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)

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)

Formalizing knowledge in multi-scale agent-based simulations. - Endre T. Somogyi; James P. Sluka; James A. Glazier (MoDELS, 2016)

Learning Everywhere: Pervasive Machine Learning for Effective High-Performance Computation. - Geoffrey C. Fox; James A. Glazier; J. C. S. Kadupitiya; Vikram Jadhao; Minje Kim; Judy Qiu; James P. Sluka; Endre T. Somogyi; Madhav V. Marathe; Abhijin Adiga; Jiangzhuo Chen; Oliver Beckstein; et al. (IPDPS Workshops, 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)

Construction and Usage of a Human Body Common Coordinate Framework Comprising Clinical, Semantic, and Spatial Ontologies. - Katy Börner; Ellen M. Quardokus; Bruce William Herr II; Leonard E. Cross; Elizabeth G. Record; Yingnan Ju; Andreas D. Bueckle; James P. Sluka; Jonathan C. Silverstein; Kristen M. Browne; Sanjay Jain 006; Clive H. Wasserfall; et al. (CoRR, 2020)

Deep learning approaches to surrogates for solving the diffusion equation for mechanistic real-world simulations. - Javier Quetzalcóatl Toledo-Marín; Geoffrey C. Fox; James P. Sluka; James A. Glazier (CoRR, 2021)

Tissue Forge: Interactive biological and biophysics simulation environment. - T. J. Sego; James P. Sluka; Herbert M. Sauro; James A. Glazier (PLoS Comput. Biol., 2023)

MOTHER-DB: A Database for Sharing Nonhuman Ovarian Histology Images. - Suzanne W. Dietrich; Wenli Ma; Yian Ding; Karen H. Watanabe; Mary B. Zelinski; James P. Sluka (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

Modelling the spatiotemporal dynamics of senescent cells in wound healing, chronic wounds, and fibrosis. - Sharmilla Chandrasegaran; James P. Sluka; Daryl P. Shanley (PLoS Comput. Biol., 2025)