developmental-biology

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

Spheroid models of morphogenesis for the GPU.

Scientific Agent for evidence-grounded evaluation of cell-therapy products.

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.

vertex model for simulating two-dimensional epithelial tissues

Deep Learning Based Models for Preimplantation Mouse and Human Development

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

Custom codes for Flysta3D paper.

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

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

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

Modeling cell differentiation as continuous developmental flow through pseudotime instead of static clusters. Inspired by Waddington’s epigenetic landscape with interactive trajectory, branching, and uncertainty visualizations.

A python toolkit for spatial domains and spatially variable genes discovery for high-resolution spatially resolved transcriptomics data.

A collection of open sourced lectures for Dr. Michael Levin

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

"Cluster Assembly Dynamics Drive Fidelity of Planar Cell Polarity Polarization" published in Nature Communications (2026)

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