Simulation and inference algorithms for stochastic biochemical reaction networks: from basic concepts to state-of-the-art

DJ Warne, RE Baker… - Journal of the Royal …, 2019 - royalsocietypublishing.org
Stochasticity is a key characteristic of intracellular processes such as gene regulation and
chemical signalling. Therefore, characterizing stochastic effects in biochemical systems is …

Parameter identifiability and model selection for sigmoid population growth models

MJ Simpson, AP Browning, DJ Warne… - Journal of theoretical …, 2022 - Elsevier
Sigmoid growth models, such as the logistic, Gompertz and Richards' models, are widely
used to study population dynamics ranging from microscopic populations of cancer cells, to …

Using experimental data and information criteria to guide model selection for reaction–diffusion problems in mathematical biology

DJ Warne, RE Baker, MJ Simpson - Bulletin of Mathematical Biology, 2019 - Springer
Reaction–diffusion models describing the movement, reproduction and death of individuals
within a population are key mathematical modelling tools with widespread applications in …

Inferring parameters for a lattice-free model of cell migration and proliferation using experimental data

AP Browning, SW McCue, RN Binny, MJ Plank… - Journal of Theoretical …, 2018 - Elsevier
Collective cell spreading takes place in spatially continuous environments, yet it is often
modelled using discrete lattice-based approaches. Here, we use data from a series of cell …

Reliable and efficient parameter estimation using approximate continuum limit descriptions of stochastic models

MJ Simpson, RE Baker, PR Buenzli… - Journal of Theoretical …, 2022 - Elsevier
Stochastic individual-based mathematical models are attractive for modelling biological
phenomena because they naturally capture the stochasticity and variability that is often …

A Bayesian sequential learning framework to parameterise continuum models of melanoma invasion into human skin

AP Browning, P Haridas, MJ Simpson - Bulletin of Mathematical Biology, 2019 - Springer
We present a novel framework to parameterise a mathematical model of cell invasion that
describes how a population of melanoma cells invades into human skin tissue. Using simple …

Invading and receding sharp-fronted travelling waves

M El-Hachem, SW McCue, MJ Simpson - Bulletin of Mathematical Biology, 2021 - Springer
Biological invasion, whereby populations of motile and proliferative individuals lead to
moving fronts that invade vacant regions, is routinely studied using partial differential …

Optimal quantification of contact inhibition in cell populations

DJ Warne, RE Baker, MJ Simpson - Biophysical Journal, 2017 - cell.com
Contact inhibition refers to a reduction in the rate of cell migration and/or cell proliferation in
regions of high cell density. Under normal conditions, contact inhibition is associated with …

Unpacking the Allee effect: determining individual-level mechanisms that drive global population dynamics

NT Fadai, ST Johnston… - Proceedings of the …, 2020 - royalsocietypublishing.org
We present a solid theoretical foundation for interpreting the origin of Allee effects by
providing the missing link in understanding how local individual-based mechanisms …

Pair correlation functions for identifying spatial correlation in discrete domains

E Gavagnin, JP Owen, CA Yates - Physical Review E, 2018 - APS
Identifying and quantifying spatial correlation are important aspects of studying the collective
behavior of multiagent systems. Pair correlation functions (PCFs) are powerful statistical …