ArticleNucleic acids research2018
Umap and Bismap: quantifying genome and methylome mappability.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 128 papers.
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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.
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Who cites it
128 citing papers in PubMed.
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- Single-Nucleus Multi-Omic Atlas Maps Regulatory Architecture and Non-Coding Variant Effects across Adult Human Tissues.bioRxiv : the preprint server for biology · 2026Article
- Clustered structural variant hotspots enable oncogenic addiction and plasticity in osteosarcoma.bioRxiv : the preprint server for biology · 2026Article
- Directionality of transcriptional regulatory elements.Nature communications · 2026Article
- Article
- Extensive binding of poorly characterized human transcription factors to genomic dark matter.Nature communications · 2026Article
- Gene regulatory innovations from transposable elements in primate cerebellum development.Nature communications · 2026Article
- Differentially Methylated Regions in Human Rhombic Lip Compartments Are Enriched in Putative Active Enhancers, Human Accelerated Regions, and Medulloblastoma Copy Number Aberrations.Cerebellum (London, England) · 2026Article
- Robust and generalizable CNV detection for single-cell sequencing assays.Nucleic acids research · 2026Article
- Systematic contextual biases in SegmentNT potentially relevant to other nucleotide transformer models.Nucleic acids research · 2026Article
- Transposable elements impact the human regulatory landscape through cell type specific epigenomic associations.Nature communications · 2026Article
- kmerRRR: A k-mer based tool for functional genomics in Repeat Rich Regions.bioRxiv : the preprint server for biology · 2026Article
- Sequence context and methylation interact to shape germline mutation rate variation at CpG sites.PLoS genetics · 2026Article
- UniversalEPI: robust prediction of cell type-specific and differential chromatin interactions from DNA sequence and chromatin accessibility.Nucleic acids research · 2026Article
- Sequence context and methylation interact to shape germline mutation rate variation at CpG sites.bioRxiv : the preprint server for biology · 2026Article
- Systematic contextual biases in SegmentNT potentially relevant to other nucleotide transformer models.bioRxiv : the preprint server for biology · 2026Article
- Chromatin accessibility landscape and its association with heterosis in maize hybrids.Nature communications · 2026Article
- Scalable and accurate rare-variant association tests for whole genome sequencing time-to-event analysis in large biobanks.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Global reorganization of genome architecture at the transition to gametogenesis.Nature structural & molecular biology · 2026Article
68 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Short-read sequencing enables assessment of genetic and biochemical traits of individual genomic regions, such as the location of genetic variation, protein binding and chemical modifications. Every region in a genome assembly has a property called 'mappability', which measures the extent to which it can be uniquely mapped by sequence reads. In regions of lower mappability, estimates of genomic and epigenomic characteristics from sequencing assays are less reliable. These regions have increased susceptibility to spurious mapping from reads from other regions of the genome with sequencing errors or unexpected genetic variation. Bisulfite sequencing approaches used to identify DNA methylation exacerbate these problems by introducing large numbers of reads that map to multiple regions. Both to correct assumptions of uniformity in downstream analysis and to identify regions where the analysis is less reliable, it is necessary to know the mappability of both ordinary and bisulfite-converted genomes. We introduce the Umap software for identifying uniquely mappable regions of any genome. Its Bismap extension identifies mappability of the bisulfite-converted genome. A Umap and Bismap track hub for human genome assemblies GRCh37/hg19 and GRCh38/hg38, and mouse assemblies GRCm37/mm9 and GRCm38/mm10 is available at https://bismap.hoffmanlab.org for use with genome browsers.
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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.