale analysis of a mathematical model of the Wnt/β-catenin signalling pathway. Journal of Mathematical Biology, 60(1), 131-160. https://doi.org/10.1007/s00285-009-0262-y

The Wnt signalling pathway is involved in stem cell maintenance, differentiation and tissue development. Its disregulation has also been implicated in many cancers. β-catenin is a protein that regulates both transcription of many genes and cell-cell... Read More about A multiple timescale analysis of a mathematical model of the Wnt/β-catenin signalling pathway.

A computational study of discrete mechanical tissue models (2009)
Journal Article
Pathmanathan, P., Cooper, J., Fletcher, A., Mirams, G., Murray, P., Osborne, J., …Chapman, S. J. (2009). A computational study of discrete mechanical tissue models. Physical Biology, 6(3), Article 036001. https://doi.org/10.1088/1478-3975/6/3/036001

A computational study of discrete 'cell-centre' approaches to modelling the evolution of a collection of cells is undertaken. The study focuses on the mechanical aspects of the tissue, in order to separate the passive mechanical response of the model... Read More about A computational study of discrete mechanical tissue models.

Hierarchical Bayesian modelling of variability and uncertainty in synthetic action potential traces
Presentation / Conference Contribution
Johnstone, R. H., Bardenet, R., Gavaghan, D. J., Polonchuk, L., Davies, M. R., & Mirams, G. R. Hierarchical Bayesian modelling of variability and uncertainty in synthetic action potential traces. Presented at 2016 Computing in Cardiology Conference (CinC), Vancouver, BC, Canada

© 2016 CCAL. There are many sources of uncertainty in the recording and modelling of membrane action potentials (APs) from cardiomyocytes. For example, there are measurement, parameter, and model uncertainties. There is also extrinsic variability bet... Read More about Hierarchical Bayesian modelling of variability and uncertainty in synthetic action potential traces.

Phenomenological modeling of cell-to-cell and beat-to-beat variability in isolated guinea pig ventricular myocytes
Presentation / Conference Contribution
Walmsley, J., Mirams, G., Bahoshy, M., Bollensdorff, C., Rodriguez, B., & Burrage, K. (2010, August). Phenomenological modeling of cell-to-cell and beat-to-beat variability in isolated guinea pig ventricular myocytes. Presented at 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC'10, Buenos Aires, Argentina

Experimental action potential (AP) recordings in isolated ventricular myoctes display significant temporal beatto- beat variability in morphology and duration. Furthermore, significant cell-to-cell differences in AP also exist even for isolated cells... Read More about Phenomenological modeling of cell-to-cell and beat-to-beat variability in isolated guinea pig ventricular myocytes.

Development, Implementation and Testing of a Multicellular Dynamic Action Potential Clamp Simulator for Drug Cardiac Safety Assessment
Presentation / Conference Contribution
Camporesi, M., Bartolucci, C., Lei, C. L., Mirams, G. R., De Boer, T. P., & Severi, S. (2020, September). Development, Implementation and Testing of a Multicellular Dynamic Action Potential Clamp Simulator for Drug Cardiac Safety Assessment. Presented at Computing in Cardiology, Rimini, Italy

© 2020 Creative Commons; the authors hold their copyright. As drugs can be multichannel blockers it is important to assess their cardiac safety taking into account multiple currents. In silico action potential (AP) models have been proposed for being... Read More about Development, Implementation and Testing of a Multicellular Dynamic Action Potential Clamp Simulator for Drug Cardiac Safety Assessment.

Derivative-based Inference for Cell and Channel Electrophysiology Models
Presentation / Conference Contribution
Clerx, M., Augustin, D., Dale-Evans, A. R., & Mirams, G. R. (2022, September). Derivative-based Inference for Cell and Channel Electrophysiology Models. Presented at 2022 Computing in Cardiology Conference, Tampere, Finland (online)

Models of ionic currents or of the cardiac action potential (AP) are frequently calibrated by defining an error function that quantifies the mismatch between simulations and data, and using numerical optimisation to find the parameter values that min... Read More about Derivative-based Inference for Cell and Channel Electrophysiology Models.

Normalisation of Action Potential Data Recorded with Sharp Electrodes Maximises Its Utility for Model Development
Presentation / Conference Contribution
Barral, Y. S. H., Polonchuk, L., R. Mirams, G., Clerx, M., Page, G., Sweat, K., Abi-Gerges, N., Wang, K., & Gavaghan, D. J. (2022, September). Normalisation of Action Potential Data Recorded with Sharp Electrodes Maximises Its Utility for Model Development. Presented at 2022 Computing in Cardiology Conference, Tampere, Finland

In silico models of cardiomyocyte electrophysiology describe the various ionic currents and fluxes that lead to the formation of action potentials (APs). Experimental data used to create such models can be recorded in adult human cardiac trabeculae u... Read More about Normalisation of Action Potential Data Recorded with Sharp Electrodes Maximises Its Utility for Model Development.

Modelling the Effect of Intracellular Calcium in the Rundown of L-Type Calcium Current
Presentation / Conference Contribution
Agrawal, A., Clerx, M., Wang, K., Polonchuk, L., Gavaghan, D. J., & Mirams, G. R. (2022, September). Modelling the Effect of Intracellular Calcium in the Rundown of L-Type Calcium Current. Presented at 2022 Computing in Cardiology Conference, Tampere, Finland

The L-type calcium current (ICaL) is a key current of the heart playing an important role in the contraction of the cardiomyocyte. Patch-clamp recordings of ionic currents can be associated with a reduction of the current magnitude with time (termed... Read More about Modelling the Effect of Intracellular Calcium in the Rundown of L-Type Calcium Current.