ArticleFrontiers in molecular biosciences2025
Visualizing mechanistic models by integrating site-specific molecular details into reaction networks.
Article in Frontiers in molecular biosciences, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
1 citing paper in PubMed.
- Rules railroad: Syntax-inspired diagrams for visualizing and understanding rule-based model specifications.PLoS computational biology · 2026Article
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4 authors.
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Abstract
Mechanistic modeling in biology aims to describe biological processes based on details on molecular mechanisms and interactions. Rule-based mechanistic modeling enables the simulation of biological systems while explicitly accounting for molecular details, such as protein domains and their specific interactions. Traditionally, mechanistic models are visually represented by reaction or pathway diagrams that depict transformations and modifications of chemical species. In contrast, rule-based descriptions are effective to encode the detailed specificity of individual interactions (e.g., how phosphorylation at a particular residue affects binding affinity elsewhere in the same protein complex) in a compact and precise form, but are complicated to integrate into comprehensive visual representations. Here, we introduce
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