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ORCIDShayn M. Peirce
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- affiliation: University of Virginia, Department of Biomedical Engineering, Charlottesville, VI, USA
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Journal Articles
- 2025
[j14]Tien Comlekoglu
, Javier Quetzalcóatl Toledo-Marín, Douglas W. DeSimone, Shayn M. Peirce, Geoffrey C. Fox, James A. Glazier:
Generative diffusion model surrogates for mechanistic agent-based biological models. Mach. Learn. Sci. Technol. 6(2): 45024 (2025)- [j13]Tien Comlekoglu, Javier Quetzalcóatl Toledo-Marín, Tina Comlekoglu, Douglas W. DeSimone, Shayn M. Peirce, Geoffrey C. Fox, James A. Glazier:
Surrogate modeling of Cellular-Potts agent-based models as a segmentation task using the U-Net neural network architecture. PLoS Comput. Biol. 21(11): 1013626 (2025) - 2024
- [j12]Tracy J. Kuper, Mohammad Mazharul Islam, Shayn M. Peirce-Cottler, Jason A. Papin, Roseanne M. Ford:
Spatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment. PLoS Comput. Biol. 20(4): 1012031 (2024) - 2023
- [j11]Nikita Sivakumar, Helen V. Warner, Shayn M. Peirce, Matthew Lazzara:
Correction: A computational modeling approach for predicting multicell spheroid patterns based on signaling-induced differential adhesion. PLoS Comput. Biol. 19(5) (2023) - [j10]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:
Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in antibiotic responses. PLoS Comput. Biol. 19(6) (2023) - 2022
- [j9]Eran Agmon, Ryan K. Spangler, Christopher J. Skalnik, William Poole, Shayn M. Peirce, Jerry H. Morrison, Markus W. Covert:
Vivarium: an interface and engine for integrative multiscale modeling in computational biology. Bioinform. 38(7): 1972-1979 (2022) - [j8]Nikita Sivakumar, Helen V. Warner, Shayn M. Peirce, Matthew Lazzara:
A computational modeling approach for predicting multicell spheroid patterns based on signaling-induced differential adhesion. PLoS Comput. Biol. 18(11): 1010701 (2022) - 2021
- [j7]Amanda M. Westman, Shayn M. Peirce, George J. Christ, Silvia S. Blemker:
Agent-based model provides insight into the mechanisms behind failed regeneration following volumetric muscle loss injury. PLoS Comput. Biol. 17(5) (2021) - 2019
- [j6]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:
CIRCOAST: a statistical hypothesis test for cellular colocalization with network structures. Bioinform. 35(3): 506-514 (2019) - [j5]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:
CIRCOAST: a statistical hypothesis test for cellular colocalization with network structures. Bioinform. 35(4): 720-721 (2019) - 2009
- [j4]Alexander M. Bailey, Michael B. Lawrence, Hulan Shang, Adam J. Katz, Shayn M. Peirce:
Agent-Based Model of Therapeutic Adipose-Derived Stromal Cell Trafficking during Ischemia Predicts Ability To Roll on P-Selectin. PLoS Comput. Biol. 5(2) (2009) - 2007
- [j3]Bryan C. Thorne, Alexander M. Bailey, Shayn M. Peirce:
Combining experiments with multi-cell agent-based modeling to study biological tissue patterning. Briefings Bioinform. 8(4): 245-257 (2007) - [j2]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:
Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior. BMC Syst. Biol. 1: 46 (2007) - 2006
- [j1]Shayn M. Peirce, Thomas C. Skalak, Jason A. Papin:
Multiscale biosystems integration: Coupling intracellular network analysis with tissue-patterning simulations. IBM J. Res. Dev. 50(6): 601-616 (2006)
Data and Artifacts
- 2025
- [d3]Tien Comlekoglu, Javier Quetzalcóatl Toledo-Marín, Tina Comlekoglu, Shayn M. Peirce, Douglas W. DeSimone, Geoffrey C. Fox, James A. Glazier:
Surrogate modeling of Cellular-Potts Agent-Based Models as a segmentation task using the U-Net neural network architecture. Zenodo, 2025
- [d2]Tien Comlekoglu, Javier Quetzalcóatl Toledo-Marín, Shayn M. Peirce, Douglas W. DeSimone, Geoffrey C. Fox, James A. Glazier:
Generative diffusion model surrogates for mechanistic agent-based biological models (Training Data). Zenodo, 2025 - [d1]Tien Comlekoglu, Javier Quetzalcóatl Toledo-Marín, Shayn M. Peirce, Douglas W. DeSimone, Geoffrey C. Fox, James A. Glazier:
Generative diffusion model surrogates for mechanistic agent-based biological models (Training Data and Trained Models). Zenodo, 2025
Informal and Other Publications
- 2025
- [i3]Tien Comlekoglu, Javier Quetzalcóatl Toledo-Marín, Tina Comlekoglu, Douglas W. DeSimone, Shayn M. Peirce, Geoffrey C. Fox, James A. Glazier:
Surrogate modeling of Cellular-Potts Agent-Based Models as a segmentation task using the U-Net neural network architecture. CoRR abs/2505.00316 (2025) - [i2]Tien Comlekoglu, Javier Quetzalcóatl Toledo-Marín, Douglas W. DeSimone, Shayn M. Peirce, Geoffrey C. Fox, James A. Glazier:
Generative diffusion model surrogates for mechanistic agent-based biological models. CoRR abs/2505.09630 (2025) - 2022
- [i1]Nikita Sivakumar, Cameron Mura, Shayn M. Peirce:
Combining Machine Learning and Agent-Based Modeling to Study Biomedical Systems. CoRR abs/2206.01092 (2022)
Coauthor Index
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