ArticleNature communications2024
Uncovering functional lncRNAs by scRNA-seq with ELATUS.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 14 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.
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
14 citing papers in PubMed.
- Long Non-Coding RNAs in Human Disease: An Overview of Biogenesis, Molecular Mechanism and Therapeutic Opportunities.Current issues in molecular biology · 2026Review
- Multiomic single-cell perturbation screens reveal critical lncRNA regulators of senescence.Nature aging · 2026Article
- The Regulatory Potential of Long Non-Coding RNAs in Bipolar Disorder.International journal of molecular sciences · 2026Review
- Tabula Sapiens reveals the non-coding RNA landscape across 22 human organs and tissues.bioRxiv : the preprint server for biology · 2026Article
- Implications of Single-Cell RNA Sequencing in Cervical Cancer: Unravelling the Molecular Landscape.ACS omega · 2025Review
- Single-cell profiling of long non-coding RNAs in the hematopoietic system.Blood science (Baltimore, Md.) · 2025Article
- The emerging roles of long non-coding RNAs in the nervous system.Nature reviews. Neuroscience · 2025Review
- Long non-coding RNAs: key orchestrators of macrophage polarization in breast cancer.Cancer cell international · 2025Review
- Identification of palmitoylation-related lncRNAs as prognostic biomarkers and immune modulators in HCC.Discover oncology · 2025Article
- Deciphering the role ofWorld journal of hepatology · 2025Review
- RACE-Nano-Seq: Profiling Transcriptome Diversity of a Genomic Locus.Bio-protocol · 2025Article
- Functions and Therapeutic Potentials of Long Noncoding RNA in Skeletal Muscle Atrophy and Dystrophy.Journal of cachexia, sarcopenia and muscle · 2025Review
- InfoScan: A New Transcript Identification Tool Based on scRNA-Seq and Its Application in Glioblastoma.International journal of molecular sciences · 2025Article
- Uncovering functional lncRNAs by scRNA-seq with ELATUS.Nature communications · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
8 authors.
Funding
Abstract
Long non-coding RNAs (lncRNAs) play fundamental roles in cellular processes and pathologies, regulating gene expression at multiple levels. Despite being highly cell type-specific, their study at single-cell (sc) level is challenging due to their less accurate annotation and low expression compared to protein-coding genes. Here, we systematically benchmark different preprocessing methods and develop a computational framework, named ELATUS, based on the combination of the pseudoaligner Kallisto with selective functional filtering. ELATUS enhances the detection of functional lncRNAs from scRNA-seq data, detecting their expression with higher concordance than standard methods with the ATAC-seq profiles in single-cell multiome data. Interestingly, the better results of ELATUS are due to its advanced performance with an inaccurate reference annotation such as that of lncRNAs. We independently confirm the expression patterns of cell type-specific lncRNAs exclusively detected with ELATUS and unveil biologically important lncRNAs, such as AL121895.1, a previously undocumented cis-repressor lncRNA, whose role in breast cancer progression is unnoticed by traditional methodologies. Our results emphasize the necessity for an alternative scRNA-seq workflow tailored to lncRNAs that sheds light on the multifaceted roles of 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.