James A. Glazier

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 21

Top Topics

Diffusion Equation

Immune Response

Top Venues

PLoS Comput. Biol.

Publications

Reinhard C. Laubenbacher, Fred Adler, Gary An, Filippo Castiglione, Stephen Eubank, Luis L. Fonseca, James A. Glazier, Tomás Helikar, Marti Jett-Tilton, Denise Kirschner, Paul Macklin, Borna Mehrad, Beth Moore, Virginia Pasour, Ilya Shmulevich, Amber Smith, Isabel Voigt, Thomas E. Yankeelov, Tjalf Ziemssen
Toward mechanistic medical digital twins: some use cases in immunology. Frontiers Digit. Health 6 (2024)
J. Quetzalcóatl Toledo-Marín, James A. Glazier, Geoffrey C. Fox
Analyzing the Performance of Deep Encoder-Decoder Networks as Surrogates for a Diffusion Equation. CoRR (2023)
T. J. Sego, James P. Sluka, Herbert M. Sauro, James A. Glazier
Tissue Forge: Interactive biological and biophysics simulation environment. PLoS Comput. Biol. 19 (10) (2023)
Reinhard C. Laubenbacher, Anna Niarakis, Tomás Helikar, Gary An, B. Shapiro, Rahuman S. Malik-Sheriff, T. J. Sego, Adam C. Knapp, Paul Macklin, James A. Glazier
Building digital twins of the human immune system: toward a roadmap. npj Digit. Medicine 5 (2022)
J. Quetzalcóatl Toledo-Marín, James A. Glazier
Using Deep LSD to build operators in GANs latent space with meaning in real space. CoRR (2021)
Josua Aponte-Serrano, Jordan J. A. Weaver, T. J. Sego, James A. Glazier, Jason E. Shoemaker
Multicellular spatial model of RNA virus replication and interferon responses reveals factors controlling plaque growth dynamics. PLoS Comput. Biol. 17 (10) (2021)
J. Quetzalcóatl Toledo-Marín, Geoffrey C. Fox, James P. Sluka, James A. Glazier
Deep learning approaches to surrogates for solving the diffusion equation for mechanistic real-world simulations. CoRR (2021)
T. J. Sego, Josua Aponte-Serrano, Juliano Ferrari Gianlupi, Samuel R. Heaps, Kira Breithaupt, Lutz Brusch, Jessica Crawshaw, James M. Osborne, Ellen M. Quardokus, Richard K. Plemper, James A. Glazier
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 Comput. Biol. 16 (12) (2020)
Geoffrey C. Fox, James A. Glazier, J. C. S. Kadupitiya, Vikram Jadhao, Minje Kim, Judy Qiu, James P. Sluka, Endre T. Somogyi, Madhav Marathe, Abhijin Adiga, Jiangzhuo Chen, Oliver Beckstein, Shantenu Jha
Learning Everywhere: Pervasive Machine Learning for Effective High-Performance Computation. CoRR (2019)
Geoffrey C. Fox, James A. Glazier, J. C. S. Kadupitiya, Vikram Jadhao, Minje Kim, Judy Qiu, James P. Sluka, Endre T. Somogyi, Madhav Marathe, Abhijin Adiga, Jiangzhuo Chen, Oliver Beckstein, Shantenu Jha
Learning Everywhere: Pervasive Machine Learning for Effective High-Performance Computation. IPDPS Workshops (2019)
Aasakiran Madamanchi, Shenika V. Poindexter, Monica E. Cardella, James A. Glazier, David M. Umulis
Qualitative Findings from Study of Interdisciplinary Education in Computational Modeling for Life Sciences Student Researchers from Emerging Research Institutions. FIE (2018)
Aasakiran Madamanchi, Monica E. Cardella, James A. Glazier, David M. Umulis
Factors Mediating Learning and Application of Computational Modeling by Life Scientists. FIE (2018)
Endre T. Somogyi, James A. Glazier
A modeling and simulation language for biological cells with coupled mechanical and chemical processes. SpringSim (TMS) (2017)
Endre T. Somogyi, James A. Glazier
A modeling and simulation language for biological cells with coupled mechanical and chemical processes. CoRR (2017)
Eran Agmon, James A. Glazier, Randall D. Beer
Structural coupling of a Potts model cell. ECAL (2017)
Endre T. Somogyi, James P. Sluka, James A. Glazier
Formalizing knowledge in multi-scale agent-based simulations. MoDELS (2016)
Julio M. Belmonte, Maciej H. Swat, James A. Glazier
Filopodial-Tension Model of Convergent-Extension of Tissues. PLoS Comput. Biol. 12 (6) (2016)
Xiao Fu, J. Scott Gens, James A. Glazier, Stephen A. Burns, Thomas J. Gast
Progression of Diabetic Capillary Occlusion: A Model. PLoS Comput. Biol. 12 (6) (2016)
Endre T. Somogyi, Amit Hagar, James A. Glazier
Towards a multi-scale agent-based programming language methodology. WSC (2016)
Endre T. Somogyi, Jean-Marie Bouteiller, James A. Glazier, Matthias König, J. Kyle Medley, Maciej H. Swat, Herbert M. Sauro
libRoadRunner: A High Performance SBML Simulation and Analysis Library. CoRR (2015)
Endre T. Somogyi, Jean-Marie Bouteiller, James A. Glazier, Matthias König, J. Kyle Medley, Maciej H. Swat, Herbert M. Sauro
libRoadRunner: a high performance SBML simulation and analysis library. Bioinform. 31 (20) (2015)
James P. Sluka, Abbas Shirinifard, Maciej Swat, Alin Cosmanescu, Randy W. Heiland, James A. Glazier
The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents. Bioinform. 30 (16) (2014)
Abbas Shirinifard, James A. Glazier, Maciej Swat, J. Scott Gens, Fereydoon Family, Yi Jiang, Hans E. Grossniklaus
Adhesion Failures Determine the Pattern of Choroidal Neovascularization in the Eye: A Computer Simulation Study. PLoS Comput. Biol. 8 (5) (2012)
Randy W. Heiland, Abbas Shirinifard, Maciej Swat, Gilberto L. Thomas, James P. Sluka, Andrew Lumsdaine, Benjamin Zaitlen, James A. Glazier
Visualizing cells and their connectivity graphs for CompuCell3D. BioVis (2012)
Dragos Amarie, James A. Glazier
Label-Free Microcavity Biosensors: Steps towards Personalized Medicine. Sensors 12 (12) (2012)
Susan D. Hester, Julio M. Belmonte, J. Scott Gens, Sherry G. Clendenon, James A. Glazier
A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation. PLoS Comput. Biol. 7 (10) (2011)
David E. Larson, Ruth I. Johnson, Maciej Swat, Julia B. Cordero, James A. Glazier, Ross L. Cagan
Pupal Eye. PLoS Comput. Biol. 6 (7) (2010)
Randy W. Heiland, Maciej Swat, Benjamin Zaitlen, James A. Glazier, Andrew Lumsdaine
Workflows for parameter studies of multi-cell modeling. SpringSim (2010)
Roeland Merks, Erica D. Perryn, Abbas Shirinifard, James A. Glazier
Contact-Inhibited Chemotaxis in De Novo and Sprouting Blood-Vessel Growth. PLoS Comput. Biol. 4 (9) (2008)
Trevor M. Cickovski, Kedar Aras, Maciej Swat, Roeland Merks, Tilmann Glimm, H. George E. Hentschel, Mark S. Alber, James A. Glazier, Stuart A. Newman, Jesús A. Izaguirre
From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development. Comput. Sci. Eng. 9 (4) (2007)
Nan Chen, James A. Glazier, Jesús A. Izaguirre, Mark S. Alber
A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis. Comput. Phys. Commun. 176 (11-12) (2007)
Nan Chen, James A. Glazier, Mark S. Alber
A Parallel Implementation of the Cellular Potts Model for Simulation of Cell-Based Morphogenesis. ACRI (2006)
Mark S. Alber, Thomas Hou, James A. Glazier, Yi Jiang
Special Issue on Multiscale Modeling in Biology. Multiscale Model. Simul. 3 (2) (2005)
Trevor M. Cickovski, Chengbang Huang, Rajiv Chaturvedi, Tilmann Glimm, H. George E. Hentschel, Mark S. Alber, James A. Glazier, Stuart A. Newman, Jesús A. Izaguirre
A Framework for Three-Dimensional Simulation of Morphogenesis. IEEE ACM Trans. Comput. Biol. Bioinform. 2 (4) (2005)
Rajiv Chaturvedi, Chengbang Huang, Jesús A. Izaguirre, Stuart A. Newman, James A. Glazier, Mark S. Alber
A Hybrid Discrete-Continuum Model for 3-D Skeletogenesis of the Vertebrate Limb. ACRI (2004)
Jesús A. Izaguirre, Rajiv Chaturvedi, Chengbang Huang, Trevor M. Cickovski, J. Coffland, Gilberto L. Thomas, Gabor Forgacs, Mark S. Alber, H. George E. Hentschel, Stuart A. Newman, James A. Glazier
COMPUCELL, a multi-model framework for simulation of morphogenesis. Bioinform. 20 (7) (2004)
Roeland Merks, Stuart A. Newman, James A. Glazier
Cell-Oriented Modeling of In Vitro Capillary Development. ACRI (2004)
Rajiv Chaturvedi, Jesús A. Izaguirre, Chengbang Huang, Trevor M. Cickovski, P. Virtue, Gilberto L. Thomas, Gabor Forgacs, Mark S. Alber, H. George E. Hentschel, Stuart A. Newman, James A. Glazier
Multi-model Simulations of Chicken Limb Morphogenesis. International Conference on Computational Science (2003)