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For: Lei CL, Ghosh S, Whittaker DG, Aboelkassem Y, Beattie KA, Cantwell CD, Delhaas T, Houston C, Novaes GM, Panfilov AV, Pathmanathan P, Riabiz M, dos Santos RW, Walmsley J, Worden K, Mirams GR, Wilkinson RD. Considering discrepancy when calibrating a mechanistic electrophysiology model. Philos Trans A Math Phys Eng Sci 2020;378:20190349. [PMID: 32448065 PMCID: PMC7287333 DOI: 10.1098/rsta.2019.0349] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/21/2020] [Indexed: 05/21/2023]
Number Cited by Other Article(s)
1
Lei CL, Whittaker DG, Mirams GR. The impact of uncertainty in hERG binding mechanism on in silico predictions of drug-induced proarrhythmic risk. Br J Pharmacol 2024;181:987-1004. [PMID: 37740435 DOI: 10.1111/bph.16250] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 08/23/2023] [Accepted: 08/28/2023] [Indexed: 09/24/2023]  Open
2
Saghafi S, Rumbell T, Gurev V, Kozloski J, Tamagnini F, Wedgwood KCA, Diekman CO. Inferring Parameters of Pyramidal Neuron Excitability in Mouse Models of Alzheimer's Disease Using Biophysical Modeling and Deep Learning. Bull Math Biol 2024;86:46. [PMID: 38528167 PMCID: PMC10963524 DOI: 10.1007/s11538-024-01273-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 02/19/2024] [Indexed: 03/27/2024]
3
Murphy RJ, Maclaren OJ, Simpson MJ. Implementing measurement error models with mechanistic mathematical models in a likelihood-based framework for estimation, identifiability analysis and prediction in the life sciences. J R Soc Interface 2024;21:20230402. [PMID: 38290560 PMCID: PMC10827430 DOI: 10.1098/rsif.2023.0402] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/03/2024] [Indexed: 02/01/2024]  Open
4
Shuttleworth JG, Lei CL, Whittaker DG, Windley MJ, Hill AP, Preston SP, Mirams GR. Empirical Quantification of Predictive Uncertainty Due to Model Discrepancy by Training with an Ensemble of Experimental Designs: An Application to Ion Channel Kinetics. Bull Math Biol 2023;86:2. [PMID: 37999811 PMCID: PMC10673765 DOI: 10.1007/s11538-023-01224-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 10/09/2023] [Indexed: 11/25/2023]
5
Colebank MJ, Taylor R, Hacker TA, Chesler NC. Biventricular Interaction During Acute Left Ventricular Ischemia in Mice: A Combined In-Vivo and In-Silico Approach. Ann Biomed Eng 2023;51:2528-2543. [PMID: 37453977 PMCID: PMC10598180 DOI: 10.1007/s10439-023-03293-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 06/17/2023] [Indexed: 07/18/2023]
6
Lei CL, Clerx M, Gavaghan DJ, Mirams GR. Model-driven optimal experimental design for calibrating cardiac electrophysiology models. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2023;240:107690. [PMID: 37478675 DOI: 10.1016/j.cmpb.2023.107690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/09/2023] [Accepted: 06/22/2023] [Indexed: 07/23/2023]
7
Farm HJ, Clerx M, Cooper F, Polonchuk L, Wang K, Gavaghan DJ, Lei CL. Importance of modelling hERG binding in predicting drug-induced action potential prolongations for drug safety assessment. Front Pharmacol 2023;14:1110555. [PMID: 37021055 PMCID: PMC10067903 DOI: 10.3389/fphar.2023.1110555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/22/2023] [Indexed: 03/30/2023]  Open
8
Lambert B, Lei CL, Robinson M, Clerx M, Creswell R, Ghosh S, Tavener S, Gavaghan DJ. Autocorrelated measurement processes and inference for ordinary differential equation models of biological systems. J R Soc Interface 2023. [PMCID: PMC9943878 DOI: 10.1098/rsif.2022.0725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]  Open
9
Corrado C, Roney CH, Razeghi O, Lemus JAS, Coveney S, Sim I, Williams SE, O'Neill MD, Wilkinson RD, Clayton RH, Niederer SA. Quantifying the impact of shape uncertainty on predicted arrhythmias. Comput Biol Med 2023;153:106528. [PMID: 36634600 DOI: 10.1016/j.compbiomed.2022.106528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/15/2022] [Accepted: 12/31/2022] [Indexed: 01/11/2023]
10
Şengül Ayan S, Süleymanoğlu S, Özdoğan H. A pilot study of ion current estimation by ANN from action potential waveforms. J Biol Phys 2022;48:461-475. [PMID: 36372807 PMCID: PMC9727005 DOI: 10.1007/s10867-022-09619-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/28/2022] [Indexed: 11/15/2022]  Open
11
Whittaker DG, Wang J, Shuttleworth JG, Venkateshappa R, Kemp JM, Claydon TW, Mirams GR. Ion channel model reduction using manifold boundaries. JOURNAL OF THE ROYAL SOCIETY, INTERFACE 2022;19:20220193. [PMID: 35946166 PMCID: PMC9363999 DOI: 10.1098/rsif.2022.0193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
12
Simpson MJ, Baker RE, Buenzli PR, Nicholson R, Maclaren OJ. Reliable and efficient parameter estimation using approximate continuum limit descriptions of stochastic models. J Theor Biol 2022;549:111201. [PMID: 35752285 DOI: 10.1016/j.jtbi.2022.111201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 11/28/2022]
13
Xavier CR, Oliveira RS, Vieira VDF, Rocha BM, Reis RF, Quintela BDM, Lobosco M, Santos RWD. Timing the race of vaccination, new variants, and relaxing restrictions during COVID-19 pandemic. JOURNAL OF COMPUTATIONAL SCIENCE 2022;61:101660. [PMID: 35432632 PMCID: PMC8990534 DOI: 10.1016/j.jocs.2022.101660] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 03/20/2022] [Accepted: 03/30/2022] [Indexed: 05/07/2023]
14
Ribeiro Xavier C, Sachetto Oliveira R, da Fonseca Vieira V, Lobosco M, Weber dos Santos R. Characterisation of Omicron Variant during COVID-19 Pandemic and the Impact of Vaccination, Transmission Rate, Mortality, and Reinfection in South Africa, Germany, and Brazil. BIOTECH 2022;11:biotech11020012. [PMID: 35822785 PMCID: PMC9264399 DOI: 10.3390/biotech11020012] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/21/2022] [Accepted: 04/21/2022] [Indexed: 02/05/2023]  Open
15
Accurate in silico simulation of the rabbit Purkinje fiber electrophysiological assay to facilitate early pharmaceutical cardiosafety assessment: Dream or reality? J Pharmacol Toxicol Methods 2022;115:107172. [DOI: 10.1016/j.vascn.2022.107172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/31/2022] [Accepted: 04/08/2022] [Indexed: 11/24/2022]
16
Sher A, Niederer SA, Mirams GR, Kirpichnikova A, Allen R, Pathmanathan P, Gavaghan DJ, van der Graaf PH, Noble D. A Quantitative Systems Pharmacology Perspective on the Importance of Parameter Identifiability. Bull Math Biol 2022;84:39. [PMID: 35132487 PMCID: PMC8821410 DOI: 10.1007/s11538-021-00982-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 11/30/2021] [Indexed: 12/31/2022]
17
Rao P, Peyron Q, Burgner-Kahrs J. Shape Representation and Modeling of Tendon-Driven Continuum Robots Using Euler Arc Splines. IEEE Robot Autom Lett 2022. [DOI: 10.1109/lra.2022.3185377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
18
van Osta N, Kirkels FP, van Loon T, Koopsen T, Lyon A, Meiburg R, Huberts W, Cramer MJ, Delhaas T, Haugaa KH, Teske AJ, Lumens J. Uncertainty Quantification of Regional Cardiac Tissue Properties in Arrhythmogenic Cardiomyopathy Using Adaptive Multiple Importance Sampling. Front Physiol 2021;12:738926. [PMID: 34658923 PMCID: PMC8514656 DOI: 10.3389/fphys.2021.738926] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022]  Open
19
Lei CL, Mirams GR. Neural Network Differential Equations For Ion Channel Modelling. Front Physiol 2021;12:708944. [PMID: 34421652 PMCID: PMC8371386 DOI: 10.3389/fphys.2021.708944] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/05/2021] [Indexed: 11/13/2022]  Open
20
Stage HB, Shingleton J, Ghosh S, Scarabel F, Pellis L, Finnie T. Shut and re-open: the role of schools in the spread of COVID-19 in Europe. Philos Trans R Soc Lond B Biol Sci 2021;376:20200277. [PMID: 34053270 PMCID: PMC8165592 DOI: 10.1098/rstb.2020.0277] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2020] [Indexed: 12/21/2022]  Open
21
Pagani S, Manzoni A. Enabling forward uncertainty quantification and sensitivity analysis in cardiac electrophysiology by reduced order modeling and machine learning. INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING 2021;37:e3450. [PMID: 33599106 PMCID: PMC8244126 DOI: 10.1002/cnm.3450] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 06/12/2023]
22
Reis RF, Oliveira RS, Quintela BDM, Campos JDO, Gomes JM, Rocha BM, Lobosco M, Dos Santos RW. The Quixotic Task of Forecasting Peaks of COVID-19: Rather Focus on Forward and Backward Projections. Front Public Health 2021;9:623521. [PMID: 33796495 PMCID: PMC8007858 DOI: 10.3389/fpubh.2021.623521] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/10/2021] [Indexed: 12/23/2022]  Open
23
McCabe KJ, Rangamani P. Computational modeling approaches to cAMP/PKA signaling in cardiomyocytes. J Mol Cell Cardiol 2021;154:32-40. [PMID: 33548239 DOI: 10.1016/j.yjmcc.2021.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/11/2021] [Accepted: 01/15/2021] [Indexed: 12/12/2022]
24
Paun LM, Husmeier D. Markov chain Monte Carlo with Gaussian processes for fast parameter estimation and uncertainty quantification in a 1D fluid-dynamics model of the pulmonary circulation. INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING 2021;37:e3421. [PMID: 33249755 PMCID: PMC7901000 DOI: 10.1002/cnm.3421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 11/07/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
25
Cai L, Ren L, Wang Y, Xie W, Zhu G, Gao H. Surrogate models based on machine learning methods for parameter estimation of left ventricular myocardium. ROYAL SOCIETY OPEN SCIENCE 2021;8:201121. [PMID: 33614068 PMCID: PMC7890479 DOI: 10.1098/rsos.201121] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/15/2020] [Indexed: 05/12/2023]
26
Paun LM, Colebank MJ, Olufsen MS, Hill NA, Husmeier D. Assessing model mismatch and model selection in a Bayesian uncertainty quantification analysis of a fluid-dynamics model of pulmonary blood circulation. J R Soc Interface 2020;17:20200886. [PMID: 33353505 PMCID: PMC7811590 DOI: 10.1098/rsif.2020.0886] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
27
Pathmanathan P, Galappaththige SK, Cordeiro JM, Kaboudian A, Fenton FH, Gray RA. Data-Driven Uncertainty Quantification for Cardiac Electrophysiological Models: Impact of Physiological Variability on Action Potential and Spiral Wave Dynamics. Front Physiol 2020;11:585400. [PMID: 33329034 PMCID: PMC7711195 DOI: 10.3389/fphys.2020.585400] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/20/2020] [Indexed: 12/23/2022]  Open
28
Fresca S, Manzoni A, Dedè L, Quarteroni A. Deep learning-based reduced order models in cardiac electrophysiology. PLoS One 2020;15:e0239416. [PMID: 33002014 PMCID: PMC7529269 DOI: 10.1371/journal.pone.0239416] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/06/2020] [Indexed: 01/06/2023]  Open
29
Lawson BAJ, Oliveira RS, Berg LA, Silva PAA, Burrage K, dos Santos RW. Variability in electrophysiological properties and conducting obstacles controls re-entry risk in heterogeneous ischaemic tissue. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020;378:20190341. [PMID: 32448068 PMCID: PMC7287337 DOI: 10.1098/rsta.2019.0341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
30
Clayton RH, Aboelkassem Y, Cantwell CD, Corrado C, Delhaas T, Huberts W, Lei CL, Ni H, Panfilov AV, Roney C, dos Santos RW. An audit of uncertainty in multi-scale cardiac electrophysiology models. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020;378:20190335. [PMID: 32448070 PMCID: PMC7287340 DOI: 10.1098/rsta.2019.0335] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/16/2020] [Indexed: 05/21/2023]
31
Lei CL, Clerx M, Whittaker DG, Gavaghan DJ, de Boer TP, Mirams GR. Accounting for variability in ion current recordings using a mathematical model of artefacts in voltage-clamp experiments. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020;378:20190348. [PMID: 32448060 PMCID: PMC7287334 DOI: 10.1098/rsta.2019.0348] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/08/2020] [Indexed: 05/21/2023]
32
Mirams GR, Niederer SA, Clayton RH. The fickle heart: uncertainty quantification in cardiac and cardiovascular modelling and simulation. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020;378:20200119. [PMID: 32448073 PMCID: PMC7287327 DOI: 10.1098/rsta.2020.0119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
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