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Items: 9


High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow.

Ozik J, Collier N, Wozniak JM, Macal C, Cockrell C, Friedman SH, Ghaffarizadeh A, Heiland R, An G, Macklin P.

BMC Bioinformatics. 2018 Dec 21;19(Suppl 18):483. doi: 10.1186/s12859-018-2510-x.


Cell death as a trigger for morphogenesis.

Aguilar B, Ghaffarizadeh A, Johnson CD, Podgorski GJ, Shmulevich I, Flann NS.

PLoS One. 2018 Mar 22;13(3):e0191089. doi: 10.1371/journal.pone.0191089. eCollection 2018.


PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems.

Ghaffarizadeh A, Heiland R, Friedman SH, Mumenthaler SM, Macklin P.

PLoS Comput Biol. 2018 Feb 23;14(2):e1005991. doi: 10.1371/journal.pcbi.1005991. eCollection 2018 Feb.


Applying attractor dynamics to infer gene regulatory interactions involved in cellular differentiation.

Ghaffarizadeh A, Podgorski GJ, Flann NS.

Biosystems. 2017 May;155:29-41. doi: 10.1016/j.biosystems.2016.12.004. Epub 2017 Feb 28.


Progress Towards Computational 3-D Multicellular Systems Biology.

Macklin P, Frieboes HB, Sparks JL, Ghaffarizadeh A, Friedman SH, Juarez EF, Jonckheere E, Mumenthaler SM.

Adv Exp Med Biol. 2016;936:225-246. Review.


Quantifying differences in cell line population dynamics using CellPD.

Juarez EF, Lau R, Friedman SH, Ghaffarizadeh A, Jonckheere E, Agus DB, Mumenthaler SM, Macklin P.

BMC Syst Biol. 2016 Sep 21;10(1):92.


BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations.

Ghaffarizadeh A, Friedman SH, Macklin P.

Bioinformatics. 2016 Apr 15;32(8):1256-8. doi: 10.1093/bioinformatics/btv730. Epub 2015 Dec 12.


Multistable switches and their role in cellular differentiation networks.

Ghaffarizadeh A, Flann NS, Podgorski GJ.

BMC Bioinformatics. 2014;15 Suppl 7:S7. doi: 10.1186/1471-2105-15-S7-S7. Epub 2014 May 28.


Modeling and visualizing cell type switching.

Ghaffarizadeh A, Podgorski GJ, Flann NS.

Comput Math Methods Med. 2014;2014:293980. doi: 10.1155/2014/293980. Epub 2014 Apr 14.

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