Abbas Shirinifard
Abbas Shirinifard, PhD
Scientist of Clinical Informatics

St. Jude Children’s Research Hospital


  • Ph.D., Physics, Indiana University, Bloomington, IN (2005-2012)
  • M.S., Physics, Sharif University of Technology, Tehran, Iran (2005)
  • B.A., Physics, Shiraz University, Shiraz, Iran (2002)



I am a scientist at St. Jude Children’s Research Hospital. My current research aims to provide mechanistic insights to cancer using computational models based on the underlying biological processes and their representations using the laws of physics. With the advent of individualized cancer therapies, characterization of individual tumors and their alterations in response to therapies become essential.I take amulti-scale approach to address this challenge by integrating data ranging fromcell and tissue to whole-body to modelspatio-temporal heterogeneities in individual tumorsand explore how theychange tumor response to therapies.

Research Interest

  • Multi-scale computational models of tissues
  • Individualized models of tumor growth and response to therapies
  • Cancer heterogeneity
  • Image-based computational biology


Professional Activities:

2012-Present Computational Modeling Scientist St. Jude’s Research Hospital, Memphis, TN
2011-2012 Research Associate The Biocomplexity Institute, Indiana University, Bloomington, IN
2012-2012 External Collaborator St. Jude Children’s Research Hospital, Memphis, TN
2006-2011 Research Assistant The Biocomplexity Institute, Indiana University, Bloomington, IN
2005-2006 Teaching Assistant Department of Physics, Indiana University, Bloomington, IN
2002-2005 Teaching Assistant Department of Physics, Sharif University Of Technology, Tehran, Iran


Honors and Awards



Book Chapters

  • Swat M., Thomas G.L., Belmonte J.M., Shirinifard A., Hmeljak M., Glazier J.A. (2012). “Multi-Scale Modeling of Tissues Using CompuCell3D.” Methods in Cell Biology, Volume 110.

Peer-reviewed Publications

  1. Swat M.H., Thomas G.L., Shirinifard A., Clendenon S.G., Glazier J.A. (2015).“Emergent Stratification in Solid Tumors Selects for Reduced Cohesion of Tumor Cells: A Multi-Cell, Virtual-Tissue Model of Tumor Evolution Using CompuCell3D.” PLoS One. 10(6):e0127972.
  2. Stewart E., Shelat A., Bradley C., Chen X., Federico S., Thiagarajan S., ShirinifardA., Bahrami A., Pappo A., Qu C., Finkelstein D., Sablauer A., Dyer M.A. (2015). “Development and characterization of a human orthotopic neuroblastoma xenograft.” Dev Biol. pii: S0012-1606(15)00060-3.
  3. Stewart E, Goshorn R, Bradley C, Griffiths L.M., Benavente C., Twarog N.R., Miller G.M., Caufield W, Freeman B.B. 3rd, Bahrami A., Pappo A., Wu J., Loh A., Karlström Å., Calabrese C., Gordon B., Tsurkan L., Hatfield M.J., Potter P.M., Snyder S.E., Thiagarajan S., Shirinifard A., Sablauer A., Shelat A.A., Dyer M.A. (2014). “Targeting the DNA repair pathway in Ewing sarcoma.” Cell Rep. 9(3):829-41.
  4. Sluka J.P., Shirinifard A., Swat M., Cosmanescu A.,  Heiland R. and Glazier J.A (2014).“The Cell Behavior Ontology: Describing the intrinsic biological behaviors of real and model cells seen as active agents.”Bioinformatics,doi: 10.1093.
  5. Shirinifard A., McCollum C.W., Bolin M.B., Gustafsson J.Å., Glazier J.A., Clendenon S.G. (2013), “3D Quantitative Analyses Of Angiogenic Sprout Growth Dynamics.”Developmental Dynamics.242(5):518-26.
  6. Steinkamp M., Kanigel-Winner K., Davies S., Muller C., Zhang Y., Hoffman R. M., Shirinifard A., Moses M., Jiang Y., Wilson B. S. (2013), “Ovarian Tumor Attachment, Invasion and Vascularization Reflect Unique Microenvironments In the Peritoneum: Insights from Xenograft and Mathematical Models.”Frontiers in Molecular and Cellular Oncology.3:97. doi: 10.3389.
  7. Shirinifard A., Glazier J.A., Swat M., Gens J.S., Family F., Jiang Y., Grossniklaus H.E. (2012) “Adhesion Failures in the Bruch’s Membrane-Retinal Pigment Epithelium-Photoreceptor Outer Segment Complex Determine the Pattern of Choroidal Neovascularization: A Computer Simulation Study.”PLoSComputBiol 8(5): e1002440. doi:10.1371/journal.pcbi.1002440.
  8. Heiland R., Swat M., Sluka J., Zaitlen B., Shirinifard A., Thomas G.L., Lumsdaine A., and Glazier J.A. “Visualizing Cells and their Connectivity Graphs for CompuCell3D.”2nd IEEE Symposium on Biological Data Visualization.
  9. Thomas G.T., Zhang Y., Swat M., Shirinifard A., Glazier J.A. (2011). “Computer simulations of cell sorting due to differential adhesion.”PLoS ONE 6(10): e24999.
  10. Popławski N.J., Shirinifard A., Ubirajara A., Gens J.S., Swat M., Glazier J.A. (2010). “Front Instabilities and Invasiveness of Simulated 3D Avascular Tumors.”PLoS ONE 5(5): e10641.
  11. Shirinifard A., Gens J.S., Zaitlen B.L., Popławski N.J., Swat M., Glazier J.A (2009). “3D multi-cell simulation of tumor growth and angiogenesis.”PLoS One. 4(10):e7190.
  12. Merks R.M., Perryn E.D., Shirinifard A., Glazier J.A. (2008). “Contact-inhibited chemotaxis in de novo and sprouting blood-vessel growth.”PLoSComput Biol. 4(9):e1000163.
  13. Popławski N.J., Shirinifard A., Swat M., Glazier J.A. (2008). “Simulation of single-species bacterial-biofilm growth using the Glazier-Graner-Hogeweg model and the CompuCell3D modeling environment.”Math Biosci Eng. Apr; 5(2):355-88.
  14. Shojai F., Shirinifard A. (2005). “Classical and Quantum Limits in Bohmian Quantum Cosmology.”International Journal of Modern Physics D, Volume 14, pp. 1333-1345 (2005).




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