ArticleF1000Research2019
Fast effect size shrinkage software for beta-binomial models of allelic imbalance.
Article in F1000Research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 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
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Who cites it
15 citing papers in PubMed.
- ThemBio · 2026Article
- Article
- Long-read RNA sequencing reveals allele-specificGenome research · 2025Article
- Long-read RNA sequencing reveals allele-specific NbioRxiv : the preprint server for biology · 2024Article
- Translatome analysis in acute ischemic stroke: Astrocytes and microglia exhibit differences in poststroke alternative splicing of expressed transcripts.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2024Article
- Detection of allele-specific expression in spatial transcriptomics with spASE.Genome biology · 2024Article
- Single-cell allele-specific expression analysis reveals dynamic and cell-type-specific regulatory effects.Nature communications · 2023Article
- The Effect of Plastic-Related Compounds on Transcriptome-Wide Gene Expression on CYP2C19-Overexpressing HepG2 Cells.Molecules (Basel, Switzerland) · 2023Article
- SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty.Genome biology · 2023Article
- Transcriptome of GH-producing pituitary neuroendocrine tumours and models are significantly affected by somatostatin analogues.Cancer cell international · 2023Article
- Inference of putative cell-type-specific imprinted regulatory elements and genes during human neuronal differentiation.Human molecular genetics · 2023Article
- Inactivation ofFrontiers in microbiology · 2023Article
- Dithranol as novel co-adjuvant for non-invasive dermal vaccination.NPJ vaccines · 2022Article
- Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets.Bioinformatics (Oxford, England) · 2022Article
- Allele-specific analysis reveals exon- and cell-type-specific regulatory effects of Alzheimer's disease-associated genetic variants.Translational psychiatry · 2022Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Allelic imbalance occurs when the two alleles of a gene are differentially expressed within a diploid organism and can indicate important differences in cis-regulation and epigenetic state across the two chromosomes. Because of this, the ability to accurately quantify the proportion at which each allele of a gene is expressed is of great interest to researchers. This becomes challenging in the presence of small read counts and/or sample sizes, which can cause estimators for allelic expression proportions to have high variance. Investigators have traditionally dealt with this problem by filtering out genes with small counts and samples. However, this may inadvertently remove important genes that have truly large allelic imbalances. Another option is to use pseudocounts or Bayesian estimators to reduce the variance. To this end, we evaluated the accuracy of four different estimators, the latter two of which are Bayesian shrinkage estimators: maximum likelihood, adding a pseudocount to each allele, approximate posterior estimation of GLM coefficients (apeglm) and adaptive shrinkage (ash). We also wrote C++ code to quickly calculate ML and apeglm estimates and integrated it into the
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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.