Rule-based modeling of biochemical systems with BioNetGen.

By James R. Faeder, Michael L. Blinov, William S. Hlavacek. Methods in molecular biology, 2009

459 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9cc4ebb5783b49dfd655ac35419b8137924aac1d

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

1. A. Barrette
2. Luis C. Santos
3. R. J. Koch
4. Mehdi Bouhaddou
5. A. Tan
6. Matthew S. DiStefano
7. E. A. Riesel
8. Alex E. Mertz

Citations in the corpus

• Statistical Model Checking: An Overview (2010, unknown): “we introduced a new tool, called BioLab, for formally reasoning about the behavior of stochastic dynamic models by integrating SPRT into the BioNetGen [15,16] framework for rule-based modeling.”
• 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”
• An Integrated Mechanistic Model of Pan-Cancer Driver Pathways Predicts Stochastic Proliferation and Death (2017, background): “Rule-based modeling (Faeder et al., 2009) and algorithmic model building (Lopez et al., 2013) could help modelers capture more biology.”