ArticleGenome biology2010
Estimating enrichment of repetitive elements from high-throughput sequence data.
Article in Genome biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 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.
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Who cites it
69 citing papers in PubMed, 115 citations in OpenAlex.
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- Foxg1 bimodally tunes L1-mRNA and -DNA dynamics in the developing murine neocortex.Development (Cambridge, England) · 2024Article
- RepEnTools: an automated repeat enrichment analysis package for ChIP-seq data reveals hUHRF1 Tandem-Tudor domain enrichment in young repeats.Mobile DNA · 2024Article
- EZH2 inhibition stimulates repetitive element expression and viral mimicry in resting splenic B cells.The EMBO journal · 2023Article
- Pediatric glioma histone H3.3 K27M/G34R mutations drive abnormalities in PML nuclear bodies.Genome biology · 2023Article
- TERRA regulates DNA G-quadruplex formation and ATRX recruitment to chromatin.Nucleic acids research · 2022Article
- The chromatin remodeller ATRX facilitates diverse nuclear processes, in a stochastic manner, in both heterochromatin and euchromatin.Nature communications · 2022Article
- CHAF1A/B mediate silencing of unintegrated HIV-1 DNAs early in infection.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Genome sequencing and resequencing identified three horizontal gene transfers and uncovered the genetic mechanism on the intraspecies adaptive evolution ofFrontiers in plant science · 2022Article
- Recent Bioinformatic Progress to Identify Epigenetic Changes Associated to Transposable Elements.Frontiers in genetics · 2022Review
- Differential enrichment of H3K9me3 at annotated satellite DNA repeats in human cell lines and during fetal development in mouse.Epigenetics & chromatin · 2021Article
- Mutations inhibiting KDM4B drive ALT activation in ATRX-mutated glioblastomas.Nature communications · 2021Article
- Innovation of heterochromatin functions drives rapid evolution of essential ZAD-ZNF genes ineLife · 2020Article
- Review
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- Early life exposures, neurodevelopmental disorders, and transposable elements.Neurobiology of stress · 2019Review
- SIRT7 mediates L1 elements transcriptional repression and their association with the nuclear lamina.Nucleic acids research · 2019Article
- Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression.PLoS computational biology · 2019Article
9 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We describe computational methods for analysis of repetitive elements from short-read sequencing data, and apply them to study histone modifications associated with the repetitive elements in human and mouse cells. Our results demonstrate that while accurate enrichment estimates can be obtained for individual repeat types and small sets of repeat instances, there are distinct combinatorial patterns of chromatin marks associated with major annotated repeat families, including H3K27me3/H3K9me3 differences among the endogenous retroviral element classes.
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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.