T. J. Sego

Tissue Forge: Interactive Biological and Biophysics Simulation Environment

Tissue Forge provides an open-source interactive environment for simulating biological and biophysical systems across multiple scales using particle-based models.

A spatialised agent-based model of NOTCH signalling pathway in Endothelial Cells predicts emergent heterogeneity due to continual dynamic phenotypic adjustments.

The paper uses a spatialised agent-based model to show NOTCH signalling pathway dynamics in endothelial cells can generate spatial heterogeneity through oscillations and phenotypic adjustments.

Generating Agent-Based Multiscale Multicellular Spatiotemporal Models from Ordinary Differential Equations of Biological Systems, with Applications in Viral Infection

This paper develops a method to convert non-spatial ODE models into spatial, agent-based models for multicellular systems, demonstrating applications in viral infection and showing how spatial models can reveal hidden biophysical mechanisms.

A Modular Framework for Multiscale Spatial Modeling of Viral Infection and Immune Response in Epithelial Tissue

The paper introduces a modular simulation platform to model viral infection and immune response in epithelial tissue, showing that early low-dose antiviral treatment is more effective than late high-dose treatment.