ArticleNature communications2021
Aptardi predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 26 citations in OpenAlex.
- TDP-43 loss induces cryptic polyadenylation in ALS/FTD.Nature neuroscience · 2025Article
- Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation.Experimental & molecular medicine · 2025Review
- Big data and deep learning for RNA biology.Experimental & molecular medicine · 2024Review
- InPACT: a computational method for accurate characterization of intronic polyadenylation from RNA sequencing data.Nature communications · 2024Article
- The genetical genomic path to understanding why rats and humans consume too much alcohol.Journal of neurobiology and physiology · 2024Article
- Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data.RNA (New York, N.Y.) · 2023Review
- Hypoviral-regulated HSP90 co-chaperone p23 (CpCop23) determines the colony morphology, virulence, and viral response of chestnut blight fungus Cryphonectria parasitica.Molecular plant pathology · 2023Article
- Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ.Genome research · 2023Article
- A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-seq, and Single-cell RNA-seq.Genomics, proteomics & bioinformatics · 2023Review
- Leveraging omic features with F3UTER enables identification of unannotated 3'UTRs for synaptic genes.Nature communications · 2022Article
- Beyond Genes: Inclusion of Alternative Splicing and Alternative Polyadenylation to Assess the Genetic Architecture of Predisposition to Voluntary Alcohol Consumption in Brain of the HXB/BXH Recombinant Inbred Rat Panel.Frontiers in genetics · 2022Article
- Aptardi predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence.Nature communications · 2021Article
- The Role of Alternative Polyadenylation in the Regulation of Subcellular RNA Localization.Frontiers in genetics · 2021Review
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Annotation of polyadenylation sites from short-read RNA sequencing alone is a challenging computational task. Other algorithms rooted in DNA sequence predict potential polyadenylation sites; however, in vivo expression of a particular site varies based on a myriad of conditions. Here, we introduce aptardi (alternative polyadenylation transcriptome analysis from RNA-Seq data and DNA sequence information), which leverages both DNA sequence and RNA sequencing in a machine learning paradigm to predict expressed polyadenylation sites. Specifically, as input aptardi takes DNA nucleotide sequence, genome-aligned RNA-Seq data, and an initial transcriptome. The program evaluates these initial transcripts to identify expressed polyadenylation sites in the biological sample and refines transcript 3'-ends accordingly. The average precision of the aptardi model is twice that of a standard transcriptome assembler. In particular, the recall of the aptardi model (the proportion of true polyadenylation sites detected by the algorithm) is improved by over three-fold. Also, the model-trained using the Human Brain Reference RNA commercial standard-performs well when applied to RNA-sequencing samples from different tissues and different mammalian species. Finally, aptardi's input is simple to compile and its output is easily amenable to downstream analyses such as quantitation and differential expression.
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Registered trials
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