ArticleCell genomics2023
Genome graphs detect human polymorphisms in active epigenomic state during influenza infection.
Article in Cell genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
11 citing papers in PubMed, 14 citations in OpenAlex.
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- Quantifying reference alignment bias in functional genomics analyses.Cell reports methods · 2026Article
- Transposable elements impact the human regulatory landscape through cell type specific epigenomic associations.Nature communications · 2026Article
- Benchmarking genome choice in functional genomics analyses.Nature communications · 2026Article
- ViMIC 2.0: an updated database of human disease-related viral mutations, integration sites, and multi-omics data.Nucleic acids research · 2026Article
- A Hitchhiker's Guide to long-read genomic analysis.Genome research · 2025Review
- Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA.Genome research · 2025Article
- Investigating mobile element variations by statistical genetics.Human genome variation · 2024Review
- Transposable elements are associated with the variable response to influenza infection.Cell genomics · 2023Article
- Genome graphs detect human polymorphisms in active epigenomic state during influenza infection.Cell genomics · 2023Article
- An assessment of bioinformatics tools for the detection of human endogenous retroviral insertions in short-read genome sequencing data.Frontiers in bioinformatics · 2022Article
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genetic variants, including mobile element insertions (MEIs), are known to impact the epigenome. We hypothesized that genome graphs, which encapsulate genetic diversity, could reveal missing epigenomic signals. To test this, we sequenced the epigenome of monocyte-derived macrophages from 35 ancestrally diverse individuals before and after influenza infection, allowing us to investigate the role of MEIs in immunity. We characterized genetic variants and MEIs using linked reads and built a genome graph. Mapping epigenetic data revealed 2.3%-3% novel peaks for H3K4me1, H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq), and ATAC-seq. Additionally, the use of a genome graph modified some quantitative trait loci estimates and revealed 375 polymorphic MEIs in an active epigenomic state. Among these is an AluYh3 polymorphism whose chromatin state changed after infection and was associated with the expression of
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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.