• L E Wadkin, J Holden, R Ettelaie, M J Holmes, J Smith, A Golightly, N G Parker, A Baggaley. Estimating the reproduction number, R0, from individual-based models of tree disease spread. Ecological Modelling. 489 110630 (2024).

We explore three different methods of estimating the reproduction number from an agent-based model of tree disease spread.

• L E Wadkin, I Makarenko, N G Parker, A Shukurov, F C Figueiredo, M Lako. Human stem cells for ophthalmology: recent advances in diagnostic image analysis and computational modelling. Current Stem Cell Reports. 9, pg 57-66 (2023)

We explore the advances and future research directions in image analysis and computational modelling of human stem cells (hSCs) for ophthalmological applications.

• A Golightly, L. E. Wadkin, S. Whitaker, A W Baggaley, N G Parker and Theodore Kypraios. Accelerating Bayesian inference for stochastic epidemic models using incidence data. Statistics and Computing. 33, 134 (2023).

We consider two approaches for marginalising over the latent process in performing inference for stochastic epidemic compartment models using incomplete time course data.

• L E Wadkin, A Golightly, J Branson, A Hoppit, N G Parker, and A W Baggaley. Quantifying invasive pest dynamics through inference of a two-node epidemic network model. Diversity. 15(4), 496 (2023).

We show the applicability of a two-node epidemic network model to describing invasive pest dynamics using the case study of the oak processionary moth.

• L E Wadkin, J Branson, A Hoppit, N G Parker, A Golightly and A W Baggaley.  Inference for epidemic models with time varying infection rates: tracking the dynamics of oak processionary moth in the UK. Ecol. Evol. 12, e8871 (2022).

Using an advanced Bayesian inference scheme we estimate the parameters for a stochastic compartmental SIR model with a time varying infection rate to describe the spread of pests.

• L E Wadkin, S Orozco-Fuentes, I Neganova, M Lako, N G Parker and A Shukurov. A mathematical modelling framework for the regulation of intra-cellular OCT4 in human pluripotent stem cells.  PLoS ONE 16.8 (2021).

An application of fractional Brownian motion and the stochastic logistic equation to describe temporal properties of the pluripotency transcription factor OCT4. 

• L E Wadkin, S Orozco-Fuentes, I Neganova, M Lako, R A Barrio, A W Baggaley, N G Parker and A Shukurov. OCT4 expression in human embryonic stem cells: spatio-temporal dynamics and fate transitions.  Physical Biology 18.2 (2021).

An analysis of the temporal behaviour of the pluripotency transcription factor OCT4, quantifying its intra-cellular self-regulation and fluctuations. The quantitative framework provides a basis for experimental comparison and developments of mathematical models. 

• L E Wadkin, S Orozco-Fuentes, I Neganova, M Lako, N G Parker and A Shukurov. An introduction to the mathematical modelling of iPSCs. Chapter 5 of Elsevier “Recent Advances in iPSC Technology”  (2021).

A chapter conveying the importance and usefulness of mathematical modelling as a tool to achieve a deeper understanding of stem cell biology, introducing key mathematical concepts (random walk theory, differential equations and agent-based modelling) for non-mathematical readers.

• L E Wadkin, S Orozco-Fuentes, I Neganova, M Lako, A Shukurov and N G Parker. The recent advances in the mathematical modelling of human pluripotent stem cells. Springer Nature Applied Sciences 2, 276 (2020).

A review of the recent developments in the mathematical modelling of the key behaviours of pluripotent stem cells, suitable for both biologists and mathematicians. 

• L E Wadkin, S Orozco-Fuentes, I Neganova, S Bojic, A Laude, M Lako, N G Parker, and A Shukurov. Seeding hESCs to achieve optimal colony clonality. Scientific Reports 9, 15299 (2019).

A stochastic exponential growth model for colony formation is developed based on experimental data. The model is a diagnostic tool for biologists to predict the time of clonality loss at varying seeding densities. 

• S Orozco-Fuentes, I Neganova, L E Wadkin, A W Baggaley, R A Barrio, M Lako, A Shukurov, and N G Parker. Quantification of the morphological characteristics of hESC colonies. Scientific Reports 9, 17569 (2019).

The morphological characteristics of hESC colonies are quantified to develop a colony characteristics database. Self-organisation of colonies is observed and quantified. 

• L E Wadkin, S Orozco-Fuentes, I Neganova, G Swan, A Laude, M Lako, A Shukurov, and N G Parker. Correlated random walks of human embryonic stem cells in vitro. Physical Biology 15.5 (2018).

Important parameters of the movement of single and pairs of cells, such as velocities, diffusivity and correlation times are extracted from analysis of experimental data.

• L E Wadkin, L F Elliot, I Neganova, N G Parker, V Chichagova, G Swan, A Laude, M Lako, and A Shukurov. Dynamics of single human embryonic stem cells and their pairs: a quantitative analysis. Scientific Reports 7, 570 (2017).

The individual motions of single and pairs of cells from experimental data are analysed. The correlated random walks and super-diffusive behaviour of cells is presented.