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SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty
Detecting allelic imbalance at the isoform level requires accounting for inferential uncertainty, caused by multi-map** of RNA-seq reads. Our...
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Stochastic allelic expression as trigger for contractile imbalance in hypertrophic cardiomyopathy
Hypertrophic cardiomyopathy (HCM), the most common inherited cardiac disease, is caused by several mostly heterozygous mutations in sarcomeric genes....
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BrewerIX enables allelic expression analysis of imprinted and X-linked genes from bulk and single-cell transcriptomes
Genomic imprinting and X chromosome inactivation (XCI) are two prototypical epigenetic mechanisms whereby a set of genes is expressed...
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Precise identification of cancer cells from allelic imbalances in single cell transcriptomes
A fundamental step of tumour single cell mRNA analysis is separating cancer and non-cancer cells. We show that the common approach to separation,...
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scDALI: modeling allelic heterogeneity in single cells reveals context-specific genetic regulation
While it is established that the functional impact of genetic variation can vary across cell types and states, capturing this diversity remains...
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Biased allelic expression in tissues of F1 hybrids between tropical and temperate lotus (Nelumbo nuicfera)
Key messageThe genome-wide allele-specific expression in F1 hybrids from the cross of tropical and temperate lotus unveils how cis -regulatory...
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Effects of Various Allelic Combinations of Starch Biosynthetic Genes on the Properties of Endosperm Starch in Rice
Rice endosperm accumulates large amounts of photosynthetic products as insoluble starch within amyloplasts by properly arranging structured, highly...
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X-chromosome inactivation in human iPSCs provides insight into X-regulated gene expression in autosomes
BackgroundVariation in X chromosome inactivation (XCI) in human-induced pluripotent stem cells (hiPSCs) can impact their ability to model biological...
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STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer
Spatial transcriptomic technologies, such as the Visium platform, measure gene expression in different regions of tissues. Here, we describe new...
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A vast resource of allelic expression data spanning human tissues
Allele expression (AE) analysis robustly measures cis -regulatory effects. Here, we present and demonstrate the utility of a vast AE resource...
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Omics-based construction of regulatory variants can be applied to help decipher pig liver-related traits
Genetic variants can influence complex traits by altering gene expression through changes to regulatory elements. However, the genetic variants that...
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Comparison of allele-specific expression in Sistani cattle and its crossbreed with Holstein, Simmental, and Montbeliarde breeds
The present study has analyzed the allelic-specific expression in Purebred Sistani (Bos Indicus) and their crossbreed with Holstein, Simmental, and...
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Genomic Imprinting and Random Monoallelic Expression
AbstractThe review discusses the mechanisms of monoallelic expression, such as genomic imprinting, in which gene transcription depends on the...
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Allelic variation and haplotype diversity of Matrilineal (MTL) gene governing in vivo maternal haploid induction in maize
Diverse haploid inducer lines with > 6% of haploid induction rate are now routinely used to develop doubled haploid lines. Though MTL gene regulates...
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Gene expression variation explains maize seed germination heterosis
BackgroundHeterosis has been extensively utilized in plant breeding, however, the underlying molecular mechanism remains largely elusive. Maize ( Zea...
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Allele-specific expression reveals genes with recurrent cis-regulatory alterations in high-risk neuroblastoma
BackgroundNeuroblastoma is a pediatric malignancy with a high frequency of metastatic disease at initial diagnosis. Neuroblastoma tumors have few...
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Co-expression network analysis of environmental canalization in the ascidian Ciona
BackgroundCanalization, or buffering, is defined as developmental stability in the face of genetic and/or environmental perturbations. Understanding...
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Polymorphisms and gene expression of metalloproteinases and their inhibitors associated with cerebral ischemic stroke in young patients with sickle cell anemia
BackgroundSickle cell anemia (SCA) is a genetic disease with great clinical heterogeneity and few viable strategies for treatment; hydroxyurea (HU)...
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Analysis of alcohol-metabolizing enzymes genetic variants and RAR/RXR expression in patients diagnosed with fetal alcohol syndrome: a case-control study
Understanding the mechanisms underlying alcohol metabolism and its regulation, including the effect of polymorphisms in alcohol-metabolizing enzymes,...
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Antagonistic regulatory effects of a single cis-acting expression quantitative trait locus between transcription and translation of the MRPL43 gene
BackgroundHeterogeneity of expression quantitative trait locus (eQTL) effects have been shown across gene expression processes. Knowledge on how to...
