Implementing measurement error models with mechanistic mathematical models in a likelihood-based framework for estimation, identifiability analysis and prediction …

RJ Murphy, OJ Maclaren… - Journal of the Royal …, 2024 - royalsocietypublishing.org
Throughout the life sciences, we routinely seek to interpret measurements and observations
using parametrized mechanistic mathematical models. A fundamental and often overlooked …

Sigmoidal curves reflect impacts and dynamics of aquatic invasive species

I Soto, DA Ahmed, P Balzani, RN Cuthbert… - Science of the Total …, 2023 - Elsevier
Identifying general patterns and trends underlying the impacts and dynamics of biological
invasions has proven elusive for scientists. Recently, the impact curve was proposed as a …

Parameter estimation and uncertainty quantification using information geometry

JA Sharp, AP Browning, K Burrage… - Journal of the Royal …, 2022 - royalsocietypublishing.org
In this work, we:(i) review likelihood-based inference for parameter estimation and the
construction of confidence regions; and (ii) explore the use of techniques from information …

[HTML][HTML] Modelling count data with partial differential equation models in biology

MJ Simpson, RJ Murphy, OJ Maclaren - Journal of Theoretical Biology, 2024 - Elsevier
Partial differential equation (PDE) models are often used to study biological phenomena
involving movement-birth–death processes, including ecological population dynamics and …

[HTML][HTML] Profile-wise analysis: a profile likelihood-based workflow for identifiability analysis, estimation, and prediction with mechanistic mathematical models

MJ Simpson, OJ Maclaren - PLoS Computational Biology, 2023 - journals.plos.org
Interpreting data using mechanistic mathematical models provides a foundation for
discovery and decision-making in all areas of science and engineering. Developing …

[HTML][HTML] The faunal Ponto-Caspianization of central and western European waterways

I Soto, RN Cuthbert, A Ricciardi, DA Ahmed… - Biological …, 2023 - Springer
As alien invasive species are a key driver of biodiversity loss, understanding patterns of
rapidly changing global species compositions depends upon knowledge of invasive species …

Computationally efficient framework for diagnosing, understanding and predicting biphasic population growth

RJ Murphy, OJ Maclaren… - Journal of the …, 2022 - royalsocietypublishing.org
Throughout the life sciences, biological populations undergo multiple phases of growth,
often referred to as biphasic growth for the commonly encountered situation involving two …

Designing experimental conditions to use the Lotka–Volterra model to infer tumor cell line interaction types

H Cho, AL Lewis, KM Storey, HM Byrne - Journal of Theoretical Biology, 2023 - Elsevier
Abstract The Lotka–Volterra model is widely used to model interactions between two
species. Here, we generate synthetic data mimicking competitive, mutualistic and …

[HTML][HTML] Geometric analysis enables biological insight from complex non-identifiable models using simple surrogates

AP Browning, MJ Simpson - PLoS Computational Biology, 2023 - journals.plos.org
An enduring challenge in computational biology is to balance data quality and quantity with
model complexity. Tools such as identifiability analysis and information criterion have been …

Parameter identifiability and model selection for partial differential equation models of cell invasion

Y Liu, K Suh, PK Maini, DJ Cohen… - Journal of the Royal …, 2024 - royalsocietypublishing.org
When employing mechanistic models to study biological phenomena, practical parameter
identifiability is important for making accurate predictions across wide ranges of unseen …