ArticleScientific reports2022
LncDC: a machine learning-based tool for long non-coding RNA detection from RNA-Seq data.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Dark matter matters: from noncoding RNA regulation to cancer immunity.Oncoimmunology · 2026Review
- Copy number evolution of conserved noncoding RNA gene families across mammals.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- Computational identification and characterization of noncoding RNA-encoded peptides: tools, databases, and in silico strategies.Amino acids · 2026Review
- Genome-wide identification and functional analysis of long noncoding RNAs responsive to abscisic acid, drought, and methyl jasmonate in Arabidopsis thaliana.Plant molecular biology · 2026Article
- Uncertainty-aware benchmarking reveals ambiguous transcripts in mRNA-lncRNA classification.bioRxiv : the preprint server for biology · 2026Article
- A novel deep learning-driven framework for improving lncRNA comprehensive annotation with LncADeep 2.0.Bioinformatics (Oxford, England) · 2026Article
- Investigation of cervical cell image segmentation technology based on deep learning and non-coding RNAs.Non-coding RNA research · 2026Article
- FLYNC: a machine-learning-driven framework for discovering long noncoding RNAs inNAR genomics and bioinformatics · 2026Article
- Prostate Cancer: Dissecting Novel Immunosuppressive Mechanisms Through Context-Specific Transcriptomic Programs and MDSC Cells.International journal of molecular sciences · 2026Article
- LncRNAs: key regulators and molecular mechanisms in lung cancer radiosensitivity.Open medicine (Warsaw, Poland) · 2026Review
- LncPlankton: a comprehensive database of candidate lncRNAs from marine microbial eukaryotes.NAR genomics and bioinformatics · 2025Article
- From nucleotides to numbers: a comprehensive review of RNA feature extraction methods for computational modelling.Briefings in bioinformatics · 2025Review
- Regulatory Landscapes of Non-Coding RNAs During Drought Stress in Plants.International journal of molecular sciences · 2025Review
- PlantLncBoost: key features for plant lncRNA identification and significant improvement in accuracy and generalization.The New phytologist · 2025Article
- AttenRNA: multi-scale deep attentive model with RNA feature variability analysis.Briefings in bioinformatics · 2025Article
- POCALI: Prediction and Insight on CAncer LncRNAs by Integrating Multi-Omics Data with Machine Learning.Small methods · 2025Article
- Ovarian transcriptome analyses indicate that weak juvenile hormone signaling underlies the molecular basis of oogenesis deficiencies in mosquitoes.BMC biology · 2025Article
- Single-Cell Transcriptomic Approaches for Decoding Non-Coding RNA Mechanisms in Colorectal Cancer.Non-coding RNA · 2025Review
- Recent advances in investigation of circRNA/lncRNA-miRNA-mRNA networks through RNA sequencing data analysis.Briefings in functional genomics · 2025Review
- Computational Resources for lncRNA Functions and Targetome.Methods in molecular biology (Clifton, N.J.) · 2025Review
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2 authors.
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Abstract
Long non-coding RNAs (lncRNAs) play an essential role in diverse biological processes and disease development. Accurate classification of lncRNAs and mRNAs is important for the identification of tissue- or disease-specific lncRNAs. Here, we present our tool LncDC (Long non-coding RNA detection) that is able to accurately predict lncRNAs with an XGBoost model using features extracted from RNA sequences, secondary structures, and translated proteins. Benchmarking experiments showed that LncDC consistently outperformed six state-of-the-art tools in distinguishing lncRNAs from mRNAs. Notably, the use of sequence and secondary structure (SASS) k-mer score features and flexible ORF features improved the classification capability of LncDC. We anticipate that LncDC will definitely promote the discovery of more and novel disease-specific lncRNAs. LncDC is implemented in Python and freely available at https://github.com/lim74/LncDC .
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