ArticleNucleic acids research2025
WarpDemuX-tRNA: barcode multiplexing for nanopore tRNA sequencing.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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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.
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Who cites it
6 citing papers in PubMed.
- Advanced deep learning strategies in nanopore RNA sequencing.RNA biology · 2026Review
- Comprehensive post-transcriptional modification profiles in individual Staphylococcus aureus tRNA species.Nucleic acids research · 2026Article
- ReadChop: a high-performance demultiplexer for long-read sequencing data.Bioinformatics (Oxford, England) · 2026Article
- tRNA isodecoder analysis using Nanopore ionic current signals and deep learning.bioRxiv : the preprint server for biology · 2025Article
- Improved long-transcript representation in Oxford Nanopore direct RNA sequencing with UltraMarathonRT.bioRxiv : the preprint server for biology · 2025Article
- Direct RNA sequencing enables improved transcriptome assessment and tracking of RNA modifications for medical applications.Nucleic acids research · 2025Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Transfer RNA (tRNA) plays an essential role in protein translation, and tRNA modifications are important to their function. Recently, nanopore direct RNA sequencing (dRNA-seq) has shown promising results in the detection of complex tRNA modifications. However, its wider adoption in the tRNA field has been limited by a lack of (de)multiplexing solutions. Here, we present WarpDemuX-tRNA: an extension to the WarpDemuX method specifically optimized for multiplexed nanopore tRNA sequencing. Using consensus-based signal analysis using (soft) dynamic time warping and barycenter averaging, our approach improves barcode feature generation and achieves more robust barcode identification. WarpDemuX-tRNA outperforms the original method and achieves 99% precision and 95% recovery for four barcodes, while reducing computational complexity and runtime to 6 min per one million reads. WarpDemuX-tRNA is an open-source and free-to-use solution to high-throughput nanopore tRNA sequencing, facilitating more accessible, cost-effective, and high-throughput studies of tRNA modifications and their regulatory mechanisms.
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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 Socratic graph.