ArticleMethods in molecular biology (Clifton, N.J.)2022
Functional Annotation of Custom Transcriptomes.
Article in Methods in molecular biology (Clifton, N.J.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 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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Who cites it
3 citing papers in PubMed, 16 citations in OpenAlex.
- CLN3 transcript complexity revealed by long-read RNA sequencing analysis.BMC medical genomics · 2024Article
- Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons.Genome biology · 2024Article
- Abiotic stress tolerance in pearl millet: Unraveling molecular mechanisms via transcriptomics.Science progressArticle
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Many eukaryotic genes can give rise to different alternative transcripts depending on stage of development, cell type, and physiological cues. Current transcriptome-wide sequencing technologies highlight the remarkable extent of this regulation in metazoans and allow for RNA isoforms to be profiled in increasingly small biological samples and with a growing confidence. Understanding biological functions of sample-specific transcripts is a major challenge in genomics and RNA processing fields. Here we describe simple bioinformatics workflows that facilitate this task by streamlining reference-guided annotation of novel transcripts. A key part of our protocol is the R package factR that rapidly matches custom-assembled transcripts to their likely host genes, deduces the sequence and domain structure of novel protein products, and predicts sensitivity of newly identified RNA isoforms to nonsense-mediated decay.
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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.