James R. Faeder

This study shows that mitotic nanotubes, influenced by Cx43 trafficking and actin remodeling, enable reduced gap junction communication during cell division.

This paper develops a rule-based kinetic model of EEEV replication in mammalian cells, calibrated with experimental data, revealing ribosome density on viral RNA as critical for rapid replication and identifying transcription as a therapeutic target.

The paper predicts gene sensitivity to JAK-STAT perturbation by linking STAT phosphorylation dynamics to gene expression using a mechanistic-to-machine learning framework.

WEBNG simplifies rare event sampling in rule-based models by integrating BioNetGen and WESTPA, enabling efficient simulation with default parameters.

This paper uses a pan-cancer pathway model to identify novel combination therapies and optimize treatment sequences for cancer cell lines.

The paper compares different computational methods for simulating cellular biochemistry and identifies discrepancies in results, emphasizing the need for critical evaluation of models.

Open-source agent-based PhysiCell model of SARS-CoV-2 infection in lung epithelium; version 5 clears virus in about 6 days in simulation, and delayed T cell arrival increases epithelial loss.

This paper uses Bayesian model reduction with Lasso to identify minimal reaction subsets in signaling networks that reproduce experimental data.