ArticlePLoS biology2016
Modelling the Structure and Dynamics of Biological Pathways.
Article in PLoS biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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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.
The trial behind it
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
17 citing papers in PubMed.
- WayFindR: investigating feedback in biological pathways.NAR genomics and bioinformatics · 2026Article
- Automatic construction of Petri net models for computational simulations of molecular interaction network.NPJ systems biology and applications · 2024Article
- Veterinary systems biology for bridging the phenotype-genotype gap via computational modeling for disease epidemiology and animal welfare.Briefings in bioinformatics · 2024Review
- Graphia: A platform for the graph-based visualisation and analysis of high dimensional data.PLoS computational biology · 2022Article
- Expression Profile of Genes Related to the Th17 Pathway in Macrophages Infected byFrontiers in cellular and infection microbiology · 2022Article
- Thompson loop: opportunities for antitubercular drug design by targeting the weak spot in demethylmenaquinone methyltransferase protein.RSC advances · 2020Article
- INDRA-IPM: interactive pathway modeling using natural language with automated assembly.Bioinformatics (Oxford, England) · 2019Article
- A genomic analysis and transcriptomic atlas of gene expression in Psoroptes ovis reveals feeding- and stage-specific patterns of allergen expression.BMC genomics · 2019Article
- A multiscale signalling network map of innate immune response in cancer reveals cell heterogeneity signatures.Nature communications · 2019Article
- Visualization and analysis of RNA-Seq assembly graphs.Nucleic acids research · 2019Article
- Reconstruction of endosomal organization and function by a combination of ODE and agent-based modeling strategies.Biology direct · 2018Article
- Modelling steroidogenesis: a framework model to support hypothesis generation and testing across endocrine studies.BMC research notes · 2018Article
- A graphical and computational modeling platform for biological pathways.Nature protocols · 2018Article
- Let Your Ideas Flow: Using Flowcharts to Convey Methods and Implications of the Results in Laboratory Exercises, Articles, Posters, and Slide Presentations.Journal of microbiology & biology education · 2018Article
- Use of Graph Theory to Characterize Human and Arthropod Vector Cell Protein Response to Infection WithFrontiers in cellular and infection microbiology · 2018Article
- From word models to executable models of signaling networks using automated assembly.Molecular systems biology · 2017Article
- Petri Net computational modelling of Langerhans cell Interferon Regulatory Factor Network predicts their role in T cell activation.Scientific reports · 2017Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
There is a need for formalised diagrams that both summarise current biological pathway knowledge and support modelling approaches that explain and predict their behaviour. Here, we present a new, freely available modelling framework that includes a biologist-friendly pathway modelling language (mEPN), a simple but sophisticated method to support model parameterisation using available biological information; a stochastic flow algorithm that simulates the dynamics of pathway activity; and a 3-D visualisation engine that aids understanding of the complexities of a system's dynamics. We present example pathway models that illustrate of the power of approach to depict a diverse range of systems.
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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.