Marco Ruscone

Hck signaling drives long-distance ECM degradation through endo-exocytosis coupling in macrophages.

This study identifies HCK signaling as a driver of long-distance ECM degradation in macrophages through endo-exocytosis coupling involving MMPs and cathepsins.

PhysiCelldFBA: Linking single-cell genome-scale metabolism to spatially explicit multicellular dynamics

PhysiCelldFBA links single-cell metabolism to multicellular spatial dynamics by integrating genome-scale metabolic models with agent-based simulations.

Intelligent Tool Orchestration for Rapid Mechanistic Model Prototyping: MCP Servers as AI-Biology Interfaces

This paper introduces an AI-assisted framework for rapid prototyping of multicellular mechanistic models using LLMs and MCP servers to integrate multiple modeling tools.

NeKo: a tool for automatic network construction from prior knowledge

NeKo automates biological network construction by integrating molecular interactions from databases, enabling efficient network building for research applications.

Open Benchmarking for Cell-Based Multiscale Models: Lessons from a Community Initiative

This paper presents a community-driven benchmarking initiative for cell-based multiscale models, highlighting variations in tool implementations and advocating for standardized benchmarks and interoperability.

PhysiMeSS - A New PhysiCell Addon for Extracellular Matrix Modelling

PhysiMeSS extends PhysiCell to model extracellular matrix fibers and their interactions, enabling more accurate simulations of cancer metastasis.

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.

Multiscale model of the different modes of cancer cell invasion

The paper presents a multiscale model of cancer cell invasion using PhysiBoSS, integrating spatial and intracellular processes to study migration modes and validate against experimental data.