184 citations · 704 across the 38 of their papers we have counts for
12 papers · 1 filter
Detecting Temporal shape changes with the Euler Characteristic Transform
Lewis Marsh, Felix Y. Zhou, Xiao Qin +3
Organoids are multi-cellular structures which are cultured in vitro from stem cells to resemble specific organs (e.g., brain, liver) in their three-dimensional composition. Dynamic…
Multiscale methods for signal selection in single-cell data
Renee S. Hoekzema, Lewis Marsh, Otto Sumray +4
Analysis of single-cell transcriptomics often relies on clustering cells and then performing differential gene expression (DGE) to identify genes that vary between these clusters.…
Structural features of microvascular networks trigger blood-flow oscillations
Yaron Ben-Ami, George W. Atkinson, Joe M. Pitt-Francis +2
We analyse mathematical models in order to understand how microstructural features of vascular networks may affect blood-flow dynamics, and to identify particular characteristics t…
Statistical and Topological Summaries Aid Disease Detection for Segmented Retinal Vascular Images
John T. Nardini, Charles W. J. Pugh, Helen M. Byrne
Disease complications can alter vascular network morphology and disrupt tissue functioning. Diabetic retinopathy, for example, is a complication of types 1 and 2 diabetes mellitus…
A method to coarse-grain multi-agent stochastic systems with regions of multistability
Daria Stepanova, Helen M. Byrne, Philip K. Maini +1
Hybrid multiscale modelling has emerged as a useful framework for modelling complex biological phenomena. However, when accounting for stochasticity in the internal dynamics of age…
Topological data analysis distinguishes parameter regimes in the Anderson-Chaplain model of angiogenesis
John T. Nardini, Bernadette J. Stolz, Kevin B. Flores +2
Angiogenesis is the process by which blood vessels form from pre-existing vessels. It plays a key role in many biological processes, including embryonic development and wound heali…
Multiscale Topology Characterises Dynamic Tumour Vascular Networks
Bernadette J. Stolz, Jakob Kaeppler, Bostjan Markelc +5
Advances in imaging techniques enable high resolution 3D visualisation of vascular networks over time and reveal abnormal structural features such as twists and loops, and their qu…
Topological Methods for Characterising Spatial Networks: A Case Study in Tumour Vasculature
Helen M Byrne, Heather A Harrington, Ruth Muschel +3
Understanding how the spatial structure of blood vessel networks relates to their function in healthy and abnormal biological tissues could improve diagnosis and treatment for dise…
Local migration quantification method for scratch assays
Ana Victoria Ponce Bobadilla, Jazmine Arévalo, Eduard Sarró +6
Motivation: The scratch assay is a standard experimental protocol used to characterize cell migration. It can be used to identify genes that regulate migration and evaluate the eff…
3D hybrid modeling of vascular network formation
Holger Perfahl, Barry D Hughes, Tomas Alaracon +4
We develop an agent-based model of vasculogenesis, the de novo formation of blood vessels. Endothelial cells in the vessel network are viewed as linearly elastic spheres and are of…
Mathematical and Statistical Techniques for Systems Medicine: The Wnt Signaling Pathway as a Case Study
Adam L. MacLean, Heather A. Harrington, Michael P. H. Stumpf +1
The last decade has seen an explosion in models that describe phenomena in systems medicine. Such models are especially useful for studying signaling pathways, such as the Wnt path…
Parameter-free methods distinguish Wnt pathway models and guide design of experiments
Adam L. MacLean, Zvi Rosen, Helen M. Byrne +1
The canonical Wnt signaling pathway, mediated by -catenin, is crucially involved in development, adult stem cell tissue maintenance and a host of diseases including cancer. We u…