VCF2Networks: applying genotype networks to single-nucleotide variants data. - Giovanni Marco Dall'Olio; Ali R. Vahdati; Jaume Bertranpetit; Andreas Wagner; Hafid Laayouni (Bioinform., 2015)

Agents.jl: agent-based modeling framework in Julia. - Ali R. Vahdati (J. Open Source Softw., 2019)

Agents.jl: A performant and feature-full agent based modelling software of minimal code complexity. - George Datseris; Ali R. Vahdati; Timothy C. DuBois (CoRR, 2021)

EvoDynamics.jl: a framework for modeling eco-evolutionary dynamics. - Ali R. Vahdati; Carlos J. Melián (J. Open Source Softw., 2022)

Agents.jl: a performant and feature-full agent-based modeling software of minimal code complexity. - George Datseris; Ali R. Vahdati; Timothy C. DuBois (Simul., 2024)