ArticleBioinformatics (Oxford, England)2021
Ranked choice voting for representative transcripts with TRaCE.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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
11 citing papers in PubMed.
- The promise of AlphaFold for gene structure annotation.Nucleic acids research · 2026Article
- SorghumBase: a knowledgebase for sorghum genomics, phenomics, and stakeholder engagement.Genetics · 2026Article
- Gramene 2025: expanded comparative genomics and pathway resources, integrated search, and pan-genome portals for crop research.Nucleic acids research · 2026Article
- Genome sequence assembly and annotation ofNAR genomics and bioinformatics · 2025Article
- A pangenome of maize provides genetic insights into drought resistance.Nature genetics · 2025Article
- Extensive genome evolution distinguishes maize within a stable tribe of grasses.bioRxiv : the preprint server for biology · 2025Article
- High-quality chromosome scale genome assemblies of two important Sorghum inbred lines, Tx2783 and RTx436.NAR genomics and bioinformatics · 2024Article
- Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice.Nature communications · 2023Article
- APPRIS principal isoforms and MANE Select transcripts define reference splice variants.Bioinformatics (Oxford, England) · 2022Article
- Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes.Frontiers in plant science · 2022Article
- De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes.Science (New York, N.Y.) · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
summaryGenome sequencing projects annotate protein-coding gene models with multiple transcripts, aiming to represent all of the available transcript evidence. However, downstream analyses often operate on only one representative transcript per gene locus, sometimes known as the canonical transcript. To choose canonical transcripts, Transcript Ranking and Canonical Election (TRaCE) holds an 'election' in which a set of RNA-seq samples rank transcripts by annotation edit distance. These sample-specific votes are tallied along with other criteria such as protein length and InterPro domain coverage. The winner is selected as the canonical transcript, but the election proceeds through multiple rounds of voting to order all the transcripts by relevance. Based on the set of expression data provided, TRaCE can identify the most common isoforms from a broad expression atlas or prioritize alternative transcripts expressed in specific contexts. AVAILABILITY AND IMPLEMENTATION: Transcript ranking code can be found on GitHub at {{https://github.com/warelab/TRaCE}}. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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What OpenQuestion holds
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.