ReviewTrends in biotechnology2010
De novo prediction of structured RNAs from genomic sequences.
Review in Trends in biotechnology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 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
38 citing papers in PubMed.
- Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes.Genomics, proteomics & bioinformatics · 2024Article
- Article
- The ensemble diversity of non-coding RNA structure is lower than random sequence.Non-coding RNA research · 2018Article
- Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots.BMC genomics · 2017Article
- The identification and functional annotation of RNA structures conserved in vertebrates.Genome research · 2017Article
- RNAscClust: clustering RNA sequences using structure conservation and graph based motifs.Bioinformatics (Oxford, England) · 2017Article
- Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures.RNA (New York, N.Y.) · 2016Article
- Mutually exclusive RNA secondary structures regulate translation initiation of DinQ in Escherichia coli.RNA (New York, N.Y.) · 2016Article
- Evolution to the rescue: using comparative genomics to understand long non-coding RNAs.Nature reviews. Genetics · 2016Review
- Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment.Bioinformatics (Oxford, England) · 2016Article
- RNA motif discovery: a computational overview.Biology direct · 2015Review
- Optimizing RNA structures by sequence extensions using RNAcop.Nucleic acids research · 2015Article
- Article
- Article
- Generation of a neuro-specific microarray reveals novel differentially expressed noncoding RNAs in mouse models for neurodegenerative diseases.RNA (New York, N.Y.) · 2014Article
- Structured RNAs and synteny regions in the pig genome.BMC genomics · 2014Article
- Identification of conserved RNA secondary structures at influenza B and C splice sites reveals similarities and differences between influenza A, B, and C.BMC research notes · 2014Article
- Widespread purifying selection on RNA structure in mammals.Nucleic acids research · 2013Article
- Review
- Structure-based whole-genome realignment reveals many novel noncoding RNAs.Genome research · 2013Article
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.
Funding
Abstract
Growing recognition of the numerous, diverse and important roles played by non-coding RNA in all organisms motivates better elucidation of these cellular components. Comparative genomics is a powerful tool for this task and is arguably preferable to any high-throughput experimental technology currently available, because evolutionary conservation highlights functionally important regions. Conserved secondary structure, rather than primary sequence, is the hallmark of many functionally important RNAs, because compensatory substitutions in base-paired regions preserve structure. Unfortunately, such substitutions also obscure sequence identity and confound alignment algorithms, which complicates analysis greatly. This paper surveys recent computational advances in this difficult arena, which have enabled genome-scale prediction of cross-species conserved RNA elements. These predictions suggest that a wealth of these elements indeed exist.
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.