ArticleNature communications2021
Exploring the effect of network topology, mRNA and protein dynamics on gene regulatory network stability.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 12 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
12 citing papers in PubMed.
- Bacterial gene regulatory neural network as a biocomputing library of mathematical solvers.NPJ systems biology and applications · 2026Article
- An Investigation into the Evolutionary Characteristics and Expression Patterns of the Basic Leucine Zipper Gene Family in the Endangered SpeciesPlants (Basel, Switzerland) · 2025Article
- Modeling and analysis of the coupling effect for large-scale multi-band optical networks.Scientific reports · 2025Article
- Topological benchmarking of algorithms to infer gene regulatory networks from single-cell RNA-seq data.Bioinformatics (Oxford, England) · 2024Article
- Adaptation in Unstable Environments and Global Gene Losses: Small but Stable Gene Networks by the May-Wigner Theory.Molecular biology and evolution · 2024Article
- Article
- Graph 'texture' features as novel metrics that can summarize complex biological graphs.Physics in medicine and biology · 2023Article
- Canalization of Phenotypes-When the Transcriptome is Constantly but Weakly Perturbed.Molecular biology and evolution · 2023Article
- Comparative expression analysis in three Brassicaceae species revealed compensatory changes of the underlying gene regulatory network.Frontiers in plant science · 2022Article
- Generation of Realistic Gene Regulatory Networks by Enriching for Feed-Forward Loops.Frontiers in genetics · 2022Article
- In vivo, in vitro and in silico: an open space for the development of microbe-based applications of synthetic biology.Microbial biotechnology · 2022Article
- Community Detection in Large-Scale Bipartite Biological Networks.Frontiers in genetics · 2021Review
Corrections and comments
- Erratum issued
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Homeostasis of protein concentrations in cells is crucial for their proper functioning, requiring steady-state concentrations to be stable to fluctuations. Since gene expression is regulated by proteins such as transcription factors (TFs), the full set of proteins within the cell constitutes a large system of interacting components, which can become unstable. We explore factors affecting stability by coupling the dynamics of mRNAs and proteins in a growing cell. We find that mRNA degradation rate does not affect stability, contrary to previous claims. However, global structural features of the network can dramatically enhance stability. Importantly, a network resembling a bipartite graph with a lower fraction of interactions that target TFs has a higher chance of being stable. Scrambling the E. coli transcription network, we find that the biological network is significantly more stable than its randomized counterpart, suggesting that stability constraints may have shaped network structure during the course of evolution.
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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.