ArticleACS synthetic biology2024
Ligify: Automated Genome Mining for Ligand-Inducible Transcription Factors.
Article in ACS synthetic biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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Who cites it
9 citing papers in PubMed.
- Using enantioselective biosensors to evolve asymmetric biocatalysts.Nature chemical biology · 2026Article
- Ligify 2.0: a web server for predicted small molecule biosensors.Nucleic acids research · 2026Article
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Advances in natural product discovery: strategies, technologies, and insights.Natural products and bioprospecting · 2026Review
- groovDB in 2026: a community-editable database of small molecule biosensors.Nucleic acids research · 2026Article
- Leveraging artificial intelligence for efficient microbial production.Bioresource technology · 2026Review
- Directed Evolution in Escherichia coli for Novel Ligand-Binding Regulators: Evolving a Progesterone-Responsive Transcription Factor to Bind Cortisol.Current protocols · 2025Article
- Biological Switches: Past and Future Milestones of Transcription Factor-Based Biosensors.ACS synthetic biology · 2025Review
- Article
Corrections and comments
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Authors and funding
4 authors.
Funding
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Abstract
Prokaryotic transcription factors can be repurposed into biosensors for the ligand-inducible control of gene expression, but the landscape of chemical ligands for which biosensors exist is extremely limited. To expand this landscape, we developed Ligify, a web application that leverages information in enzyme reaction databases to predict transcription factors that may be responsive to user-defined chemicals. Candidate transcription factors are then incorporated into automatically generated plasmid sequences that are designed to express GFP in response to the target chemical. Our benchmarking analyses demonstrated that Ligify correctly predicted 31/100 previously validated biosensors and highlighted strategies for further improvement. We then used Ligify to build a panel of genetic circuits that could induce a 47-fold, 5-fold, 9-fold, and 27-fold change in fluorescence in response to D-ribose, L-sorbose, isoeugenol, and 4-vinylphenol, respectively. Ligify should enhance the ability of researchers to quickly develop biosensors for an expanded range of chemicals and is publicly available at https://ligify.groov.bio.
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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.