ArticleG3 (Bethesda, Md.)2013
Accurate identification and analysis of human mRNA isoforms using deep long read sequencing.
Article in G3 (Bethesda, Md.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 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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Who cites it
38 citing papers in PubMed.
- Article
- Long-read Sequencing of Nascent RNA from Budding and Fission Yeasts.bioRxiv : the preprint server for biology · 2025Article
- Chromosome-scale genome assembly and annotation of two geographically distinct strains of malaria vector Anopheles albimanus.Scientific reports · 2025Article
- Single-cell long-read targeted sequencing reveals transcriptional variation in ovarian cancer.Nature communications · 2024Article
- Identification of Splice Variants and Isoforms in Transcriptomics and Proteomics.Annual review of biomedical data science · 2023Review
- Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns.Genome research · 2022Article
- Single-cell isoform analysis in human immune cells.Genome biology · 2022Article
- Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification ofLife (Basel, Switzerland) · 2021Article
- Article
- How Machine Learning and Statistical Models Advance Molecular Diagnostics of Rare Disorders Via Analysis of RNA Sequencing Data.Frontiers in molecular biosciences · 2021Review
- Application of Next Generation Sequencing in Laboratory Medicine.Annals of laboratory medicine · 2021Review
- Annotation of Full-Length Long Noncoding RNAs with Capture Long-Read Sequencing (CLS).Methods in molecular biology (Clifton, N.J.) · 2021Article
- SMRT- and Illumina-based RNA-seq analyses unveil the ginsinoside biosynthesis and transcriptomic complexity in Panax notoginseng.Scientific reports · 2020Article
- Full-length transcript sequencing accelerates the transcriptome research of Gymnocypris namensis, an iconic fish of the Tibetan Plateau.Scientific reports · 2020Article
- Full-Length Transcript-Based Proteogenomics of Rice Improves Its Genome and Proteome Annotation.Plant physiology · 2020Article
- Identifying Candidate Genes Involved in the Regulation of Early Growth Using Full-Length Transcriptome and RNA-Seq Analyses of Frontal and Parietal Bones and Vertebral Bones in Bighead Carp (Frontiers in genetics · 2020Article
- Single-Molecule Long-Read Sequencing Reveals the Diversity of Full-Length Transcripts in Leaves ofInternational journal of molecular sciences · 2019Article
- Realizing the potential of full-length transcriptome sequencing.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Review
- Analysis of Chromosomal Numbers, Mitochondrial Genome, and Full-Length Transcriptome of Onychostoma brevibarba.Marine biotechnology (New York, N.Y.) · 2019Article
- Analysis of transcripts and splice isoforms in Medicago sativa L. by single-molecule long-read sequencing.Plant molecular biology · 2019Article
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Authors and funding
6 authors.
Funding
Abstract
Precise identification of RNA-coding regions and transcriptomes of eukaryotes is a significant problem in biology. Currently, eukaryote transcriptomes are analyzed using deep short-read sequencing experiments of complementary DNAs. The resulting short-reads are then aligned against a genome and annotated junctions to infer biological meaning. Here we use long-read complementary DNA datasets for the analysis of a eukaryotic transcriptome and generate two large datasets in the human K562 and HeLa S3 cell lines. Both data sets comprised at least 4 million reads and had median read lengths greater than 500 bp. We show that annotation-independent alignments of these reads provide partial gene structures that are very much in-line with annotated gene structures, 15% of which have not been obtained in a previous de novo analysis of short reads. For long-noncoding RNAs (i.e., lncRNA) genes, however, we find an increased fraction of novel gene structures among our alignments. Other important aspects of transcriptome analysis, such as the description of cell type-specific splicing, can be performed in an accurate, reliable and completely annotation-free manner, making it ideal for the analysis of transcriptomes of newly sequenced genomes. Furthermore, we demonstrate that long read sequence can be assembled into full-length transcripts with considerable success. Our method is applicable to all long read sequencing technologies.
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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.