ReviewPLoS computational biology2011
From structure prediction to genomic screens for novel non-coding RNAs.
Review in PLoS computational biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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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.
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Who cites it
27 citing papers in PubMed, 44 citations in OpenAlex.
- Computational discovery of conserved RNA structures and functional characterization of a structured lncRNA inNon-coding RNA research · 2025Article
- Clusters of mammalian conserved RNA structures in UTRs associate with RBP binding sites.NAR genomics and bioinformatics · 2024Article
- Does rapid sequence divergence preclude RNA structure conservation in vertebrates?Nucleic acids research · 2022Article
- BML: a versatile web server for bipartite motif discovery.Briefings in bioinformatics · 2022Article
- Article
- Expression profiles of microRNAs in skeletal muscle of sheep by deep sequencing.Asian-Australasian journal of animal sciences · 2019Article
- MicroRNAs or Long Noncoding RNAs in Diagnosis and Prognosis of Coronary Artery Disease.Aging and disease · 2019Review
- Identification and characterization of novel conserved RNA structures in Drosophila.BMC genomics · 2018Article
- Fine mapping of a QTL affecting levels of skatole on pig chromosome 7.BMC genetics · 2017Article
- Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq).Nature communications · 2016Article
- Probing-directed identification of novel structured RNAs.RNA biology · 2016Article
- RNA motif discovery: a computational overview.Biology direct · 2015Review
- Systematic exploration of autonomous modules in noisy microRNA-target networks for testing the generality of the ceRNA hypothesis.BMC genomics · 2014Article
- Identification of non-coding RNAs with a new composite feature in the Hybrid Random Forest Ensemble algorithm.Nucleic acids research · 2014Article
- Interconversion between parallel and antiparallel conformations of a 4H RNA junction in domain 3 of foot-and-mouth disease virus IRES captured by dynamics simulations.Biophysical journal · 2014Article
- Fast selection of miRNA candidates based on large-scale pre-computed MFE sets of randomized sequences.BMC research notes · 2014Article
- Functional transcriptomics in the post-ENCODE era.Genome research · 2013Article
- Widespread purifying selection on RNA structure in mammals.Nucleic acids research · 2013Article
- Structure-based whole-genome realignment reveals many novel noncoding RNAs.Genome research · 2013Article
- Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Non-coding RNAs (ncRNAs) are receiving more and more attention not only as an abundant class of genes, but also as regulatory structural elements (some located in mRNAs). A key feature of RNA function is its structure. Computational methods were developed early for folding and prediction of RNA structure with the aim of assisting in functional analysis. With the discovery of more and more ncRNAs, it has become clear that a large fraction of these are highly structured. Interestingly, a large part of the structure is comprised of regular Watson-Crick and GU wobble base pairs. This and the increased amount of available genomes have made it possible to employ structure-based methods for genomic screens. The field has moved from folding prediction of single sequences to computational screens for ncRNAs in genomic sequence using the RNA structure as the main characteristic feature. Whereas early methods focused on energy-directed folding of single sequences, comparative analysis based on structure preserving changes of base pairs has been efficient in improving accuracy, and today this constitutes a key component in genomic screens. Here, we cover the basic principles of RNA folding and touch upon some of the concepts in current methods that have been applied in genomic screens for de novo RNA structures in searches for novel ncRNA genes and regulatory RNA structure on mRNAs. We discuss the strengths and weaknesses of the different strategies and how they can complement each other.
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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.