Published BioNetGen Models
This page links to publications that have applied a BioNetGen rule-based model to a specific biological system. Note: This list is a work in progress and may not be complete.
- NF-κB-Chromatin Interactions Drive Diverse Phenotypes by Modulating Transcriptional Noise. Cell Reports
- Computational modeling of synergistic interaction between αVβ3 integrin and VEGFR2 in endothelial cells: Implications for the mechanism of action of angiogenesis-modulating integrin-binding peptides. J. Theor. Biol.
- Needs updated
- Modelling intracellular competition for calcium: kinetic and thermodynamic control of different molecular modes of signal decoding. Sci. Rep.
- Feedbacks, Bifurcations, and Cell Fate Decision-Making in the p53 System. PLOS Comput. Biol.
- Integrated Stochastic Model of DNA Damage Repair by Non-homologous End Joining and p53/p21- Mediated Early Senescence Signalling. PLOS Comput. Biol.
- Use of mechanistic models to integrate and analyze multiple proteomic datasets. Biophys. J.
- Cutting Edge: Differential Regulation of PTEN by TCR, Akt, and FoxO1 Controls CD4+ T Cell Fate Decisions. J. Immunol.
- Computational analysis of an autophagy/translation switch based on mutual inhibition of MTORC1 and ULK1. PLOS One
- Analytical reduction of combinatorial complexity arising from multiple protein modification sites. J. R. Soc. Interface
- Multi-level kinetic model of mRNA delivery via transfection of lipoplexes. PLOS One
- Phosphorylation site dynamics of early T-cell receptor signaling. PLOS One
- Biosensor architectures for high-fidelity reporting of cellular signaling. Biophys. J.
- An Interaction Library for the FcεRI Signaling Network. Frontiers Immunol.
- Recruitment of the adaptor protein Grb2 to EGFR tetramers. Biochemistry
- Spatial rule-based modeling: a method and its application to the human mitotic kinetochore. Cells
- Spontaneous NF-κB activation by autocrine TNFα signaling: a computational analysis. PLOS One
- Pleomorphic ensembles: formation of large clusters composed of weakly interacting multivalent molecules. Biophys. J.
- Modeling the effect of APC truncation on destruction complex function in colorectal cancer cells. PLOS Comput. Biol.
- Prediction stability in a data-based, mechanistic model of σF regulation during sporulation in Bacillus subtilis. Sci. Rep.
- Exploring higher-order EGFR oligomerisation and phosphorylation–a combined experimental and theoretical approach. Mol. Biosyst.
- Disease-enhancing antibodies improve the efficacy of bacterial toxin-neutralizing antibodies. Cell Host Microbe
- Systems model of T cell receptor proximal signaling reveals emergent ultrasensitivity. PLOS Comput. Biol.
- Single-cell measurements of IgE-mediated FcεRI signaling using an integrated microfluidic platform. PLOS One
- Computational analysis of Rho GTPase cycling. PLOS Comput. Biol.
- A predictive mathematical model of the DNA damage G2 checkpoint. J. Theor. Biol.
- A mechanistic model of early FcεRI signaling: lipid rafts and the question of protection from dephosphorylation. PLOS One
- Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling. BMC Syst. Biol.
- A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn. J. Immunol.
- CaMKII activation and dynamics are independent of the holoenzyme structure: an infinite subunit holoenzyme approximation. Phys. Biol.
- The interplay of double phosphorylation and scaffolding in MAPK pathways. J. Theor. Biol.
- A computational analysis of the dynamic roles of talin, Dok1, and PIPKI for integrin activation. PLOS One
- Ultrasensitivity in multisite phosphorylation of membrane-anchored proteins. Biophys. J.
- Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range. PNAS
- Shaping the response: the role of FcεRI and Syk expression levels in mast cell signaling. IET Syst. Biol.
- A detailed mathematical model predicts that serial engagement of IgE-FcεRI complexes can enhance Syk activation in mast cells. J. Immunol.
- Modeling multivalent ligand-receptor interactions with steric constraints on configurations of cell-surface receptor aggregates. Biophys. J.
- Analysis and verification of the HMGB1 signaling pathway. BMC Bioinformatics
- Adaptable functionality of transcriptional feedback in bacterial two-component systems. PLOS Comput. Biol.
- A role for rebinding in rapid and reliable T cell responses to antigen. PLOS Comput. Biol.
- A bipolar clamp mechanism for activation of Jak-family protein tyrosine kinases. PLOS Comput. Biol.
- Detailed qualitative dynamic knowledge representation using a BioNetGen model of TLR-4 signaling and preconditioning. Math. Biosci.
- Aggregation of membrane proteins by cytosolic cross-linkers: theory and simulation of the LAT-Grb2-SOS1 system. Biophys. J.
- Computational models of tandem SRC homology 2 domain interactions and application to phosphoinositide 3-kinase. J. Biol. Chem.
- Carbon-fate maps for metabolic reactions. Bioinformatics
- A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity. Biosystems
- Combinatorial complexity and dynamical restriction of network flows in signal transduction. IET Syst. Biol.