ArticleBMC genomics2025
Genome annotations matter: characterizing Ensembl hg38 annotations from 2014 to 2023.
Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 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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3 citing papers in PubMed.
- Systematic contextual biases in SegmentNT potentially relevant to other nucleotide transformer models.Nucleic acids research · 2026Article
- Systematic contextual biases in SegmentNT potentially relevant to other nucleotide transformer models.bioRxiv : the preprint server for biology · 2026Article
- A bioinformatic survey of RNA isoform diversity and expression across 9 GTEx tissues using long-read sequencing data.BMC genomics · 2025Article
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Authors and funding
5 authors.
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Abstract
backgroundAn accurate genome annotation is essential in many contexts, including RNA sequencing studies. Annotations include known genes and isoforms, detailing their location (chromosome, start, and end) and coding sequence, among other important metadata.
resultsWe characterized changes in human Ensembl annotations from 2014 to 2023 and the important gains in our biological understanding in recent years. While generally gene and isoform annotations increased (2014: 58,812 genes ; 2023: 62,710), some years dropped (e.g., 2016). A similar pattern exists for the gene and isoform biotypes; both 2015 (19,825) and 2017 (19,828) have fewer genes annotated as protein-coding than 2014 (19,953) and 2016 (19,961)- 2023 has the most (20,048). PCBP1-AS1 had the most annotated isoforms (296). We quantified expression for isoforms that were new between 2019 and 2023 across nine GTEx tissues (58 samples) to demonstrate our significant gains in understanding recently. We saw 2,054 of these 'new' isoforms expressed in cerebellar hemisphere (594 in liver). For many genes, we saw that the relative expression of the 'new' isoforms was much greater than the previously known isoforms.
conclusionsThis study demonstrates the importance of an accurate genome annotation to truly understand the underlying complexity of biology that is often oversimplified by ignoring transcriptional complexity.
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