ArticleNature communications2021
Contextual dependencies expand the re-usability of genetic inverters.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Challenges and Future Directives of Synthetic Biology in Engineering Plant-Microbe Partnerships for Sustainable Agriculture.Biotechnology and bioengineering · 2026Review
- Product-Responsive Regulation of NADPH and Malonyl-CoA Allocation Enhances 3-Hydroxypropionic Acid Production inACS synthetic biology · 2026Article
- Growth control as a central regulator for tuning the cellular context.Journal of biological engineering · 2026Article
- Dynamics of genetic circuits in Pseudomonas protegens.Cell systems · 2026Article
- Genomic perplexity and the evolution of context-dependent function.Molecular biology and evolution · 2026Article
- Exploring the computing power of microbes that shapes the environment.Current opinion in microbiology · 2026Review
- Design of CRISPRi-Based Synthetic Gene Circuits in Bacteria.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Broad-Host-Range Synthetic Biology: Rethinking Microbial Chassis as a Design Variable.ACS synthetic biology · 2025Review
- Parameter Evolvability in Gene Expression Models Drives Phenotypic Adaptation.ALIFE : proceedings of the artificial life conference. International Conference on Artificial Life · 2025Article
- Why cellular computations challenge our design principles.Seminars in cell & developmental biology · 2025Review
- Context-Aware Biosensor Design Through Biology-Guided Machine Learning and Dynamical Modeling.ACS synthetic biology · 2025Article
- Standardized Quorum Sensing Tools for Gram-Negative Bacteria.ACS synthetic biology · 2025Article
- Genetic designs for stochastic and probabilistic biocomputing.Physical review. E · 2025Article
- CRISPRi-based circuits to control gene expression in plants.Nature biotechnology · 2025Article
- Rational Design Assisted by Evolutionary Engineering Allows (De)Construction and Optimization of Complex Phenotypes in Pseudomonas putida KT2440.Microbial biotechnology · 2025Article
- The switch-liker's guide to plant synthetic gene circuits.The Plant journal : for cell and molecular biology · 2025Review
- Fine-Tuning Genetic Circuits via Host Context and RBS Modulation.ACS synthetic biology · 2025Article
- Article
- Transfer learning for cross-context prediction of protein expression from 5'UTR sequence.Nucleic acids research · 2024Article
- Biocomputation: Moving Beyond Turing with Living Cellular Computers.Communications of the ACM · 2024Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The implementation of Boolean logic circuits in cells have become a very active field within synthetic biology. Although these are mostly focussed on the genetic components alone, the context in which the circuit performs is crucial for its outcome. We characterise 20 genetic NOT logic gates in up to 7 bacterial-based contexts each, to generate 135 different functions. The contexts we focus on are combinations of four plasmid backbones and three hosts, two Escherichia coli and one Pseudomonas putida strains. Each gate shows seven different dynamic behaviours, depending on the context. That is, gates can be fine-tuned by changing only contextual parameters, thus improving the compatibility between gates. Finally, we analyse portability by measuring, scoring, and comparing gate performance across contexts. Rather than being a limitation, we argue that the effect of the genetic background on synthetic constructs expands functionality, and advocate for considering context as a fundamental design parameter.
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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.