Search Results - "Gavaghan, David"

Chaste: an open source C++ library for computational physiology and biology by Mirams, Gary R, Arthurs, Christopher J, Bernabeu, Miguel O, Bordas, Rafel, Cooper, Jonathan, Corrias, Alberto, Davit, Yohan, Dunn, Sara-Jane, Fletcher, Alexander G, Harvey, Daniel G, Marsh, Megan E, Osborne, James M, Pathmanathan, Pras, Pitt-Francis, Joe, Southern, James, Zemzemi, Nejib, Gavaghan, David J

“…Chaste - Cancer, Heart And Soft Tissue Environment - is an open source C++ library for the computational simulation of mathematical models developed for…”
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Comparing individual-based approaches to modelling the self-organization of multicellular tissues by Osborne, James M, Fletcher, Alexander G, Pitt-Francis, Joe M, Maini, Philip K, Gavaghan, David J

“…The coordinated behaviour of populations of cells plays a central role in tissue growth and renewal. Cells react to their microenvironment by modulating…”
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Four Ways to Fit an Ion Channel Model by Clerx, Michael, Beattie, Kylie A., Gavaghan, David J., Mirams, Gary R.

“…Mathematical models of ionic currents are used to study the electrophysiology of the heart, brain, gut, and several other organs. Increasingly, these models…”
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The role of the Hes1 crosstalk hub in Notch-Wnt interactions of the intestinal crypt by Kay, Sophie K, Harrington, Heather A, Shepherd, Sarah, Brennan, Keith, Dale, Trevor, Osborne, James M, Gavaghan, David J, Byrne, Helen M

“…The Notch pathway plays a vital role in determining whether cells in the intestinal epithelium adopt a secretory or an absorptive phenotype. Cell fate…”
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Rapid Characterization of hERG Channel Kinetics I: Using an Automated High-Throughput System by Lei, Chon Lok, Clerx, Michael, Gavaghan, David J., Polonchuk, Liudmila, Mirams, Gary R., Wang, Ken

“…Predicting how pharmaceuticals may affect heart rhythm is a crucial step in drug development and requires a deep understanding of a compound’s action on ion…”
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A Monte Carlo method to estimate cell population heterogeneity from cell snapshot data by Lambert, Ben, Gavaghan, David J., Tavener, Simon J.

“…•Determining sources of cellular variation is crucial for a range of applications.•A statistical method for determining cellular variation from snapshot data…”
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Retuning the Catalytic Bias and Overpotential of a [NiFe]-Hydrogenase via a Single Amino Acid Exchange at the Electron Entry/Exit Site by Adamson, Hope, Robinson, Martin, Wright, John J, Flanagan, Lindsey A, Walton, Julia, Elton, Darrell, Gavaghan, David J, Bond, Alan M, Roessler, Maxie M, Parkin, Alison

“…The redox chemistry of the electron entry/exit site in Escherichia coli hydrogenase-1 is shown to play a vital role in tuning biocatalysis. Inspired by nature,…”
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Simulation of multiple ion channel block provides improved early prediction of compounds' clinical torsadogenic risk by Mirams, Gary R., Cui, Yi, Sher, Anna, Fink, Martin, Cooper, Jonathan, Heath, Bronagh M., McMahon, Nick C., Gavaghan, David J., Noble, Denis

“…Aims The level of inhibition of the human Ether-à-go-go-related gene (hERG) channel is one of the earliest preclinical markers used to predict the risk of a…”
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Importance of modelling hERG binding in predicting drug-induced action potential prolongations for drug safety assessment by Farm, Hui Jia, Clerx, Michael, Cooper, Fergus, Polonchuk, Liudmila, Wang, Ken, Gavaghan, David J, Lei, Chon Lok

“…Reduction of the rapid delayed rectifier potassium current ( ) drug binding to the human Ether-à-go-go-Related Gene (hERG) channel is a well recognised…”
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Model-driven optimal experimental design for calibrating cardiac electrophysiology models by Lei, Chon Lok, Clerx, Michael, Gavaghan, David J., Mirams, Gary R.

“…•Current models of cardiac action potentials reflect only an average cell behaviour and ignore cell-to-cell variability.•Optimal single-cell experiments are…”
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Implementing vertex dynamics models of cell populations in biology within a consistent computational framework by Fletcher, Alexander G., Osborne, James M., Maini, Philip K., Gavaghan, David J.

“…The dynamic behaviour of epithelial cell sheets plays a central role during development, growth, disease and wound healing. These processes occur as a result…”
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Ten simple rules for training scientists to make better software by Gallagher, Kit, Creswell, Richard, Lambert, Ben, Robinson, Martin, Lok Lei, Chon, Mirams, Gary R, Gavaghan, David J

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Rapid Characterization of hERG Channel Kinetics II: Temperature Dependence by Lei, Chon Lok, Clerx, Michael, Beattie, Kylie A., Melgari, Dario, Hancox, Jules C., Gavaghan, David J., Polonchuk, Liudmila, Wang, Ken, Mirams, Gary R.

“…Ion channel behavior can depend strongly on temperature, with faster kinetics at physiological temperatures leading to considerable changes in currents…”
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Uncertainty and variability in models of the cardiac action potential: Can we build trustworthy models? by Johnstone, Ross H, Chang, Eugene T.Y, Bardenet, Rémi, de Boer, Teun P, Gavaghan, David J, Pathmanathan, Pras, Clayton, Richard H, Mirams, Gary R

“…Abstract Cardiac electrophysiology models have been developed for over 50 years, and now include detailed descriptions of individual ion currents and…”
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Accounting for variability in ion current recordings using a mathematical model of artefacts in voltage-clamp experiments by Lei, Chon Lok, Clerx, Michael, Whittaker, Dominic G, Gavaghan, David J, de Boer, Teun P, Mirams, Gary R

“…Mathematical models of ion channels, which constitute indispensable components of action potential models, are commonly constructed by fitting to whole-cell…”
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A Spotter’s guide to dispersion in non-catalytic surface-confined voltammetry experiments by Lloyd-Laney, Henry O., Robinson, Martin J., Bond, Alan M., Parkin, Alison, Gavaghan, David J.

“…•Effects of thermodynamic and kinetic dispersion in surface confined voltammetry.•Distinguishing dispersed from non-dispersed cases by looking at voltammetry…”
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Review of automatic pulmonary lobe segmentation methods from CT by Doel, Tom, Gavaghan, David J, Grau, Vicente

“…Highlights • A detailed review of automated segmentation methods for the pulmonary lobes from clinical CT data. • Formulation of a modular description,…”
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Simulating clinical trials for model-informed precision dosing: using warfarin treatment as a use case by Augustin, David, Lambert, Ben, Robinson, Martin, Wang, Ken, Gavaghan, David

“…Treatment response variability across patients is a common phenomenon in clinical practice. For many drugs this inter-individual variability does not require…”
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Sinusoidal voltage protocols for rapid characterisation of ion channel kinetics by Beattie, Kylie A., Hill, Adam P., Bardenet, Rémi, Cui, Yi, Vandenberg, Jamie I., Gavaghan, David J., Boer, Teun P., Mirams, Gary R.

“…Key points Ion current kinetics are commonly represented by current–voltage relationships, time constant–voltage relationships and subsequently mathematical…”
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Filter inference: A scalable nonlinear mixed effects inference approach for snapshot time series data by Augustin, David, Lambert, Ben, Wang, Ken, Walz, Antje-Christine, Robinson, Martin, Gavaghan, David

“…Variability is an intrinsic property of biological systems and is often at the heart of their complex behaviour. Examples range from cell-to-cell variability…”
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