ArticleGenome biology2015
Tools and best practices for data processing in allelic expression analysis.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 248 papers.
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Who cites it
248 citing papers in PubMed.
- High-throughput transcriptome analyses from ASPIRO, a phase 1/2/3 study of gene replacement therapy for X-linked myotubular myopathy.American journal of human genetics · 2023Trial
- The landscape of allele-specific expression in human kidneys.Science advances · 2026Article
- Allele-specific expression is associated with lower translational efficiency in mouse embryos and stem cells.bioRxiv : the preprint server for biology · 2026Article
- The promise of long-read RNA-seq: reducing bias in analyses of allele imbalance.NAR genomics and bioinformatics · 2026Article
- Bridging precision agriculture and human medicine through comparative genetics.Nature reviews. Genetics · 2026Review
- Article
- Network-based stratification of allele-specific expression reveals patient subgroups in Huntington's disease.Bioinformatics (Oxford, England) · 2026Article
- Multi-tissue analyses of allele-specific chromatin accessibility nominate likely functional variants for type 2 diabetes.medRxiv : the preprint server for health sciences · 2026Article
- Mapping the landscape of allele-specific expression in porcine genomes.Genome biology · 2026Article
- predNMD: prediction of nonsense-mediated mRNA decay for improved clinical variant pathogenicity classification.bioRxiv : the preprint server for biology · 2026Article
- LongAllele: a joint inference framework for allele-specific analysis on long-read bulk and single-cell RNA sequencing.bioRxiv : the preprint server for biology · 2026Article
- Gene expression is stable despite widespread cis and trans regulatory divergence inbioRxiv : the preprint server for biology · 2026Article
- Allele specific expression in Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Article
- Analysis of Human Uniparental Embryonic Stem Cells Reveals New Putative Imprinted Loci.Cell proliferation · 2026Article
- Identification and functional assessment of CDSN gene variants associated with horn phenotypes in sheep.BMC genomics · 2026Article
- Divergent cis-regulatory haplotypes at Tlr2 are associated with immune responsiveness.Molecular biology and evolution · 2026Article
- Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning.Nature communications · 2026Article
- Experimental and computational methods for allelic imbalance analysis from single-nucleus RNA-seq data.Genome biology · 2026Article
- Confounding factors in assessing the enriched expression of somatic mutant alleles in bulk tumor samples.Genome research · 2026Article
- Assessment of forensic individual identification and kinship analysis using transcript SNPs derived from public transcriptome sequencing data.BMC genomics · 2026Article
188 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
Allelic expression analysis has become important for integrating genome and transcriptome data to characterize various biological phenomena such as cis-regulatory variation and nonsense-mediated decay. We analyze the properties of allelic expression read count data and technical sources of error, such as low-quality or double-counted RNA-seq reads, genotyping errors, allelic mapping bias, and technical covariates due to sample preparation and sequencing, and variation in total read depth. We provide guidelines for correcting such errors, show that our quality control measures improve the detection of relevant allelic expression, and introduce tools for the high-throughput production of allelic expression data from RNA-sequencing data.
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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.