ReviewNature reviews. Genetics2025
Transcriptomics in the era of long-read sequencing.
Review in Nature reviews. Genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 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.
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Who cites it
70 citing papers in PubMed.
- The novel transcripts we keep rediscovering.Nature biotechnology · 2026Article
- LRP2: A proteogenomics pipeline for long-read informed protein isoform analysis and discovery.bioRxiv : the preprint server for biology · 2026Article
- Nanopore long-read transcriptome sequencing reveals miR-22-3p-mediated transcriptomic remodeling and alternative splicing in chicken pectoral muscle.Poultry science · 2026Article
- Long-read transcriptome analysis using IsoRanker for identifying pathogenic variants in Mendelian conditions.American journal of human genetics · 2026Article
- New insights on Plasmodium gene expression from direct RNA sequencing.Trends in parasitology · 2026Review
- Integrated Transcriptomic Analysis and Machine Learning Identify THY1 as a Key Regulator of Cancer-Associated Fibroblast Infiltration, Promoting Malignant Progression and Immune Escape in Gastric Cancer.Journal of gastroenterology and hepatology · 2026Article
- Long-read sequencing reveals widespread novel splicing and neojunction-derived neoantigens in nasopharyngeal carcinoma.Genome research · 2026Article
- Integration of Multi-Omics Data To Understand the Multifaceted Role of RAMP1 across Different Cancer Types.Cell biochemistry and biophysics · 2026Review
- A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq nanopore long reads data.NAR genomics and bioinformatics · 2026Article
- Handling biological replicates in long-read RNA sequencing data by joining or not joining.Nature communications · 2026Article
- Advances in Poultry RNA-Omics Research: Technologies, RNA Information Layers, and Applications in Complex Traits.Animals : an open access journal from MDPI · 2026Review
- Leveraging long read RNA-seq to decipher neuronal regulation of alternative polyadenylation.Nature communications · 2026Article
- Article
- Orthology-based comparative transcriptomic analysis reveals conserved osmoadaptive responses in Bacillus velezensis and Bacillus paralicheniformis.Archives of microbiology · 2026Article
- Benchmarking RNA-seq with the Quartet and MAQC reference materials to establish best practices for accurate alternative splicing analysis.Nature communications · 2026Article
- A poly(A)-independent PacBio strategy for organellar transcriptome profiling.Plant physiology · 2026Article
- Beyond the gene: isoform diversity as a key contributor to human brain disorders.Current opinion in genetics & development · 2026Review
- Uncultured Amniocytes Enable Rapid and Clinically Informative Prenatal RNA Sequencing for Genetic Diagnosis.International journal of molecular sciences · 2026Article
- AI-Augmented Multi-Omics for Abiotic Stress Responses: A New Frontier in Plant Hormone Systems Biology.Plants (Basel, Switzerland) · 2026Review
- Meis1 isoform diversity orchestrates neural progenitor differentiation by regulating ATOH1 degradation at distinct subcellular compartments.PLoS biology · 2026Article
10 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
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcriptome sequencing revolutionized the analysis of gene expression, providing an unbiased approach to gene detection and quantification that enabled the discovery of novel isoforms, alternative splicing events and fusion transcripts. However, although short-read sequencing technologies have surpassed the limited dynamic range of previous technologies such as microarrays, they have limitations, for example, in resolving full-length transcripts and complex isoforms. Over the past 5 years, long-read sequencing technologies have matured considerably, with improvements in instrumentation and analytical methods, enabling their application to RNA sequencing (RNA-seq). Benchmarking studies are beginning to identify the strengths and limitations of long-read RNA-seq, although there remains a need for comprehensive resources to guide newcomers through the intricacies of this approach. In this Review, we provide a comprehensive overview of the long-read RNA-seq workflow, from library preparation and sequencing challenges to core data processing, downstream analyses and emerging developments. We present an extensive inventory of experimental and analytical methods and discuss current challenges and prospects.
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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.