SynthesisScience advances2024
A meta-analysis of Boolean network models reveals design principles of gene regulatory networks.
Synthesis in Science advances, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- From prior knowledge to data-informed models: a review of Boolean network inference.Briefings in bioinformatics · 2026Review
- BoolForge: controlled generation and analysis of Boolean functions and networks.Bioinformatics (Oxford, England) · 2026Article
- AstroLogics: a simulation-based framework for the analysis of boolean model ensembles.Bioinformatics (Oxford, England) · 2026Article
- ChEA-KG and ChEA-KG-TS: a network-based transcription factor enrichment analysis tool with an accompanying time-series workflow.Nucleic acids research · 2026Article
- A Dataset of Benchmark Boolean Models for Gene Regulatory Networks.Scientific data · 2026Article
- Network hypermotifs in biological systems: structure, dynamics, and functional implications.NPJ systems biology and applications · 2026Review
- Dynamics of attractor transitions in Boolean networks under noise.Chaos (Woodbury, N.Y.) · 2026Article
- Canalization as a stabilizing principle of gene regulatory networks: a discrete dynamical systems perspective.NPJ systems biology and applications · 2026Review
- BioLogical: a universal analysis framework for biosystem logical dynamics.Computational and structural biotechnology journal · 2026Article
- Attractors are less stable than their basins: Canalization creates a coherence gap in gene regulatory networks.bioRxiv : the preprint server for biology · 2025Article
- CANA v1.0.0: efficient quantification of canalization in automata networks.Bioinformatics (Oxford, England) · 2025Article
- Upper bound for the stability of Boolean networks.Physical review. E · 2025Article
- Data-driven inference of Boolean networks from transcriptomes to predict cellular differentiation and reprogramming.NPJ systems biology and applications · 2025Article
- A novel quantum algorithm for efficient attractor search in gene regulatory networks.Patterns (New York, N.Y.) · 2025Article
- Review
- Reverse control of biological networks to restore phenotype landscapes.Science advances · 2025Article
- Critical assessment of the ability of Boolean threshold models to describe gene regulatory network dynamics.PNAS nexus · 2025Article
- Article
- Automated model refinement using perturbation-observation pairs.NPJ systems biology and applications · 2025Article
- An open problem: Why are motif-avoidant attractors so rare in asynchronous Boolean networks?Journal of mathematical biology · 2025Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene regulatory networks (GRNs) play a central role in cellular decision-making. Understanding their structure and how it impacts their dynamics constitutes thus a fundamental biological question. GRNs are frequently modeled as Boolean networks, which are intuitive, simple to describe, and can yield qualitative results even when data are sparse. We assembled the largest repository of expert-curated Boolean GRN models. A meta-analysis of this diverse set of models reveals several design principles. GRNs exhibit more canalization, redundancy, and stable dynamics than expected. Moreover, they are enriched for certain recurring network motifs. This raises the important question why evolution favors these design mechanisms.
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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 Socratic graph.