Helen Mary Byrne

This paper introduces a mechanical model to simulate subcellular and tissue remodelling in epithelial monolayers, showing how deformation history affects tissue recovery.

The paper develops SPOT, a tool for analyzing 3D morpho-dynamics from 2D live-cell imaging, and applies it to organoids to identify phenotype-genotype-function relationships.

MuSpAn, a Python library of over 100 spatial methods, quantifies multiscale tissue organisation and maps cancer-associated fibroblast subtypes to distinct immune niches in mouse colorectal tumours.

This study maps spatial changes in the aging mouse thymus, revealing stromal reorganization that disrupts T cell selection and tolerance.

This paper introduces a deep attention network model to infer cell-cell interaction dynamics from trajectory data, providing interpretable insights into how interactions affect cell movement.

The paper introduces netPCF, a geometry-aware method for quantifying spatial organisation on complex biological domains, showing its utility in biological applications.

This paper develops an agent-based model to simulate vascular remodelling and its impact on tumour growth and response to radiotherapy, showing that friction forces significantly influence vessel compression and tumour regrowth.

The paper develops a universal imaging phenome using SAM features and SPOT tool, showing it outperforms deep learning models in capturing dynamic cell behaviors.

This paper develops a multiscale model to study how cell-ECM interactions affect ECM fibre alignment and cell detachment through mechanical cues.

This study shows mechanical confinement drives phenotype switching in melanoma via chromatin remodeling mediated by HMGB2.

This study develops a mathematical model to analyze how antibody-antigen interactions affect mAb potency, efficacy, and the avidity effect.

This study models tumor growth and macrophage dynamics in a multiphase system, showing how macrophage heterogeneity affects tumor progression and proposing an immunotherapeutic strategy.

This study develops a mathematical model to simulate cancer cell responses to cyclic hypoxia and shows varying cell responses based on oxygen fluctuation dynamics.

The paper develops spatial descriptors using mathematical tools to analyze cell interactions in colorectal cancer progression and demonstrates their utility in identifying disease-related pathways.

The paper develops a mathematical model of flavivirus dynamics within mosquitoes, showing that higher viral doses and multiple blood feeds shorten the extrinsic incubation period.

This paper identifies vascular features that enhance perfusion after radiotherapy and develops a computational model to explore their impact on tumour response.

This study uses topological data analysis to quantify ECM architecture and spatial patterns in lung adenocarcinoma, revealing progressive changes linked to immune exclusion and metabolic shifts.

This paper introduces a new spatial statistic, the weighted pair correlation function (wPCF), to analyze spatial and phenotypic heterogeneity in agent-based models and multiplex imaging data.

This paper introduces a multiscale model of angiogenesis that reproduces vascular network features through cell rearrangements and uses a mixing measure to quantify cell mixing as a potential biomarker for pathological angiogenesis.

This study shows radiation-resistant prostate cancer cells enhance survival and resistance of sensitive cells in spheroids through competitive and antagonistic interactions.

This study investigates how acute and chronic inflammatory cell death affects epithelial cell migration in the intestinal villi using computational models and cell-tracking methods.

This paper introduces an agent-based model of kidney branching morphogenesis and uses Bayesian inference to show that growth factor-dependent cell division is essential for branching.

The paper develops a hierarchical Bayesian framework to model spatiotemporal dynamics of intestinal epithelium proliferation and migration under different conditions, concluding a proliferation-driven model is sufficient for most time-scales.

Microvessel Chaste provides an open-source library for building and simulating 3D spatial models of vascularized tissue growth, integrating with experimental data and Python tools.