ReviewBriefings in bioinformatics2019
LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information and physicochemical property.
Review in Briefings in bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 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.
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Who cites it
84 citing papers in PubMed.
- Integrative Transcriptomic Network Modeling Coupled with Patient-Derived Validation for Circulating lncRNA Biomarker Discovery in NAFLD: A Comprehensive Workflow.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Profiling maize embryonic leaf development and discovering new genes using high-resolution spatial long-read isoform sequencing.Nature plants · 2026Article
- Article
- Post-Transcriptional Regulatory Network of Non-Coding RNAs in Yaks: Molecular Mechanisms of Hypoxia Adaptation and Productive Traits.Animals : an open access journal from MDPI · 2026Review
- Transcriptome Dynamics Reveal the Potential Roles of Long Non-Coding RNAs in Regulating Flower Color of Safflowers (International journal of molecular sciences · 2026Article
- Benchmarking reveals the superiority of nucleic acid foundation models in predicting lncRNA coding potential.Genome 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
- Interleukin-4 changes the transcriptome, ECM-associated components and function of mare endometrial fibroblast: Insights from healthy and fibrotic cells.Cell and tissue research · 2026Article
- Diversity of lncRNAs in the pan-transcriptome of maize inbred lines.BMC genomics · 2026Article
- Characterization of long non-coding RNAs during compatible and incompatible pollination inFrontiers in plant science · 2026Article
- A novel super-enhancer-driven lncRNA LINC00973 governs head and neck squamous cell carcinoma progression through EN2.Cell death & disease · 2025Article
- LncPlankton: a comprehensive database of candidate lncRNAs from marine microbial eukaryotes.NAR genomics and bioinformatics · 2025Article
- Interpretation of RNA Universe and Coding Potential Using IntRNA.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- From nucleotides to numbers: a comprehensive review of RNA feature extraction methods for computational modelling.Briefings in bioinformatics · 2025Review
- Precise detection of differential RNA editing sites across varied biological conditions using the CADRES pipeline.Scientific reports · 2025Article
- InfoScan: A New Transcript Identification Tool Based on scRNA-Seq and Its Application in Glioblastoma.International journal of molecular sciences · 2025Article
- Recent advances in investigation of circRNA/lncRNA-miRNA-mRNA networks through RNA sequencing data analysis.Briefings in functional genomics · 2025Review
- TetraRNA, a tetra-class machine learning model for deciphering the coding potential derivation of RNA world.Computational and structural biotechnology journal · 2025Article
- MLA-ac4C: A N4-Acetylcytidine Site Prediction Model Based on Multi-Layer Attention, Bidirectional GRU, and DenseNet.Current genomics · 2025Article
24 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Discovering new long non-coding RNAs (lncRNAs) has been a fundamental step in lncRNA-related research. Nowadays, many machine learning-based tools have been developed for lncRNA identification. However, many methods predict lncRNAs using sequence-derived features alone, which tend to display unstable performances on different species. Moreover, the majority of tools cannot be re-trained or tailored by users and neither can the features be customized or integrated to meet researchers' requirements. In this study, features extracted from sequence-intrinsic composition, secondary structure and physicochemical property are comprehensively reviewed and evaluated. An integrated platform named LncFinder is also developed to enhance the performance and promote the research of lncRNA identification. LncFinder includes a novel lncRNA predictor using the heterologous features we designed. Experimental results show that our method outperforms several state-of-the-art tools on multiple species with more robust and satisfactory results. Researchers can additionally employ LncFinder to extract various classic features, build classifier with numerous machine learning algorithms and evaluate classifier performance effectively and efficiently. LncFinder can reveal the properties of lncRNA and mRNA from various perspectives and further inspire lncRNA-protein interaction prediction and lncRNA evolution analysis. It is anticipated that LncFinder can significantly facilitate lncRNA-related research, especially for the poorly explored species. LncFinder is released as R package (https://CRAN.R-project.org/package=LncFinder). A web server (http://bmbl.sdstate.edu/lncfinder/) is also developed to maximize its availability.
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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.