immune-response

Developed code using the Hybrid Automata Library (HAL) to create a spatial agent-based model of radio-immune response to spatially fractionated radiotherapy. This project was in association with the Cleveland Clinic Lerner Research Institute, Jacob Scott Lab.

Code and data associated with Billings et al., "High dose inactivated influenza vaccine inconsistently improves heterologous antibody responses in an elderly human cohort", JID 2025.

Code and reproducibility materials for “Phage-antibiotic therapy under density-dependent bacterial defense,” including ODE simulations, equilibrium/stability analysis, bifurcation diagrams, and figure generation scripts.

scRNA-seq analysis pipeline of mice lung immune response to House Dust Mites

Physics-informed and pure-mechanistic Universal Differential Equations (UDEs) for modeling tumor–immune dynamics. Dual Julia pipelines: Enhanced PI-NODE with residual/correction subnetworks for hybrid physics-neural learning, and Pure-Mechanistic UDE with biologically-constrained Gompertz growth and saturating immune-killing.

Created code to develop and analyze statistical graphs for the spatial radiotherapy model, which can be found at https://github.com/hannahgsimon/HALModeling2024. This project was in association with the Cleveland Clinic Lerner Research Institute, Jacob Scott Lab.