Profile of James Glazier

Dr. Glazier received his B.A. in Physics and Mathematics from Harvard University in 1983 and his M.S. and Ph.D. in Physics from the University of Chicago in 1987 and 1989. He has held faculty positions in Physics at the University of Notre Dame and Indiana University Bloomington and visiting positions at the University of California Santa Barbara, the University of Western Australia, the University of Grenoble in France and Tohoku University in Japan. Dr. Glazier’s research focuses on applying physics-based computer simulations to understand embryonic development, developmental and chronic toxicity, and developmental and infectious diseases. He has worked extensively on vascular development and disfunction in Age-Related Macular Degeneration and Diabetic Retinopathy, on segmentation during early development, on Autosomal Dominant Polycystic Kidney Disease and on viral infection and immune response. He also applies these simulations to develop and optimize disease treatment. He is an active member of numerous international research collaboration between experimental and computational biomedical scientists and is eager to develop new collaborations. He leads the collaborative development of the open-source CompuCell3D multi-scale modeling environment and participates in the development of Tissue Forge. He actively disseminates these methods, teaching an annual (now virtual) week-long workshop on multiscale virtual-tissue modeling with distribution on YouTube. He is a fellow of the American Association for the Advancement of Science, the American Physical Society and the Institute of Physics (London) and has served as Chair of the Division of Biological Physics of the American Physical Society. He is active in the development of infrastructure for medical digital twins and currently co-leads the IMAG/MSM Working Group on Multiscale Modeling and Viral Pandemics and the Global Alliance for Immune Prediction and Intervention (GLIMPRINT)

Recent Grants:

1. National Science Foundation, NSF 2303695, “POSE: PHASE II: Open VT - A Standardized Ecosystem for Virtual Tissue Simulation." Role: PI, co-PIs Paul Macklin, David Wild, Herbert Sauro.
2. Proctor and Gamble Corporation, “Virtual Cornea." Role: PI.
3. Johns Hopkins University, APL, “Immunity Twin Propulsion Grant." Role: PI on IUB subcontract.
4. National Science Foundation, NSF 2120200, “BII: Emergent Mechanisms in Biology of Robustness, Integration & Organization (EMBRIO),” Role: co-Investigator, PI on IUB Subcontract. David Umulis, Purdue University is project PI.
5. National Institutes of Health, National Institute of Biomedical Imaging and Bioengineering, U24 EB028887, “Dissemination of libRoadRunner and CompuCell3D." Role MPI. MPI Herbert Sauro (University of Washington), MPI TJ Sego, MPI James Sluka.

Awards:

1. 2025 Klaus Schulten and Zaida Luthey-Schulten Computational Biophysics Lecture Award, Biophysical Society (2024).
2. Fellow in Physics, American Academy for the Advancement of Science, January 30th, 2023.
3. Fellow of the American Physical Society (2006).
4. Fellow of the Institute of Physics (London) (2005).

Research:

Web Resources: www.youtube.com/@jamesglazier6340

Frameworks for Virtual Tissue Modeling:

1. “Tissue forge: interactive biological and biophysics simulation environment,” T. J. Sego, James P. Sluka, Herbert M. Sauro, and James A. Glazier. PLOS Computational Biology 19, e1010768. Doi: 10.1371/journal.pcbi.1010768. (2023).  
2. “General, open-source vertex modeling in biological applications using Tissue Forge,” T. J. Sego, Tien Comlekoglu, Shayn M. Peirce, Douglas W. Desimone, James A. Glazier. Scientific Reports 13, 17886, (2023).
3. “Multi-Scale Modeling of Tissues Using CompuCell3D.” Maciej H. Swat, Gilberto L. Thomas, Julio M. Belmonte, Abbas Shirinifard, Dimitrij Hmeljak, James A. Glazier, in Computational Methods in Cell Biology, Anand R Asthagiri Adam P Arkin, editors (Methods in Cell Biology 110, Academic Press, USA, 2012), p. 325-366,

Machine Learning and Artificial Intelligence:

1. “Deep Learning Approaches to Surrogates for Solving the Diffusion Equation for Mechanistic Real-World Simulations,” Javier Quetzalcóatl Toledo-Marín, Geoffrey Fox, James P. Sluka, James A. Glazier, Frontiers in Physiology 12, 908 (2021).
2. “Using deep LSD to build operators in GANs latent space with meaning in real space,” Javier Quetzalcóatl Toledo-Marín, James A. Glazier. PLoS ONE 18, e0287736, doi: 10.1371/journal.pone.0287736 (2023). 

Medical Digital Twins:

1. “Using digital twins in viral infection,” Reinhard Laubenbacher, James P. Sluka, James A. Glazier, Science 371: 1105-1106 (2021). 
2. “Building digital twins of the human immune system: toward a roadmap,” Reinhard Laubenbacher, Anna Niarakis, Tomas Helikar, Gary An, Bruce Shapiro, Rahuman S. Malik-Sheriff, T J. Sego, Adam Knapp, Paul Macklin, and James A. Glazier, npj Digital Medicine 5, 64 (2022). 

Infectious Diseases:

1. “A multiscale multicellular spatiotemporal model of local influenza infection and immune response,” TJ Sego, Ericka D. Mochan, G. Bard Ermentrout, James A. Glazier, Journal of Theoretical Biology 532 ,110918 (2022).
2. “Multiscale Model of Antiviral Timing, Potency, and Heterogeneity Effects on an Epithelial Tissue Patch Infected by SARS-CoV-2,” Juliano Ferrari Gianlupi, Tarunendu Mapder, T. J. Sego, James P. Sluka, Sara K. Quinney, Morgan Craig, Robert E. Stratford Jr, and James A. Glazier, Viruses 14, 605 (2022). 
3. “Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection,” Rita MC de Almeida, Gilberto L. Thomas, and James A. Glazier. NAR Genomics and Bioinformatics 4, (2022). 

Developmental Biology and Disease:

1. “A computational dynamic systems model for in silico prediction of neural tube closure defects,” Berkhout, Job H., James A. Glazier, Aldert H. Piersma, Julio M. Belmonte, Juliette Legler, Richard M. Spencer, Thomas B. Knudsen, Harm J. Heusinkveld. Current Research in Toxicology (2024): 100210. 
2. "Sequential changes in cellular properties accompanying amniote somite formation,” Agnieszka M. Piatkowska, Kaustubh Adhikari, Adam A. Moverley, Mark Turmaine, James A. Glazier, Nicolas Plachta, Susan E. Evans, and Claudio D. Stern. Journal of Anatomy 242, 417-435 (2023). 
3. “Computational modelling of nephron progenitor cell movement and aggregation during kidney organogenesis,” Pauli Tikka, Moritz Mercker, Ilya Skovorodkin, Ulla Saarela, Seppo Vainio, Veli-Pekka Ronkainen, James P. Sluka, James A. Glazier, Anna Marciniak-Czochra, Franz Schaefer, Mathematical Biosciences 344, 108759 (2022).  
4. “A Mechanical Model of Early Somite Segmentation,” Priyom Adhyapok, Agnieszka M. Piatkowska, Michael J. Norman, Sherry G. Clendenon, Claudio D. Stern, James A. Glazier, Julio M. Belmonte, iScience 24, 102317 (2021). 
5. "Modeling of xenobiotic transport and metabolism in virtual hepatic lobule models," Xiao Fu, James P. Sluka, Sherry G. Clendenon, Kenneth W. Dunn, Zemin Wang, James E. Klaunig, and James A. Glazier. PLoS ONE 13: e0198060, (2018). 
6. “A Notch positive feedback in the intestinal stem cell niche is essential for stem cell self-renewal,” Kai-Yuan Chen, Tara Srinivasan, Kuei-Ling Tung, Julio M. Belmonte, Lihua Wang, Preetish Kadur Lakshminarasimha Murthy, Jiahn Choi, Nikolai Rakhilin, Sarah King, Anastasia Kristine Varanko, Mavee Witherspoon, Nozomi Nishimura, James A. Glazier, Steven M. Lipkin, Pengcheng Bu, Xiling Shen, Molecular Systems Biology 13, 927,  (2017). 
7. “Transcriptome Analysis Reveals Manifold Mechanisms of Cyst Development in ADPKD,” Rita M. C. de Almeida, Sherry G. Clendenon, William G. Richards, Michael Boedigheimer, Michael Damore, Sandro Rossetti, Peter C. Harris, Britney-Shea Herbert, Wei Min Xu, Angela Wandinger-Ness, Heather H. Ward, James A. Glazier, Robert L. Bacallao, Human Genomics 10, (2016). 
8. “A Liver-Centric Multiscale Modeling Framework for Xenobiotics,” James P. Sluka, Xiao Fu, Maciej Swat, Julio M. Belmonte, Alin Cosmanescu, Sherry G. Clendenon, John F. Wambaugh, James A. Glazier, PLoS ONE 11: e0162428 (2016). 
9. “A Computational Model of Peripheral Photocoagulation for the Prevention of Progressive Diabetic Capillary Occlusion,” Thomas J. Gast, Xiao Fu, John Scott Gens, James A. Glazier, Journal of Diabetes Research 2016: Article ID 2508381 (2016).
10. Virtual-Tissue Computer Simulations Define the Roles of Cell Adhesion and Proliferation in the Onset of Kidney Cystic Disease,” Julio M. Belmonte, Sherry G. Clendenon, Guilherme M. Oliveira, Maciej H. Swat, Evan V. Greene, Srividhya Jeyaraman, James A. Glazier, Robert L. Bacallao, Molecular Biology of the Cell  (2016). 
11. “Emergent Stratification in Solid Tumors Selects for Reduced Cohesion of Tumor Cells: A Multi-Cell, Virtual-Tissue Model of Tumor Evolution Using CompuCell3D,” Maciej H. Swat, Gilberto L. Thomas, Abbas Shirinifard, Sherry G. Clendenon, James A. Glazier, PLoS ONE 10, e0127972 (2015).
12. “Somites Without a Clock,” Ana S. Dias, Irene de Almeida, Julio M. Belmonte, James A. Glazier, Claudio D. Stern, Science 343, 791-795, doi: 10.1126/science.1247575 (2014).