Nicholson T. Collier

Modeling in vitro cell-to-cell spread of hepatitis C viral infection using an agent-based approach

This paper develops an agent-based model to simulate HCV cell-to-cell spread in vitro, incorporating cell proliferation, size changes, and foci merging, and shows it fits experimental data well.

Modeling of hepatitis B virus infection spread in primary human hepatocytes

The paper models HBV infection spread in primary human hepatocytes using agent-based modeling, identifying viral kinetic patterns and estimating the efficacy of an entry inhibitor.

Multiphasic hepatitis B virus kinetic patterns in humanized chimeric mice can be explained via stochastic agent-based modeling of intracellular virion production cycles

The paper develops a stochastic agent-based model to explain multiphasic HBV kinetics in humanized mice by simulating intracellular virion production cycles.

Iterative community-driven development of a SARS-CoV-2 tissue simulator

Open-source agent-based PhysiCell model of SARS-CoV-2 infection in lung epithelium; version 5 clears virus in about 6 days in simulation, and delayed T cell arrival increases epithelial loss.

Learning-accelerated Discovery of Immune-Tumour Interactions

The paper presents a framework combining agent-based simulation and active learning to discover optimal cancer regression regions in immunotherapy models.

High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow

This paper introduces a high-throughput framework integrating PhysiCell and EMEWS to test cancer hypotheses through mechanistic simulations and optimize therapeutic strategies.