ArticleJournal of the Royal Society, Interface2016
Form and function in gene regulatory networks: the structure of network motifs determines fundamental properties of their dynamical state space.
Article in Journal of the Royal Society, Interface, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- Dissecting reversible and irreversible single cell state transitions from gene regulatory networks.Molecular systems biology · 2026Article
- Symmetries in metabolic networks ofPNAS nexus · 2025Article
- Dynamics and bifurcations in genetic circuits with fibration symmetries.Journal of the Royal Society, Interface · 2024Article
- Evolution of miRNA-Binding Sites and Regulatory Networks in Cichlids.Molecular biology and evolution · 2022Article
- Generation of Realistic Gene Regulatory Networks by Enriching for Feed-Forward Loops.Frontiers in genetics · 2022Article
- Cell-Free Characterization of Coherent Feed-Forward Loop-Based Synthetic Genetic Circuits.ACS synthetic biology · 2021Article
- Dynamical modules in metabolism, cell and developmental biology.Interface focus · 2021Article
- Testing biological network motif significance with exponential random graph models.Applied network science · 2021Article
- Populations of genetic circuits are unable to find the fittest solution in a multilevel genotype-phenotype map.Journal of the Royal Society, Interface · 2020Article
- Circuits with broken fibration symmetries perform core logic computations in biological networks.PLoS computational biology · 2020Article
- Article
- Next Generation Networks: Featuring the Potential Role of Emerging Applications in Translational Oncology.Journal of clinical medicine · 2019Article
- A spectrum of modularity in multi-functional gene circuits.Molecular systems biology · 2017Article
- Identification of Critical Molecular Factors and Side Effects Underlying the Response to Thalicthuberine in Prostate Cancer: A Systems Biology Approach.Avicenna journal of medical biotechnologyArticle
- A Motif-Based Network Analysis of Regulatory Patterns in Doxorubicin Effects on Treating Breast Cancer, a Systems Biology Study.Avicenna journal of medical biotechnologyArticle
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2 authors.
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Abstract
Network motifs have been studied extensively over the past decade, and certain motifs, such as the feed-forward loop, play an important role in regulatory networks. Recent studies have used Boolean network motifs to explore the link between form and function in gene regulatory networks and have found that the structure of a motif does not strongly determine its function, if this is defined in terms of the gene expression patterns the motif can produce. Here, we offer a different, higher-level definition of the 'function' of a motif, in terms of two fundamental properties of its dynamical state space as a Boolean network. One is the basin entropy, which is a complexity measure of the dynamics of Boolean networks. The other is the diversity of cyclic attractor lengths that a given motif can produce. Using these two measures, we examine all 104 topologically distinct three-node motifs and show that the structural properties of a motif, such as the presence of feedback loops and feed-forward loops, predict fundamental characteristics of its dynamical state space, which in turn determine aspects of its functional versatility. We also show that these higher-level properties have a direct bearing on real regulatory networks, as both basin entropy and cycle length diversity show a close correspondence with the prevalence, in neural and genetic regulatory networks, of the 13 connected motifs without self-interactions that have been studied extensively in the literature.
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