ArticleMolecular ecology resources2013
Allelic imbalance metre (Allim), a new tool for measuring allele-specific gene expression with RNA-seq data.
Article in Molecular ecology resources, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 47 citations in OpenAlex.
- The promise of long-read RNA-seq: reducing bias in analyses of allele imbalance.NAR genomics and bioinformatics · 2026Article
- A two-phase clustering procedure based on allele specific expression.BMC bioinformatics · 2026Article
- Deep resequencing unveils novel SNPs, InDels, and large structural variants for the clonal fingerprinting of sweet orange [Citrus sinensis (L.) Osbeck].The plant genome · 2025Article
- Statistical framework for calling allelic imbalance in high-throughput sequencing data.Nature communications · 2025Article
- Transcriptional misexpression in hybrids between species linked by gene flow is associated with patterns of sequence divergence.Genome biology and evolution · 2023Article
- The genomes of 204 Vitis vinifera accessions reveal the origin of European wine grapes.Nature communications · 2021Article
- Article
- Power calculator for detecting allelic imbalance using hierarchical Bayesian model.BMC research notes · 2021Article
- Open chromatin in grapevine marks candidate CREs and with other chromatin features correlates with gene expression.The Plant journal : for cell and molecular biology · 2021Article
- Personalized and graph genomes reveal missing signal in epigenomic data.Genome biology · 2020Article
- Modeling allele-specific expression at the gene and SNP levels simultaneously by a Bayesian logistic mixed regression model.BMC bioinformatics · 2019Article
- Is it time to change the reference genome?Genome biology · 2019Article
- AltHapAlignR: improved accuracy of RNA-seq analyses through the use of alternative haplotypes.Bioinformatics (Oxford, England) · 2018Article
- IDP-ASE: haplotyping and quantifying allele-specific expression at the gene and gene isoform level by hybrid sequencing.Nucleic acids research · 2017Article
- Gene expression allelic imbalance in ovine brown adipose tissue impacts energy homeostasis.PloS one · 2017Article
- ASEQ: fast allele-specific studies from next-generation sequencing data.BMC medical genomics · 2015Article
- A hidden Markov approach for ascertaining cSNP genotypes from RNA sequence data in the presence of allelic imbalance by exploiting linkage disequilibrium.BMC bioinformatics · 2015Article
- Transcriptomic response to heat stress among ecologically divergent populations of redband trout.BMC genomics · 2015Article
- Temperature stress mediates decanalization and dominance of gene expression in Drosophila melanogaster.PLoS genetics · 2015Article
- Natural genetic variation impacts expression levels of coding, non-coding, and antisense transcripts in fission yeast.Molecular systems biology · 2014Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Estimating differences in gene expression among alleles is of high interest for many areas in biology and medicine. Here, we present a user-friendly software tool, Allim, to estimate allele-specific gene expression. Because mapping bias is a major problem for reliable estimates of allele-specific gene expression using RNA-seq, Allim combines two different strategies to account for the mapping biases. In order to reduce the mapping bias, Allim first generates a polymorphism-aware reference genome that accounts for the sequence variation between the alleles. Then, a sequence-specific simulation tool estimates the residual mapping bias. Statistical tests for allelic imbalance are provided that can be used with the bias corrected RNA-seq data.
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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.