ArticleNature microbiology2017
An integrative circuit-host modelling framework for predicting synthetic gene network behaviours.
Article in Nature microbiology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed.
- Review
- Coarse-grained resource allocation modeling for decoding and rewiring microbial metabolism.Trends in microbiology · 2026Review
- Opportunities for artificial intelligence and synthetic biology in designing living drug delivery systems.Advanced drug delivery reviews · 2026Review
- Overriding Bioprocess Perturbations With a Cell-Machine Interface for Reliable Microbial Stress-Response Control.Microbial biotechnology · 2026Article
- Resolving emergent transient oscillations in gene circuits with a growth-coupled model.Science advances · 2026Article
- Quantitative Coarse-Grained Modeling of Microbial Metabolism: Uncovering Growth Laws, Environmental Responses, and Host-Circuit Coupling.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Coupled Perturbations of Gene Circuit Dynamics by Resource Competition and Growth Dilution.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Article
- Article
- Systematic modulation of bacterial resource allocation by perturbing RNA polymerase availability via synthetic transcriptional switches.Nucleic acids research · 2025Article
- Gene Expression Depends on the Interplay Among Growth, Resource Biogenesis, and Nutrient Quality.ACS synthetic biology · 2025Article
- Coarse-Grained Modeling Elucidates Differential Metabolism ofACS synthetic biology · 2025Article
- Resource competition-driven bistability and stochastic switching amplify gene expression noise.PLoS computational biology · 2025Article
- Mitigating Winner-Take-All Resource Competition through Antithetic Control Mechanism.ACS synthetic biology · 2024Article
- Plasmid-encoded phosphatase RapP enhances cell growth in non-domesticated Bacillus subtilis strains.Nature communications · 2024Article
- Phase Separation to Resolve Growth-Related Circuit Failures.bioRxiv : the preprint server for biology · 2024Article
- Modulating bacterial function utilizing A knowledge base of transcriptional regulatory modules.Nucleic acids research · 2024Article
- Computational Synthetic Biology Enabled through JAX: A Showcase.ACS synthetic biology · 2024Article
- How DoesACS synthetic biology · 2024Article
- Context-dependent redesign of robust synthetic gene circuits.Trends in biotechnology · 2024Review
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3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
One fundamental challenge in synthetic biology is the lack of quantitative tools that accurately describe and predict the behaviours of engineered gene circuits. This challenge arises from multiple factors, among which the complex interdependence of circuits and their host is a leading cause. Here we present a gene circuit modelling framework that explicitly integrates circuit behaviours with host physiology through bidirectional circuit-host coupling. The framework consists of a coarse-grained but mechanistic description of host physiology that involves dynamic resource partitioning, multilayered circuit-host coupling including both generic and system-specific interactions, and a detailed kinetic module of exogenous circuits. We showed that, following training, the framework was able to capture and predict a large set of experimental data concerning the host and its foreign gene overexpression. To demonstrate its utility, we applied the framework to examine a growth-modulating feedback circuit whose dynamics is qualitatively altered by circuit-host interactions. Using an extended version of the framework, we further systematically revealed the behaviours of a toggle switch across scales from single-cell dynamics to population structure and to spatial ecology. This work advances our quantitative understanding of gene circuit behaviours and also benefits the rational design of synthetic gene networks.
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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.