ArticleProceedings of the National Academy of Sciences of the United States of America2013
Characterization of the human ESC transcriptome by hybrid sequencing.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 193 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.
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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
193 citing papers in PubMed.
- Review
- Tools and tactics for studying alternative splicing.Nature reviews. Genetics · 2026Review
- Quantifying transcript complexity via the condition number of gene-specific random matrix.Briefings in bioinformatics · 2026Article
- The changing landscape of gene expression analysis.Briefings in bioinformatics · 2026Review
- Improving gene isoform quantification with miniQuant.Nature biotechnology · 2026Article
- Decoding exon inclusion in the human brain reveals more divergent splicing mechanisms in neurons than glia.Genome biology · 2026Article
- ImmunoPepper: extracting personalized peptides from complex splicing graphs.Bioinformatics (Oxford, England) · 2026Article
- From Genomic Fossils to Functional Elements: The Evolving Story of Pseudogenes.Advanced genetics (Hoboken, N.J.) · 2025Review
- Nano3P-seq: charting the coding and noncoding transcriptome at single-molecule resolution.Nature protocols · 2025Review
- A single-cell, long-read, isoform-resolved case-control study of FTD reveals cell-type-specific and broad splicing dysregulation in human brain.Cell reports · 2025Article
- NRCAM variant defined by microexon skipping is a targetable cell surface proteoform in high-grade gliomas.Cell reports · 2025Article
- Zygotic activation of transposable elements during zebrafish early embryogenesis.Nature communications · 2025Article
- Deciphering the genetic basis of sex differentiation in silver-lipped pearl oyster (Zoological research · 2025Article
- Long-read RNA sequencing: A transformative technology for exploring transcriptome complexity in human diseases.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics.Genome research · 2024Review
- Challenges in identifying mRNA transcript starts and ends from long-read sequencing data.Genome research · 2024Review
- Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads.Genome research · 2024Article
- Integrative analyses of long and short-read RNA sequencing reveal the spliced isoform regulatory network of seedling growth dynamics in upland cotton.Functional & integrative genomics · 2024Article
- Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing.Scientific data · 2024Article
- Direct transposition of native DNA for sensitive multimodal single-molecule sequencing.Nature genetics · 2024Article
133 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Although transcriptional and posttranscriptional events are detected in RNA-Seq data from second-generation sequencing, full-length mRNA isoforms are not captured. On the other hand, third-generation sequencing, which yields much longer reads, has current limitations of lower raw accuracy and throughput. Here, we combine second-generation sequencing and third-generation sequencing with a custom-designed method for isoform identification and quantification to generate a high-confidence isoform dataset for human embryonic stem cells (hESCs). We report 8,084 RefSeq-annotated isoforms detected as full-length and an additional 5,459 isoforms predicted through statistical inference. Over one-third of these are novel isoforms, including 273 RNAs from gene loci that have not previously been identified. Further characterization of the novel loci indicates that a subset is expressed in pluripotent cells but not in diverse fetal and adult tissues; moreover, their reduced expression perturbs the network of pluripotency-associated genes. Results suggest that gene identification, even in well-characterized human cell lines and tissues, is likely far from complete.
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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.