ArticleNature methods2014
Comprehensive analysis of RNA-protein interactions by high-throughput sequencing-RNA affinity profiling.
Article in Nature methods, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 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
82 citing papers in PubMed, 139 citations in OpenAlex.
- Decoding RNA-protein interactions using high-throughput methods.RNA biology · 2026Review
- Article
- A High-Throughput Platform for Rapid Adaptation of DNA Aptamers to SARS-CoV-2 Evolution.bioRxiv : the preprint server for biology · 2026Article
- Automated high-throughput selection of DNA aptamers using a common optical next-generation sequencer.Nucleic acids research · 2026Article
- Multiplexed single-molecule characterization at the library scale.Nature protocols · 2026Review
- Single-molecule parallel analysis for rapid exploration of sequence space.Nature protocols · 2026Review
- Systematic analysis of cotranscriptional RNA folding using transcription elongation complex display.Nature communications · 2025Article
- Structure-Based Prediction of lncRNA-Protein Interactions by Deep Learning.Methods in molecular biology (Clifton, N.J.) · 2025Article
- The Times-Divide Expression: An Intuitive Approach for Describing Right-Skewed Data in Nursing Practice.Journal of nursing management · 2025Article
- Massively parallel dissection of RNA in RNA-protein interactions in vivo.Nucleic acids research · 2024Article
- Rapid discovery of high-affinity antibodies via massively parallel sequencing, ribosome display and affinity screening.Nature biomedical engineering · 2024Article
- Massively parallel profiling of RNA-targeting CRISPR-Cas13d.Nature communications · 2024Article
- Repurposing CRISPR/Cas to Discover SARS-CoV-2 Detecting and Neutralizing Aptamers.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- High-throughput biochemistry in RNA sequence space: predicting structure and function.Nature reviews. Genetics · 2023Review
- Massively Parallel Profiling of RNA-targeting CRISPR-Cas13d.bioRxiv : the preprint server for biology · 2023Article
- Generation of Functional-RNA Arrays by In Vitro Transcription and In Situ RNA Capture for the Detection of RNA-RNA Interactions.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Using the structural diversity of RNA: protein interfaces to selectively target RNA with small molecules in cells: methods and perspectives.Frontiers in molecular biosciences · 2023Review
- Massively Parallel Selection of NanoCluster Beacons.Advanced materials (Deerfield Beach, Fla.) · 2022Article
- A comprehensive thermodynamic model for RNA binding by the Saccharomyces cerevisiae Pumilio protein PUF4.Nature communications · 2022Article
- Simple synthesis of massively parallel RNA microarrays via enzymatic conversion from DNA microarrays.Nature communications · 2022Article
22 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
6 authors at 2 institutions in 1 country.
Funding
Abstract
RNA-protein interactions play critical roles in gene regulation, but methods to quantitatively analyze these interactions at a large scale are lacking. We have developed a high-throughput sequencing-RNA affinity profiling (HiTS-RAP) assay by adapting a high-throughput DNA sequencer to quantify the binding of fluorescently labeled protein to millions of RNAs anchored to sequenced cDNA templates. Using HiTS-RAP, we measured the affinity of mutagenized libraries of GFP-binding and NELF-E-binding aptamers to their respective targets and identified critical regions of interaction. Mutations additively affected the affinity of the NELF-E-binding aptamer, whose interaction depended mainly on a single-stranded RNA motif, but not that of the GFP aptamer, whose interaction depended primarily on secondary structure.
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.