Contact-Inhibited Chemotaxis in De Novo and Sprouting Blood-Vessel Growth. - Roeland Merks; Erica D. Perryn; Abbas Shirinifard; James A. Glazier (PLoS Comput. Biol., 2008)

Visualizing cells and their connectivity graphs for CompuCell3D. - Randy W. Heiland; Abbas Shirinifard; Maciej Swat; Gilberto L. Thomas; James P. Sluka; Andrew Lumsdaine; Benjamin Zaitlen; James A. Glazier (BioVis, 2012)

Adhesion Failures Determine the Pattern of Choroidal Neovascularization in the Eye: A Computer Simulation Study. - Abbas Shirinifard; James A. Glazier; Maciej Swat; J. Scott Gens; Fereydoon Family; Yi Jiang; Hans E. Grossniklaus (PLoS Comput. Biol., 2012)

The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents. - James P. Sluka; Abbas Shirinifard; Maciej Swat; Alin Cosmanescu; Randy W. Heiland; James A. Glazier (Bioinform., 2014)

A 2.5d Yolo-Based Fusion Algorithm for 3d Localization Of Cells. - Amirkoushyar Ziabari; Derek C. Rose; Matthew R. Eicholtz; David J. Solecki; Abbas Shirinifard (ACSSC, 2019)

A Two-Tier Convolutional Neural Network for Combined Detection and Segmentation in Biological Imagery. - Amirkoushyar Ziabari; Abbas Shirinifard; Matthew R. Eicholtz; David J. Solecki; Derek C. Rose (GlobalSIP, 2019)

YOLO2U-Net: Detection-guided 3D instance segmentation for microscopy. - Amirkoushyar Ziabari; Derek C. Rose; Abbas Shirinifard; David J. Solecki (Pattern Recognit. Lett., 2024)

Ethome: tools for machine learning of animal behavior. - Benjamin Lansdell; Abbas Shirinifard (J. Open Source Softw., 2024)