Simulation and inference algorithms for stochastic biochemical reaction networks: from basic concepts to state-of-the-art
Stochasticity is a key characteristic of intracellular processes such as gene regulation and
chemical signalling. Therefore, characterizing stochastic effects in biochemical systems is …
chemical signalling. Therefore, characterizing stochastic effects in biochemical systems is …
Parameter identifiability and model selection for sigmoid population growth models
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 …
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
Reaction–diffusion models describing the movement, reproduction and death of individuals
within a population are key mathematical modelling tools with widespread applications in …
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
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 …
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
Stochastic individual-based mathematical models are attractive for modelling biological
phenomena because they naturally capture the stochasticity and variability that is often …
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
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 …
describes how a population of melanoma cells invades into human skin tissue. Using simple …
Invading and receding sharp-fronted travelling waves
Biological invasion, whereby populations of motile and proliferative individuals lead to
moving fronts that invade vacant regions, is routinely studied using partial differential …
moving fronts that invade vacant regions, is routinely studied using partial differential …
Optimal quantification of contact inhibition in cell populations
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 …
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 …
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 …
behavior of multiagent systems. Pair correlation functions (PCFs) are powerful statistical …