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BioNetGen

Published BioNetGen Models

This page lists publications that have applied a BioNetGen rule-based model to a specific biological system. It is automatically maintained, but if you feel we have missed a publication please post a GitHub issue. Click a column header to sort. 149 publications.

Year System Authors Title Journal PMID RuleHub Entry
2026 RNA Pol II CTD phosphorylation Callenbach A et al. Quantitative modelling of P-TEFb mediated CTD phosphorylation identifies local cooperativity. PLOS Comput. Biol. 42531208
2026 FcεRI signaling Linhart B et al. IgE Occupancy and Antigen Valency Cooperate to Control FcεRI Aggregation Geometry and Signaling Efficiency. Int. J. Mol. Sci. 41279798
2026 Viral evolution Mohanty V et al. Biophysical fitness landscape design traps viral evolution. PNAS 40236159
2026 RAF/MEK/ERK signaling Imoto H et al. Dual RAF inhibition outperforms RAF-MEK combinations for suppressing ERK signaling in KRAS mutant cells. NPJ Syst. Biol. Appl. 41986383
2026 MAPK/ERK signaling Kocieniewski P et al. A computational rule-based model of MAPK/ERK system regulation. Sci. Rep. 41865127
2025 VEGFR signaling Sarabipour S et al. Impact of ligand binding on VEGFR1, VEGFR2, and NRP1 localization in human endothelial cells. PLOS Comput. Biol. 40668864
2025 Viral replication Larkin CI et al. A detailed kinetic model of Eastern equine encephalitis virus replication in a susceptible host cell. PLOS Comput. Biol. 40465541
2025 Ang-Tie/Src signaling Zhang Y et al. Promoting vascular stability through Src inhibition and Tie2 activation: A model-based analysis. iScience 40491479
2025 CaMKII signaling Bartol TM et al. A spatial model of autophosphorylation of CaMKII predicts that the lifetime of phospho-CaMKII after induction of synaptic plasticity is greatly prolonged by CaM-trapping. Front. Synaptic Neurosci. 40255983
2025 NK cell/CAR signaling Millan AJ et al. SYK negatively regulates ITAM-mediated human NK cell signaling and CD19-CAR NK cell efficacy. J. Immunol. 40073103
2024 VEGFR signaling Sarabipour S et al. Trafficking dynamics of VEGFR1, VEGFR2, and NRP1 in human endothelial cells. PLOS Comput. Biol. 38324585
2024 RAF/ERK signaling Sevrin T et al. Cell-specific models reveal conformation-specific RAF inhibitor combinations that synergistically inhibit ERK signaling in pancreatic cancer cells. Cell Reports 39240715
2024 RAF/MEK signaling Goetz A et al. Computational Modeling of Drug Response Identifies Mutant-Specific Constraints for Dosing panRAF and MEK Inhibitors in Melanoma. Cancers 39199684
2024 Hepatic stellate cell signaling Bouguéon M et al. A rule-based multiscale model of hepatic stellate cell plasticity: Critical role of the inactivation loop in fibrosis progression. PLOS Comput. Biol. 39074160
2024 Cell cycle Lang P et al. Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells. PLOS Comput. Biol. 38190398 Lang2024
2024 JAK-STAT signaling Cheemalavagu N et al. Predicting gene-level sensitivity to JAK-STAT signaling perturbation using a mechanistic-to-machine learning framework. Cell Systems 38198893 CheemalavaguJAKSTAT
2023 Interferon signaling Korwek Z et al. Non-self RNA rewires IFNβ signaling: A mathematical model of the innate immune response. Sci. Signaling 38085817 Korwek2023
2023 VEGF/CD47 signaling Zhang Y et al. Combining Multikinase Tyrosine Kinase Inhibitors Targeting the Vascular Endothelial Growth Factor and Cluster of Differentiation 47 Signaling Pathways Is Predicted to Increase theEfficacy of Antiangiogenic Combination Therapies. ACS Pharmacol. Transl. Sci. 37200806 Zhang2023
2023 Calcium signaling (Huntington's) Sameni S et al. Computer simulations predict the impact of neuronal atrophy on the calcium dynamics in Huntington's disease. PNAS Nexus 38222468
2023 NLRP3 inflammasome Krantz M et al. A detailed molecular network map and model of the NLRP3 inflammasome. Front. Immunol. 38077364
2023 RAF signaling Imoto H et al. A Combination of Conformation-Specific RAF Inhibitors Overcome Drug Resistance Brought about by RAF Overexpression. Biomolecules 37627277
2023 MAPK signaling Fröhlich F et al. Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance. Mol. Syst. Biol. 36700386
2023 Biomolecular condensation Chattaraj A et al. The maximum solubility product marks the threshold for condensation of multivalent biomolecules. Biophys. J. 36987392
2022 PLCγ1 signaling 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. 35367415 Nosbisch2022
2022 Cell fate/MAPK signaling Rukhlenko OS et al. Control of cell state transitions. Nature 36104561
2022 Proliferation/death signaling Erdem C et al. A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling. Nat. Commun. 35729113
2022 T cell engager QSP Abrams RE et al. Quantitative systems pharmacology modeling sheds light into the dose response relationship of a trispecific T cell engager in multiple myeloma. Sci. Rep. 35768621
2022 Aquaporin trafficking Leberecht C et al. A multiscale model of the regulation of aquaporin 2 recycling. NPJ Syst. Biol. Appl. 35534498
2022 Transcriptional noise Bullock ME et al. A transcriptional cycling model recapitulates chromatin-dependent features of noisy inducible transcription. PLOS Comput. Biol. 36084132
2022 CAR/NF-κB signaling Tserunyan V et al. Computational analysis of 4-1BB-induced NFκB signaling suggests improvements to CAR cell design. Cell Commun. Signal. 36028884
2022 DARPP-32 signaling Wysocka E et al. Comparison of rule- and ordinary differential equation-based dynamic model of DARPP-32 signalling network. PeerJ 36540795
2022 Translational regulation Bottorff T et al. Translational buffering by ribosome stalling in upstream open reading frames. PLoS Genetics 36315596
2022 Gene expression noise Loell K et al. Activation domains can decouple the mean and noise of gene expression. Cell Reports 35858548
2021 TNF/TNFR signaling McMillan D et al. Structural insights into the disruption of TNF-TNFR1 signalling by small molecules stabilising a distorted TNF. Nat. Commun. 33495441 McMillan2021
2021 Ang-Tie signaling Zhang Y et al. A systems biology model of junctional localization and downstream signaling of the Ang-Tie signaling pathway. NPJ Syst. Biol. Appl. 34417472 Zhang2021
2021 PI3K/Akt signaling Erdem C et al. Inhibition of RPS6K reveals context-dependent Akt activity in luminal breast cancer cells. PLOS Comput. Biol. 34191793 Erdem2021
2021 WNT signaling Haack F et al. Receptor/Raft Ratio Is a Determinant for LRP6 Phosphorylation and WNT/β-Catenin Signaling. Front. Cell Dev. Biol. 34485292
2021 Tumor cell-state heterogeneity Hayford CE et al. An in vitro model of tumor heterogeneity resolves genetic, epigenetic, and stochastic sources of cell state variability. PLOS Biology 34061819
2020 Rho GTPase signaling Bolado-Carrancio A et al. Periodic propagating waves coordinate RhoGTPase network dynamics at the leading and trailing edges during cell migration. Elife 32705984
2020 CaMKII signaling Ordyan M et al. Interactions between calmodulin and neurogranin govern the dynamics of CaMKII as a leaky integrator. PLOS Comput. Biol. 32678848 Ordyan2020
2020 JNK/p38 signaling Kirsch K et al. Co-regulation of the transcription controlling ATF2 phosphoswitch by JNK and p38. Nat. Commun. 33188182
2020 CAR signaling Salzer B et al. Engineering AvidCARs for combinatorial antigen recognition and reversible control of CAR function. Nat. Commun. 32820173
2020 VEGF/eNOS signaling Wu Q, Finley SD. Mathematical Model Predicts Effective Strategies to Inhibit VEGF-eNOS Signaling. J. Clin. Med. 32357492
2020 Ferroptosis/lipid signaling Kapralov AA et al. Redox lipid reprogramming commands susceptibility of macrophages and microglia to ferroptotic death. Nat. Chem. Biol. 32080625
2020 DNA repair (RAD51) Paoletti F et al. Molecular flexibility of DNA as a key determinant of RAD51 recruitment. EMBO J. 31943278
2020 EGFR signaling Salazar-Cavazos E et al. Multisite EGFR phosphorylation is regulated by adaptor protein abundances and dimer lifetimes. Mol. Biol. Cell 31913761
2020 TNF/TNFR signaling Prada J et al. A systems-biology model of the tumor necrosis factor (TNF) interactions with TNF receptor 1 and 2. Bioinformatics 32991680
2020 Epidemiology (COVID-19) Kochańczyk M et al. Super-spreading events initiated the exponential growth phase of COVID-19 with R0 higher than initially estimated. R. Soc. Open Sci. 33047040
2020 Cancer radiotherapy Hat B et al. Model-based optimization of combination protocols for irradiation-insensitive cancers. Sci. Rep. 32724100
2020 NK cell signaling Makaryan SZ et al. Enhancing network activation in natural killer cells: predictions from in silico modeling. Integrative Biology 32409824
2019 IGF1R signaling Erickson KE et al. Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor. PLOS Comput. Biol. 30653502
2019 Metabolomics/NMR Nikolaev Y et al. Systems NMR: single-sample quantification of RNA, proteins and metabolites for biomolecular network analysis. Nat. Methods 31363225
2019 Simulation methods Lin YT, Feng S, Hlavacek WS. Scaling methods for accelerating kinetic Monte Carlo simulations of chemical reaction networks. J. Chem. Phys. 31255063
2019 CaMKII signaling Pharris MC et al. A multi-state model of the CaMKII dodecamer suggests a role for calmodulin in maintenance of autophosphorylation. PLOS Comput. Biol. 31869343
2019 CAR T cell signaling Cess CG et al. Data-driven analysis of a mechanistic model of CAR T cell signaling predicts effects of cell-to-cell heterogeneity. J. Theor. Biol. 31866395
2019 Fn14/NF-κB signaling Khetan J et al. Analysis of Fn14–NF-κB signaling response dynamics using a mechanistic model. J. Theor. Biol. 31374284
2019 Angiogenesis Li D et al. Exploring the Extracellular Regulation of the Tumor Angiogenic Interaction Network Using a Systems Biology Model. Front. Physiol. 31379588
2019 Cell cycle (yeast) Münzner U et al. A comprehensive, mechanistically detailed, and executable model of the cell division cycle in Saccharomyces cerevisiae. Nat. Commun. 30899000
2018 NF-κB signaling Wong VC et al. NF-κB-Chromatin Interactions Drive Diverse Phenotypes by Modulating Transcriptional Noise. Cell Reports 29346759
2018 Integrin/VEGFR2 signaling 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. 30036530
2018 Epigenetic switching Tse MJ et al. Rare-event sampling of epigenetic landscapes and phenotype transitions. PLOS Comput. Biol. 30074987
2018 Metabolic gene expression Singh M et al. Shift from stochastic to spatially-ordered expression of serine-glycine synthesis enzymes in 3D microtumors. Sci. Rep. 29925909
2018 CAR signaling Rohrs JA et al. Computational Model of Chimeric Antigen Receptors Explains Site-Specific Phosphorylation Kinetics. Biophys. J. 30197180
2018 TCR/ITAM signaling James JR. Tuning ITAM multiplicity on T cell receptors can control potency and selectivity to ligand density. Sci. Signal 29789296
2018 Antiviral signaling Czerkies M et al. Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways. Nat. Commun. 29402958
2018 RAF/RAS signaling Rukhlenko OS et al. Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling Cell Syst. 30007540
2018 VEGF/eNOS signaling Bazzazi H et al. Computer Simulation of TSP1 Inhibition of VEGF–Akt–eNOS: An Angiogenesis Triple Threat. Front. Physiol. 29899706
2018 Pan-cancer signaling Bouhaddou M et al. A mechanistic pan-cancer pathway model informed by multi-omics data interprets stochastic cell fate responses to drugs and mitogens. PLOS Comput. Biol. 29579036
2018 Stem cell pluripotency Lin YT et al. A stochastic and dynamical view of pluripotency in mouse embryonic stem cells. PLOS Comput. Biol. 29451874
2018 Signal detection/decoding Antunes G et al. Molecular mechanisms of detection and discrimination of dynamic signals. Sci. Rep. 29410522
2018 FcεRI signaling Shahinuzzaman M et al. A spatio-temporal model reveals self-limiting FcεRI cross-linking by multivalent antigens. R. Soc. Open Sci. 30839725
2018 Angiogenesis Li D et al. The impact of tumor receptor heterogeneity on the response to anti-angiogenic cancer treatment. Integrative Biology 29623971
2017 FcεRI/IgE signaling Harmon B et al. Timescale Separation of Positive and Negative Signaling Creates History-Dependent Responses to IgE Receptor Stimulation. Sci. Rep. 29138425 Harmon2017
2017 Translational regulation 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. 27928055
2017 VEGFR2 signaling 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. 28220078
2017 VEGFR2 signaling 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. 28178265
2017 RAF/ERK signaling Varga A et al. RAF1/BRAF dimerization integrates the signal from RAS to ERK and ROKα. Sci. Signaling 28270557
2017 SHP-1 phosphatase signaling Goyette J et al. Biophysical assay for tethered signaling reactions reveals tether-controlled activity for the phosphatase SHP-1. Sci. Adv. 28378014
2017 RNA granule biophysics Falkenberg CV et al. Multivalent Molecules as Modulators of RNA Granule Size and Composition. Biophys. J. 28242011
2017 MAPK signaling Kochańczyk M et al. Relaxation oscillations and hierarchy of feedbacks in MAPK signaling. Sci. Rep. 28045041
2017 NF-κB signaling Tudelska K et al. Information processing in the NF-κB pathway. Sci. Rep. 29162874
2016 Calcium signaling 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. 27033299
2016 Synaptic plasticity (LTP/LTD) Antunes G, Roque AC, Simoes de Souza FM. Stochastic Induction of Long-Term Potentiation and Long-Term Depression Sci. Rep. 27485552
2016 p53 signaling Hat B et al. Feedbacks, Bifurcations, and Cell Fate Decision-Making in the p53 System. PLOS Comput. Biol. 26928575 Hat2016
2016 VEGF/TSP1 signaling Rohrs JA, Sulistio CD, Finley SD. Predictive model of thrombospondin-1 and vascular endothelial growth factor in breast tumor tissue. NPJ Syst. Biol. Appl. 28713587
2016 NF-κB signaling Korwek Z et al. Importins promote high-frequency NF-κB oscillations increasing information channel capacity. Biol. Direct 27835978
2016 Insulin signaling Camillo BD et al. A rule-based model of insulin signalling pathway. BMC Syst. Biol. 27245161
2016 AMPK/mTOR signaling Dalle Pezze P et al. A systems study reveals concurrent activation of AMPK and mTOR by amino acids. Nat. Commun. 27869123
2016 ErbB signaling Das AA et al. Agent-based re-engineering of ErbB signaling: a modeling pipeline for integrative systems biology. Bioinformatics 27998938
2015 DNA damage repair 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. 26020242 Dolan2015
2015 Proteomics integration Stites EC et al. Use of mechanistic models to integrate and analyze multiple proteomic datasets. Biophys. J. 25863072
2015 TCR/PTEN/Akt signaling Hawse WF et al. Cutting Edge: Differential Regulation of PTEN by TCR, Akt, and FoxO1 Controls CD4+ T Cell Fate Decisions. J. Immunol. 25855357
2015 Autophagy/mTORC1 signaling Szymańska P et al. Computational analysis of an autophagy/translation switch based on mutual inhibition of MTORC1 and ULK1. PLOS One 25761126
2015 Model reduction theory Birtwistle MR. Analytical reduction of combinatorial complexity arising from multiple protein modification sites. J. R. Soc. Interface 25519995
2015 JNK signaling Fey D et al. Signaling pathway models as biomarkers: Patient-specific simulations of JNK activity predict the survival of neuroblastoma patients. Sci. Signaling 26696630
2015 Gene network switching Tse MJ et al. DNA-Binding Kinetics Determines the Mechanism of Noise-Induced Switching in Gene Networks. Biophys. J. 26488666
2015 WNT/ROS signaling Haack F et al. Spatio-temporal Model of Endogenous ROS and Raft-Dependent WNT/Beta-Catenin Signaling Driving Cell Fate Commitment in Human Neural Progenitor Cells. PLOS Comput. Biol. 25793621
2015 CDK2/HGF signaling Mueller S et al. T160-phosphorylated CDK2 defines threshold for HGF-dependent proliferation in primary hepatocytes. Mol. Syst. Biol. 26148348
2014 mRNA delivery Ligon TS, Leonhardt C, Rädler JO. Multi-level kinetic model of mRNA delivery via transfection of lipoplexes. PLOS One 25237886 Ligon2014
2014 TCR signaling Chylek LA et al. Phosphorylation site dynamics of early T-cell receptor signaling. PLOS One 25147952
2014 Biosensor design Dushek O et al. Biosensor architectures for high-fidelity reporting of cellular signaling. Biophys. J. 25099816 Dushek2014
2014 FcεRI signaling Chylek LA et al. An Interaction Library for the FcεRI Signaling Network. Frontiers Immunol. 24782869
2014 EGFR/Grb2 signaling Kozer N et al. Recruitment of the adaptor protein Grb2 to EGFR tetramers. Biochemistry 24697349 Kozer2014
2013 Mitotic kinetochore Ibrahim B et al. Spatial rule-based modeling: a method and its application to the human mitotic kinetochore. Cells 24709796
2013 NF-κB signaling Pękalski J et al. Spontaneous NF-κB activation by autocrine TNFα signaling: a computational analysis. PLOS One 24324544
2013 Multivalent clustering biophysics Falkenberg CV, Blinov MJ, Loew LM. Pleomorphic ensembles: formation of large clusters composed of weakly interacting multivalent molecules. Biophys. J. 24314076
2013 Wnt/APC signaling Barua D, Hlavacek WS. Modeling the effect of APC truncation on destruction complex function in colorectal cancer cells. PLOS Comput. Biol. 24086117 Barua2013
2013 Sporulation (B. subtilis) Fengos G, Iber D. Prediction stability in a data-based, mechanistic model of σF regulation during sporulation in Bacillus subtilis. Sci. Rep. 24067622
2013 EGFR signaling Kozer N et al. Exploring higher-order EGFR oligomerisation and phosphorylation--a combined experimental and theoretical approach. Mol. Biosyst. 23629589 Kozer2013
2013 Antibody/toxin neutralization Chow SK et al. Disease-enhancing antibodies improve the efficacy of bacterial toxin-neutralizing antibodies. Cell Host Microbe 23601104
2013 TCR signaling Mukhopadhyay H et al. Systems model of T cell receptor proximal signaling reveals emergent ultrasensitivity. PLOS Comput. Biol. 23555234 Mukhopadhyay2013
2013 FcεRI signaling Liu Y et al. Single-cell measurements of IgE-mediated FcεRI signaling using an integrated microfluidic platform. PLOS One 23544131
2013 Rho GTPase signaling Falkenberg CV, Loew LM. Computational analysis of Rho GTPase cycling. PLOS Comput. Biol. 23326220
2013 DNA damage checkpoint Kesseler KJ et al. A predictive mathematical model of the DNA damage G2 checkpoint. J. Theor. Biol. 23266715 Kesseler2013
2013 ErbB signaling Kiel C et al. Integration of Protein Abundance and Structure Data Reveals Competition in the ErbB Signaling Network. Sci. Signaling 24345680
2013 Bacterial chemotaxis Pontius W et al. Adaptation Dynamics in Densely Clustered Chemoreceptors. PLOS Comput. Biol. 24068908
2013 MAPK/ERK signaling Kocieniewski P et al. MEK1 and MEK2 differentially control the duration and amplitude of the ERK cascade response. Phys. Biol. 23735655
2013 RNA Pol II CTD phosphorylation Aitken S et al. A rule-based kinetic model of RNA polymerase II C-terminal domain phosphorylation. J. R. Soc. Interface 23804443
2013 Insulin signaling Smith GR et al. Computational modelling of the regulation of Insulin signalling by oxidative stress. BMC Syst. Biol. 23705851
2012 FcεRI signaling Barua D, Goldstein B. A mechanistic model of early FcεRI signaling: lipid rafts and the question of protection from dephosphorylation. PLOS One 23284735
2012 ErbB signaling Creamer MS et al. Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling. BMC Syst. Biol. 22913808
2012 B cell receptor signaling 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. 22711887
2012 CaMKII signaling Michalski PJ, Loew LM. CaMKII activation and dynamics are independent of the holoenzyme structure: an infinite subunit holoenzyme approximation. Phys. Biol. 22683827
2012 MAPK signaling Kocieniewski P, Faeder JR, Lipniacki T. The interplay of double phosphorylation and scaffolding in MAPK pathways. J. Theor. Biol. 22123371 Kocieniewski2012
2012 Autophagy Martin KR et al. Computational model for autophagic vesicle dynamics in single cells. Autophagy 23196898
2012 Membrane receptor clustering Radhakrishnan K et al. Mathematical Simulation of Membrane Protein Clustering for Efficient Signal Transduction. Ann. Biomed. Eng. 22669501
2012 Membrane signaling bistability Abel SM et al. The Membrane Environment Can Promote or Suppress Bistability in Cell Signaling Networks. J. Phys. Chem. B 22332778
2011 Integrin signaling Geier F, Fengos G, Iber D. A computational analysis of the dynamic roles of talin, Dok1, and PIPKI for integrin activation. PLOS One 22110576
2011 Multisite phosphorylation Dushek O, van der Merwe PA, Shahrezaei V. Ultrasensitivity in multisite phosphorylation of membrane-anchored proteins. Biophys. J. 21354391 Dushek2011
2011 Yeast signaling scaffolds Thomson TM et al. Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range. PNAS 22114196
2011 Endothelial cell signaling Bauer AL et al. Investigating the Role of Cross-Talk Between Chemical and Stromal Factors in Endothelial Cell Phenotype Determination. Modeling Tumor Vasculature
2011 IL-2/T cell signaling Feinerman O et al. Single-cell quantification of IL-2 response by effector and regulatory T cells reveals critical plasticity in immune response. Mol. Syst. Biol. 21119631
2010 FcεRI signaling Nag A, Faeder JR, Goldstein B. Shaping the response: the role of FcεRI and Syk expression levels in mast cell signaling. IET Syst. Biol. 21073233
2010 FcεRI signaling 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. 20733205
2010 Multivalent receptor aggregation Monine MI et al. Modeling multivalent ligand-receptor interactions with steric constraints on configurations of cell-surface receptor aggregates. Biophys. J. 20085718
2010 HMGB1 signaling Gong J et al. Analysis and verification of the HMGB1 signaling pathway. BMC Bioinformatics 21106117
2010 Bacterial two-component systems Ray JC, Igoshin OA. Adaptable functionality of transcriptional feedback in bacterial two-component systems. PLOS Comput. Biol. 20168997
2009 TCR signaling Dushek O, Das R, Coombs D. A role for rebinding in rapid and reliable T cell responses to antigen. PLOS Comput. Biol. 19956745
2009 JAK kinase activation Barua D, Faeder JR, Haugh JM. A bipolar clamp mechanism for activation of Jak-family protein tyrosine kinases. PLOS Comput. Biol. 19381268 Barua2009
2009 TLR-4 signaling An GC, Faeder JR. Detailed qualitative dynamic knowledge representation using a BioNetGen model of TLR-4 signaling and preconditioning. Math. Biosci. 18835283 An2009
2009 LAT/Grb2 signaling Nag A et al. Aggregation of membrane proteins by cytosolic cross-linkers: theory and simulation of the LAT-Grb2-SOS1 system. Biophys. J. 19348745 Nag2009
2008 SH2/PI3K signaling Barua D, Faeder JR, Haugh JM. Computational models of tandem SRC homology 2 domain interactions and application to phosphoinositide 3-kinase. J. Biol. Chem. 18204097
2008 TCR signaling Lipniacki T et al. Stochastic effects and bistability in T cell receptor signaling. J. Theor. Biol. 18556025
2007 Metabolic networks Mu F et al. Carbon-fate maps for metabolic reactions. Bioinformatics 17933853
2007 Shp2 signaling Barua D, Faeder JR, Haugh JM. Structure-based kinetic models of modular signaling protein function: focus on Shp2. Biophys. J. 17208977 Barua2007
2006 EGFR signaling Blinov ML et al. A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity. Biosystems 16233948 Blinov2006
2006 EGFR/Gab1 signaling Kiyatkin A et al. Scaffolding Protein Grb2-associated Binder 1 Sustains Epidermal Growth Factor-induced Mitogenic and Survival Signaling by Multiple Positive Feedback Loops. J. Biol. Chem. 16687399
2005 Signal transduction theory Faeder JR et al. Combinatorial complexity and dynamical restriction of network flows in signal transduction. IET Syst. Biol. 17091578
2003 FcεRI signaling Faeder JR et al. Investigation of early events in FcεRI-mediated signaling using a detailed mathematical model. J. Immunol. 12646643 Faeder2003