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Four Ways to Fit an Ion Channel Model.

Clerx M, Beattie KA, Gavaghan DJ, Mirams GR.

Biophys J. 2019 Aug 6. pii: S0006-3495(19)30666-6. doi: 10.1016/j.bpj.2019.08.001. [Epub ahead of print]


Rapid Characterization of hERG Channel Kinetics II: Temperature Dependence.

Lei CL, Clerx M, Beattie KA, Melgari D, Hancox JC, Gavaghan DJ, Polonchuk L, Wang K, Mirams GR.

Biophys J. 2019 Jul 25. pii: S0006-3495(19)30598-3. doi: 10.1016/j.bpj.2019.07.030. [Epub ahead of print]


Rapid Characterization of hERG Channel Kinetics I: Using an Automated High-Throughput System.

Lei CL, Clerx M, Gavaghan DJ, Polonchuk L, Mirams GR, Wang K.

Biophys J. 2019 Jul 25. pii: S0006-3495(19)30597-1. doi: 10.1016/j.bpj.2019.07.029. [Epub ahead of print]


Representation of Multiple Cellular Phenotypes Within Tissue-Level Simulations of Cardiac Electrophysiology.

Bowler LA, Gavaghan DJ, Mirams GR, Whiteley JP.

Bull Math Biol. 2019 Jan;81(1):7-38. doi: 10.1007/s11538-018-0516-1. Epub 2018 Oct 5.


Reproducible model development in the cardiac electrophysiology Web Lab.

Daly AC, Clerx M, Beattie KA, Cooper J, Gavaghan DJ, Mirams GR.

Prog Biophys Mol Biol. 2018 Nov;139:3-14. doi: 10.1016/j.pbiomolbio.2018.05.011. Epub 2018 May 26.


Sinusoidal voltage protocols for rapid characterisation of ion channel kinetics.

Beattie KA, Hill AP, Bardenet R, Cui Y, Vandenberg JI, Gavaghan DJ, de Boer TP, Mirams GR.

J Physiol. 2018 May 15;596(10):1813-1828. doi: 10.1113/JP275733. Epub 2018 Apr 17.


Early afterdepolarisation tendency as a simulated pro-arrhythmic risk indicator.

McMillan B, Gavaghan DJ, Mirams GR.

Toxicol Res (Camb). 2017 Nov 1;6(6):912-921. doi: 10.1039/c7tx00141j. Epub 2017 Sep 14.


Tailoring Mathematical Models to Stem-Cell Derived Cardiomyocyte Lines Can Improve Predictions of Drug-Induced Changes to Their Electrophysiology.

Lei CL, Wang K, Clerx M, Johnstone RH, Hortigon-Vinagre MP, Zamora V, Allan A, Smith GL, Gavaghan DJ, Mirams GR, Polonchuk L.

Front Physiol. 2017 Dec 12;8:986. doi: 10.3389/fphys.2017.00986. eCollection 2017.


Comparing two sequential Monte Carlo samplers for exact and approximate Bayesian inference on biological models.

Daly AC, Cooper J, Gavaghan DJ, Holmes C.

J R Soc Interface. 2017 Sep;14(134). pii: 20170340. doi: 10.1098/rsif.2017.0340.


Retuning the Catalytic Bias and Overpotential of a [NiFe]-Hydrogenase via a Single Amino Acid Exchange at the Electron Entry/Exit Site.

Adamson H, Robinson M, Wright JJ, Flanagan LA, Walton J, Elton D, Gavaghan DJ, Bond AM, Roessler MM, Parkin A.

J Am Chem Soc. 2017 Aug 9;139(31):10677-10686. doi: 10.1021/jacs.7b03611. Epub 2017 Jul 26.


Ten simple rules for surviving an interdisciplinary PhD.

Demharter S, Pearce N, Beattie K, Frost I, Leem J, Martin A, Oppenheimer R, Regep C, Rukat T, Skates A, Trendel N, Gavaghan DJ, Deane CM, Knapp B.

PLoS Comput Biol. 2017 May 25;13(5):e1005512. doi: 10.1371/journal.pcbi.1005512. eCollection 2017 May. No abstract available.


The role of the Hes1 crosstalk hub in Notch-Wnt interactions of the intestinal crypt.

Kay SK, Harrington HA, Shepherd S, Brennan K, Dale T, Osborne JM, Gavaghan DJ, Byrne HM.

PLoS Comput Biol. 2017 Feb 28;13(2):e1005400. doi: 10.1371/journal.pcbi.1005400. eCollection 2017 Feb.


Comparing individual-based approaches to modelling the self-organization of multicellular tissues.

Osborne JM, Fletcher AG, Pitt-Francis JM, Maini PK, Gavaghan DJ.

PLoS Comput Biol. 2017 Feb 13;13(2):e1005387. doi: 10.1371/journal.pcbi.1005387. eCollection 2017 Feb.


Analysis of HypD Disulfide Redox Chemistry via Optimization of Fourier Transformed ac Voltammetric Data.

Adamson H, Robinson M, Bond PS, Soboh B, Gillow K, Simonov AN, Elton DM, Bond AM, Sawers RG, Gavaghan DJ, Parkin A.

Anal Chem. 2017 Feb 7;89(3):1565-1573. doi: 10.1021/acs.analchem.6b03589. Epub 2017 Jan 19.


Hierarchical Bayesian inference for ion channel screening dose-response data.

Johnstone RH, Bardenet R, Gavaghan DJ, Mirams GR.

Wellcome Open Res. 2016 Nov 15;1:6. doi: 10.12688/wellcomeopenres.9945.2. eCollection 2016.


Multiparameter Estimation in Voltammetry When an Electron Transfer Process Is Coupled to a Chemical Reaction.

Simonov AN, Morris GP, Mashkina E, Bethwaite B, Gillow K, Baker RE, Gavaghan DJ, Bond AM.

Anal Chem. 2016 May 3;88(9):4724-32. doi: 10.1021/acs.analchem.5b04820. Epub 2016 Apr 15.


Hodgkin-Huxley revisited: reparametrization and identifiability analysis of the classic action potential model with approximate Bayesian methods.

Daly AC, Gavaghan DJ, Holmes C, Cooper J.

R Soc Open Sci. 2015 Dec 23;2(12):150499. doi: 10.1098/rsos.150499. eCollection 2015 Dec.


Uncertainty and variability in models of the cardiac action potential: Can we build trustworthy models?

Johnstone RH, Chang ETY, Bardenet R, de Boer TP, Gavaghan DJ, Pathmanathan P, Clayton RH, Mirams GR.

J Mol Cell Cardiol. 2016 Jul;96:49-62. doi: 10.1016/j.yjmcc.2015.11.018. Epub 2015 Dec 2.


Theoretical Analysis of the Relative Significance of Thermodynamic and Kinetic Dispersion in the dc and ac Voltammetry of Surface-Confined Molecules.

Morris GP, Baker RE, Gillow K, Davis JJ, Gavaghan DJ, Bond AM.

Langmuir. 2015 May 5;31(17):4996-5004. doi: 10.1021/la5042635. Epub 2015 Apr 24.


Uncertainty quantification of fast sodium current steady-state inactivation for multi-scale models of cardiac electrophysiology.

Pathmanathan P, Shotwell MS, Gavaghan DJ, Cordeiro JM, Gray RA.

Prog Biophys Mol Biol. 2015 Jan;117(1):4-18. doi: 10.1016/j.pbiomolbio.2015.01.008. Epub 2015 Feb 7. Review.


Cardiac tissue slices: preparation, handling, and successful optical mapping.

Wang K, Lee P, Mirams GR, Sarathchandra P, Borg TK, Gavaghan DJ, Kohl P, Bollensdorff C.

Am J Physiol Heart Circ Physiol. 2015 May 1;308(9):H1112-25. doi: 10.1152/ajpheart.00556.2014. Epub 2015 Jan 16.


Review of automatic pulmonary lobe segmentation methods from CT.

Doel T, Gavaghan DJ, Grau V.

Comput Med Imaging Graph. 2015 Mar;40:13-29. doi: 10.1016/j.compmedimag.2014.10.008. Epub 2014 Oct 28. Review.


Living cardiac tissue slices: an organotypic pseudo two-dimensional model for cardiac biophysics research.

Wang K, Terrar D, Gavaghan DJ, Mu-U-Min R, Kohl P, Bollensdorff C.

Prog Biophys Mol Biol. 2014 Aug;115(2-3):314-27. doi: 10.1016/j.pbiomolbio.2014.08.006. Epub 2014 Aug 11.


Prediction of Thorough QT study results using action potential simulations based on ion channel screens.

Mirams GR, Davies MR, Brough SJ, Bridgland-Taylor MH, Cui Y, Gavaghan DJ, Abi-Gerges N.

J Pharmacol Toxicol Methods. 2014 Nov-Dec;70(3):246-54. doi: 10.1016/j.vascn.2014.07.002. Epub 2014 Jul 31.


Inappropriate use of the quasi-reversible electrode kinetic model in simulation-experiment comparisons of voltammetric processes that approach the reversible limit.

Simonov AN, Morris GP, Mashkina EA, Bethwaite B, Gillow K, Baker RE, Gavaghan DJ, Bond AM.

Anal Chem. 2014 Aug 19;86(16):8408-17. doi: 10.1021/ac5019952. Epub 2014 Jul 31.


Ten simple rules for effective computational research.

Osborne JM, Bernabeu MO, Bruna M, Calderhead B, Cooper J, Dalchau N, Dunn SJ, Fletcher AG, Freeman R, Groen D, Knapp B, McInerny GJ, Mirams GR, Pitt-Francis J, Sengupta B, Wright DW, Yates CA, Gavaghan DJ, Emmott S, Deane C.

PLoS Comput Biol. 2014 Mar 27;10(3):e1003506. doi: 10.1371/journal.pcbi.1003506. eCollection 2014 Mar. No abstract available.


The free energy landscape of dimerization of a membrane protein, NanC.

Dunton TA, Goose JE, Gavaghan DJ, Sansom MS, Osborne JM.

PLoS Comput Biol. 2014 Jan;10(1):e1003417. doi: 10.1371/journal.pcbi.1003417. Epub 2014 Jan 9.


A comparison of fully automated methods of data analysis and computer assisted heuristic methods in an electrode kinetic study of the pathologically variable [Fe(CN)6](3-/4-) process by AC voltammetry.

Morris GP, Simonov AN, Mashkina EA, Bordas R, Gillow K, Baker RE, Gavaghan DJ, Bond AM.

Anal Chem. 2013 Dec 17;85(24):11780-7. doi: 10.1021/ac4022105. Epub 2013 Dec 3.


Implementing vertex dynamics models of cell populations in biology within a consistent computational framework.

Fletcher AG, Osborne JM, Maini PK, Gavaghan DJ.

Prog Biophys Mol Biol. 2013 Nov;113(2):299-326. doi: 10.1016/j.pbiomolbio.2013.09.003. Epub 2013 Oct 9. Review.


Colorectal cancer through simulation and experiment.

Kershaw SK, Byrne HM, Gavaghan DJ, Osborne JM.

IET Syst Biol. 2013 Jun;7(3):57-73. Review.


Variability in high-throughput ion-channel screening data and consequences for cardiac safety assessment.

Elkins RC, Davies MR, Brough SJ, Gavaghan DJ, Cui Y, Abi-Gerges N, Mirams GR.

J Pharmacol Toxicol Methods. 2013 Jul-Aug;68(1):112-22. doi: 10.1016/j.vascn.2013.04.007. Epub 2013 May 5.


Evaluation of an in silico cardiac safety assay: using ion channel screening data to predict QT interval changes in the rabbit ventricular wedge.

Beattie KA, Luscombe C, Williams G, Munoz-Muriedas J, Gavaghan DJ, Cui Y, Mirams GR.

J Pharmacol Toxicol Methods. 2013 Jul-Aug;68(1):88-96. doi: 10.1016/j.vascn.2013.04.004. Epub 2013 Apr 25.


Chaste: an open source C++ library for computational physiology and biology.

Mirams GR, Arthurs CJ, Bernabeu MO, Bordas R, Cooper J, Corrias A, Davit Y, Dunn SJ, Fletcher AG, Harvey DG, Marsh ME, Osborne JM, Pathmanathan P, Pitt-Francis J, Southern J, Zemzemi N, Gavaghan DJ.

PLoS Comput Biol. 2013;9(3):e1002970. doi: 10.1371/journal.pcbi.1002970. Epub 2013 Mar 14.


Access to enhanced differences in Marcus-Hush and Butler-Volmer electron transfer theories by systematic analysis of higher order AC harmonics.

Stevenson GP, Baker RE, Kennedy GF, Bond AM, Gavaghan DJ, Gillow K.

Phys Chem Chem Phys. 2013 Feb 14;15(6):2210-21. doi: 10.1039/c2cp43193a. Epub 2012 Dec 10.


Computational modelling of cardiac electrophysiology: explanation of the variability of results from different numerical solvers.

Pathmanathan P, Bernabeu MO, Niederer SA, Gavaghan DJ, Kay D.

Int J Numer Method Biomed Eng. 2012 Aug;28(8):890-903. doi: 10.1002/cnm.2467. Epub 2012 Feb 28.


A two-dimensional model of the colonic crypt accounting for the role of the basement membrane and pericryptal fibroblast sheath.

Dunn SJ, Appleton PL, Nelson SA, Näthke IS, Gavaghan DJ, Osborne JM.

PLoS Comput Biol. 2012;8(5):e1002515. doi: 10.1371/journal.pcbi.1002515. Epub 2012 May 24.


Theoretical analysis of the two-electron transfer reaction and experimental studies with surface-confined cytochrome c peroxidase using large-amplitude Fourier transformed AC voltammetry.

Stevenson GP, Lee CY, Kennedy GF, Parkin A, Baker RE, Gillow K, Armstrong FA, Gavaghan DJ, Bond AM.

Langmuir. 2012 Jun 26;28(25):9864-77. doi: 10.1021/la205037e. Epub 2012 Jun 14.


Modelling tissue electrophysiology with multiple cell types: applications of the extended bidomain framework.

Corrias A, Pathmanathan P, Gavaghan DJ, Buist ML.

Integr Biol (Camb). 2012 Feb;4(2):192-201. doi: 10.1039/c2ib00100d. Epub 2012 Jan 5.


Modelling the role of the basement membrane beneath a growing epithelial monolayer.

Dunn SJ, Fletcher AG, Chapman SJ, Gavaghan DJ, Osborne JM.

J Theor Biol. 2012 Apr 7;298:82-91. doi: 10.1016/j.jtbi.2011.12.013. Epub 2011 Dec 22.


Leveraging e-Science infrastructure for electrochemical research.

Peachey T, Mashkina E, Lee CY, Enticott C, Abramson D, Bond AM, Elton D, Gavaghan DJ, Stevenson GP, Kennedy GF.

Philos Trans A Math Phys Eng Sci. 2011 Aug 28;369(1949):3336-52. doi: 10.1098/rsta.2011.0146.


The role of photon scattering in voltage-calcium fluorescent recordings of ventricular fibrillation.

Bishop MJ, Rowley A, Rodriguez B, Plank G, Gavaghan DJ, Bub G.

Biophys J. 2011 Jul 20;101(2):307-18. doi: 10.1016/j.bpj.2011.06.012.


Simulation of multiple ion channel block provides improved early prediction of compounds' clinical torsadogenic risk.

Mirams GR, Cui Y, Sher A, Fink M, Cooper J, Heath BM, McMahon NC, Gavaghan DJ, Noble D.

Cardiovasc Res. 2011 Jul 1;91(1):53-61. doi: 10.1093/cvr/cvr044. Epub 2011 Feb 7.


A global sensitivity tool for cardiac cell modeling: Application to ionic current balance and hypertrophic signaling.

Sher AA, Cooling MT, Bethwaite B, Tan J, Peachey T, Enticott C, Garic S, Gavaghan DJ, Noble D, Abramson D, Crampin EJ.

Conf Proc IEEE Eng Med Biol Soc. 2010;2010:1498-502. doi: 10.1109/IEMBS.2010.5626841.


A numerical guide to the solution of the bi-domain equations of cardiac electrophysiology.

Pathmanathan P, Bernabeu MO, Bordas R, Cooper J, Garny A, Pitt-Francis JM, Whiteley JP, Gavaghan DJ.

Prog Biophys Mol Biol. 2010 Jun-Jul;102(2-3):136-55. doi: 10.1016/j.pbiomolbio.2010.05.006. Epub 2010 May 27. Review.


Development of an anatomically detailed MRI-derived rabbit ventricular model and assessment of its impact on simulations of electrophysiological function.

Bishop MJ, Plank G, Burton RA, Schneider JE, Gavaghan DJ, Grau V, Kohl P.

Am J Physiol Heart Circ Physiol. 2010 Feb;298(2):H699-718. doi: 10.1152/ajpheart.00606.2009. Epub 2009 Nov 20.


An integrative computational model for intestinal tissue renewal.

van Leeuwen IM, Mirams GR, Walter A, Fletcher A, Murray P, Osborne J, Varma S, Young SJ, Cooper J, Doyle B, Pitt-Francis J, Momtahan L, Pathmanathan P, Whiteley JP, Chapman SJ, Gavaghan DJ, Jensen OE, King JR, Maini PK, Waters SL, Byrne HM.

Cell Prolif. 2009 Oct;42(5):617-36. doi: 10.1111/j.1365-2184.2009.00627.x. Epub 2009 Jul 20.


CHASTE: incorporating a novel multi-scale spatial and temporal algorithm into a large-scale open source library.

Bernabeu MO, Bordas R, Pathmanathan P, Pitt-Francis J, Cooper J, Garny A, Gavaghan DJ, Rodriguez B, Southern JA, Whiteley JP.

Philos Trans A Math Phys Eng Sci. 2009 May 28;367(1895):1907-30. doi: 10.1098/rsta.2008.0309.


Predicting tumor location by modeling the deformation of the breast.

Pathmanathan P, Gavaghan DJ, Whiteley JP, Chapman SJ, Brady JM.

IEEE Trans Biomed Eng. 2008 Oct;55(10):2471-80. doi: 10.1109/TBME.2008.925714.


Chaste: using agile programming techniques to develop computational biology software.

Pitt-Francis J, Bernabeu MO, Cooper J, Garny A, Momtahan L, Osborne J, Pathmanathan P, Rodriguez B, Whiteley JP, Gavaghan DJ.

Philos Trans A Math Phys Eng Sci. 2008 Sep 13;366(1878):3111-36. doi: 10.1098/rsta.2008.0096.


Photon scattering effects in optical mapping of propagation and arrhythmogenesis in the heart.

Bishop MJ, Gavaghan DJ, Trayanova NA, Rodriguez B.

J Electrocardiol. 2007 Nov-Dec;40(6 Suppl):S75-80. Review.

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