BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains

By Michael L. Blinov, James R. Faeder, B. Goldstein, William S. Hlavacek. Bioinform., 2004

455 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/ab2f8a8beda2d4681b64f77e86e6fdf0c6f65e26

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In Molecular Biology

Citations in the corpus

Cell-signalling dynamics in time and space (2006, methodology): “Multiple software tools can assist in quantitative modelling 56,58,107–109 , and several databases of biological models have been developed, offering an interesting environment to generate and test novel hypotheses by using a computer keyboard 110–112 .”
Signaling pathway models as biomarkers: Patient-specific simulations of JNK activity predict the survival of neuroblastoma patients (2015, methodology): “4A, a dynamic model was constructed by rule-based modelling (34), which develops the ODEs based on a framework of rules”
Input–output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data (2009, background): “However, systematic computational treatment of combinatorial complexity places severe demands on parameter optimization because repeated cycles of numerical integration are required (Blinov et al , 2004).”
Weighted Ensemble Simulation: Review of Methodology, Applications, and Software (2017, unknown): “To our knowledge, the first freely available, highly scalable, and interoperable WE software package was WESTPA (74), which has been widely applied to a variety of systems ranging in scale from atomistic to cellular (2–4, 21, 22, 59, 62, 63, 75, 76) and interfaced with a diversity of dynamics engine”
Rule-based modeling of biochemical systems with BioNetGen. (2009, methodology): “These transformations are ( 1 ) add a bond, (2) delete a bond, (3) change a component state label, (4) delete a molecule, or (5) add a molecule.”