ArticleJournal of biological engineering2014
In silico design and in vivo implementation of yeast gene Boolean gates.
Article in Journal of biological engineering, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 29 citations in OpenAlex.
- Cell-free recombinase-integrated Boolean output system.Cell systems · 2025Article
- Scaffold RNA engineering in type V CRISPR-Cas systems: a potent way to enhance gene expression in the yeast Saccharomyces cerevisiae.Nucleic acids research · 2024Article
- RNAi-based Boolean gates in the yeastFrontiers in bioengineering and biotechnology · 2024Article
- Hybrid Synthetic Promoters in Saccharomyces cerevisiae Built on Foreign Promoter Sequences.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Design of Gene Boolean Gates and Circuits with Convergent Promoters.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Hybrid Boolean gates show that Cas12c controls transcription activation effectively in the yeastFrontiers in bioengineering and biotechnology · 2023Article
- Engineering a two-gene system to operate as a highly sensitive biosensor or a sharp switch upon induction with β-estradiol.Scientific reports · 2022Article
- NOT Gates Based on Protein Degradation as a Case Study for a New Modular Modeling via SBML Level 3-Comp Package.Frontiers in bioengineering and biotechnology · 2022Article
- Review
- Synthetic Toolkit for Complex Genetic Circuit Engineering in Saccharomyces cerevisiae.ACS synthetic biology · 2018Article
- Anti-CRISPR-based biosensors in the yeastJournal of biological engineering · 2018Article
- Review
- Can terminators be used as insulators into yeast synthetic gene circuits?Journal of biological engineering · 2016Article
- Exploiting the dynamic properties of covalent modification cycle for the design of synthetic analog biomolecular circuitry.Journal of biological engineering · 2016Article
- Artificial cell-cell communication as an emerging tool in synthetic biology applications.Journal of biological engineering · 2015Article
- Developments in the tools and methodologies of synthetic biology.Frontiers in bioengineering and biotechnology · 2014Review
- Synthetic biology outside the cell: linking computational tools to cell-free systems.Frontiers in bioengineering and biotechnology · 2014Review
- Parts & pools: a framework for modular design of synthetic gene circuits.Frontiers in bioengineering and biotechnology · 2014Review
Corrections and comments
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Authors and funding
1 author at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In our previous computational work, we showed that gene digital circuits can be automatically designed in an electronic fashion. This demands, first, a conversion of the truth table into Boolean formulas with the Karnaugh map method and, then, the translation of the Boolean formulas into circuit schemes organized into layers of Boolean gates and Pools of signal carriers. In our framework, gene digital circuits that take up to three different input signals (chemicals) arise from the composition of three kinds of basic Boolean gates, namely YES, NOT, and AND. Here we present a library of YES, NOT, and AND gates realized via plasmidic DNA integration into the yeast genome. Boolean behavior is reproduced via the transcriptional control of a synthetic bipartite promoter that contains sequences of the yeast VPH1 and minimal CYC1 promoters together with operator binding sites for bacterial (i.e. orthogonal) repressor proteins. Moreover, model-driven considerations permitted us to pinpoint a strategy for re-designing gates when a better digital performance is required. Our library of well-characterized Boolean gates is the basis for the assembly of more complex gene digital circuits. As a proof of concepts, we engineered two 2-input OR gates, designed by our software, by combining YES and NOT gates present in our library.
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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.