Multiscale biosystems integration: Coupling intracellular network analysis with tissue-patterning simulations. - Shayn M. Peirce; Thomas C. Skalak; Jason A. Papin (IBM J. Res. Dev., 2006)

Combining experiments with multi-cell agent-based modeling to study biological tissue patterning. - Bryan C. Thorne; Alexander M. Bailey; Shayn M. Peirce (Briefings Bioinform., 2007)

Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior. - Scott H. Robertson; Chris K. Smith; Anna L. Langhans; Sara E. McLinden; Matthew A. Oberhardt; Karoly R. Jakab; Bette Dzamba; Douglas W. DeSimone; Jason A. Papin; Shayn M. Peirce (BMC Syst. Biol., 2007)

Agent-Based Model of Therapeutic Adipose-Derived Stromal Cell Trafficking during Ischemia Predicts Ability To Roll on P-Selectin. - Alexander M. Bailey; Michael B. Lawrence; Hulan Shang; Adam J. Katz; Shayn M. Peirce (PLoS Comput. Biol., 2009)

CIRCOAST: a statistical hypothesis test for cellular colocalization with network structures. - Bruce A. Corliss; H. Clifton Ray; James T. Patrie; Jennifer Mansour; Sam Kesting; Janice H. Park; Gustavo K. Rohde; Paul A. Yates; Kevin A. Janes; Shayn M. Peirce (Bioinform., 2019)

Agent-based model provides insight into the mechanisms behind failed regeneration following volumetric muscle loss injury. - Amanda M. Westman; Shayn M. Peirce; George J. Christ; Silvia S. Blemker (PLoS Comput. Biol., 2021)

Vivarium: an interface and engine for integrative multiscale modeling in computational biology. - Eran Agmon; Ryan K. Spangler; Christopher J. Skalnik; William Poole; Shayn M. Peirce; Jerry H. Morrison; Markus W. Covert (Bioinform., 2022)

Combining Machine Learning and Agent-Based Modeling to Study Biomedical Systems. - Nikita Sivakumar; Cameron Mura; Shayn M. Peirce (CoRR, 2022)

A computational modeling approach for predicting multicell spheroid patterns based on signaling-induced differential adhesion. - Nikita Sivakumar; Helen V. Warner; Shayn M. Peirce; Matthew Lazzara (PLoS Comput. Biol., 2022)

Correction: A computational modeling approach for predicting multicell spheroid patterns based on signaling-induced differential adhesion. - Nikita Sivakumar; Helen V. Warner; Shayn M. Peirce; Matthew Lazzara (PLoS Comput. Biol., 2023)

Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in antibiotic responses. - Christopher J. Skalnik; Sean Y. Cheah; Mica Y. Yang; Mattheus B. Wolff; Ryan K. Spangler; Lee Talman; Jerry H. Morrison; Shayn M. Peirce; Eran Agmon; Markus W. Covert (PLoS Comput. Biol., 2023)

Spatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment. - Tracy J. Kuper; Mohammad Mazharul Islam; Shayn M. Peirce-Cottler; Jason A. Papin; Roseanne M. Ford (PLoS Comput. Biol., 2024)

Surrogate modeling of Cellular-Potts Agent-Based Models as a segmentation task using the U-Net neural network architecture. - Tien Comlekoglu; Javier Quetzalcóatl Toledo-Marín; Tina Comlekoglu; Douglas W. DeSimone; Shayn M. Peirce; Geoffrey C. Fox; James A. Glazier (CoRR, 2025)

Generative diffusion model surrogates for mechanistic agent-based biological models. - Tien Comlekoglu; Javier Quetzalcóatl Toledo-Marín; Douglas W. DeSimone; Shayn M. Peirce; Geoffrey C. Fox; James A. Glazier (CoRR, 2025)