ReviewAnnual review of biophysics2014
Computational analysis of conserved RNA secondary structure in transcriptomes and genomes.
Review in Annual review of biophysics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed.
- Genomic indicators of gene function: a systematic assessment of the human genome.G3 (Bethesda, Md.) · 2026Article
- Markov models of SHAPE data improve secondary structure prediction.bioRxiv : the preprint server for biology · 2026Article
- UFold-X: an enhanced Dual & Dynamic U-Mamba model for long-range RNA secondary structure prediction.Nucleic acids research · 2026Article
- An efficient algorithm for exploring RNA branching conformations under the nearest-neighbor thermodynamic model.Algorithms for molecular biology : AMB · 2026Article
- Deep learning for RNA secondary structure determination: gauging generalizability and broadening the scope of traditional methods.RNA (New York, N.Y.) · 2026Review
- Conservation of extended sequence and structure in the branchpoint-to-3' splice site region upstream of neural microexons.bioRxiv : the preprint server for biology · 2026Article
- Designing molecular RNA switches with Restricted Boltzmann machines.Nature communications · 2025Article
- A method for estimating energy parameters of RNAs by differentiating base-pairing probabilities.NAR genomics and bioinformatics · 2025Article
- Deep Learning for RNA Secondary Structure Determination: Gauging Generalizability and Broadening the Scope of Traditional Methods.bioRxiv : the preprint server for biology · 2025Article
- Improving RNA Secondary Structure Prediction Through Expanded Training Data.bioRxiv : the preprint server for biology · 2025Article
- Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data.RNA (New York, N.Y.) · 2025Article
- Enhanced RNA secondary structure prediction through integrative deep learning and structural context analysis.Nucleic acids research · 2025Article
- Measuring intramolecular connectivity in long RNA molecules using two-dimensional DNA patch-probe arrays.Nucleic acids research · 2025Article
- Consistent features observed in structural probing data of eukaryotic RNAs.NAR genomics and bioinformatics · 2025Article
- Targeting RNA with small molecules, from RNA structures to precision medicines: IUPHAR review: 40.British journal of pharmacology · 2024Review
- Heterobifunctional small molecules to modulate RNA function.Trends in pharmacological sciences · 2024Review
- How Parameters Influence SHAPE-Directed Predictions.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Mutation signature filtering enables high-fidelity RNA structure probing at all four nucleobases with DMS.Nucleic acids research · 2023Article
- RNA contact prediction by data efficient deep learning.Communications biology · 2023Article
- RNA Secondary Structure Analysis Using RNAstructure.Current protocols · 2023Article
19 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
1 author.
Funding
Abstract
Transcriptomics experiments and computational predictions both enable systematic discovery of new functional RNAs. However, many putative noncoding transcripts arise instead from artifacts and biological noise, and current computational prediction methods have high false positive rates. I discuss prospects for improving computational methods for analyzing and identifying functional RNAs, with a focus on detecting signatures of conserved RNA secondary structure. An interesting new front is the application of chemical and enzymatic experiments that probe RNA structure on a transcriptome-wide scale. I review several proposed approaches for incorporating structure probing data into the computational prediction of RNA secondary structure. Using probabilistic inference formalisms, I show how all these approaches can be unified in a well-principled framework, which in turn allows RNA probing data to be easily integrated into a wide range of analyses that depend on RNA secondary structure inference. Such analyses include homology search and genome-wide detection of new structural RNAs.
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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.