ArticleGenome biology2025
DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing.
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Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Systematic benchmarking of dorado basecalling models for RNA modification detection with highly multiplexed nanopore sequencing.Nucleic acids research · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Advancements and Emerging Trends in the Detection of Sweet Potato Diseases: A Comprehensive Review.ACS omega · 2026Review
- Advances and challenges in non-canonical nucleic acids data storage.Nature communications · 2026Review
- RMPore: a comprehensive database of single-molecule RNA modifications detected by Nanopore direct RNA sequencing.Nucleic acids research · 2026Article
- Mapping isoforms and regulatory mechanisms from spatial transcriptomics data with SPLISOSM.Nature biotechnology · 2026Article
- Dysregulation of piRNA biogenesis-associated proteins in cancer: mechanisms, evidence, and translational constraints.Frontiers in molecular biosciences · 2026Review
- Advances in Detecting RNA Modifications Using Direct RNA Nanopore Sequencing.Advanced genetics (Hoboken, N.J.) · 2025Review
- DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing.Genome biology · 2025Article
- Therapeutic frontiers in viral myocarditis: targeting inflammation, viruses, oxidative stress, and myocardial repair.Frontiers in immunology · 2025Review
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Authors and funding
28 authors.
Junwei Song *Department of Laboratory Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
Li-An Lin *Department of Laboratory Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
Chao Tang *Department of Laboratory Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
Chuan Chen *Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China.
Qingxin YangDepartment of Laboratory Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
Dan ZhangDepartment of Laboratory Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
Yuancun ZhaoDepartment of Laboratory Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
Han-Cheng WeiDepartment of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China.
Kepan LinghuDepartment of Laboratory Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
Zijie XuDepartment of Laboratory Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
Tingfeng ChenDepartment of Laboratory Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
Zhifeng HeDepartment of Laboratory Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
Defu LiuDepartment of Laboratory Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
Yu ZhongBiosafety Laboratory, lnternational Center for Biological and Translational Research, West China Hospital, Sichuan University, Chengdu, 610041, China.
Weizhen ZhuDepartment of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
Wanqin ZengDepartment of Laboratory Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
Li ChenDepartment of Laboratory Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
Guiqin SongSchool of Pharmacy, School of Basic Medical Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong, 637000, China.
Mutian ChenDepartment of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China.
Juan JiangPrecision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, China.
Juan ZhouDepartment of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China.
Jing WangPrecision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, China.
Bojiang ChenPrecision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, China.
Binwu YingDepartment of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China.
Yuan WangDepartment of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China.
Jia GengDepartment of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China. geng.jia@scu.edu.cn.
Jing-Wen LinDepartment of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China. lin.jingwen@scu.edu.cn.
Lu ChenDepartment of Laboratory Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China. luchen@scu.edu.cn.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nanopore direct RNA sequencing (DRS) is a powerful tool for RNA biology but suffers from low basecalling accuracy, low throughput, and high input requirements. We present DEMINERS, a novel DRS toolkit combining an RNA multiplexing workflow, a Random Forest-based barcode classifier, and an optimized convolutional neural network basecaller with species-specific training. DEMINERS enables accurate demultiplexing of up to 24 samples, reducing RNA input and runtime. Applications include clinical metagenomics, cancer transcriptomics, and parallel transcriptomic comparisons, uncovering microbial diversity in COVID-19 and m
Indexed as
Gene Expression ProfilingMetagenomicsNanopore SequencingSequence Analysis, RNASoftwareTranscriptomeCOVID-19HumansNanoporesSARS-CoV-2BasecallingDemultiplexMachine learningNanopore direct RNA sequencingRNA modification
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