Chaste - Cancer Heart And Soft Tissue Environment - main public repository.

Spheroid models of morphogenesis for the GPU.

vertex model implementation to simulate biological tissue in 3D

"Scutoids are a geometrical solution to three-dimensional packing of epithelia" - https://www.nature.com/articles/s41467-018-05376-1.

Deep Learning Based Models for Preimplantation Mouse and Human Development

vertex model for simulating two-dimensional epithelial tissues

Matlab scripts to recreate figures of the JR Soc Interface article "Model reduction enables Turing instability analysis of large reaction-diffusion models"

Ontology of human developmental anatomy

Python code to model the syncytial development of a cricket in 3D. Additional Mathematica Code for rendering mesh2 objects in povray.

Analysis scripts for the Ebbing et manuscript: "Spatially-resolved transcriptomics in C. elegans identifies sex-specific differences in gene expression patterns"

Custom codes for Flysta3D paper.

Analysis scripts for the Vertesy 2018 paper: "Parental haplotype specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells"

"Theoretical tool bridging cell polarities with development of robust morphologies" published in eLife (2018)

R scripts for analyzing Edar and Xedar gene expression data in mouse and rat tail development

Expression of Wnt signaling components in the brachiopod Terebratalia transversa

"Cluster Assembly Dynamics Drive Fidelity of Planar Cell Polarity Polarization" published in bioRxiv (2025)

"Transcriptional Heterogeneity and Cell Cycle Regulation as Central Determinants of Primitive Endoderm Priming" published in eLife (2022)

deep-learning for metadata extraction from the C. elegans embryo