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.

Help keep this page current by sending your publications to our email or Twitter.

2023

• Korwek Z et al. Non-self RNA rewires IFNβ signaling: A mathematical model of the innate immune response. Sci. Signaling
• Zhang Y et al. Combining Multikinase Tyrosine Kinase Inhibitors Targeting the Vascular Endothelial Growth Factor andCluster ofDifferentiation 47 Signaling Pathways IsPredicted toIncrease theEfficacy of Antiangiogenic Combination Therapies ACS Pharmacol. Transl. Sci.

2022

• Nosbisch JL et al. A kinetic model of phospholipase C-γ1 linking structure-based insights to dynamics of enzyme autoinhibition and activation. J. Biol. Chem.

2021

• McMillan D et al. Structural insights into the disruption of TNF-TNFR1 signalling by small molecules stabilising a distorted TNF. Nat. Commun.
• Zhang Y et al. A systems biology model of junctional localization and downstream signaling of the Ang-Tie signaling pathway. NPJ Syst. Biol. Appl.
• Erdem C et al. Inhibition of RPS6K reveals context-dependent Akt activity in luminal breast cancer cells. PLOS Comput. Biol.

2020

• Bolado-Carrancio A et al. Periodic propagating waves coordinate RhoGTPase network dynamics at the leading and trailing edges during cell migration. Elife
• Ordyan M et al. Interactions between calmodulin and neurogranin govern the dynamics of CaMKII as a leaky integrator. PLOS Comput. Biol.
• Kirsch K et al. Co-regulation of the transcription controlling ATF2 phosphoswitch by JNK and p38. Nat. Commun.
• Salzer B et al. Engineering AvidCARs for combinatorial antigen recognition and reversible control of CAR function. Nat. Commun.
• Wu Q, Finley SD. Mathematical Model Predicts Effective Strategies to Inhibit VEGF-eNOS Signaling. J. Clin. Med.
• Kapralov AA et al. Redox lipid reprogramming commands susceptibility of macrophages and microglia to ferroptotic death. Nat. Chem. Biol.
• Paoletti F et al. Molecular flexibility of DNA as a key determinant of RAD51 recruitment. EMBO J.
• Salazar-Cavazos E et al. Multisite EGFR phosphorylation is regulated by adaptor protein abundances and dimer lifetimes. Mol. Biol. Cell

2019

• Erickson KE et al. Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor. PLOS Comput. Biol.
• Nikolaev Y et al. Systems NMR: single-sample quantification of RNA, proteins and metabolites for biomolecular network analysis. Nat. Methods
• Lin YT, Feng S, Hlavacek WS. Scaling methods for accelerating kinetic Monte Carlo simulations of chemical reaction networks. J. Chem. Phys.

2018

• Wong VC et al. NF-κB-Chromatin Interactions Drive Diverse Phenotypes by Modulating Transcriptional Noise. Cell Reports
• Bazzazi J et al.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.
• Tse MJ et al. Rare-event sampling of epigenetic landscapes and phenotype transitions. PLOS Comput. Biol.
• Singh M et al. Shift from stochastic to spatially-ordered expression of serine-glycine synthesis enzymes in 3D microtumors. Sci. Rep.
• Rohrs JA et al. Computational Model of Chimeric Antigen Receptors Explains Site-Specific Phosphorylation Kinetics. Biophys. J.
• James JR. Tuning ITAM multiplicity on T cell receptors can control potency and selectivity to ligand density. Sci. Signal
• Czerkies M et al. Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways. Nat. Commun.
• Rukhlenko OS et al. Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling Cell Syst.

2017

• Harmon B et al. Timescale Separation of Positive and Negative Signaling Creates History-Dependent Responses to IgE Receptor Stimulation. Sci. Rep.
• Meng X et al. Minimum-noise production of translation factor eIF4G maps to a mechanistically determined optimal rate control window for protein synthesis. Nucleic Acids Res.
• Bazzazi J, Isenberg JS, Popel AS. Inhibition of VEGFR2 Activation and Its Downstream Signaling to ERK1/2 and Calcium by Thrombospondin-1 (TSP1): In silico Investigation. Front Physiol.
• Bazzazi J, Popel AS. Computational investigation of sphingosine kinase 1 (SphK1) and calcium dependent ERK1/2 activation downstream of VEGFR2 in endothelial cells. PLoS Comput. Biol.

2016

• Antunes G, Roque AC, Simoes de Souza FM. Modelling intracellular competition for calcium: kinetic and thermodynamic control of different molecular modes of signal decoding. Sci. Rep.
• Antunes G, Roque AC, Simoes de Souza FM. Stochastic Induction of Long-Term Potentiation and Long-Term Depression Sci. Rep.
• Hat B et al. Feedbacks, Bifurcations, and Cell Fate Decision-Making in the p53 System. PLOS Comput. Biol.
• Rohrs JA, Sulistio CD, Finley SD. Predictive model of thrombospondin-1 and vascular endothelial growth factor in breast tumor tissue. NPJ Syst. Biol. Appl.
• Korwek Z et al. Importins promote high-frequency NF-κB oscillations increasing information channel capacity. Biol. Direct
• Camillo BD et al. A rule-based model of insulin signalling pathway. BMC Syst. Biol.

2015

• Dolan DWP et al. Integrated Stochastic Model of DNA Damage Repair by Non-homologous End Joining and p53/p21- Mediated Early Senescence Signalling. PLOS Comput. Biol.
• Stites EC et al. Use of mechanistic models to integrate and analyze multiple proteomic datasets. Biophys. J.
• Hawse WF et al. Cutting Edge: Differential Regulation of PTEN by TCR, Akt, and FoxO1 Controls CD4+ T Cell Fate Decisions. J. Immunol.
• Szymańska P et al. Computational analysis of an autophagy/translation switch based on mutual inhibition of MTORC1 and ULK1. PLOS One
• Birtwistle MR. Analytical reduction of combinatorial complexity arising from multiple protein modification sites. J. R. Soc. Interface

2014

• Ligon TS, Leonhardt C, Rädler JO. Multi-level kinetic model of mRNA delivery via transfection of lipoplexes. PLOS One
• Chylek LA et al. Phosphorylation site dynamics of early T-cell receptor signaling. PLOS One
• Dushek O et al. Biosensor architectures for high-fidelity reporting of cellular signaling. Biophys. J.
• Chylek LA et al. An Interaction Library for the FcεRI Signaling Network. Frontiers Immunol.
• Kozer N et al. Recruitment of the adaptor protein Grb2 to EGFR tetramers. Biochemistry

2013

• Ibrahim B et al. Spatial rule-based modeling: a method and its application to the human mitotic kinetochore. Cells
• Pękalski J et al. Spontaneous NF-κB activation by autocrine TNFα signaling: a computational analysis. PLOS One
• Falkenberg CV, Blinov MJ, Loew LM. Pleomorphic ensembles: formation of large clusters composed of weakly interacting multivalent molecules. Biophys. J.
• Barua D, Hlavacek WS. Modeling the effect of APC truncation on destruction complex function in colorectal cancer cells. PLOS Comput. Biol.
• Fengos G, Iber D. Prediction stability in a data-based, mechanistic model of σF regulation during sporulation in Bacillus subtilis. Sci. Rep.
• Kozer N et al. Exploring higher-order EGFR oligomerisation and phosphorylation–a combined experimental and theoretical approach. Mol. Biosyst.
• Chow SK et al. Disease-enhancing antibodies improve the efficacy of bacterial toxin-neutralizing antibodies. Cell Host Microbe
• Mukhopadhyay H et al. Systems model of T cell receptor proximal signaling reveals emergent ultrasensitivity. PLOS Comput. Biol.
• Liu Y et al. Single-cell measurements of IgE-mediated FcεRI signaling using an integrated microfluidic platform. PLOS One
• Falkenberg CV, Loew LM.Computational analysis of Rho GTPase cycling. PLOS Comput. Biol.
• Kesseler KJ et al. A predictive mathematical model of the DNA damage G2 checkpoint. J. Theor. Biol.

2012

• Barua D, Goldstein B. A mechanistic model of early FcεRI signaling: lipid rafts and the question of protection from dephosphorylation. PLOS One
• Creamer MS et al. Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling. BMC Syst. Biol.
• Barua D, Hlavacek WS, Lipniacki T. A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn. J. Immunol.
• Michalski PJ, Loew LM. CaMKII activation and dynamics are independent of the holoenzyme structure: an infinite subunit holoenzyme approximation. Phys. Biol.
• Kocieniewski P, Faeder JR, Lipniacki T.The interplay of double phosphorylation and scaffolding in MAPK pathways. J. Theor. Biol.

2011

• Geier F, Fengos G, Iber D. A computational analysis of the dynamic roles of talin, Dok1, and PIPKI for integrin activation. PLOS One
• Dushek O, van der Merwe PA, Shahrezaei V. Ultrasensitivity in multisite phosphorylation of membrane-anchored proteins. Biophys. J.
• Thomson TM et al. Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range. PNAS

2010

• Nag A, Faeder JR, Goldstein B. Shaping the response: the role of FcεRI and Syk expression levels in mast cell signaling. IET Syst. Biol.
• Nag A et al. A detailed mathematical model predicts that serial engagement of IgE-FcεRI complexes can enhance Syk activation in mast cells. J. Immunol.
• Monine MI et al. Modeling multivalent ligand-receptor interactions with steric constraints on configurations of cell-surface receptor aggregates. Biophys. J.
• Gong J et al. Analysis and verification of the HMGB1 signaling pathway. BMC Bioinformatics
• Ray JC, Igoshin OA. Adaptable functionality of transcriptional feedback in bacterial two-component systems. PLOS Comput. Biol.

2009

• Dushek O, Das R, Coombs D. A role for rebinding in rapid and reliable T cell responses to antigen. PLOS Comput. Biol.
• Barua D, Faeder JR, Haugh JM. A bipolar clamp mechanism for activation of Jak-family protein tyrosine kinases. PLOS Comput. Biol.
• An GC, Faeder JR. Detailed qualitative dynamic knowledge representation using a BioNetGen model of TLR-4 signaling and preconditioning. Math. Biosci.
• Nag A et al. Aggregation of membrane proteins by cytosolic cross-linkers: theory and simulation of the LAT-Grb2-SOS1 system. Biophys. J.

2008

• Barua D, Faeder JR, Haugh JM. Computational models of tandem SRC homology 2 domain interactions and application to phosphoinositide 3-kinase. J. Biol. Chem.

2007

• Mu F et al. Carbon-fate maps for metabolic reactions. Bioinformatics
• Barua D, Faeder JR, Haugh JM. Structure-based kinetic models of modular signaling protein function: focus on Shp2. Biophys. J.

2006

• Blinov ML et al. A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity. Biosystems

2005

• Faeder JR et al. Combinatorial complexity and dynamical restriction of network flows in signal transduction. IET Syst. Biol.

2003

• Faeder JR et al. Investigation of early events in FcεRI-mediated signaling using a detailed mathematical model. J. Immunol.