ArticleBioinformatics (Oxford, England)2016
BioNetGen 2.2: advances in rule-based modeling.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 128 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
128 citing papers in PubMed.
- Antimony 3: Extending human-readable model definitions for SBML Level 3 Core and Packages.PLoS computational biology · 2026Article
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- IgE Occupancy and Antigen Valency Cooperate to Control FcεRI Aggregation Geometry and Signaling Efficiency.International journal of molecular sciences · 2026Article
- Multiscale predictive cellular modeling: integrating hypothesis grammars, digital twins, and multi-omics for In silico oncology and precision theranostics.Functional & integrative genomics · 2026Review
- Dual RAF inhibition outperforms RAF-MEK combinations for suppressing ERK signaling in KRAS mutant cells.NPJ systems biology and applications · 2026Article
- A computational rule-based model of MAPK/ERK system regulation.Scientific reports · 2026Article
- A Computational Model of Tumor Interactions with Bone-Resident Cells Predicts Tumor-Type-Specific Responses to Perturbations.bioRxiv : the preprint server for biology · 2026Article
- Rules railroad: Syntax-inspired diagrams for visualizing and understanding rule-based model specifications.PLoS computational biology · 2026Article
- Artificial intelligence in mitotic checkpoint modeling: transforming our understanding of cellular division through machine learning and predictive biology.Briefings in bioinformatics · 2026Review
- Using PyBioNetFit to leverage qualitative and quantitative data in biological model parameterization and uncertainty quantification.Frontiers in immunology · 2026Article
- Article
- Spatially structured models of viral dynamics: a scoping review.Microbiology and molecular biology reviews : MMBR · 2025Article
- Coupling Molecular and Cellular Dynamics in a Large-Scale Monte Carlo Simulation.International journal of molecular sciences · 2025Article
- IgE occupancy and antigen valency cooperate to control FcεRI aggregation geometry and signaling efficiency.bioRxiv : the preprint server for biology · 2025Article
- Impact of ligand binding on VEGFR1, VEGFR2, and NRP1 localization in human endothelial cells.PLoS computational biology · 2025Article
- Promoting vascular stability through Src inhibition and Tie2 activation: A model-based analysis.iScience · 2025Article
- A detailed kinetic model of Eastern equine encephalitis virus replication in a susceptible host cell.PLoS computational biology · 2025Article
- Leveraging public AI tools to explore systems biology resources in mathematical modeling.NPJ systems biology and applications · 2025Article
- SIMPROV: Provenance capturing for simulation studies.PloS one · 2025Article
- Visualizing mechanistic models by integrating site-specific molecular details into reaction networks.Frontiers in molecular biosciences · 2025Article
68 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
Abstract
: BioNetGen is an open-source software package for rule-based modeling of complex biochemical systems. Version 2.2 of the software introduces numerous new features for both model specification and simulation. Here, we report on these additions, discussing how they facilitate the construction, simulation and analysis of larger and more complex models than previously possible. AVAILABILITY AND IMPLEMENTATION: Stable BioNetGen releases (Linux, Mac OS/X and Windows), with documentation, are available at http://bionetgen.org Source code is available at http://github.com/RuleWorld/bionetgen CONTACT: bionetgen.help@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.