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ORCIDJames A. Glazier
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2020 – today
- 2024
[j20]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)- 2023
- [j19]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) - [i6]Javier Quetzalcóatl Toledo-Marín, James A. Glazier, Geoffrey C. Fox:
Analyzing the Performance of Deep Encoder-Decoder Networks as Surrogates for a Diffusion Equation. CoRR abs/2302.03786 (2023) - 2022
- [j18]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:
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. Briefings Bioinform. 23(4) (2022) - [j17]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) - 2021
- [j16]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) - [i5]Javier Quetzalcóatl Toledo-Marín, James A. Glazier:
Using Deep LSD to build operators in GANs latent space with meaning in real space. CoRR abs/2102.05132 (2021) - [i4]Javier 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 abs/2102.05527 (2021) - 2020
- [j15]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:
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)
2010 – 2019
- 2019
- [c13]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:
Learning Everywhere: Pervasive Machine Learning for Effective High-Performance Computation. IPDPS Workshops 2019: 422-429 - [i3]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:
Learning Everywhere: Pervasive Machine Learning for Effective High-Performance Computation. CoRR abs/1902.10810 (2019) - 2018
- [c12]Aasakiran Madamanchi, Monica E. Cardella, James A. Glazier, David M. Umulis:
Factors Mediating Learning and Application of Computational Modeling by Life Scientists. FIE 2018: 1-5 - [c11]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: 1-5 - 2017
- [c10]Eran Agmon, James A. Glazier, Randall D. Beer:
Structural coupling of a Potts model cell. ECAL 2017: 13-20 - [c9]Endre T. Somogyi, James A. Glazier:
A modeling and simulation language for biological cells with coupled mechanical and chemical processes. SpringSim (TMS) 2017: 14:1-14:12 - [i2]Endre T. Somogyi, James A. Glazier:
A modeling and simulation language for biological cells with coupled mechanical and chemical processes. CoRR abs/1701.00317 (2017) - 2016
- [j14]Julio M. Belmonte, Maciej H. Swat, James A. Glazier:
Filopodial-Tension Model of Convergent-Extension of Tissues. PLoS Comput. Biol. 12(6) (2016) - [j13]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) - [c8]Endre T. Somogyi, James P. Sluka, James A. Glazier:
Formalizing knowledge in multi-scale agent-based simulations. MoDELS 2016: 115-122 - [c7]Endre T. Somogyi, Amit Hagar, James A. Glazier:
Towards a multi-scale agent-based programming language methodology. WSC 2016: 1230-1240 - 2015
- [j12]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): 3315-3321 (2015) - [i1]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 abs/1503.01095 (2015) - 2014
- [j11]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): 2367-2374 (2014) - 2012
- [j10]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) - [j9]Dragos Amarie, James A. Glazier:
Label-Free Microcavity Biosensors: Steps towards Personalized Medicine. Sensors 12(12): 17262-17294 (2012) - [c6]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: 85-90 - 2011
- [j8]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) - 2010
- [j7]David E. Larson, Ruth I. Johnson, Maciej Swat, Julia B. Cordero, James A. Glazier, Ross L. Cagan:
Computer Simulation of Cellular Patterning Within the Drosophila Pupal Eye. PLoS Comput. Biol. 6(7) (2010) - [c5]Randy W. Heiland, Maciej Swat, Benjamin Zaitlen, James A. Glazier, Andrew Lumsdaine:
Workflows for parameter studies of multi-cell modeling. SpringSim 2010: 94
2000 – 2009
- 2008
- [j6]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) - 2007
- [j5]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): 670-681 (2007) - [j4]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): 50-60 (2007) - 2006
- [c4]Nan Chen, James A. Glazier, Mark S. Alber:
A Parallel Implementation of the Cellular Potts Model for Simulation of Cell-Based Morphogenesis. ACRI 2006: 58-67 - 2005
- [j3]Mark S. Alber, Thomas Yizhao Hou, James A. Glazier, Yi Jiang:
Special Issue on Multiscale Modeling in Biology. Multiscale Model. Simul. 3(2) (2005) - [j2]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): 273-288 (2005) - 2004
- [j1]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): 1129-1137 (2004) - [c3]Roeland Merks, Stuart A. Newman, James A. Glazier:
Cell-Oriented Modeling of In Vitro Capillary Development. ACRI 2004: 425-434 - [c2]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: 543-552 - 2003
- [c1]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: 39-49 - [p1]Mark S. Alber, Maria A. Kiskowski, James A. Glazier, Yi Jiang:
On Cellular Automaton Approaches to Modeling Biological Cells. Mathematical Systems Theory in Biology, Communications, Computation, and Finance 2003: 1-39
Coauthor Index
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