ArticlePLoS computational biology2014
Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
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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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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.
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Who cites it
27 citing papers in PubMed, 45 citations in OpenAlex.
- Distribution of prophage-encoded Pas sRNAs across pathogenicbioRxiv : the preprint server for biology · 2026Article
- RNA cis-regulators are important for Streptococcus pneumoniae in vivo success.PLoS genetics · 2024Article
- High-Resolution Small RNAs Landscape Provides Insights into Alkane Adaptation in the Marine Alkane-Degrader Alcanivorax dieselolei B-5International journal of molecular sciences · 2022Article
- A Peroxide-Responding sRNA Evolved from a Peroxidase mRNA.Molecular biology and evolution · 2022Article
- Divergently Transcribed ncRNAs inFrontiers in molecular biosciences · 2021Article
- A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron.Nature communications · 2020Article
- Regulatory context drives conservation of glycine riboswitch aptamers.PLoS computational biology · 2019Article
- Identification of receptors for UNCG and GNRA Z-turns and their occurrence in rRNA.Nucleic acids research · 2018Article
- Regulatory RNAs in Virulence and Host-Microbe Interactions.Microbiology spectrum · 2018Review
- Origin, Evolution, and Loss of Bacterial Small RNAs.Microbiology spectrum · 2018Review
- rRNA Mimicry in RNA Regulation of Gene Expression.Microbiology spectrum · 2018Review
- GLASSgo - Automated and Reliable Detection of sRNA Homologs From a Single Input Sequence.Frontiers in genetics · 2018Article
- Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution.BMC genomics · 2017Article
- The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq.Nucleic acids research · 2017Article
- Emergence of New sRNAs in Enteric Bacteria is Associated with Low Expression and Rapid Evolution.Journal of molecular evolution · 2017Article
- A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life.Bioinformatics (Oxford, England) · 2017Article
- Small Regulatory RNAs of Rickettsia conorii.Scientific reports · 2016Article
- Molecular phenotyping of infection-associated small non-coding RNAs.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2016Review
- RNA regulators responding to ribosomal protein S15 are frequent in sequence space.Nucleic acids research · 2016Article
- Article
Corrections and comments
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Authors and funding
12 authors at 3 institutions in 3 countries.
Funding
Abstract
Noncoding RNAs are integral to a wide range of biological processes, including translation, gene regulation, host-pathogen interactions and environmental sensing. While genomics is now a mature field, our capacity to identify noncoding RNA elements in bacterial and archaeal genomes is hampered by the difficulty of de novo identification. The emergence of new technologies for characterizing transcriptome outputs, notably RNA-seq, are improving noncoding RNA identification and expression quantification. However, a major challenge is to robustly distinguish functional outputs from transcriptional noise. To establish whether annotation of existing transcriptome data has effectively captured all functional outputs, we analysed over 400 publicly available RNA-seq datasets spanning 37 different Archaea and Bacteria. Using comparative tools, we identify close to a thousand highly-expressed candidate noncoding RNAs. However, our analyses reveal that capacity to identify noncoding RNA outputs is strongly dependent on phylogenetic sampling. Surprisingly, and in stark contrast to protein-coding genes, the phylogenetic window for effective use of comparative methods is perversely narrow: aggregating public datasets only produced one phylogenetic cluster where these tools could be used to robustly separate unannotated noncoding RNAs from a null hypothesis of transcriptional noise. Our results show that for the full potential of transcriptomics data to be realized, a change in experimental design is paramount: effective transcriptomics requires phylogeny-aware sampling.
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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.