Posts by Collection

preprints

A nonlinear and time-dependent leak current in the presence of calcium fluoride patch-clamp seal enhancer

Published in Wellcome Open Research, 2020

This paper studies a nonlinear-in-voltage and time-dependent leak current due to the effect of a commonly-used seal enhancer in patch-clamping.

Recommended citation: Lei, C.L., Fabbri, A., Whittaker, D.G., et al. (2020). "A nonlinear and time-dependent leak current in the presence of calcium fluoride patch-clamp seal enhancer." Wellcome Open Research, 5:152. https://doi.org/10.12688/wellcomeopenres.15968.1

publications

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

Published in Frontiers in Physiology, 2017

This paper shows that tailoring a mathematical model of hiPSC-CMs to a specific cell line, even using limited data and a relatively simple approach, leads to improved predictions of baseline behavior and response to drugs.

Recommended citation: Lei, C.L., Wang, K., Clerx, M., Johnstone, R.H., et al. (2017). "Tailoring Mathematical Models to Stem-Cell Derived Cardiomyocyte Lines Can Improve Predictions of Drug-Induced Changes to Their Electrophysiology." Frontiers in Physiology, 8, 986. https://doi.org/10.3389/fphys.2017.00986

Probabilistic Inference on Noisy Time Series (PINTS)

Published in Journal of Open Research Software, 2019

This paper introduces our open-source Python library, PINTS, that provides researchers with a broad suite of non-linear optimisation and sampling methods.

Recommended citation: Clerx, M., Robinson, M., Lambert, B., Lei, C.L., et al. (2019). "Probabilistic Inference on Noisy Time Series (PINTS)." Journal of Open Research Software, 7(1), p.23. https://doi.org/10.5334/jors.252

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

Published in Biophysical Journal, 2019

This paper presents a method for high-throughput characterization of hERG potassium channel kinetics via fitting a mathematical model to results of over 100 single-cell patch-clamp measurements collected simultaneously on an automated voltage-clamp platform.

Recommended citation: Lei, C.L., Clerx, M., Gavaghan, D.J., et al. (2019). "Rapid Characterization of hERG Channel Kinetics I: Using an Automated High-Throughput System." Biophysical Journal, 117, 12, p.2438-2454. https://doi.org/10.1016/j.bpj.2019.07.029

Rapid Characterization of hERG Channel Kinetics II: Temperature Dependence

Published in Biophysical Journal, 2019

This paper shows that the commonly used Q10 and Eyring formulations are incapable of describing the parameters’ temperature dependence, and care is needed to avoid misleading extrapolations in their many scientific and industrial pharmaceutical applications.

Recommended citation: Lei, C.L., Clerx, M., Beattie, K.A., et al. (2019). "Rapid Characterization of hERG Channel Kinetics II: Temperature Dependence." Biophysical Journal, 117, 12, p.2455-2470. https://doi.org/10.1016/j.bpj.2019.07.030

An audit of uncertainty in multi-scale cardiac electrophysiology models

Published in Philosophical Transactions of the Royal Society A, 2020

This paper reviews the source of uncertainty in multi-scale cardiac electrophysiology models.

Recommended citation: Clayton, R.H., Aboelkassem, T., Cantwell, C.D., Corrado, C., Delhaas, T., Huberts, W., Lei, C.L., et al. (2020). "An audit of uncertainty in multi-scale cardiac electrophysiology models." Phil. Trans. R. Soc. A. 378: 20190335. https://doi.org/10.1098/rsta.2019.0335

Accounting for variability in ion current recordings using a mathematical model of artefacts in voltage-clamp experiments

Published in Philosophical Transactions of the Royal Society A, 2020

This paper studies the source of variability of the ion channel recordings by constructing a model that describes not just ion current dynamics, but the entire voltage-clamp experiment.

Recommended citation: Lei, C.L., Clerx, M., Whittaker, D.G., et al. (2020). "Accounting for variability in ion current recordings using a mathematical model of artefacts in voltage-clamp experiments." Phil. Trans. R. Soc. A. 378: 20190348. https://doi.org/10.1098/rsta.2019.0348

Considering discrepancy when calibrating a mechanistic electrophysiology model

Published in Philosophical Transactions of the Royal Society A, 2020

This paper reviews the pitfalls and methods to account for the uncertainty in the model/equations structure, and provides detailed examples with electrophysiology models.

Recommended citation: Lei, C.L., Ghosh, S., Whittaker, D.G., et al. (2020). "Considering discrepancy when calibrating a mechanistic electrophysiology model." Phil. Trans. R. Soc. A. 378: 20190349. https://doi.org/10.1098/rsta.2019.0349

talks

teaching

Mathematical Methods

Undergraduate tutorial, University of Oxford, University College, 2018

This tutorial is a part of the Mathematical Methods course for the second year Physics undergraduate degree at the University of Oxford.

Essential Mathematics

Postgraduate course, University of Oxford, Doctoral Training Centre, 2019

This course gives students a solid grounding in mathematical topics essential for the analysis of biological systems.

Research Software Engineering

Postgraduate practical session, University of Oxford, Doctoral Training Centre, 2019

This course provides the basics for research software engineering (RSE).

Scientific Computing

Postgraduate practical session, University of Oxford, Doctoral Training Centre, 2019

This course gives a solid introduction to different methods and algorithms in scientific computing with applications in biological science.