ArticleNucleic acids research2015
Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 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
35 citing papers in PubMed.
- Male specific conserved LncRNA TSCL1 regulated target mRNA translation by interaction with PIWIL1.Cell death and differentiation · 2026Article
- Associating cancer-related RNA structure disrupting SNPs in LincRNAs to function.BMC genomics · 2025Article
- VariantFoldRNA: a flexible, containerized, and scalable pipeline for genome-wide riboSNitch prediction.NAR genomics and bioinformatics · 2025Article
- Identification of candidate causal variants and target genes at 41 breast cancer risk loci through differential allelic expression analysis.Scientific reports · 2024Article
- Rock, scissors, paper: How RNA structure informs function.The Plant cell · 2023Article
- RNAsmc: A integrated tool for comparing RNA secondary structure and evaluating allosteric effects.Computational and structural biotechnology journal · 2023Article
- RNA Secondary Structure Alteration Caused by Single Nucleotide Variants.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Disease-associated human genetic variation through the lens of precursor and mature RNA structure.Human genetics · 2022Review
- RNANetMotif: Identifying sequence-structure RNA network motifs in RNA-protein binding sites.PLoS computational biology · 2022Article
- Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis.Genome biology · 2022Article
- Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Wheat in vivo RNA structure landscape reveals a prevalent role of RNA structure in modulating translational subgenome expression asymmetry.Genome biology · 2021Article
- Article
- Identification and analysis of RNA structural disruptions induced by single nucleotide variants using Riprap and RiboSNitchDB.NAR genomics and bioinformatics · 2020Article
- Alternate RNA Structures.Cold Spring Harbor perspectives in biology · 2020Review
- Integrative Analysis of Somatic Mutations in Non-coding Regions Altering RNA Secondary Structures in Cancer Genomes.Scientific reports · 2019Article
- Pairwise visual comparison of small RNA secondary structures with base pair probabilities.BMC bioinformatics · 2019Article
- Genome-Wide Discovery of DEAD-Box RNA Helicase Targets Reveals RNA Structural Remodeling in Transcription Termination.Genetics · 2019Article
- High-throughput determination of RNA structures.Nature reviews. Genetics · 2018Review
- Allele-specific SHAPE-MaP assessment of the effects of somatic variation and protein binding on mRNA structure.RNA (New York, N.Y.) · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Ribonucleic acid (RNA) secondary structure prediction continues to be a significant challenge, in particular when attempting to model sequences with less rigidly defined structures, such as messenger and non-coding RNAs. Crucial to interpreting RNA structures as they pertain to individual phenotypes is the ability to detect RNAs with large structural disparities caused by a single nucleotide variant (SNV) or riboSNitches. A recently published human genome-wide parallel analysis of RNA structure (PARS) study identified a large number of riboSNitches as well as non-riboSNitches, providing an unprecedented set of RNA sequences against which to benchmark structure prediction algorithms. Here we evaluate 11 different RNA folding algorithms' riboSNitch prediction performance on these data. We find that recent algorithms designed specifically to predict the effects of SNVs on RNA structure, in particular remuRNA, RNAsnp and SNPfold, perform best on the most rigorously validated subsets of the benchmark data. In addition, our benchmark indicates that general structure prediction algorithms (e.g. RNAfold and RNAstructure) have overall better performance if base pairing probabilities are considered rather than minimum free energy calculations. Although overall aggregate algorithmic performance on the full set of riboSNitches is relatively low, significant improvement is possible if the highest confidence predictions are evaluated independently.
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.