ArticleNature communications2025
Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed.
- Advanced deep learning strategies in nanopore RNA sequencing.RNA biology · 2026Review
- The stability of m6A-marked transcripts is linked to cell identity in planarians.Nucleic acids research · 2026Article
- Oxford Nanopore Sequencing, a Promising Technology for Precision Diagnostics in Intensive Care Units: A Narrative Review.Biomedicines · 2026Review
- Systematic benchmarking of dorado basecalling models for RNA modification detection with highly multiplexed nanopore sequencing.Nucleic acids research · 2026Article
- Extended poly(A) tails are a shared feature of herpesvirus mRNAs.PLoS pathogens · 2026Article
- ReadChop: a high-performance demultiplexer for long-read sequencing data.Bioinformatics (Oxford, England) · 2026Article
- NanoSimFormer: an end-to-end transformer-based nanopore signal simulator with basecaller guidance.Bioinformatics (Oxford, England) · 2026Article
- Umi-pipeline-nf: a modular and scalable workflow for UMI-tagged nanopore amplicon analysis with real-time sequencing integration and GPU-acceleration.Bioinformatics (Oxford, England) · 2026Article
- Nanopore direct RNA sequencing for RNA modification analysis: workflow assessment and computational tool benchmarking.Advanced biotechnology · 2026Article
- ADAM-tRNA-seq: an optimized approach for demultiplexing and enhanced hierarchal mapping in direct tRNA sequencing.Nucleic acids research · 2026Article
- Defining expansions and perturbations to the RNA polymerase III transcriptome and epitranscriptome by modified direct RNA nanopore sequencing.Nature communications · 2026Article
- The potential of mRNA markers in body fluids and personal source analysis based on the QNome nanopore sequencing.International journal of legal medicine · 2026Article
- Article
- Resolving METTL5 Specificity: Direct RNA Sequencing Reveals No Compelling Evidence for METTL5 mediated mRNA m6A Methylation in mESCs.microPublication biology · 2026Article
- DNA-guided 3D pathway reconfiguration of composite nanopores for ion transport regulation.Journal of nanobiotechnology · 2025Article
- Extended poly(A) tails are a shared feature of herpesvirus mRNAs.bioRxiv : the preprint server for biology · 2025Article
- Review
- RNA stability enhancers for durable base-modified mRNA therapeutics.Nature biotechnology · 2025Article
- DemuxTrans: Transformer and temporal convolution network for accurate barcode demultiplexing in nanopore sequencing.Bioinformatics (Oxford, England) · 2025Article
- mRNA poly(A)-tail length is a battleground for coronavirus-host competition.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Nanopore direct RNA sequencing (dRNA-seq) enables unique insights into RNA biology. However, applications are currently limited by the lack of accurate and cost-effective sample multiplexing. Here we introduce WarpDemuX, an ultra-fast and highly accurate adapter-barcoding and demultiplexing approach for dRNA-seq with SQK-RNA002 and SQK-RNA004 chemistries. WarpDemuX enhances speed and accuracy by fast processing of the raw nanopore signal, use of a light-weight machine-learning algorithm and design of optimized barcode sets. We demonstrate its utility by performing rapid phenotypic profiling of different SARS-CoV-2 viruses through multiplexed sequencing of longitudinal samples on a single flowcell, identifying systematic differences in transcript abundance and poly(A) tail lengths during infection. Additionally, integrating WarpDemuX into sequencing control software enables real-time enrichment of target molecules through barcode-specific adaptive sampling, which we demonstrate by enriching low abundance viral RNA. In summary, WarpDemuX represents a broadly applicable, high-performance, economical multiplexing solution for dRNA-seq, facilitating advanced (epi-) transcriptomic research.
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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.