ArticleNature genetics2018
Functional classification of long non-coding RNAs by k-mer content.
Article in Nature genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 127 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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Who cites it
127 citing papers in PubMed, 270 citations in OpenAlex.
- Article
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- RNA-Lexis: a probabilistic algorithm using a non-parametric segmentation logic to detect meaningful sequences in RNA.Nucleic acids research · 2026Article
- An integrative workflow for lncRNA orthology detection and its application to 13 evolutionarily diverse species.Nucleic acids research · 2026Article
- Scanning transcriptomes for nonlinear, domain-level similarities using hmSEEKR.bioRxiv : the preprint server for biology · 2026Article
- Correlated protein-RNA associations and a requirement for HNRNPU in the long-range recruitment of Polycomb Repressive Complexes by the lncRNAs Airn and Kcnq1ot1.PLoS genetics · 2026Article
- Machine and Deep Learning Reveal Sequence Determinants Encoding Bivalent Histone Modifications.Communications biology · 2026Article
- Association of tumour-associated macrophage states with nonconserved lncRNAs in lung cancer.Genes and immunity · 2026Article
- Retentive Network promotes efficient RNA language modeling of long sequences.Communications biology · 2026Article
- Deciphering Sequence Determinants of Zygotic Genome Activation Genes: Insights From Machine Learning and the ZGAExplorer Platform.Cell proliferation · 2025Article
- From nucleotides to numbers: a comprehensive review of RNA feature extraction methods for computational modelling.Briefings in bioinformatics · 2025Review
- Noncoding and coding mechanisms of aging-related heart failure with preserved ejection fraction associated with thyroid dysfunction.Disease models & mechanisms · 2025Article
- Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox.Nature communications · 2025Article
- POCALI: Prediction and Insight on CAncer LncRNAs by Integrating Multi-Omics Data with Machine Learning.Small methods · 2025Article
- Activation of Pvt1b isoform contributes to local Pvt1 abundance to repress Myc during stress.PLoS genetics · 2025Article
- LncRNA Subcellular Localization Across Diverse Cell Lines: An Exploration Using Deep Learning with InexactNon-coding RNA · 2025Article
- Unraveling the cohesin-chromatin interface: identifying protein interactions that modulate chromosome structure and function.Epigenetics & chromatin · 2025Article
- Isogenic comparison of Airn and Xist reveals core principles of Polycomb recruitment by lncRNAs.Molecular cell · 2025Article
- Considerations for Social Networks and Health Data Sharing: An Overview.Annals of epidemiology · 2025Review
- Roles for the long non-coding RNAiScience · 2025Article
67 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
16 authors at 1 institution in 1 country.
Funding
Abstract
The functions of most long non-coding RNAs (lncRNAs) are unknown. In contrast to proteins, lncRNAs with similar functions often lack linear sequence homology; thus, the identification of function in one lncRNA rarely informs the identification of function in others. We developed a sequence comparison method to deconstruct linear sequence relationships in lncRNAs and evaluate similarity based on the abundance of short motifs called k-mers. We found that lncRNAs of related function often had similar k-mer profiles despite lacking linear homology, and that k-mer profiles correlated with protein binding to lncRNAs and with their subcellular localization. Using a novel assay to quantify Xist-like regulatory potential, we directly demonstrated that evolutionarily unrelated lncRNAs can encode similar function through different spatial arrangements of related sequence motifs. K-mer-based classification is a powerful approach to detect recurrent relationships between sequence and function in lncRNAs.
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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.