ArticleScientific reports2018
Prediction of LncRNA Subcellular Localization with Deep Learning from Sequence Features.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
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Who cites it
85 citing papers in PubMed.
- RNA-Binding Protein Occupancy Composition Predicts Long Noncoding RNA Subcellular Localization.International journal of molecular sciences · 2026Article
- A comprehensive review on RNA subcellular localization prediction.Briefings in functional genomics · 2026Review
- High-throughput Screening of Sequence Elements Associated with RNA Localization.Computational and structural biotechnology journal · 2026Article
- Functions and mechanisms of long non-coding RNA in esophageal squamous cell carcinoma (Review).Oncology letters · 2025Review
- Loc4Lnc: Accurate prediction of long noncoding RNA subcellular localization via enhanced RNA sequence representation.Quantitative biology (Beijing, China) · 2025Article
- PlantLncBoost: key features for plant lncRNA identification and significant improvement in accuracy and generalization.The New phytologist · 2025Article
- LncRNA Subcellular Localization Across Diverse Cell Lines: An Exploration Using Deep Learning with InexactNon-coding RNA · 2025Article
- Identification and characterization of long non-coding RNA (lncRNA) in wild and semi-wild cucumbers.BMC plant biology · 2025Article
- BiGM-lncLoc: Bi-level Multi-Graph Meta-Learning for Predicting Cell-Specific Long Noncoding RNAs Subcellular Localization.Interdisciplinary sciences, computational life sciences · 2025Article
- Role of lncRNAs in pathophysiology of obesity.Current opinion in physiology · 2025Article
- Elucidating long non-coding RNA networks in tomato plants in response to Funneliformis mosseae colonization and cucumber mosaic virus infection.BMC plant biology · 2025Article
- RNALoc-LM: RNA subcellular localization prediction using pre-trained RNA language model.Bioinformatics (Oxford, England) · 2025Article
- Decoding subcellular RNA localization one molecule at a time.Genome biology · 2025Review
- An ensemble deep learning framework for multi-class LncRNA subcellular localization with innovative encoding strategy.BMC biology · 2025Article
- Long Non-coding RNAs as Key Modulators in Hypoxic-Ischemic Brain Injury: Implications for Neuroprotection.Current pharmaceutical design · 2025Review
- Investigating the role of exosomal long non-coding RNAs in drug resistance within female reproductive system cancers.Frontiers in cell and developmental biology · 2025Review
- LncLSTA: a versatile predictor unveiling subcellular localization of lncRNAs through long-short term attention.Bioinformatics advances · 2025Article
- LncSL: A Novel Stacked Ensemble Computing Tool for Subcellular Localization of lncRNA by Amino Acid-Enhanced Features and Two-Stage Automated Selection Strategy.International journal of molecular sciences · 2024Article
- Prediction of viral oncoproteins through the combination of generative adversarial networks and machine learning techniques.Scientific reports · 2024Article
- Long non‑coding RNAs as diagnostic and prognostic biomarkers for colorectal cancer (Review).Oncology letters · 2024Review
25 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
Long non-coding RNAs are involved in biological processes throughout the cell including the nucleus, chromatin and cytosol. However, most lncRNAs remain unannotated and functional annotation of lncRNAs is difficult due to their low conservation and their tissue and developmentally specific expression. LncRNA subcellular localization is highly informative regarding its biological function, although it is difficult to discover because few prediction methods currently exist. While protein subcellular localization prediction is a well-established research field, lncRNA localization prediction is a novel research problem. We developed DeepLncRNA, a deep learning algorithm which predicts lncRNA subcellular localization directly from lncRNA transcript sequences. We analyzed 93 strand-specific RNA-seq samples of nuclear and cytosolic fractions from multiple cell types to identify differentially localized lncRNAs. We then extracted sequence-based features from the lncRNAs to construct our DeepLncRNA model, which achieved an accuracy of 72.4%, sensitivity of 83%, specificity of 62.4% and area under the receiver operating characteristic curve of 0.787. Our results suggest that primary sequence motifs are a major driving force in the subcellular localization of lncRNAs.
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