ArticleNature methods2015
High-throughput cellular RNA device engineering.
Article in Nature methods, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
62 citing papers in PubMed.
- High-throughput engineering of ligand-activated splicing ribozyme through domain insertion.bioRxiv : the preprint server for biology · 2026Article
- Scalable and cost-efficient custom gene library assembly from oligopools.Science advances · 2026Article
- A Versatile Plasmid System for Translational Control and Secretion of Recombinant Proteins in Mycobacteria.ACS synthetic biology · 2026Article
- Conditional guide RNA deactivation by mRNA and small molecule triggers in Saccharomyces cerevisiae.New biotechnology · 2025Article
- Generative and predictive neural networks for the design of functional RNA molecules.Nature communications · 2025Article
- Prevention of ribozyme catalysis through cDNA synthesis enables accurate RT-qPCR measurements of context-dependent ribozyme activity.RNA (New York, N.Y.) · 2025Article
- Structural investigation of an RNA device that regulates PD-1 expression in mammalian cells.Nucleic acids research · 2025Article
- RNA folding kinetics control riboswitch sensitivity in vivo.Nature communications · 2025Article
- RNA folding kinetics control riboswitch sensitivity in vivo.bioRxiv : the preprint server for biology · 2024Article
- Non-invasive single cell aptasensing in live cells and animals.Chemical science · 2024Article
- Deep generative design of RNA family sequences.Nature methods · 2024Article
- Encoding Genetic Circuits with DNA Barcodes Paves the Way for High-Throughput Profiling of Dose-Response Curves of Metabolite Biosensors.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Advances in ligand-specific biosensing for structurally similar molecules.Cell systems · 2023Review
- Deep-learning-assisted Sort-Seq enables high-throughput profiling of gene expression characteristics with high precision.Science advances · 2023Article
- Genome-wide promoter responses to CRISPR perturbations of regulators reveal regulatory networks in Escherichia coli.Nature communications · 2023Article
- Article
- Effective design and inference for cell sorting and sequencing based massively parallel reporter assays.Bioinformatics (Oxford, England) · 2023Article
- Real-Time Assessment of Intracellular Metabolites in Single Cells through RNA-Based Sensors.Biomolecules · 2023Review
- Article
- Engineering Ag43 Signal Peptides with Bacterial Display and Selection.Methods and protocols · 2022Article
2 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Methods for rapidly assessing sequence-structure-function landscapes and developing conditional gene-regulatory devices are critical to our ability to manipulate and interface with biology. We describe a framework for engineering RNA devices from preexisting aptamers that exhibit ligand-responsive ribozyme tertiary interactions. Our methodology utilizes cell sorting, high-throughput sequencing and statistical data analyses to enable parallel measurements of the activities of hundreds of thousands of sequences from RNA device libraries in the absence and presence of ligands. Our tertiary-interaction RNA devices performed better in terms of gene silencing, activation ratio and ligand sensitivity than optimized RNA devices that rely on secondary-structure changes. We applied our method to build biosensors for diverse ligands and determine consensus sequences that enable ligand-responsive tertiary interactions. These methods advance our ability to develop broadly applicable genetic tools and to elucidate the underlying sequence-structure-function relationships that empower rational design of complex biomolecules.
Indexed as
Identifiers
What OpenQuestion holds
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.