ArticleNucleic acids research2014
Profiling small RNA reveals multimodal substructural signals in a Boltzmann ensemble.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed.
- When does additional information improve accuracy of RNA secondary structure prediction?bioRxiv : the preprint server for biology · 2026Article
- Can geometric combinatorics improve RNA branching predictions?BMC bioinformatics · 2025Article
- The R-loop grammar predicts R-loop formation under different topological constraints.PLoS computational biology · 2025Article
- How Parameters Influence SHAPE-Directed Predictions.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Led-Seq: ligation-enhanced double-end sequence-based structure analysis of RNA.Nucleic acids research · 2023Article
- On the Problem of Reconstructing a Mixture of RNA Structures.Bulletin of mathematical biology · 2020Article
- Article
- Helix-Based RNA Landscape Partition and Alternative Secondary Structure Determination.ACS omega · 2019Article
- The roles of structural dynamics in the cellular functions of RNAs.Nature reviews. Molecular cell biology · 2019Review
- ENTRNA: a framework to predict RNA foldability.BMC bioinformatics · 2019Article
- Analyzing Secondary Structure Patterns in DNA Aptamers Identified via CompELS.Molecules (Basel, Switzerland) · 2019Article
- Towards an understanding of RNA structural modalities: a riboswitch case study.Computational and mathematical biophysics · 2019Article
- Challenges and approaches to predicting RNA with multiple functional structures.RNA (New York, N.Y.) · 2018Review
- SSMART: sequence-structure motif identification for RNA-binding proteins.Bioinformatics (Oxford, England) · 2018Article
- Characterization and visualization of RNA secondary structure Boltzmann ensemble via information theory.BMC bioinformatics · 2018Article
- Statistical modeling of RNA structure profiling experiments enables parsimonious reconstruction of structure landscapes.Nature communications · 2018Article
- Conditioning and Robustness of RNA Boltzmann Sampling under Thermodynamic Parameter Perturbations.Biophysical journal · 2017Article
- Article
- New insights from cluster analysis methods for RNA secondary structure prediction.Wiley interdisciplinary reviews. RNA · 2016Review
- Multiple conformations are a conserved and regulatory feature of the RB1 5' UTR.RNA (New York, N.Y.) · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
As the biomedical impact of small RNAs grows, so does the need to understand competing structural alternatives for regions of functional interest. Suboptimal structure analysis provides significantly more RNA base pairing information than a single minimum free energy prediction. Yet computational enhancements like Boltzmann sampling have not been fully adopted by experimentalists since identifying meaningful patterns in this data can be challenging. Profiling is a novel approach to mining RNA suboptimal structure data which makes the power of ensemble-based analysis accessible in a stable and reliable way. Balancing abstraction and specificity, profiling identifies significant combinations of base pairs which dominate low-energy RNA secondary structures. By design, critical similarities and differences are highlighted, yielding crucial information for molecular biologists. The code is freely available via http://gtfold.sourceforge.net/profiling.html.
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.