List of works - James A. Glazier

3D multi-cell simulation of tumor growth and angiogenesis

scientific article (publication date: 2009)

3D quantitative analyses of angiogenic sprout growth dynamics.

scientific article

3D simulations of wet foam coarsening evidence a self similar growth regime.

scientific article

A Computational Model of Peripheral Photocoagulation for the Prevention of Progressive Diabetic Capillary Occlusion

scientific article

A Liver-Centric Multiscale Modeling Framework for Xenobiotics

scientific article

A MODELING AND SIMULATION LANGUAGE FOR BIOLOGICAL CELLS WITH COUPLED MECHANICAL AND CHEMICAL PROCESSES

A Notch positive feedback in the intestinal stem cell niche is essential for stem cell self-renewal.

scientific article

A computational model of liver tissue damage and repair

scientific article published on 21 December 2020

A framework for three-dimensional simulation of morphogenesis

scientific article published in October 2005

A modular framework for multiscale multicellular spatial modeling of viral infection, immune response and drug therapy timing and efficacy in epithelial tissues

scientific article published on 29 April 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

scientific article published on 21 December 2020

A multi-cell, multi-scale model of vertebrate segmentation and somite formation

scientific article (publication date: October 2011)

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

scientific article published on June 2007

A simple automated method for continuous fieldwise measurement of microvascular hemodynamics

scientific article published on 28 November 2018

A threaded Java concurrent implementation of the Monte-Carlo Metropolis Ising model ⬇️

scientific article published on 01 June 2009

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

scientific article published on May 3, 2012

Adhesion between cells, diffusion of growth factors, and elasticity of the AER produce the paddle shape of the chick limb

scientific article published on 01 January 2007

Analysis of tissue flow patterns during primitive streak formation in the chick embryo

scientific article

Anomalous diffusion and non-Gaussian velocity distribution of Hydra cells in cellular aggregates

article published in 2001

Bulk elastic properties of chicken embryos during somitogenesis

scientific article published on 30 March 2010

Cell elongation is key to in silico replication of in vitro vasculogenesis and subsequent remodeling

scientific article published on December 2005

Cell movement during chick primitive streak formation

scientific article published in August 2006

Coarsening foams robustly reach a self-similar growth regime.

scientific article

Compact microfluidic structures for generating spatial and temporal gradients

scientific article published on 14 November 2007

Computer simulation of cellular patterning within the Drosophila pupal eye

scientific article (publication date: 2010)

Computer simulations of cell sorting due to differential adhesion

scientific article

Contact-inhibited chemotaxis in de novo and sprouting blood-vessel growth

scientific article

Coordinated action of N-CAM, N-cadherin, EphA4, and ephrinB2 translates genetic prepatterns into structure during somitogenesis in chick

scientific article published on January 2008

Development of a coupled simulation toolkit for computational radiation biology based on Geant4 and CompuCell3D

scientific article published on 18 December 2020

Dynamic mechanisms of blood vessel growth.

scientific article published on January 2006

Dynamical mechanisms for skeletal pattern formation in the vertebrate limb

scientific article published on 01 August 2004

Emergent Stratification in Solid Tumors Selects for Reduced Cohesion of Tumor Cells: A Multi-Cell, Virtual-Tissue Model of Tumor Evolution Using CompuCell3D

2015 scientific article

Evidence against ‘ultrahard’ thermal turbulence at very high Rayleigh numbers

scientific article published in Nature

Experimental growth law for bubbles in a moderately "wet" 3D liquid foam

scientific article published on 02 August 2007

Filopodial-Tension Model of Convergent-Extension of Tissues

scientific article (publication date: June 2016)

Formalizing Knowledge in Multi-Scale Agent-Based Simulations

scientific article published on 01 October 2016

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

scientific article published on January 2007

Front instabilities and invasiveness of simulated 3D avascular tumors ⬇️

scientific article

Front instabilities and invasiveness of simulated avascular tumors ⬇️

scientific article published on 21 February 2009

General, open-source vertex modeling in biological applications using Tissue Forge

scientific article published in 2023

Generation of multicellular spatiotemporal models of population dynamics from ordinary differential equations, with applications in viral infection

scientific article published in 2021

Interplay between activator-inhibitor coupling and cell-matrix adhesion in a cellular automaton model for chondrogenic patterning

scientific article published in July 2004

Label-free microcavity biosensors: steps towards personalized medicine

scientific article

Microfluidic devices integrating microcavity surface-plasmon-resonance sensors: glucose oxidase binding-activity detection

scientific article published on January 2010

Mitochondrial depolarization and repolarization in the early stages of acetaminophen hepatotoxicity in mice

scientific article published on 18 April 2020

Modeling gastrulation in the chick embryo: formation of the primitive streak

scientific article published in 2010

Modeling of xenobiotic transport and metabolism in virtual hepatic lobule models

scientific article published in PLoS ONE

Molecular jenga: the percolation phase transition (collapse) in virus capsids

Multi-scale modeling of tissues using CompuCell3D

2012 scientific article

Multicell simulations of development and disease using the CompuCell3D simulation environment

2009 scientific article

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

scientific article published on 25 October 2021

Progression of Diabetic Capillary Occlusion: A Model

scientific article

Rapid community-driven development of a SARS-CoV-2 tissue simulator ⬇️

scientific article published on 06 April 2020

Self-similar mitochondrial DNA.

scientific article published in January 2004

Simulating convergent extension by way of anisotropic differential adhesion ⬇️

scientific article published on May 21, 2003

Simulation of biological cell sorting using a two-dimensional extended Potts model

scientific article

Simulation of single-species bacterial-biofilm growth using the Glazier-Graner-Hogeweg model and the CompuCell3D modeling environment

scientific article published on April 2008

Solving the advection-diffusion equations in biological contexts using the cellular Potts model

scientific article published on 10 October 2005

Somites without a clock.

scientific article

Spatial Temporal Analysis of Fieldwise Flow in Microvasculature

scientific article published on 18 November 2019

TOWARDS A MULTI-SCALE AGENT-BASED PROGRAMMING LANGUAGE METHODOLOGY.

scientific article published in December 2016

The 2019 mathematical oncology roadmap

scientific article published on 19 June 2019

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

scientific article

Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection

scientific article published on 16 June 2020

Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection

scientific article published on 15 March 2022

Transcriptome analysis reveals manifold mechanisms of cyst development in ADPKD.

scientific article

Unification of aggregate growth models by emergence from cellular and intracellular mechanisms

scientific article published on 12 August 2020

Virtual-tissue computer simulations define the roles of cell adhesion and proliferation in the onset of kidney cystic disease

scientific article

Viscous instabilities in flowing foams: a Cellular Potts Model approach

scientific article published on January 2006

libRoadRunner: a high performance SBML simulation and analysis library

scientific article published on 17 June 2015

List of works by James A. Glazier

3D multi-cell simulation of tumor growth and angiogenesis

3D quantitative analyses of angiogenic sprout growth dynamics.

3D simulations of wet foam coarsening evidence a self similar growth regime.

A Computational Model of Peripheral Photocoagulation for the Prevention of Progressive Diabetic Capillary Occlusion

A Liver-Centric Multiscale Modeling Framework for Xenobiotics

A MODELING AND SIMULATION LANGUAGE FOR BIOLOGICAL CELLS WITH COUPLED MECHANICAL AND CHEMICAL PROCESSES

A Notch positive feedback in the intestinal stem cell niche is essential for stem cell self-renewal.

A computational model of liver tissue damage and repair

A framework for three-dimensional simulation of morphogenesis

A modular framework for multiscale multicellular spatial modeling of viral infection, immune response and drug therapy timing and efficacy in epithelial tissues

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

A multi-cell, multi-scale model of vertebrate segmentation and somite formation

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

A simple automated method for continuous fieldwise measurement of microvascular hemodynamics

A threaded Java concurrent implementation of the Monte-Carlo Metropolis Ising model ⬇️

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

Adhesion between cells, diffusion of growth factors, and elasticity of the AER produce the paddle shape of the chick limb

Analysis of tissue flow patterns during primitive streak formation in the chick embryo

Anomalous diffusion and non-Gaussian velocity distribution of Hydra cells in cellular aggregates

Bulk elastic properties of chicken embryos during somitogenesis

Cell elongation is key to in silico replication of in vitro vasculogenesis and subsequent remodeling

Cell movement during chick primitive streak formation

Coarsening foams robustly reach a self-similar growth regime.

Compact microfluidic structures for generating spatial and temporal gradients

Computer simulation of cellular patterning within the Drosophila pupal eye

Computer simulations of cell sorting due to differential adhesion

Contact-inhibited chemotaxis in de novo and sprouting blood-vessel growth

Coordinated action of N-CAM, N-cadherin, EphA4, and ephrinB2 translates genetic prepatterns into structure during somitogenesis in chick

Development of a coupled simulation toolkit for computational radiation biology based on Geant4 and CompuCell3D

Dynamic mechanisms of blood vessel growth.

Dynamical mechanisms for skeletal pattern formation in the vertebrate limb

Emergent Stratification in Solid Tumors Selects for Reduced Cohesion of Tumor Cells: A Multi-Cell, Virtual-Tissue Model of Tumor Evolution Using CompuCell3D

Evidence against ‘ultrahard’ thermal turbulence at very high Rayleigh numbers

Experimental growth law for bubbles in a moderately "wet" 3D liquid foam

Filopodial-Tension Model of Convergent-Extension of Tissues

Formalizing Knowledge in Multi-Scale Agent-Based Simulations

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

Front instabilities and invasiveness of simulated 3D avascular tumors ⬇️

Front instabilities and invasiveness of simulated avascular tumors ⬇️

General, open-source vertex modeling in biological applications using Tissue Forge

Generation of multicellular spatiotemporal models of population dynamics from ordinary differential equations, with applications in viral infection

Interplay between activator-inhibitor coupling and cell-matrix adhesion in a cellular automaton model for chondrogenic patterning

Label-free microcavity biosensors: steps towards personalized medicine

Microfluidic devices integrating microcavity surface-plasmon-resonance sensors: glucose oxidase binding-activity detection

Mitochondrial depolarization and repolarization in the early stages of acetaminophen hepatotoxicity in mice

Modeling gastrulation in the chick embryo: formation of the primitive streak

Modeling of xenobiotic transport and metabolism in virtual hepatic lobule models

Molecular jenga: the percolation phase transition (collapse) in virus capsids

Multi-scale modeling of tissues using CompuCell3D

Multicell simulations of development and disease using the CompuCell3D simulation environment

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

Progression of Diabetic Capillary Occlusion: A Model

Rapid community-driven development of a SARS-CoV-2 tissue simulator ⬇️

Self-similar mitochondrial DNA.

Simulating convergent extension by way of anisotropic differential adhesion ⬇️

Simulation of biological cell sorting using a two-dimensional extended Potts model

Simulation of single-species bacterial-biofilm growth using the Glazier-Graner-Hogeweg model and the CompuCell3D modeling environment

Solving the advection-diffusion equations in biological contexts using the cellular Potts model

Somites without a clock.

Spatial Temporal Analysis of Fieldwise Flow in Microvasculature

TOWARDS A MULTI-SCALE AGENT-BASED PROGRAMMING LANGUAGE METHODOLOGY.

The 2019 mathematical oncology roadmap

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

Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection

Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection

Transcriptome analysis reveals manifold mechanisms of cyst development in ADPKD.

Unification of aggregate growth models by emergence from cellular and intracellular mechanisms

Virtual-tissue computer simulations define the roles of cell adhesion and proliferation in the onset of kidney cystic disease

Viscous instabilities in flowing foams: a Cellular Potts Model approach

libRoadRunner: a high performance SBML simulation and analysis library