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Empirical Quantification of Predictive Uncertainty Due to Model Discrepancy by Training with an Ensemble of Experimental Designs: An Application to Ion Channel Kinetics (2023)
Journal Article
Shuttleworth, J. G., Lei, C. L., Whittaker, D. G., Windley, M. J., Hill, A. P., Preston, S. P., & Mirams, G. R. (2024). Empirical Quantification of Predictive Uncertainty Due to Model Discrepancy by Training with an Ensemble of Experimental Designs: An Application to Ion Channel Kinetics. Bulletin of Mathematical Biology, 86(1), Article 2. https://doi.org/10.1007/s11538-023-01224-6

When using mathematical models to make quantitative predictions for clinical or industrial use, it is important that predictions come with a reliable estimate of their accuracy (uncertainty quantification). Because models of complex biological system... Read More about Empirical Quantification of Predictive Uncertainty Due to Model Discrepancy by Training with an Ensemble of Experimental Designs: An Application to Ion Channel Kinetics.

The impact of uncertainty in hERG binding mechanism on in silico predictions of drug-induced proarrhythmic risk (2023)
Journal Article
Lei, C. L., Whittaker, D. G., & Mirams, G. R. (2024). The impact of uncertainty in hERG binding mechanism on in silico predictions of drug-induced proarrhythmic risk. British Journal of Pharmacology, 181(7), 987-1004. https://doi.org/10.1111/bph.16250

Background and Purpose Drug-induced reduction of the rapid delayed rectifier potassium current carried by the human Ether-à-go-go-Related Gene (hERG) channel is associated with increased risk of arrhythmias. Recent updates to drug safety regulatory... Read More about The impact of uncertainty in hERG binding mechanism on in silico predictions of drug-induced proarrhythmic risk.

Computational Cardiac Safety Testing (2023)
Book Chapter
Mirams, G. R. (2023). Computational Cardiac Safety Testing. In F. J. Hock, M. R. Gralinski, & M. K. Pugsley (Eds.), Drug Discovery and Evaluation: Safety and Pharmacokinetic Assays (1-33). Springer. https://doi.org/10.1007/978-3-030-73317-9_137-1

In recent years, computational cardiac electrophysiology simulations using mathematical models have begun to be used in industrial and regulatory assessment of the proarrhythmic risk of candidate drug compounds. The aim of this chapter is to equip th... Read More about Computational Cardiac Safety Testing.

The role of mathematical models in designing mechanopharmacological therapies for asthma (2022)
Journal Article
Irons, L., & Brook, B. S. (2022). The role of mathematical models in designing mechanopharmacological therapies for asthma. Frontiers in Systems Biology, 2, Article 929426. https://doi.org/10.3389/fsysb.2022.929426

Healthy lung function depends on a complex system of interactions which regulate the mechanical and biochemical environment of individual cells to the whole organ. Perturbations from these regulated processes give rise to significant lung dysfunction... Read More about The role of mathematical models in designing mechanopharmacological therapies for asthma.

Ion channel model reduction using manifold boundaries (2022)
Journal Article
Whittaker, D. G., Wang, J., Shuttleworth, J., Venkateshappa, R., Kemp, J. M., Claydon, T. W., & Mirams, G. R. (2022). Ion channel model reduction using manifold boundaries. Journal of the Royal Society, Interface, 19(193), Article 20220193. https://doi.org/10.1098/rsif.2022.0193

Mathematical models of voltage-gated ion channels are used in basic research, industrial and clinical settings. These models range in complexity, but typically contain numerous variables representing the proportion of channels in a given state, and p... Read More about Ion channel model reduction using manifold boundaries.

Modelling the emergence of cities and urban patterning using coupled integro-differential equations (2022)
Journal Article
Whiteley, T. D., Avitabile, D., Siebers, P. O., Robinson, D., & Owen, M. R. (2022). Modelling the emergence of cities and urban patterning using coupled integro-differential equations. Journal of the Royal Society, Interface, 19(190), Article 20220176. https://doi.org/10.1098/rsif.2022.0176

Human residential population distributions show patterns of higher density clustering around local services such as shops and places of employment, displaying characteristic length scales; Fourier transforms and spatial autocorrelation show the lengt... Read More about Modelling the emergence of cities and urban patterning using coupled integro-differential equations.

A Parameter Representing Missing Charge Should Be Considered when Calibrating Action Potential Models (2022)
Journal Article
Barral, Y. H. M., Shuttleworth, J., Clerx, M., Whittaker, D. G., Wang, K., Polonchuk, L., …Mirams, G. R. (2022). A Parameter Representing Missing Charge Should Be Considered when Calibrating Action Potential Models. Frontiers in Physiology, 13, Article 879035. https://doi.org/10.3389/fphys.2022.879035

Computational models of the electrical potential across a cell membrane are longstanding and vital tools in electrophysiology research and applications. These models describe how ionic currents, internal fluxes, and buffering interact to determine me... Read More about A Parameter Representing Missing Charge Should Be Considered when Calibrating Action Potential Models.

chaste codegen: automatic CellML to C++ code generation with fixes for singularities and automatically generated Jacobians (2022)
Journal Article
Hendrix, M., Clerx, M., Tamuri, A. U., Keating, S. M., Johnstone, R. H., Cooper, J., & Mirams, G. R. (2022). chaste codegen: automatic CellML to C++ code generation with fixes for singularities and automatically generated Jacobians. Wellcome Open Research, 6, Article 261. https://doi.org/10.12688/wellcomeopenres.17206.1

Hundreds of different mathematical models have been proposed for describing electrophysiology of various cell types. These models are quite complex (nonlinear systems of typically tens of ODEs and sometimes hundreds of parameters) and software packag... Read More about chaste codegen: automatic CellML to C++ code generation with fixes for singularities and automatically generated Jacobians.

A Quantitative Systems Pharmacology Perspective on the Importance of Parameter Identifiability (2022)
Journal Article
Sher, A., Niederer, S. A., Mirams, G. R., Kirpichnikova, A., Allen, R., Pathmanathan, P., …Noble, D. (2022). A Quantitative Systems Pharmacology Perspective on the Importance of Parameter Identifiability. Bulletin of Mathematical Biology, 84(3), Article 39. https://doi.org/10.1007/s11538-021-00982-5

There is an inherent tension in Quantitative Systems Pharmacology (QSP) between the need to incorporate mathematical descriptions of complex physiology and drug targets with the necessity of developing robust, predictive and well-constrained models.... Read More about A Quantitative Systems Pharmacology Perspective on the Importance of Parameter Identifiability.

Exorcising Malthusian ghosts: Vaccinating the Nexus to advance integrated water, energy and food resource resilience (2021)
Journal Article
Kemp, P. S., Acuto, M., Larcom, S., Lumbroso, D., & Owen, M. R. (2022). Exorcising Malthusian ghosts: Vaccinating the Nexus to advance integrated water, energy and food resource resilience. Current Research in Environmental Sustainability, 4, Article 100108. https://doi.org/10.1016/j.crsust.2021.100108

Water-Energy-Food (WEF) Nexus interactions vary from seemingly negative and intractable wicked problems to opportunities for enhanced sustainability. The aim of this paper is to review the current state of understanding on WEF resource interactions a... Read More about Exorcising Malthusian ghosts: Vaccinating the Nexus to advance integrated water, energy and food resource resilience.

A nonlinear and time-dependent leak current in the presence of calcium fluoride patch-clamp seal enhancer (2021)
Journal Article
Lei, C. L., Fabbri, A., Whittaker, D. G., Clerx, M., Windley, M. J., Hill, A. P., …de Boer, T. P. (2021). A nonlinear and time-dependent leak current in the presence of calcium fluoride patch-clamp seal enhancer. Wellcome Open Research, 5, 1-34. https://doi.org/10.12688/wellcomeopenres.15968.2

Automated patch-clamp platforms are widely used and vital tools in both academia and industry to enable high-throughput studies such as drug screening. A leak current to ground occurs whenever the seal between a pipette and cell (or internal solution... Read More about A nonlinear and time-dependent leak current in the presence of calcium fluoride patch-clamp seal enhancer.

Neural Network Differential Equations For Ion Channel Modelling (2021)
Journal Article
Lei, C. L., & Mirams, G. R. (2021). Neural Network Differential Equations For Ion Channel Modelling. Frontiers in Physiology, 12, Article 708944. https://doi.org/10.3389/fphys.2021.708944

Mathematical models of cardiac ion channels have been widely used to study and predict the behaviour of ion currents. Typically models are built using biophysically-based mechanistic principles such as Hodgkin-Huxley or Markov state transitions. Thes... Read More about Neural Network Differential Equations For Ion Channel Modelling.

Cardiac TdP risk stratification modelling of anti-infective compounds including chloroquine and hydroxychloroquine (2021)
Journal Article
Whittaker, D. G., Capel, R. A., Hendrix, M., Chan, X. H. S., Herring, N., White, N. J., …Burton, R. A. B. (2021). Cardiac TdP risk stratification modelling of anti-infective compounds including chloroquine and hydroxychloroquine. Royal Society Open Science, 8(4), https://doi.org/10.1098/rsos.210235

Hydroxychloroquine (HCQ), the hydroxyl derivative of chloroquine (CQ), is widely used in the treatment of rheumatological conditions (systemic lupus erythematosus, rheumatoid arthritis) and is being studied for the treatment and prevention of COVID-1... Read More about Cardiac TdP risk stratification modelling of anti-infective compounds including chloroquine and hydroxychloroquine.

Agent-based modelling of juvenile eel migration via selective tidal stream transport (2021)
Journal Article
Benson, T., de Bie, J., Gaskell, J., Vezza, P., Kerr, J. R., Lumbroso, D., …Kemp, P. S. (2021). Agent-based modelling of juvenile eel migration via selective tidal stream transport. Ecological Modelling, 443, Article 109448. https://doi.org/10.1016/j.ecolmodel.2021.109448

Recruitment of temperate eel species Anguilla anguilla, A. rostrata & A. japonica has declined over the last few decades due to human activities, such as overfishing and construction of migratory barriers (e.g. dams, weirs and sluices) and hazardous... Read More about Agent-based modelling of juvenile eel migration via selective tidal stream transport.

Development, Implementation and Testing of a Multicellular Dynamic Action Potential Clamp Simulator for Drug Cardiac Safety Assessment (2020)
Conference Proceeding
Camporesi, M., Bartolucci, C., Lei, C. L., Mirams, G. R., De Boer, T. P., & Severi, S. (2020). Development, Implementation and Testing of a Multicellular Dynamic Action Potential Clamp Simulator for Drug Cardiac Safety Assessment. . https://doi.org/10.22489/CinC.2020.416

© 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.

Use of Patient Health Records to Quantify Drug-Related Pro-arrhythmic Risk (2020)
Journal Article
Davies, M. R., Martinec, M., Walls, R., Schwarz, R., Mirams, G. R., Wang, K., …Polonchuk, L. (2020). Use of Patient Health Records to Quantify Drug-Related Pro-arrhythmic Risk. Cell Reports Medicine, 1(5), Article 100076. https://doi.org/10.1016/j.xcrm.2020.100076

There is an increasing expectation that computational approaches may supplement existing human decision-making. Frontloading of models for cardiac safety prediction is no exception to this trend, and ongoing regulatory initiatives propose use of high... Read More about Use of Patient Health Records to Quantify Drug-Related Pro-arrhythmic Risk.

Accounting for variability in ion current recordings using a mathematical model of artefacts in voltage-clamp experiments (2020)
Journal Article
Clerx, M., Lei, C. L., Whittaker, D. G., Gavaghan, D. J., de Boer, T. P., & Mirams, G. R. (2020). Accounting for variability in ion current recordings using a mathematical model of artefacts in voltage-clamp experiments. Philosophical Transactions A: Mathematical, Physical and Engineering Sciences, 378(2173), Article 20190348. https://doi.org/10.1098/rsta.2019.0348

Mathematical models of ion channels, which constitute indispensable components of action potential models, are commonly constructed by fitting to whole-cell patch-clamp data. In a previous study, we fitted cell-specific models to hERG1a (Kv11.1) reco... Read More about Accounting for variability in ion current recordings using a mathematical model of artefacts in voltage-clamp experiments.

Calibration of ionic and cellular cardiac electrophysiology models (2020)
Journal Article
Whittaker, D. G., Clerx, M., Lei, C. L., Christini, D. J., & Mirams, G. R. (2020). Calibration of ionic and cellular cardiac electrophysiology models. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 12(4), https://doi.org/10.1002/wsbm.1482

© 2020 The Authors. WIREs Systems Biology and Medicine published by Wiley Periodicals, Inc. Cardiac electrophysiology models are among the most mature and well-studied mathematical models of biological systems. This maturity is bringing new challenge... Read More about Calibration of ionic and cellular cardiac electrophysiology models.

Rapid characterisation of hERG channel kinetics II: temperature dependence (2019)
Journal Article
Lei, C. L., Clerx, M., Beattie, K. A., Melgari, D., Hancox, J. C., Gavaghan, D. J., …Mirams, G. R. (2019). Rapid characterisation of hERG channel kinetics II: temperature dependence. Biophysical Journal, 117(12), 2455-2470. https://doi.org/10.1101/609719

Ion channel behavior can depend strongly on temperature, with faster kinetics at physiological temperatures leading to considerable changes in currents relative to room temperature. These temperature-dependent changes in voltage-dependent ion channel... Read More about Rapid characterisation of hERG channel kinetics II: temperature dependence.