ArticleGenome research2020
Molecular barcoding of native RNAs using nanopore sequencing and deep learning.
Article in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed.
- The TENT5A-ATXN2 axis modulates germline and somatic cell survival during heat stress.Cell death & disease · 2026Article
- Single-molecule mbioRxiv : the preprint server for biology · 2026Article
- rDNAmine: A New Tool for the Analysis of Long Repetitive Sequences.Yeast (Chichester, England) · 2026Article
- 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
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- TENT5C extends Odf1 poly(A) tail to sustain sperm morphogenesis and fertility.Nature communications · 2026Article
- Defining the RNA Modification Landscape of Multiple Myeloma Reveals METTL3-Dependent mbioRxiv : the preprint server for biology · 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
- Genomic language model mitigates chimera artifacts in nanopore direct RNA sequencing.Nature communications · 2026Article
- Nanopore based RNA methylation profiling of a circulating lung cancer biomarker.Communications medicine · 2025Article
- Extended poly(A) tails are a shared feature of herpesvirus mRNAs.bioRxiv : the preprint server for biology · 2025Article
- Structural insights into cauliflower mitoribosome in translation state and in association with a late assembly factor.Nature communications · 2025Article
- Direct RNA sequencing enables improved transcriptome assessment and tracking of RNA modifications for medical applications.Nucleic acids research · 2025Article
- Motif caller for sequence reconstruction in motif-based DNA storage.Scientific reports · 2025Article
- Saskemycin, a potent and selective antimycobacterial agent targeting a unique site on the ribosome.Research square · 2025Article
- DemuxTrans: Transformer and temporal convolution network for accurate barcode demultiplexing in nanopore sequencing.Bioinformatics (Oxford, England) · 2025Article
- Empowering low-crosstalk, dynamic-decision random access of DNA storage via 384-multiplexed nanopore signatures.Nature communications · 2025Article
- Noncanonical Poly(A) Polymerase TENT4 Drives Expression of Subgenomic Hepatitis A Virus RNAs in Infected Cells.Viruses · 2025Article
3 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
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nanopore sequencing enables direct measurement of RNA molecules without conversion to cDNA, thus opening the gates to a new era for RNA biology. However, the lack of molecular barcoding of direct RNA nanopore sequencing data sets severely affects the applicability of this technology to biological samples, where RNA availability is often limited. Here, we provide the first experimental protocol and associated algorithm to barcode and demultiplex direct RNA nanopore sequencing data sets. Specifically, we present a novel and robust approach to accurately classify raw nanopore signal data by transforming current intensities into images or arrays of pixels, followed by classification using a deep learning algorithm. We demonstrate the power of this strategy by developing the first experimental protocol for barcoding and demultiplexing direct RNA sequencing libraries. Our method, DeePlexiCon, can classify 93% of reads with 95.1% accuracy or 60% of reads with 99.9% accuracy. The availability of an efficient and simple multiplexing strategy for native RNA sequencing will improve the cost-effectiveness of this technology, as well as facilitate the analysis of lower-input biological samples. Overall, our work exemplifies the power, simplicity, and robustness of signal-to-image conversion for nanopore data analysis using deep learning.
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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.