ArticleNature communications2014
A unified design space of synthetic stripe-forming networks.
Article in Nature communications, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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Who cites it
70 citing papers in PubMed.
- A novel reaction-diffusion architecture for engineering self-organized patterns in mammalian cells.bioRxiv : the preprint server for biology · 2026Article
- Network hypermotifs in biological systems: structure, dynamics, and functional implications.NPJ systems biology and applications · 2026Review
- Design of CRISPRi-Based Synthetic Gene Circuits in Bacteria.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A tool for modeling gene regulatory networks (GRN_modeler) and its applications to synthetic biology.Molecular systems biology · 2025Article
- Engineering Tunable, Low Latency Spatial Computation with Dual Input Quorum Sensing Promoters.ACS synthetic biology · 2024Article
- Automatic design of gene regulatory mechanisms for spatial pattern formation.NPJ systems biology and applications · 2024Article
- Spatial biology of Ising-like synthetic genetic networks.BMC biology · 2023Article
- Dynamics of an incoherent feedforward loop drive ERK-dependent pattern formation in the early Drosophila embryo.Development (Cambridge, England) · 2023Article
- Article
- Environment-dependent epistasis increases phenotypic diversity in gene regulatory networks.Science advances · 2023Article
- Robustness and innovation in synthetic genotype networks.Nature communications · 2023Article
- Dynamics of an incoherent feedforward loop drive ERK-dependent pattern formation in the earlybioRxiv : the preprint server for biology · 2023Article
- A quantitative evaluation of topological motifs and their coupling in gene circuit state distributions.iScience · 2023Article
- Construction of the genetic switches in response to mannitol based on artificial MtlR box.Bioresources and bioprocessing · 2023Article
- What Makes a Functional Gene Regulatory Network? A Circuit Motif Analysis.The journal of physical chemistry. B · 2022Article
- Article
- Advances and challenges in programming pattern formation using living cells.Current opinion in chemical biology · 2022Review
- Synthetic spatial patterning in bacteria: advances based on novel diffusible signals.Microbial biotechnology · 2022Review
- Ecological drivers of division of labour in Streptomyces.Current opinion in microbiology · 2022Review
- Bacterial Growth, Communication, and Guided Chemotaxis in 3D-Bioprinted Hydrogel Environments.ACS applied materials & interfaces · 2022Article
10 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Synthetic biology is a promising tool to study the function and properties of gene regulatory networks. Gene circuits with predefined behaviours have been successfully built and modelled, but largely on a case-by-case basis. Here we go beyond individual networks and explore both computationally and synthetically the design space of possible dynamical mechanisms for 3-node stripe-forming networks. First, we computationally test every possible 3-node network for stripe formation in a morphogen gradient. We discover four different dynamical mechanisms to form a stripe and identify the minimal network of each group. Next, with the help of newly established engineering criteria we build these four networks synthetically and show that they indeed operate with four fundamentally distinct mechanisms. Finally, this close match between theory and experiment allows us to infer and subsequently build a 2-node network that represents the archetype of the explored design space.
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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.