Ahmadreza Ghaffarizadeh

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.

Quantification of Cancer Cell Migration with an Integrated Experimental-Computational Pipeline

This paper introduces an experimental-computational pipeline to quantify cancer cell migration, showing that blocking sAGR2 reduces migration of MDA-MB-231 cells.

PhysiCell: an Open Source Physics-Based Cell Simulator for 3-D Multicellular Systems

Open source off-lattice agent-based C++ simulator PhysiCell, coupled to the BioFVM diffusion solver, simulates 3-D multicellular tissues with cost linear in cell number, reaching roughly 10^6 cells.

MultiCellDS: a standard and a community for sharing multicellular data

The paper introduces MultiCellDS, a standard and community-driven initiative for sharing multicellular data to enhance research in cell biology.

MultiCellDS: a community-developed standard for curating microenvironment-dependent multicellular data

The paper introduces MultiCellDS, a standard for multicellular data curation, and presents MultiCellDB as a database to store associated data, enhancing data sharing and utility in biological and clinical research.

Estimating cell cycle model parameters using systems identification

The paper describes a method to estimate cell cycle model parameters using optimization tools with flow cytometry and synthetic viability data, demonstrated on simulated data.

Agent-based simulation of large tumors in 3-D microenvironments

The paper introduces PhysiCell, an agent-based model for simulating tumor growth in 3-D microenvironments, and reports its scalability to large cell systems.

Simulating multi-substrate diffusive transport in 3-D tissues with BioFVM

The paper introduces BioFVM, a reaction-diffusion solver for simulating chemical transport in 3-D tissues, supporting multiple compounds and demonstrating efficient computational scaling.