ArticleBioinformatics (Oxford, England)2013
Accurate identification of polyadenylation sites from 3' end deep sequencing using a naive Bayes classifier.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed, 36 citations in OpenAlex.
- PolyAseqTrap: a universal tool for genome-wide identification and quantification of polyadenylation sites from different 3' end sequencing data.Genome biology · 2026Article
- Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation.Experimental & molecular medicine · 2025Review
- Quantifying 3'UTR length from scRNA-seq data reveals changes independent of gene expression.Nature communications · 2024Article
- Polyadenylation-related isoform switching in human evolution revealed by full-length transcript structure.Briefings in bioinformatics · 2021Article
- Proposed criteria for nevoid basal cell carcinoma syndrome in children assessed using statistical optimization.Scientific reports · 2021Article
- Article
- Alternative polyadenylation: methods, mechanism, function, and role in cancer.Journal of experimental & clinical cancer research : CR · 2021Review
- Article
- Evolutionarily conserved pachytene piRNA loci are highly divergent among modern humans.Nature ecology & evolution · 2020Article
- Article
- Detection of Differentially Expressed Cleavage Site Intervals Within 3' Untranslated Regions Using CSI-UTR Reveals Regulated Interaction Motifs.Frontiers in genetics · 2019Article
- Article
- Alterations in mRNA 3' UTR Isoform Abundance Accompany Gene Expression Changes in Human Huntington's Disease Brains.Cell reports · 2017Article
- FLT1 and transcriptome-wide polyadenylation site (PAS) analysis in preeclampsia.Scientific reports · 2017Article
- Defining the 5΄ and 3΄ landscape of the Drosophila transcriptome with Exo-seq and RNaseH-seq.Nucleic acids research · 2017Article
- Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing.Cancer informatics · 2014Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
motivation3' end processing is important for transcription termination, mRNA stability and regulation of gene expression. To identify 3' ends, most techniques use an oligo-dT primer to construct deep sequencing libraries. However, this approach can lead to identification of artifactual polyadenylation sites due to internal priming in homopolymeric stretches of adenines. Although heuristic filters have been applied in these cases, they typically result in a high proportion of both false-positive and -negative classifications. Therefore, there is a need to develop improved algorithms to better identify mis-priming events in oligo-dT primed sequences.
resultsBy analyzing sequence features flanking 3' ends derived from oligo-dT-based sequencing, we developed a naïve Bayes classifier to classify them as true or false/internally primed. The resulting algorithm is highly accurate, outperforms previous heuristic filters and facilitates identification of novel polyadenylation sites.
Indexed as
Identifiers
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.