ArticleNature communications2024
A coarse-grained bacterial cell model for resource-aware analysis and design of synthetic gene circuits.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Coarse-grained resource allocation modeling for decoding and rewiring microbial metabolism.Trends in microbiology · 2026Review
- Systems engineering of engineered live biotherapeutics: A discovery-to-translation framework for streamlining microbiome therapeutic development.Journal of controlled release : official journal of the Controlled Release Society · 2026Review
- The proportional scaling of mRNA and ribosome concentrations controls eukaryotic cell growth.Nature cell biology · 2026Article
- Host-aware Identification of Intrinsic Gene Expression Biopart Parameters using Combinatorial Libraries.Nature communications · 2026Article
- Bacterial-based cancer therapy: mechanisms and therapeutic advances.Molecular biomedicine · 2026Review
- Modular Scalable Synthetic Gene Circuits for Complex Functions Within Minimal Computational Layers in Human Cells.Nature communications · 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
- Engineering bacteria for enhanced tumor therapy: from surface modification to synthetic genetic circuits.Journal of hematology & oncology · 2025Review
- Gene Expression Depends on the Interplay Among Growth, Resource Biogenesis, and Nutrient Quality.ACS synthetic biology · 2025Article
- Multi-Layer Autocatalytic Feedback Enables Integral Control Amidst Resource Competition and Across Scales.ACS synthetic biology · 2025Article
- Model-guided gene circuit design for engineering genetically stable cell populations in diverse applications.Journal of the Royal Society, Interface · 2025Article
- Mitigating Winner-Take-All Resource Competition through Antithetic Control Mechanism.ACS synthetic biology · 2024Article
- Noise Reduction in Resource-Coupled Multi-Module Gene Circuits through Antithetic Feedback Control.Proceedings of the ... IEEE Conference on Decision & Control. IEEE Conference on Decision & Control · 2024Article
- Energy Aware Technology Mapping of Genetic Logic Circuits.ACS synthetic biology · 2024Article
- Energy Aware Technology Mapping of Genetic Logic Circuits.bioRxiv : the preprint server for biology · 2024Article
- Computational Synthetic Biology Enabled through JAX: A Showcase.ACS synthetic biology · 2024Article
- Context-dependent redesign of robust synthetic gene circuits.Trends in biotechnology · 2024Review
- A coarse-grained bacterial cell model for resource-aware analysis and design of synthetic gene circuits.Nature communications · 2024Article
- Competition and evolutionary selection among core regulatory motifs in gene expression control.Nature communications · 2023Article
Corrections and comments
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4 authors.
Funding
Abstract
Within a cell, synthetic and native genes compete for expression machinery, influencing cellular process dynamics through resource couplings. Models that simplify competitive resource binding kinetics can guide the design of strategies for countering these couplings. However, in bacteria resource availability and cell growth rate are interlinked, which complicates resource-aware biocircuit design. Capturing this interdependence requires coarse-grained bacterial cell models that balance accurate representation of metabolic regulation against simplicity and interpretability. We propose a coarse-grained E. coli cell model that combines the ease of simplified resource coupling analysis with appreciation of bacterial growth regulation mechanisms and the processes relevant for biocircuit design. Reliably capturing known growth phenomena, it provides a unifying explanation to disparate empirical relations between growth and synthetic gene expression. Considering a biomolecular controller that makes cell-wide ribosome availability robust to perturbations, we showcase our model's usefulness in numerically prototyping biocircuits and deriving analytical relations for design guidance.
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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.