James A. Glazier

According to our database, James A. Glazier authored at least 37 papers between 2003 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Toward mechanistic medical digital twins: some use cases in immunology.

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

Frontiers Digit. Health, 2024

2023

Tissue Forge: Interactive biological and biophysics simulation environment.

T. J. Sego, James P. Sluka, Herbert M. Sauro, James A. Glazier

PLoS Comput. Biol., October, 2023

Analyzing the Performance of Deep Encoder-Decoder Networks as Surrogates for a Diffusion Equation.

Javier Quetzalcóatl Toledo-Marín, James A. Glazier, Geoffrey C. Fox

CoRR, 2023

2022

Building digital twins of the human immune system: toward a roadmap.

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

npj Digit. Medicine, 2022

Addressing <i>barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology</i>.

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

Briefings Bioinform., 2022

2021

Multicellular spatial model of RNA virus replication and interferon responses reveals factors controlling plaque growth dynamics.

Josua Aponte-Serrano, Jordan J. A. Weaver, T. J. Sego, James A. Glazier, Jason E. Shoemaker

PLoS Comput. Biol., 2021

Deep learning approaches to surrogates for solving the diffusion equation for mechanistic real-world simulations.

Javier Quetzalcóatl Toledo-Marín, Geoffrey C. Fox, James P. Sluka, James A. Glazier

CoRR, 2021

Using Deep LSD to build operators in GANs latent space with meaning in real space.

Javier Quetzalcóatl Toledo-Marín, James A. Glazier

CoRR, 2021

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.

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

PLoS Comput. Biol., 2020

2019

Learning Everywhere: Pervasive Machine Learning for Effective High-Performance Computation.

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

Proceedings of the IEEE International Parallel and Distributed Processing Symposium Workshops, 2019

2018

Qualitative Findings from Study of Interdisciplinary Education in Computational Modeling for Life Sciences Student Researchers from Emerging Research Institutions.

Aasakiran Madamanchi, Shenika V. Poindexter, Monica E. Cardella, James A. Glazier, David M. Umulis

Proceedings of the IEEE Frontiers in Education Conference, 2018

Factors Mediating Learning and Application of Computational Modeling by Life Scientists.

Aasakiran Madamanchi, Monica E. Cardella, James A. Glazier, David M. Umulis

Proceedings of the IEEE Frontiers in Education Conference, 2018

2017

A modeling and simulation language for biological cells with coupled mechanical and chemical processes.

Endre T. Somogyi, James A. Glazier

Proceedings of the Symposium on Theory of Modeling & Simulation, Virginia Beach, VA, USA, April 23, 2017

Structural coupling of a Potts model cell.

Eran Agmon, James A. Glazier, Randall D. Beer

Proceedings of the Fourteenth European Conference Artificial Life, 2017

2016

Progression of Diabetic Capillary Occlusion: A Model.

Xiao Fu, J. Scott Gens, James A. Glazier, Stephen A. Burns, Thomas J. Gast

PLoS Comput. Biol., 2016

Filopodial-Tension Model of Convergent-Extension of Tissues.

Julio M. Belmonte, Maciej H. Swat, James A. Glazier

PLoS Comput. Biol., 2016

Towards a multi-scale agent-based programming language methodology.

Endre T. Somogyi, Amit Hagar, James A. Glazier

Proceedings of the Winter Simulation Conference, 2016

Formalizing knowledge in multi-scale agent-based simulations.

Endre T. Somogyi, James P. Sluka, James A. Glazier

Proceedings of the ACM/IEEE 19th International Conference on Model Driven Engineering Languages and Systems, 2016

2015

libRoadRunner: a high performance SBML simulation and analysis library.

Endre T. Somogyi, Jean-Marie Bouteiller, James A. Glazier, Matthias König, J. Kyle Medley, Maciej H. Swat, Herbert M. Sauro

Bioinform., 2015

2014

The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents.

James P. Sluka, Abbas Shirinifard, Maciej Swat, Alin Cosmanescu, Randy W. Heiland, James A. Glazier

Bioinform., 2014

2012

Label-Free Microcavity Biosensors: Steps towards Personalized Medicine.

Dragos Amarie, James A. Glazier

Sensors, 2012

Adhesion Failures Determine the Pattern of Choroidal Neovascularization in the Eye: A Computer Simulation Study.

Abbas Shirinifard, James A. Glazier, Maciej Swat, J. Scott Gens, Fereydoon Family, Yi Jiang, Hans E. Grossniklaus

PLoS Comput. Biol., 2012

Visualizing cells and their connectivity graphs for CompuCell3D.

Randy W. Heiland, Abbas Shirinifard, Maciej Swat, Gilberto L. Thomas, James P. Sluka, Andrew Lumsdaine, Benjamin Zaitlen, James A. Glazier

Proceedings of the 2012 IEEE Symposium on Biological Data Visualization, 2012

2011

A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation.

Susan D. Hester, Julio M. Belmonte, J. Scott Gens, Sherry G. Clendenon, James A. Glazier

PLoS Comput. Biol., 2011

2010

Computer Simulation of Cellular Patterning Within the <i>Drosophila</i> Pupal Eye.

David E. Larson, Ruth I. Johnson, Maciej Swat, Julia B. Cordero, James A. Glazier, Ross L. Cagan

PLoS Comput. Biol., 2010

Workflows for parameter studies of multi-cell modeling.

Randy W. Heiland, Maciej Swat, Benjamin Zaitlen, James A. Glazier, Andrew Lumsdaine

Proceedings of the 2010 Spring Simulation Multiconference, 2010

2008

Contact-Inhibited Chemotaxis in De Novo and Sprouting Blood-Vessel Growth.

Roeland Merks, Erica D. Perryn, Abbas Shirinifard, James A. Glazier

PLoS Comput. Biol., 2008

2007

From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development.

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

Comput. Sci. Eng., 2007

A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis.

Nan Chen, James A. Glazier, Jesús A. Izaguirre, Mark S. Alber

Comput. Phys. Commun., 2007

2006

A Parallel Implementation of the Cellular Potts Model for Simulation of Cell-Based Morphogenesis.

Nan Chen, James A. Glazier, Mark S. Alber

Proceedings of the Cellular Automata, 2006

2005

A Framework for Three-Dimensional Simulation of Morphogenesis.

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

IEEE ACM Trans. Comput. Biol. Bioinform., 2005

Special Issue on Multiscale Modeling in Biology.

Mark S. Alber, Thomas Yizhao Hou, James A. Glazier, Yi Jiang

Multiscale Model. Simul., 2005

2004

COMPUCELL, a multi-model framework for simulation of morphogenesis.

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

Bioinform., 2004

Cell-Oriented Modeling of In Vitro Capillary Development.

Roeland Merks, Stuart A. Newman, James A. Glazier

Proceedings of the Cellular Automata, 2004

A Hybrid Discrete-Continuum Model for 3-D Skeletogenesis of the Vertebrate Limb.

Rajiv Chaturvedi, Chengbang Huang, Jesús A. Izaguirre, Stuart A. Newman, James A. Glazier, Mark S. Alber

Proceedings of the Cellular Automata, 2004

2003

Multi-model Simulations of Chicken Limb Morphogenesis.

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

Proceedings of the Computational Science - ICCS 2003, 2003

On Cellular Automaton Approaches to Modeling Biological Cells.

Mark S. Alber, Maria A. Kiskowski, James A. Glazier, Yi Jiang

Proceedings of the Mathematical Systems Theory in Biology, 2003