ArticleNucleic acids research2021
DM3Loc: multi-label mRNA subcellular localization prediction and analysis based on multi-head self-attention mechanism.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
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74 citing papers in PubMed.
- Peptide language pragmatic analysis and two-stage hierarchical learning framework for therapeutic peptide prediction.BMC biology · 2026Article
- Graph-based RNA structural representation reveals determinants of subcellular localization.Briefings in bioinformatics · 2026Article
- UTR-DynaPro: a CNN-transformer multimodal language model for decoding 5'UTR regulatory mechanisms.Scientific reports · 2026Article
- Predicting circRNA subcellular localization by fusing circRNA sequence and network information.Scientific reports · 2026Article
- Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning.Briefings in bioinformatics · 2026Article
- A comprehensive review on RNA subcellular localization prediction.Briefings in functional genomics · 2026Review
- CellSP enables module discovery and visualization for subcellular spatial transcriptomics data.Communications biology · 2025Article
- Decoding the interactions and functions of non-coding RNA with artificial intelligence.Nature reviews. Molecular cell biology · 2025Review
- Knowledge based convolutional transformer for joint estimation of PMScientific reports · 2025Article
- LOCAS: multilabel mRNA localization with supervised contrastive learning.Briefings in bioinformatics · 2025Article
- RNALoc-LM: RNA subcellular localization prediction using pre-trained RNA language model.Bioinformatics (Oxford, England) · 2025Article
- LncLSTA: a versatile predictor unveiling subcellular localization of lncRNAs through long-short term attention.Bioinformatics advances · 2025Article
- EDCLoc: a prediction model for mRNA subcellular localization using improved focal loss to address multi-label class imbalance.BMC genomics · 2024Article
- A versatile attention-based neural network for chemical perturbation analysis and its potential to aid surgical treatment: an experimental study.International journal of surgery (London, England) · 2024Article
- Deep learning modeling of RNA ac4C deposition reveals the importance of plant alternative splicing.Plant molecular biology · 2024Article
- Deciphering 3'UTR Mediated Gene Regulation Using Interpretable Deep Representation Learning.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- MSlocPRED: deep transfer learning-based identification of multi-label mRNA subcellular localization.Briefings in bioinformatics · 2024Article
- DRpred: A Novel Deep Learning-Based Predictor for Multi-Label mRNA Subcellular Localization Prediction by Incorporating Bayesian Inferred Prior Label Relationships.Biomolecules · 2024Article
- Advancing mRNA subcellular localization prediction with graph neural network and RNA structure.Bioinformatics (Oxford, England) · 2024Article
- scLEGA: an attention-based deep clustering method with a tendency for low expression of genes on single-cell RNA-seq data.Briefings in bioinformatics · 2024Article
14 more citing papers are in PubMed but not listed here.
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7 authors.
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Abstract
Subcellular localization of messenger RNAs (mRNAs), as a prevalent mechanism, gives precise and efficient control for the translation process. There is mounting evidence for the important roles of this process in a variety of cellular events. Computational methods for mRNA subcellular localization prediction provide a useful approach for studying mRNA functions. However, few computational methods were designed for mRNA subcellular localization prediction and their performance have room for improvement. Especially, there is still no available tool to predict for mRNAs that have multiple localization annotations. In this paper, we propose a multi-head self-attention method, DM3Loc, for multi-label mRNA subcellular localization prediction. Evaluation results show that DM3Loc outperforms existing methods and tools in general. Furthermore, DM3Loc has the interpretation ability to analyze RNA-binding protein motifs and key signals on mRNAs for subcellular localization. Our analyses found hundreds of instances of mRNA isoform-specific subcellular localizations and many significantly enriched gene functions for mRNAs in different subcellular localizations.
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