Publications by authors named "James Faeder"

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STAT3 S727 phosphorylation drives pathogenic Th17 differentiation and neuroinflammation in autoimmune disease.
Douglas S Prado, Achyudhan R Kutuva, Richard T Cattley, Andreza Buzolin Sonego, Parth Sutariya, James R Faeder

J Neuroinflammation· October 2025

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A detailed kinetic model of Eastern equine encephalitis virus replication in a susceptible host cell.
Caroline I Larkin, Matthew D Dunn, Jason E Shoemaker, William B Klimstra, James R Faeder

PLoS Comput Biol· June 2025

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From FAIR to CURE: Guidelines for Computational Models of Biological Systems.
Herbert M Sauro, Eran Agmon, Michael L Blinov, John H Gennari, Joe Hellerstein, James R Faeder

ArXiv· February 2025

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A detailed kinetic model of Eastern equine encephalitis virus replication in a susceptible host cell.
Caroline I Larkin, Matthew D Dunn, Jason E Shoemaker, William B Klimstra, James R Faeder

bioRxiv· December 2024

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MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface.
Adam Husar, Mariam Ordyan, Guadalupe C Garcia, Joel G Yancey, Ali S Saglam, James R Faeder

PLoS Comput Biol· April 2024

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Predicting gene-level sensitivity to JAK-STAT signaling perturbation using a mechanistic-to-machine learning framework.
Neha Cheemalavagu, Karsen E Shoger, Yuqi M Cao, Brandon A Michalides, Samuel A Botta, James R Faeder

Cell Syst· January 2024

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Predicting gene level sensitivity to JAK-STAT signaling perturbation using a mechanistic-to-machine learning framework.
Neha Cheemalavagu, Karsen E Shoger, Yuqi M Cao, Brandon A Michalides, Samuel A Botta, James R Faeder

bioRxiv· May 2023

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A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0].
Anthony T Bogetti, Jeremy M G Leung, John D Russo, She Zhang, Jeff P Thompson, James R Faeder

Living J Comput Mol Sci· January 2023

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BioSimulators: a central registry of simulation engines and services for recommending specific tools.
Bilal Shaikh, Lucian P Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, James R Faeder

Nucleic Acids Res· July 2022

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Model Integration in Computational Biology: The Role of Reproducibility, Credibility and Utility.
Jonathan Karr, Rahuman S Malik-Sheriff, James Osborne, Gilberto Gonzalez-Parra, Eric Forgoston, James R Faeder

Front Syst Biol· March 2022

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Combination treatment optimization using a pan-cancer pathway model.
Robin Schmucker, Gabriele Farina, James Faeder, Fabian Fröhlich, Ali Sinan Saglam

PLoS Comput Biol· December 2021

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Iterative community-driven development of a SARS-CoV-2 tissue simulator.
Michael Getz, Yafei Wang, Gary An, Maansi Asthana, Andrew Becker, James R Faeder

bioRxiv· November 2021

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SBML Level 3: an extensible format for the exchange and reuse of biological models.
Sarah M Keating, Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, James R Faeder

Mol Syst Biol· August 2020

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Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2.
Fengkai Zhang, Lucian P Smith, Michael L Blinov, James Faeder, William S Hlavacek

J Integr Bioinform· July 2020

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Parallel Tempering with Lasso for model reduction in systems biology.
Sanjana Gupta, Robin E C Lee, James R Faeder

PLoS Comput Biol· March 2020

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Harnessing Human Microphysiology Systems as Key Experimental Models for Quantitative Systems Pharmacology.
D Lansing Taylor, Albert Gough, Mark E Schurdak, Lawrence Vernetti, Chakra S Chennubhotla, James R Faeder

Handb Exp Pharmacol· January 2020

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MCell-R: A Particle-Resolution Network-Free Spatial Modeling Framework.
Jose-Juan Tapia, Ali Sinan Saglam, Jacob Czech, Robert Kuczewski, Thomas M Bartol, James R Faeder

Methods Mol Biol· July 2019

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Heterogeneities in Axonal Structure and Transporter Distribution Lower Dopamine Reuptake Efficiency.
Cihan Kaya, Mary H Cheng, Ethan R Block, Tom M Bartol, Terrence J Sejnowski, James R Faeder

eNeuro· January 2019

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Shift from stochastic to spatially-ordered expression of serine-glycine synthesis enzymes in 3D microtumors.
Manjulata Singh, Katsuhiko Warita, Tomoko Warita, James R Faeder, Robin E C Lee

Sci Rep· June 2018

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Evaluation of Parallel Tempering to Accelerate Bayesian Parameter Estimation in Systems Biology.
Sanjana Gupta, Liam Hainsworth, Justin S Hogg, Robin E C Lee, James R Faeder

Proc Euromicro Int Conf Parallel Distrib Netw Based Process· March 2018

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NF-κB Dynamics Discriminate between TNF Doses in Single Cells.
Qiuhong Zhang, Sanjana Gupta, David L Schipper, Gabriel J Kowalczyk, Allison E Mancini, James R Faeder

Cell Syst· December 2017

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Automated visualization of rule-based models.
John Arul Prakash Sekar, Jose-Juan Tapia, James R Faeder

PLoS Comput Biol· November 2017

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Demystifying the cytokine network: Mathematical models point the way.
Penelope A Morel, Robin E C Lee, James R Faeder

Cytokine· October 2017

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BioNetGen 2.2: advances in rule-based modeling.
Leonard A Harris, Justin S Hogg, José-Juan Tapia, John A P Sekar, Sanjana Gupta, James R Faeder

Bioinformatics· November 2016

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Reductionism Is Dead: Long Live Reductionism! Systems Modeling Needs Reductionist Experiments.
James R Faeder, Penelope A Morel

Biophys J· April 2016

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