James A. Glazier

Also affiliated with Biocom

Biochemistry, Genetics and Molecular BiologyMathematicsMaterials Science

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 35 papers. Top paper: “Immune digital twins for complex human pathologies: applications, limitations, and challenges”.

Immune digital twins for complex human pathologies: applications, limitations, and challenges

npj Systems Biology and Applications(2024)10.1038/s41540-024-00450-5

N/A

0.652DataRank · unranked

76 citations

Reinhard Laubenbacher, Gary An, Yaron Ilan, Jasmin Fisher, Åsmund Flobak +42 more

Iterative community-driven development of a SARS-CoV-2 tissue simulator

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.02.019075

N/A

0.641DataRank · unranked

71 citations

Yafei Wang, Gary An, Maansi Asthana, Andrew Becker, Chase Cockrell +30 more

Multiscale Model of Antiviral Timing, Potency, and Heterogeneity Effects on an Epithelial Tissue Patch Infected by SARS-CoV-2

Viruses(2022)10.3390/v14030605

N/A

0.470DataRank · unranked

22 citations

Tarunendu Mapder, T. J. Sego, James P. Sluka, Sara K. Quinney, Morgan Craig +3 more

Advancing therapies for viral infections using mechanistic computational models of the dynamic interplay between the virus and host immune response

Current Opinion in Virology(2021)10.1016/j.coviro.2021.07.007

N/A

0.416DataRank · unranked

15 citations

Juliano F. Gianlupi, Amit Hagar, T. J. Sego, James A. Glazier, Veronika I. Zarnitsyna

Generating Agent-Based Multiscale Multicellular Spatiotemporal Models from Ordinary Differential Equations of Biological Systems, with Applications in Viral Infection

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.28.428647

N/A

0.175DataRank · unranked

2 citations

Josua O. Aponte-Serrano, Juliano F. Gianlupi, James A. Glazier, T. J. Sego

Modeling the roles of cohesotaxis, cell-intercalation, and tissue geometry in collective cell migration of Xenopus mesendoderm

Biology Open(2024)10.1242/bio.060615

N/A

0.165DataRank · unranked

2 citations

Bette J. Dzamba, Gustavo G. Pacheco, David Shook, T. J. Sego, James A. Glazier +3 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.27.064139

N/A

0DataRank · unranked

16 citations

Josua O. Aponte-Serrano, Juliano Ferrari Gianlupi, Samuel Heaps, Kira Breithaupt, Lutz Brusch +6 more

Development of a Coupled Simulation Toolkit for Computational Radiation Biology Based on Geant4 and CompuCell3D

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.09.034926

N/A

0DataRank · unranked

3 citations

Kathryn A. Higley, Maciej Swat, Mark A. J. Chaplain, Gibin Powathil, James A. Glazier +1 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.16.155267

N/A

0DataRank · unranked

2 citations

Gilberto L. Thomas, James A. Glazier, Rita M. C. de Almeida

A mechanical model of early somite segmentation

iScience(2021)10.1016/j.isci.2021.102317

N/A

0DataRank · unranked

22 citations

Agnieszka Piątkowska, Michael J. Norman, Sherry G. Clendenon, Claudio D. Stern, James A. Glazier +2 more

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

PLoS Computational Biology(2021)10.1371/journal.pcbi.1008874

N/A

0DataRank · unranked

17 citations

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

Deep Learning Approaches to Surrogates for Solving the Diffusion Equation for Mechanistic Real-World Simulations

Frontiers in Physiology(2021)10.3389/fphys.2021.667828

N/A

0DataRank · unranked

2 citations

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

Exact solution for the Anisotropic Ornstein–Uhlenbeck process

Physica A Statistical Mechanics and its Applications(2021)10.1016/j.physa.2021.126526

N/A

0DataRank · unranked

1 citations

Guilherme S. Y. Giardini, Mendeli H. Vainstein, James A. Glazier, Gilberto L. Thomas, Rita M. C. de Almeida

A Multiscale Multicellular Spatiotemporal Model of Local Influenza Infection and Immune Response

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.20.432089

N/A

0DataRank · unranked

1 citations

Ericka Mochan, G. Bard Ermentrout, James A. Glazier, T. J. Sego

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

npj Digital Medicine(2022)10.1038/s41746-022-00610-z

N/A

0DataRank · unranked

160 citations

Anna Niarakis, Tomáš Helikar, Gary An, Bruce E. Shapiro, Rahuman S. Malik‐Sheriff +5 more

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology

Briefings in Bioinformatics(2022)10.1093/bib/bbac212

N/A

0DataRank · unranked

30 citations

Dagmar Waltemath, James A. Glazier, Falk Schreiber, Sarah Keating, David P Nickerson +8 more

Model Integration in Computational Biology: The Role of Reproducibility, Credibility and Utility

Frontiers in Systems Biology(2022)10.3389/fsysb.2022.822606

N/A

0DataRank · unranked

17 citations

Rahuman S. Malik‐Sheriff, James M. Osborne, Gilberto González‐Parra, Eric Forgoston, Ruth Bowness +13 more

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

NAR Genomics and Bioinformatics(2022)10.1093/nargab/lqac020

N/A

0DataRank · unranked

6 citations

Gilberto L. Thomas, James A. Glazier, Rita M. C. de Almeida

Tissue Forge: Interactive Biological and Biophysics Simulation Environment

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.28.518300

N/A

0DataRank · unranked

3 citations

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

Tissue Forge: Interactive biological and biophysics simulation environment

PLoS Computational Biology(2023)10.1371/journal.pcbi.1010768

N/A

0DataRank · unranked

20 citations

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

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

Scientific Reports(2023)10.1038/s41598-023-45127-x

N/A

0DataRank · unranked

11 citations

Tien Comlekoglu, Shayn M. Peirce, Douglas W. DeSimone, James A. Glazier, T. J. Sego

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

PLoS ONE(2023)10.1371/journal.pone.0287736

N/A

0DataRank · unranked

4 citations

James A. Glazier, J. Quetzalcóatl Toledo-Marín

Modeling the roles of cohesotaxis, cell-intercalation, and tissue geometry in collective cell migration of Xenopus mesendoderm

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.16.562601

N/A

0DataRank · unranked

1 citations

Bette J. Dzamba, Gustavo G. Pacheco, David Shook, T. J. Sego, James A. Glazier +3 more

Forum on immune digital twins: a meeting report

arXiv (Cornell University)(2023)10.48550/arxiv.2310.18374

N/A

0DataRank · unranked

1 citations

Fred Adler, Gary An, Filippo Castiglione, Stephen Eubank, Luís L. Fonseca +14 more

Cell Modeling in Jupyter Notebook using CompuCell3D

Zenodo (CERN European Organization for Nuclear Research)(2023)10.5281/zenodo.7600786

N/A

0DataRank · unranked

0 citations

T. J. Sego, James A. Glazier, Trinity Chung

General, Open-Source Vertex Modeling in Biological Applications Using Tissue Forge

Research Square(2023)10.21203/rs.3.rs-2886960/v1

N/A

0DataRank · unranked

0 citations

Tien Comlekoglu, Shayn M. Peirce, Douglas W. DeSimone, James A. Glazier, T. J. Sego

Forum on immune digital twins: a meeting report

npj Systems Biology and Applications(2024)10.1038/s41540-024-00345-5

N/A

0DataRank · unranked

24 citations

Fred Adler, Gary An, Filippo Castiglione, Stephen Eubank, Luís L. Fonseca +14 more

EFECT: A Method to Quantify the Reproducibility of Stochastic Simulations

arXiv (Cornell University)(2024)10.48550/arxiv.2406.16820

N/A

0DataRank · unranked

0 citations

Matthias König, Luís L. Fonseca, Pathirana, Dilan, Bergmann, Frank T., Grecco, Hernán E. +11 more

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 Computational Biology(2020)10.1371/journal.pcbi.1008451

N/A

0DataRank · unranked

75 citations

Josua O. Aponte-Serrano, Juliano F. Gianlupi, Samuel Heaps, Kira Breithaupt, Lutz Brusch +6 more

Modeling Epithelial Morphogenesis and Cell Rearrangement during Zebrafish Epiboly: Tissue Deformation, Cell-Cell Coupling, and the Mechanical Response to Stress

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.02.12.637977

N/A

0DataRank · unranked

1 citations

T. J. Sego, David M. Umulis, Mary C. Mullins, James A. Glazier, Sharon B. Minsuk

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

Physics in Medicine and Biology(2020)10.1088/1361-6560/abd4f9

N/A

0DataRank · unranked

19 citations

Kathryn A. Higley, Maciej Swat, Mark A. J. Chaplain, Gibin Powathil, James A. Glazier +1 more

A computational model of liver tissue damage and repair

PLoS ONE(2020)10.1371/journal.pone.0243451

N/A

0DataRank · unranked

17 citations

Xiao Fu, James P. Sluka, Sherry G. Clendenon, Victoria D. Sluka, Zemin Wang +4 more

Parameterizing cell movement when the instantaneous cell migration velocity is ill-defined

Physica A Statistical Mechanics and its Applications(2020)10.1016/j.physa.2020.124493

N/A

0DataRank · unranked

15 citations

Ismael Fortuna, Gabriel C. Perrone, James A. Glazier, Julio M. Belmonte, Rita M. C. de Almeida +1 more

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

Toxicology(2020)10.1016/j.tox.2020.152464

N/A

0DataRank · unranked

11 citations

Michelle Martínez, Zemin Wang, Henry Mang, Sherry G. Clendenon, James P. Sluka +3 more

CompuCell3D Simulations Reproduce Mesenchymal Cell Migration on Flat Substrates

Biophysical Journal(2020)10.1016/j.bpj.2020.04.024

N/A

0DataRank · unranked

37 citations

Gabriel C. Perrone, Monique Siebra Krug, Eduarda Susin, Julio M. Belmonte, Gilberto L. Thomas +3 more