Heber Lima da Rocha

UQ-PhysiCell: An extensible Python framework for uncertainty quantification and model analysis in PhysiCell

UQ-PhysiCell provides a Python framework for uncertainty quantification, calibration, and model analysis in PhysiCell simulations, enabling scalable and reproducible uncertainty-aware analysis of agent-based models.

Quantitative Calibration of a Spatial QSP Model Identifies Fibroblast Impact on HCC Immunotherapy

The paper calibrates a spatial QSP model using CODEX data to predict TME states and identify biomarkers for HCC immunotherapy response.

Tumor-immune trajectory context connects static tissue architecture to clinical outcomes

This paper introduces a trajectory-centric framework to model dynamic tumor-immune interactions, showing that treatment-phase TME states predict immunotherapy response better than pre-treatment states.

Drug-loaded nanoparticles for cancer therapy: a high-throughput multicellular agent-based modeling study

This study develops a multicellular agent-based model to simulate nanoparticle interactions in cancer therapy and evaluates how pharmacokinetic parameters and therapeutic strategies affect tumor dynamics.

PhysiGym: bridging the gap between the Gymnasium reinforcement learning application interface and the PhysiCell agent-based model software

PhysiGym integrates PhysiCell with Gymnasium to enable reinforcement learning control of in silico biological processes, demonstrating tumor elimination in a case study.

Digitize your Biology! Modeling multicellular systems through interpretable cell behavior

The paper introduces a framework for mathematical modeling of multicellular systems using interpretable cell behavior rules derived from biological knowledge and multi-omics data.

A multiscale model of immune surveillance in micrometastases: towards cancer patient digital twins

The paper develops a multiscale mathematical model of immune surveillance in micrometastases to simulate patient trajectories and identify key parameters affecting immunosurveillance outcomes.

PhysiCell Studio: a graphical tool to make agent-based modeling more accessible

PhysiCell Studio is a graphical tool that simplifies the creation and editing of multicellular models by providing a user-friendly interface for XML-based model definition.