Sauro HM, Agmon E, Blinov ML, Gennari JH, Hellerstein JL, Heydarabadipour A, Jardine BE, May E, Nickerson DP, Smith LP, Bader GD, Bergmann FT, Boyle PM, Dräger A, Faeder JR, Feng S, Freire J, Fröhlich F, Glazier JA, Gorochowski TE, Helikar T, Hermjakob H, Hoops S, Hunter P, Imoukhuede PI, Keating SM, König M, Laubenbacher R, Loew LM, Lopez CF, Lytton WW, Malik-Sheriff RS, McCulloch A, Mendes P, Mulugeta L, Myers CJ, Myers JG Jr., Niarakis A, Niekerk DDV, Olivier BG, Patrie AA, Quardokus EM, Radde N, Rohwer JM, Sahle S, Schaff JC, Schreiber F, Sego TJ, Shin J, Snoep JL, Vadigepalli R, Wiley HS, Waltemath D, Moraru II. (2026). From FAIR to CURE: guidelines for computational models of biological systems. NPJ systems biology and applications
Minsuk SB, Sego TJ, Umulis DM, Mullins MC, Glazier JA. (2026). Modeling epithelial deformation and cell rearrangement in response to external forces during Zebrafish epiboly. NPJ systems biology and applications
Vanin J, Hagar A, Glazier JA. (2026). Who's afraid of synthetic data? Hybrid approaches to deliver medical digital twins. Informatics in medicine unlocked, (61)
Comlekoglu T, Quetzalcoatl Toledo-Marín J, DeSimone DW, Peirce SM, Fox G, Glazier JA. (2025). Generative diffusion model surrogates for mechanistic agent-based biological models. Machine learning: science and technology, 6(4)
Vanin J, Getz M, Mahony C, Knudsen TB, Glazier JA. (2025). V-Cornea: A computational model of corneal epithelium homeostasis, injury, and recovery. PLoS computational biology, 21(12)
Sauro HM, Agmon E, Blinov ML, Gennari JH, Hellerstein J, Heydarabadipour A, Hunter P, Jardine BE, May E, Nickerson DP, Smith LP, Bader GD, Bergmann F, Boyle PM, Dräger A, Faeder JR, Feng S, Freire J, Fröhlich F, Glazier JA, Gorochowski TE, Helikar T, Hoops S, Imoukhuede P, Keating SM, Konig M, Laubenbacher R, Loew LM, Lopez CF, Lytton WW, McCulloch A, Mendes P, Myers CJ, Myers JG, Mulugeta L, Niarakis A, van Niekerk DD, Olivier BG, Patrie AA, Quardokus EM, Radde N, Rohwer JM, Sahle S, Schaff JC, Sego TJ, Shin J, Snoep JL, Vadigepalli R, Wiley HS, Waltemath D, Moraru I. (2025). From FAIR to CURE: Guidelines for Computational Models of Biological Systems. ArXiv
Minsuk SB, Sego TJ, Umulis DM, Mullins MC, Glazier JA. (2025). Modeling Epithelial Morphogenesis and Cell Rearrangement during Zebrafish Epiboly: Tissue Deformation, Cell-Cell Coupling, and the Mechanical Response to Stress. bioRxiv : the preprint server for biology
Comlekoglu T, Toledo-Marín JQ, Comlekoglu T, Desimone DW, Peirce SM, Fox G, Glazier JA. (2025). Surrogate modeling of Cellular-Potts Agent-Based Models as a segmentation task using the U-Net neural network architecture. ArXiv
Comlekoglu T, Quetzalcóatl Toledo-Marín J, Comlekoglu T, DeSimone DW, Peirce SM, Fox G, Glazier JA. (2025). Surrogate modeling of Cellular-Potts agent-based models as a segmentation task using the U-Net neural network architecture. PLoS computational biology, 21(11)
Niarakis A, Laubenbacher R, An G, Ilan Y, Fisher J, Flobak Å, Reiche K, Rodríguez Martínez M, Geris L, Ladeira L, Veschini L, Blinov ML, Messina F, Fonseca LL, Ferreira S, Montagud A, Noël V, Marku M, Tsirvouli E, Torres MM, Harris LA, Sego TJ, Cockrell C, Shick AE, Balci H, Salazar A, Rian K, Hemedan AA, Esteban-Medina M, Staumont B, Hernandez-Vargas E, Martis B S, Madrid-Valiente A, Karampelesis P, Sordo Vieira L, Harlapur P, Kulesza A, Nikaein N, Garira W, Malik Sheriff RS, Thakar J, Tran VDT, Carbonell-Caballero J, Safaei S, Valencia A, Zinovyev A, Glazier JA. (2024). Immune digital twins for complex human pathologies: applications, limitations, and challenges. NPJ systems biology and applications, 10(1)
Berkhout JH, Glazier JA, Piersma AH, Belmonte JM, Legler J, Spencer RM, Knudsen TB, Heusinkveld HJ. (2024). A computational dynamic systems model for in silico prediction of neural tube closure defects. Current research in toxicology, (8)
Laubenbacher R, Adler F, An G, Castiglione F, Eubank S, Fonseca LL, Glazier J, Helikar T, Jett-Tilton M, Kirschner D, Macklin P, Mehrad B, Moore B, Pasour V, Shmulevich I, Smith A, Voigt I, Yankeelov TE, Ziemssen T. (2024). Forum on immune digital twins: a meeting report. NPJ systems biology and applications, 10(1)
Comlekoglu T, Dzamba BJ, Pacheco GG, Shook DR, Sego TJ, Glazier JA, Peirce SM, DeSimone DW. (2024). Modeling the roles of cohesotaxis, cell-intercalation, and tissue geometry in collective cell migration of Xenopus mesendoderm. Biology open, 13(8)
Laubenbacher R, Adler F, An G, Castiglione F, Eubank S, Fonseca LL, Glazier J, Helikar T, Jett-Tilton M, Kirschner D, Macklin P, Mehrad B, Moore B, Pasour V, Shmulevich I, Smith A, Voigt I, Yankeelov TE, Ziemssen T. (2024). Toward mechanistic medical digital twins: some use cases in immunology. Frontiers in digital health, (6)
Toledo-Marín JQ, Glazier JA. (2023). Using deep LSD to build operators in GANs latent space with meaning in real space. PloS one, 18(6)
Sego TJ, Sluka JP, Sauro HM, Glazier JA. (2023). Tissue Forge: Interactive biological and biophysics simulation environment. PLoS computational biology, 19(10)
Sego TJ, Comlekoglu T, Peirce SM, Desimone DW, Glazier JA. (2023). General, open-source vertex modeling in biological applications using Tissue Forge. Scientific reports, 13(1)
Sego TJ, Comlekoglu T, Peirce SM, Desimone D, Glazier JA. (2023). General, Open-Source Vertex Modeling in Biological Applications Using Tissue Forge. Research square
Rosenbauer J, Berghoff M, Glazier JA, Schug A. (2023). Multiscale Modeling of Spheroid Tumors: Effect of Nutrient Availability on Tumor Evolution. The journal of physical chemistry. B, 127(16)
de Almeida RMC, Giardini GSY, Vainstein M, Glazier JA, Thomas GL. (2022). Exact solution for the Anisotropic Ornstein-Uhlenbeck process. Physica A, (587)
de Almeida RMC, Thomas GL, Glazier JA. (2022). Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection. NAR genomics and bioinformatics, 4(1)
Piatkowska AM, Adhikari K, Moverley AA, Turmaine M, Glazier JA, Plachta N, Evans SE, Stern CD. (2023). Sequential changes in cellular properties accompanying amniote somite formation. Journal of anatomy, 242(3)
Ferrari Gianlupi J, Mapder T, Sego TJ, Sluka JP, Quinney SK, Craig M, Stratford RE Jr., Glazier JA. (2022). Multiscale Model of Antiviral Timing, Potency, and Heterogeneity Effects on an Epithelial Tissue Patch Infected by SARS-CoV-2. Viruses, 14(3)
Niarakis A, Waltemath D, Glazier J, Schreiber F, Keating SM, Nickerson D, Chaouiya C, Siegel A, Noël V, Hermjakob H, Helikar T, Soliman S, Calzone L. (2022). Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. Briefings in bioinformatics
Karr J, Malik-Sheriff RS, Osborne J, Gonzalez-Parra G, Forgoston E, Bowness R, Liu Y, Thompson R, Garira W, Barhak J, Rice J, Torres M, Dobrovolny HM, Tang T, Waites W, Glazier JA, Faeder JR, Kulesza A. (2022). Model Integration in Computational Biology: The Role of Reproducibility, Credibility and Utility. Frontiers in systems biology, (2)
Sego TJ, Mochan ED, Bard Ermentrout G, Glazier JA. (2021). A Multiscale Multicellular Spatiotemporal Model of Local Influenza Infection and Immune Response. Journal of theoretical biology
Aponte-Serrano JO, Weaver JJA, Sego TJ, Glazier JA, Shoemaker JE. (2021). Multicellular spatial model of RNA virus replication and interferon responses reveals factors controlling plaque growth dynamics. PLoS computational biology, 17(10)
Toledo-Marín JQ, Fox G, Sluka JP, Glazier JA. (2021). Deep Learning Approaches to Surrogates for Solving the Diffusion Equation for Mechanistic Real-World Simulations. Frontiers in physiology, (12)
Zarnitsyna VI, Gianlupi JF, Hagar A, Sego TJ, Glazier JA. (2021). Advancing therapies for viral infections using mechanistic computational models of the dynamic interplay between the virus and host immune response. Current opinion in virology, (50)
Adhyapok P, Piatkowska AM, Norman MJ, Clendenon SG, Stern CD, Glazier JA, Belmonte JM. (2021). A mechanical model of early somite segmentation. iScience, 24(4)
Laubenbacher R, Sluka JP, Glazier JA. (2021). Using digital twins in viral infection. Science (New York, N.Y.), 371(6534)
Sego TJ, Aponte-Serrano JO, Gianlupi JF, Glazier JA. (2021). Generation of multicellular spatiotemporal models of population dynamics from ordinary differential equations, with applications in viral infection. BMC biology, 19(1)
Sego TJ, Aponte-Serrano JO, Ferrari Gianlupi J, Heaps SR, Breithaupt K, Brusch L, Crawshaw J, Osborne JM, Quardokus EM, Plemper RK, Glazier JA. (2020). A modular framework for multiscale, multicellular, spatiotemporal modeling of acute primary viral infection and immune response in epithelial tissues and its application to drug therapy timing and effectiveness. PLoS computational biology, 16(12)
Dunn KW, Martinez MM, Wang Z, Mang HE, Clendenon SG, Sluka JP, Glazier JA, Klaunig JE. (2020). Mitochondrial depolarization and repolarization in the early stages of acetaminophen hepatotoxicity in mice. Toxicology, (439)
Adhyapok P, Fu X, Sluka JP, Clendenon SG, Sluka VD, Wang Z, Dunn K, Klaunig JE, Glazier JA. (2020). A computational model of liver tissue damage and repair. PloS one, 15(12)
Liu R, Higley KA, Swat MH, Chaplain MAJ, Powathil GG, Glazier JA. (2021). Development of a coupled simulation toolkit for computational radiation biology based on Geant4 and CompuCell3D. Physics in medicine and biology, 66(4)
Fortuna I, Perrone GC, Krug MS, Susin E, Belmonte JM, Thomas GL, Glazier JA, de Almeida RMC. (2020). CompuCell3D Simulations Reproduce Mesenchymal Cell Migration on Flat Substrates. Biophysical journal, 118(11)
Sego TJ, Aponte-Serrano JO, Gianlupi JF, Heaps SR, Breithaupt K, Brusch L, Crawshaw J, Osborne JM, Quardokus EM, Plemper RK, Glazier JA. (2020). A modular framework for multiscale, multicellular, spatiotemporal modeling of acute primary viral infection and immune response in epithelial tissues and its application to drug therapy timing and effectiveness: A multiscale model of viral infection in epithelial tissues. bioRxiv : the preprint server for biology
Getz M, Wang Y, An G, Asthana M, Becker A, Cockrell C, Collier N, Craig M, Davis CL, Faeder JR, Versypt ANF, Mapder T, Gianlupi JF, Glazier JA, Hamis S, Heiland R, Hillen T, Hou D, Islam MA, Jenner AL, Kurtoglu F, Larkin CI, Liu B, Macfarlane F, Maygrundter P, Morel PA, Narayanan A, Ozik J, Pienaar E, Rangamani P, Saglam AS, Shoemaker JE, Smith AM, Weaver JJA, Macklin P. (2020). Rapid community-driven development of a SARS-CoV-2 tissue simulator. bioRxiv : the preprint server for biology
Sego TJ, Glazier JA, Tovar A. (2020). Unification of aggregate growth models by emergence from cellular and intracellular mechanisms. Royal Society open science, 7(8)
Clendenon SG, Fu X, Von Hoene RA, Clendenon JL, Sluka JP, Winfree S, Mang H, Martinez M, Filson A, Klaunig JE, Glazier JA, Dunn KW. (2019). Spatial Temporal Analysis of Fieldwise Flow in Microvasculature. Journal of visualized experiments : JoVE, 153
Fu X, Sluka JP, Clendenon SG, Dunn KW, Wang Z, Klaunig JE, Glazier JA. (2018). Modeling of xenobiotic transport and metabolism in virtual hepatic lobule models. PloS one, 13(9)
Clendenon SG, Fu X, Von Hoene RA, Clendenon JL, Sluka JP, Winfree S, Mang H, Martinez M, Filson AJ, Klaunig JE, Glazier JA, Dunn KW. (2019). A simple automated method for continuous fieldwise measurement of microvascular hemodynamics. Microvascular research, (123)
Chen KY, Srinivasan T, Tung KL, Belmonte JM, Wang L, Murthy PKL, Choi J, Rakhilin N, King S, Varanko AK, Witherspoon M, Nishimura N, Glazier JA, Lipkin SM, Bu P, Shen X. (2017). A Notch positive feedback in the intestinal stem cell niche is essential for stem cell self-renewal. Molecular systems biology, 13(4)
Somogyi E, Glazier JA. (2017). A MODELING AND SIMULATION LANGUAGE FOR BIOLOGICAL CELLS WITH COUPLED MECHANICAL AND CHEMICAL PROCESSES. Symposium on Theory of Modeling & Simulation : DEVS Integrative M&S Symposium (TMS-DEVS). Symposium on Theory of Modeling and Simulation, (2017)
Somogyi E, Hagar A, Glazier JA. (2016). TOWARDS A MULTI-SCALE AGENT-BASED PROGRAMMING LANGUAGE METHODOLOGY. Proceedings of the ... Winter Simulation Conference. Winter Simulation Conference, (2016)
Somogyi E, Sluka JP, Glazier JA. (2016). Formalizing Knowledge in Multi-Scale Agent-Based Simulations. Model driven engineering languages and systems : ... International Conference, MoDELS ... : proceedings. MODELS (Conference), (16)
Sluka JP, Fu X, Swat M, Belmonte JM, Cosmanescu A, Clendenon SG, Wambaugh JF, Glazier JA. (2016). A Liver-Centric Multiscale Modeling Framework for Xenobiotics. PloS one, 11(9)
Sluka JP, Shirinifard A, Swat M, Cosmanescu A, Heiland RW, Glazier JA. (2014). The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents. Bioinformatics (Oxford, England), 30(16)
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