ReviewGenome research2024
Challenges in identifying mRNA transcript starts and ends from long-read sequencing data.
Review in Genome research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 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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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
25 citing papers in PubMed.
- Review
- Long-read cDNA sequencing reveals novel isoforms and spliceosome-mutant-enriched transcripts in AML and MDS.bioRxiv : the preprint server for biology · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Multi-platform profiling reveals host- and cell -type-specific pseudorabies virus gene expression.Scientific reports · 2026Article
- Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods.Nature reviews. Molecular cell biology · 2026Review
- Review
- Benchmarking methods for genome annotation using nanopore direct RNA in a non-model crop plant.Bioinformatics advances · 2026Article
- Article
- Article
- Boosting Transcript Assembly via Delineating Transcript Start and End Sites.bioRxiv : the preprint server for biology · 2025Article
- mRNA initiation and termination are spatially coordinated.Science (New York, N.Y.) · 2025Article
- Bacterial Systematic Genetics and Integrated Multi-Omics: Beyond Static Genomics Toward Predictive Models.International journal of molecular sciences · 2025Review
- The generation and consequences of N-terminal proteoform diversity.Cell reports · 2025Review
- Perplexity as a Metric for Isoform Diversity in the Human Transcriptome.bioRxiv : the preprint server for biology · 2025Article
- A Hitchhiker's Guide to long-read genomic analysis.Genome research · 2025Review
- Mapping the temporal transcriptomic signature of a viral pathogen through CAGE and nanopore sequencing.PloS one · 2025Article
- Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics.Genome research · 2024Review
- Direct RNA sequencing in plants: Practical applications and future perspectives.Plant communications · 2024Review
- Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads.Genome research · 2024Article
- Exploring the transcriptomic profile of human monkeypox virus via CAGE and native RNA sequencing approaches.mSphere · 2024Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Long-read sequencing (LRS) technologies have the potential to revolutionize scientific discoveries in RNA biology through the comprehensive identification and quantification of full-length mRNA isoforms. Despite great promise, challenges remain in the widespread implementation of LRS technologies for RNA-based applications, including concerns about low coverage, high sequencing error, and robust computational pipelines. Although much focus has been placed on defining mRNA exon composition and structure with LRS data, less careful characterization has been done of the ability to assess the terminal ends of isoforms, specifically, transcription start and end sites. Such characterization is crucial for completely delineating full mRNA molecules and regulatory consequences. However, there are substantial inconsistencies in both start and end coordinates of LRS reads spanning a gene, such that LRS reads often fail to accurately recapitulate annotated or empirically derived terminal ends of mRNA molecules. Here, we describe the specific challenges of identifying and quantifying mRNA terminal ends with LRS technologies and how these issues influence biological interpretations of LRS data. We then review recent experimental and computational advances designed to alleviate these problems, with ideal use cases for each approach. Finally, we outline anticipated developments and necessary improvements for the characterization of terminal ends from LRS data.
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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.