James A. Glazier

44 papers A 1C 2Misc 2Journal 30Unranked 8
YearRankTypeTitle / Venue / Authors
2025 J jnl
Generative diffusion model surrogates for mechanistic agent-based biological models.
CoRR
Tien Comlekoglu, Javier Quetzalcóatl Toledo-Marín, Douglas W. DeSimone, Shayn M. Peirce, Geoffrey C. Fox, James A. Glazier
2025 J jnl
Generative diffusion model surrogates for mechanistic agent-based biological models.
Mach. Learn. Sci. Technol.
Tien Comlekoglu, Javier Quetzalcóatl Toledo-Marín, Douglas W. DeSimone, Shayn M. Peirce, Geoffrey C. Fox, James A. Glazier
2025 J jnl
Surrogate modeling of Cellular-Potts Agent-Based Models as a segmentation task using the U-Net neural network architecture.
CoRR
Tien Comlekoglu, Javier Quetzalcóatl Toledo-Marín, Tina Comlekoglu, Douglas W. DeSimone, Shayn M. Peirce, Geoffrey C. Fox, James A. Glazier
2025 J jnl
Surrogate modeling of Cellular-Potts agent-based models as a segmentation task using the U-Net neural network architecture.
PLoS Comput. Biol.
Tien Comlekoglu, Javier Quetzalcóatl Toledo-Marín, Tina Comlekoglu, Douglas W. DeSimone, Shayn M. Peirce, Geoffrey C. Fox, James A. Glazier
2024 J jnl
Toward mechanistic medical digital twins: some use cases in immunology.
Frontiers Digit. Health
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
2023 J jnl
Analyzing the Performance of Deep Encoder-Decoder Networks as Surrogates for a Diffusion Equation.
CoRR
Javier Quetzalcóatl Toledo-Marín, James A. Glazier, Geoffrey C. Fox
2023 J jnl
Tissue Forge: Interactive biological and biophysics simulation environment.
PLoS Comput. Biol.
T. J. Sego, James P. Sluka, Herbert M. Sauro, James A. Glazier
2022 J jnl
Addressing
Briefings Bioinform.
Anna Niarakis, Dagmar Waltemath, James A. Glazier, Falk Schreiber, Sarah M. Keating, David P. Nickerson, Claudine Chaouiya, Anne Siegel, Vincent Noël, Henning Hermjakob, Tomás Helikar, Sylvain Soliman, Laurence Calzone
2022 J jnl
Building digital twins of the human immune system: toward a roadmap.
npj Digit. Medicine
Reinhard C. Laubenbacher, Anna Niarakis, Tomás Helikar, Gary An, Bruce Shapiro, Rahuman S. Malik-Sheriff, T. J. Sego, Adam C. Knapp, Paul Macklin, James A. Glazier
2021 J jnl
Deep learning approaches to surrogates for solving the diffusion equation for mechanistic real-world simulations.
CoRR
Javier Quetzalcóatl Toledo-Marín, Geoffrey C. Fox, James P. Sluka, James A. Glazier
2021 J jnl
Multicellular spatial model of RNA virus replication and interferon responses reveals factors controlling plaque growth dynamics.
PLoS Comput. Biol.
Josua Aponte-Serrano, Jordan J. A. Weaver, T. J. Sego, James A. Glazier, Jason E. Shoemaker
2021 J jnl
Using Deep LSD to build operators in GANs latent space with meaning in real space.
CoRR
Javier Quetzalcóatl Toledo-Marín, James A. Glazier
2020 J jnl
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.
T. J. Sego, Josua Aponte-Serrano, Juliano Ferrari Gianlupi, Samuel R. Heaps, Kira Breithaupt, Lutz Brusch, Jessica R. Crawshaw, James M. Osborne, Ellen M. Quardokus, Richard K. Plemper, James A. Glazier
2019 — conf
Learning Everywhere: Pervasive Machine Learning for Effective High-Performance Computation.
IPDPS Workshops
Geoffrey C. Fox, James A. Glazier, J. C. S. Kadupitiya, Vikram Jadhao, Minje Kim, Judy Qiu, James P. Sluka, Endre T. Somogyi, Madhav V. Marathe, Abhijin Adiga, Jiangzhuo Chen, Oliver Beckstein, Shantenu Jha
2019 J jnl
Learning Everywhere: Pervasive Machine Learning for Effective High-Performance Computation.
CoRR
Geoffrey C. Fox, James A. Glazier, J. C. S. Kadupitiya, Vikram Jadhao, Minje Kim, Judy Qiu, James P. Sluka, Endre T. Somogyi, Madhav V. Marathe, Abhijin Adiga, Jiangzhuo Chen, Oliver Beckstein, Shantenu Jha
2018 C conf
Factors Mediating Learning and Application of Computational Modeling by Life Scientists.
FIE
Aasakiran Madamanchi, Monica E. Cardella, James A. Glazier, David M. Umulis
2018 C conf
Qualitative Findings from Study of Interdisciplinary Education in Computational Modeling for Life Sciences Student Researchers from Emerging Research Institutions.
FIE
Aasakiran Madamanchi, Shenika V. Poindexter, Monica E. Cardella, James A. Glazier, David M. Umulis
2017 — conf
A modeling and simulation language for biological cells with coupled mechanical and chemical processes.
SpringSim (TMS)
Endre T. Somogyi, James A. Glazier
2017 J jnl
A modeling and simulation language for biological cells with coupled mechanical and chemical processes.
CoRR
Endre T. Somogyi, James A. Glazier
2017 — conf
Structural coupling of a Potts model cell.
ECAL
Eran Agmon, James A. Glazier, Randall D. Beer
2016 J jnl
Filopodial-Tension Model of Convergent-Extension of Tissues.
PLoS Comput. Biol.
Julio M. Belmonte, Maciej H. Swat, James A. Glazier
2016 A conf
Formalizing knowledge in multi-scale agent-based simulations.
MoDELS
Endre T. Somogyi, James P. Sluka, James A. Glazier
2016 J jnl
Progression of Diabetic Capillary Occlusion: A Model.
PLoS Comput. Biol.
Xiao Fu, J. Scott Gens, James A. Glazier, Stephen A. Burns, Thomas J. Gast
2016 Misc conf
Towards a multi-scale agent-based programming language methodology.
WSC
Endre T. Somogyi, Amit Hagar, James A. Glazier
2015 J jnl
libRoadRunner: A High Performance SBML Simulation and Analysis Library.
CoRR
Endre T. Somogyi, Jean-Marie Bouteiller, James A. Glazier, Matthias König, J. Kyle Medley, Maciej H. Swat, Herbert M. Sauro
2015 J jnl
libRoadRunner: a high performance SBML simulation and analysis library.
Bioinform.
Endre T. Somogyi, Jean-Marie Bouteiller, James A. Glazier, Matthias König, J. Kyle Medley, Maciej H. Swat, Herbert M. Sauro
2014 J jnl
The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents.
Bioinform.
James P. Sluka, Abbas Shirinifard, Maciej Swat, Alin Cosmanescu, Randy W. Heiland, James A. Glazier
2012 J jnl
Adhesion Failures Determine the Pattern of Choroidal Neovascularization in the Eye: A Computer Simulation Study.
PLoS Comput. Biol.
Abbas Shirinifard, James A. Glazier, Maciej Swat, J. Scott Gens, Fereydoon Family, Yi Jiang, Hans E. Grossniklaus
2012 J jnl
Label-Free Microcavity Biosensors: Steps towards Personalized Medicine.
Sensors
Dragos Amarie, James A. Glazier
2012 — conf
Visualizing cells and their connectivity graphs for CompuCell3D.
BioVis
Randy W. Heiland, Abbas Shirinifard, Maciej Swat, Gilberto L. Thomas, James P. Sluka, Andrew Lumsdaine, Benjamin Zaitlen, James A. Glazier
2011 J jnl
A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation.
PLoS Comput. Biol.
Susan D. Hester, Julio M. Belmonte, J. Scott Gens, Sherry G. Clendenon, James A. Glazier
2010 J jnl
Computer Simulation of Cellular Patterning Within the
PLoS Comput. Biol.
David E. Larson, Ruth I. Johnson, Maciej Swat, Julia B. Cordero, James A. Glazier, Ross L. Cagan
2010 — conf
Workflows for parameter studies of multi-cell modeling.
SpringSim
Randy W. Heiland, Maciej Swat, Benjamin Zaitlen, James A. Glazier, Andrew Lumsdaine
2008 J jnl
Contact-Inhibited Chemotaxis in De Novo and Sprouting Blood-Vessel Growth.
PLoS Comput. Biol.
Roeland Merks, Erica D. Perryn, Abbas Shirinifard, James A. Glazier
2007 J jnl
A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis.
Comput. Phys. Commun.
Nan Chen, James A. Glazier, Jesús A. Izaguirre, Mark S. Alber
2007 J jnl
From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development.
Comput. Sci. Eng.
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
2006 — conf
A Parallel Implementation of the Cellular Potts Model for Simulation of Cell-Based Morphogenesis.
ACRI
Nan Chen, James A. Glazier, Mark S. Alber
2005 J jnl
A Framework for Three-Dimensional Simulation of Morphogenesis.
IEEE ACM Trans. Comput. Biol. Bioinform.
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
2005 J jnl
Special Issue on Multiscale Modeling in Biology.
Multiscale Model. Simul.
Mark S. Alber, Thomas Yizhao Hou, James A. Glazier, Yi Jiang
2004 — conf
A Hybrid Discrete-Continuum Model for 3-D Skeletogenesis of the Vertebrate Limb.
ACRI
Rajiv Chaturvedi, Chengbang Huang, Jesús A. Izaguirre, Stuart A. Newman, James A. Glazier, Mark S. Alber
2004 J jnl
COMPUCELL, a multi-model framework for simulation of morphogenesis.
Bioinform.
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
2004 — conf
Cell-Oriented Modeling of In Vitro Capillary Development.
ACRI
Roeland Merks, Stuart A. Newman, James A. Glazier
2003 Misc conf
Multi-model Simulations of Chicken Limb Morphogenesis.
International Conference on Computational Science
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
2003 — ch.
On Cellular Automaton Approaches to Modeling Biological Cells.
Mathematical Systems Theory in Biology, Communications, Computation, and Finance
Mark S. Alber, Maria A. Kiskowski, James A. Glazier, Yi Jiang