ArticleMolecular systems biology2010
An atlas of gene regulatory networks reveals multiple three-gene mechanisms for interpreting morphogen gradients.
Article in Molecular systems biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers, 1 of them a synthesis that pooled it.
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Who cites it
90 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A meta-analysis of Boolean network models reveals design principles of gene regulatory networks.Science advances · 2024Pooled it
- Computational model of flower pattern evolution predicts spontaneous emergence of boundary cell types across the petal epidermis.Development (Cambridge, England) · 2026Article
- A Dataset of Benchmark Boolean Models for Gene Regulatory Networks.Scientific data · 2026Article
- Gene regulatory networks: from correlative models to causal explanations.Nature reviews. Genetics · 2026Review
- System drift in the evolution of plant meristem development.PLoS genetics · 2026Article
- Generative epigenetic landscapes map the topology and topography of cell fates.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A tool for modeling gene regulatory networks (GRN_modeler) and its applications to synthetic biology.Molecular systems biology · 2025Article
- AI-driven automated discovery tools reveal diverse behavioral competencies of biological networks.eLife · 2025Article
- Open problems in synthetic multicellularity.NPJ systems biology and applications · 2024Article
- Stable developmental patterns of gene expression without morphogen gradients.PLoS computational biology · 2024Article
- Understanding developmental system drift.Development (Cambridge, England) · 2024Review
- Fundamental constraints to the logic of living systems.Interface focus · 2024Review
- Morphogens in the evolution of size, shape and patterning.Development (Cambridge, England) · 2024Review
- Automatic design of gene regulatory mechanisms for spatial pattern formation.NPJ systems biology and applications · 2024Article
- A bistable autoregulatory module in the developing embryo commits cells to binary expression fates.Current biology : CB · 2023Article
- Environment-dependent epistasis increases phenotypic diversity in gene regulatory networks.Science advances · 2023Article
- Robustness and innovation in synthetic genotype networks.Nature communications · 2023Article
- A shark-inspired general model of tooth morphogenesis unveils developmental asymmetries in phenotype transitions.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Deduction of signaling mechanisms from cellular responses to multiple cues.NPJ systems biology and applications · 2022Article
- Article
30 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
The interpretation of morphogen gradients is a pivotal concept in developmental biology, and several mechanisms have been proposed to explain how gene regulatory networks (GRNs) achieve concentration-dependent responses. However, the number of different mechanisms that may exist for cells to interpret morphogens, and the importance of design features such as feedback or local cell-cell communication, is unclear. A complete understanding of such systems will require going beyond a case-by-case analysis of real morphogen interpretation mechanisms and mapping out a complete GRN 'design space.' Here, we generate a first atlas of design space for GRNs capable of patterning a homogeneous field of cells into discrete gene expression domains by interpreting a fixed morphogen gradient. We uncover multiple very distinct mechanisms distributed discretely across the atlas, thereby expanding the repertoire of morphogen interpretation network motifs. Analyzing this diverse collection of mechanisms also allows us to predict that local cell-cell communication will rarely be responsible for the basic dose-dependent response of morphogen interpretation networks.
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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.