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)

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)

Harmonizing semantic annotations for computational models in biology. - Maxwell Lewis Neal; Matthias König 003; David P. Nickerson; Goksel Misirli; Reza Kalbasi; Andreas Dräger; Koray Atalag; Vijayalakshmi Chelliah; Michael T. Cooling; Daniel L. Cook; Sharon M. Crook; Miguel de Alba; et al. (Briefings Bioinform., 2019)

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. - Michael P. Snyder; Shin Lin; Amanda Posgai; Mark Atkinson; Aviv Regev; Jennifer Rood; Orit Rozenblatt-Rosen; Leslie Gaffney; Anna Hupalowska; Rahul Satija; Nils Gehlenborg; Jay Shendure; et al. (Nat., 2019)

Application of Distributed Agent-based Modeling to Investigate Opioid Use Outcomes in Justice Involved Populations. - Eric Tatara; John A. Schneider; Madeline Quasebarth; Nicholson T. Collier; Harold Pollack; Basmattee Boodram; Samuel H. Friedman; Elizabeth Salisbury-Afshar; Mary Ellen Mackesy-Amiti; Jonathan Ozik (IPDPS Workshops, 2021)