Sorting unsigned permutations by reversals using multi-objective evolutionary algorithms with variable size individuals. - Ahmadreza Ghaffarizadeh; Kamilia Ahmadi; Nicholas S. Flann (IEEE Congress on Evolutionary Computation, 2011)

Quantitative Trait Loci Mapping Problem: An Extinction-Based Multi-Objective Evolutionary Algorithm Approach. - Ahmadreza Ghaffarizadeh; Mehdi Eftekhari; Ali K. Esmailizadeh; Nicholas S. Flann (Algorithms, 2013)

History Based Coalition Formation in Hedonic Context Using Trust. - Ahmadreza Ghaffarizadeh; Vicki H. Allan (CoRR, 2013)

Multistable switches and their role in cellular differentiation networks. - Ahmadreza Ghaffarizadeh; Nicholas S. Flann; Gregory J. Podgorski (BMC Bioinform., 2014)

Modeling and Visualizing Cell Type Switching. - Ahmadreza Ghaffarizadeh; Gregory J. Podgorski; Nicholas S. Flann (Comput. Math. Methods Medicine, 2014)

BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations. - Ahmadreza Ghaffarizadeh; Samuel H. Friedman; Paul Macklin (Bioinform., 2016)

Quantifying differences in cell line population dynamics using CellPD. - Edwin F. Juarez; Roy Lau; Samuel H. Friedman; Ahmadreza Ghaffarizadeh; Edmond A. Jonckheere; David B. Agus; Shannon M. Mumenthaler; Paul Macklin (BMC Syst. Biol., 2016)

Applying attractor dynamics to infer gene regulatory interactions involved in cellular differentiation. - Ahmadreza Ghaffarizadeh; Gregory J. Podgorski; Nicholas S. Flann (Biosyst., 2017)

High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow. - Jonathan Ozik; Nicholson T. Collier; Justin M. Wozniak; Charles M. Macal; Chase Cockrell; Samuel H. Friedman; Ahmadreza Ghaffarizadeh; Randy W. Heiland; Gary An; Paul Macklin (BMC Bioinform., 2018)

PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems. - Ahmadreza Ghaffarizadeh; Randy W. Heiland; Samuel H. Friedman; Shannon M. Mumenthaler; Paul Macklin (PLoS Comput. Biol., 2018)