ArticleScientific reports2017
MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 116 papers.
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Who cites it
116 citing papers in PubMed.
- Updated guide to RNA quantification by RNA sequencing and reverse transcription-qPCR.Molecules and cells · 2026Article
- Fraction-Seq: An Integrated Experimental and Computational Workflow for Determining the Localization and Abundance of Small Non-Coding RNAs in Subcellular Compartments.Non-coding RNA · 2026Article
- tRNA-Derived Small RNAs in Digestive Cancers: From Translational Regulation to Immune and Extracellular Communication.Cancer science · 2026Review
- Altered sncRNA Signatures in Semen Extracellular Vesicles Between Patients with Benign and Malignant Prostate Disease as Potential Non-Invasive Biomarkers in the PSA Grey Zone.International journal of molecular sciences · 2026Article
- Stress-induced breakup: tRNA-derived small RNAs in biology.Trends in cell biology · 2026Review
- 5'tRNA-derived fragments modulate β-cell homeostasis and islet macrophage activation in type 2 diabetes.Nature communications · 2026Article
- Profiling of Small Noncoding RNAs During Bovine Conceptus Elongation Identifies Let-7 as a Candidate Regulator of Proliferation and Differentiation.Animals : an open access journal from MDPI · 2026Article
- Hidden in plain sight: illuminating the tRNA landscape by sequencing.Genome biology · 2026Review
- Several novel classes of small regulatory RNAs show widespread changes in schizophrenia and bipolar disorder and extensive linkages to critical brain processes.Translational psychiatry · 2026Article
- tRNA-Derived Fragment tRF-22 Promotes Immunosuppression by Inhibiting HnRNPAB Ubiquitination in Esophageal Squamous Cell Carcinoma.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Comprehensive and bias-aware analysis of small RNA NGS data for biomarker detection with caRNAge.Extracellular vesicles and circulating nucleic acids · 2026Article
- tRNA regulatory ecosystem states shape tissue and circulating small-RNA landscapes in gastric cancer.Frontiers in cell and developmental biology · 2026Article
- Conserved small RNA networks link inflammation to pain signaling in mice and men.Translational psychiatry · 2025Article
- 5'-transfer RNA halve-lysine-CTT as a promising biomarker for early detection of hepatocellular carcinoma.World journal of gastrointestinal oncology · 2025Article
- Organism-Specific Sequence Motifs Link Ribosomal RNAs to Brain Disorders.Molecular biology and evolution · 2025Article
- Maternal prenatal stress induces sex-dependent changes in tRNA fragment families and cholinergic pathways in newborns.Molecular psychiatry · 2025Article
- Emerging roles of transfer RNA fragments in the CNS.Brain : a journal of neurology · 2025Review
- Re-Analyses of Samples From Amyotrophic Lateral Sclerosis Patients and Controls Identify Many Novel Small RNAs With Diagnostic And Prognostic Potential.Molecular neurobiology · 2025Article
- Non-coding Y RNA fragments in a complex with YBX1 modulate PARP1 residency at DNA double strand breaks.Nucleic acids research · 2025Article
- CorrAdjust unveils biologically relevant transcriptomic correlations by efficiently eliminating hidden confounders.Nucleic acids research · 2025Article
56 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
Transfer RNA fragments (tRFs) are an established class of constitutive regulatory molecules that arise from precursor and mature tRNAs. RNA deep sequencing (RNA-seq) has greatly facilitated the study of tRFs. However, the repeat nature of the tRNA templates and the idiosyncrasies of tRNA sequences necessitate the development and use of methodologies that differ markedly from those used to analyze RNA-seq data when studying microRNAs (miRNAs) or messenger RNAs (mRNAs). Here we present MINTmap (for MItochondrial and Nuclear TRF mapping), a method and a software package that was developed specifically for the quick, deterministic and exhaustive identification of tRFs in short RNA-seq datasets. In addition to identifying them, MINTmap is able to unambiguously calculate and report both raw and normalized abundances for the discovered tRFs. Furthermore, to ensure specificity, MINTmap identifies the subset of discovered tRFs that could be originating outside of tRNA space and flags them as candidate false positives. Our comparative analysis shows that MINTmap exhibits superior sensitivity and specificity to other available methods while also being exceptionally fast. The MINTmap codes are available through https://github.com/TJU-CMC-Org/MINTmap/ under an open source GNU GPL v3.0 license.
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