ArticleNature communications2016
A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals.
Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed.
- Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning.Nature communications · 2026Article
- Confounding factors in assessing the enriched expression of somatic mutant alleles in bulk tumor samples.Genome research · 2026Article
- NEXT-scASV: a Nextflow pipeline for allele-specific variant calling from single-cell RNA-seq data.GigaScience · 2026Article
- baal-nf identifies motif-disrupting variants that decrease transcription factor binding affinity.Genome biology · 2026Article
- Self-organizing maps for allele specific expression data reconstruction and identification of anomalous genomic regions.Frontiers in bioinformatics · 2026Article
- Disease-linked regulatory DNA variants and homeostatic transcription factors in epidermis.Nature communications · 2025Article
- Article
- Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis.Genome research · 2025Article
- SNPeBoT: a tool for predicting transcription factor allele specific binding.BMC bioinformatics · 2025Article
- A T2T-CHM13 recombination map and globally diverse haplotype reference panel improves phasing and imputation.bioRxiv : the preprint server for biology · 2025Article
- Statistical framework for calling allelic imbalance in high-throughput sequencing data.Nature communications · 2025Article
- Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants.Science (New York, N.Y.) · 2025Article
- Benchmarking and building DNA binding affinity models using allele-specific and allele-agnostic transcription factor binding data.Genome biology · 2024Article
- Ornaments for efficient allele-specific expression estimation with bias correction.American journal of human genetics · 2024Article
- The correlation between CpG methylation and gene expression is driven by sequence variants.Nature genetics · 2024Article
- Single-cell genomics and regulatory networks for 388 human brains.Science (New York, N.Y.) · 2024Article
- Single-cell genomics and regulatory networks for 388 human brains.bioRxiv : the preprint server for biology · 2024Article
- Allele-specific binding (ASB) analyzer for annotation of allele-specific binding SNPs.BMC bioinformatics · 2023Article
- SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty.Genome biology · 2023Article
- Article
3 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
Funding
Abstract
Large-scale sequencing in the 1000 Genomes Project has revealed multitudes of single nucleotide variants (SNVs). Here, we provide insights into the functional effect of these variants using allele-specific behaviour. This can be assessed for an individual by mapping ChIP-seq and RNA-seq reads to a personal genome, and then measuring 'allelic imbalances' between the numbers of reads mapped to the paternal and maternal chromosomes. We annotate variants associated with allele-specific binding and expression in 382 individuals by uniformly processing 1,263 functional genomics data sets, developing approaches to reduce the heterogeneity between data sets due to overdispersion and mapping bias. Since many allelic variants are rare, aggregation across multiple individuals is necessary to identify broadly applicable 'allelic elements'. We also found SNVs for which we can anticipate allelic imbalance from the disruption of a binding motif. Our results serve as an allele-specific annotation for the 1000 Genomes variant catalogue and are distributed as an online resource (alleledb.gersteinlab.org).
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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.