ArticleBriefings in bioinformatics2023
Comparative epigenome analysis using Infinium DNA methylation BeadChips.
Article in Briefings in bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 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
27 citing papers in PubMed.
- Age-associated DNA methylation patterns in mouse blood and tail: feasibility of tissue-specific epigenetic clock development.GeroScience · 2026Article
- DNA methylation biomarkers-based pan-cancer classifier: predictive modeling for cancer classification.Genome medicine · 2026Article
- Article
- Estimating population structure using epigenome-wide methylation data.Briefings in bioinformatics · 2026Article
- DNA Methylation in Blood Samples from Malignant Mammary Tumors of Companion Dogs: A Pilot Study.Computational and structural biotechnology journal · 2026Article
- Decoding epigenetic and transcriptional landscapes: DNA methylome-transcriptome integration reveals novel drivers in 4NQO-Induced esophageal squamous cell carcinoma mouse model.Clinical epigenetics · 2025Article
- DNA methylation signatures of frailty beyond age: a longitudinal study of female and male mice.bioRxiv : the preprint server for biology · 2025Article
- CD8 T cells mediate immunosurveillance for neoantigen+ epithelial stem cells in the colon.bioRxiv : the preprint server for biology · 2025Article
- A ternary-code DNA methylome atlas of mouse tissues.Genome biology · 2025Article
- The EBV-Positive Tumor Methylome Is Distinct from EBV-Negative in Diffuse Large B-Cell Lymphoma.Cancers · 2025Article
- Scalable screening of ternary-code DNA methylation dynamics associated with human traits.Cell genomics · 2025Article
- Estimating population structure using epigenome-wide methylation data.medRxiv : the preprint server for health sciences · 2025Article
- Epigenomic Interactions Between Chronic Pain and Recurrent Pressure Injuries After Spinal Cord Injury.Epigenomes · 2025Article
- Methylation risk score of C-reactive protein associates sleep health with related health outcomes.Communications biology · 2025Article
- CMImpute: cross-species and tissue imputation of species-level DNA methylation samples across mammalian species.Genome biology · 2025Article
- Characteristics and outcomes of diffuse non-midline gliomas with H3F3A gene mutation in the Kansai Molecular Diagnosis Network for CNS Tumors (Kansai Network): multicenter retrospective cohort study.Acta neuropathologica communications · 2025Article
- Epigenetic Changes in Cerebrospinal Fluid and Blood of People With Neurosyphilis.The Journal of infectious diseases · 2025Article
- Unraveling the intricate molecular landscape and potential biomarkers in lung adenocarcinoma through integrative epigenomic and transcriptomic profiling.Scientific reports · 2025Article
- DNA hypomethylation promotes UHRF1-and SUV39H1/H2-dependent crosstalk between H3K18ub and H3K9me3 to reinforce heterochromatin states.Molecular cell · 2025Article
- Exploratory DNA methylation analysis in post-mortem heart tissue of sudden unexplained death.Clinical epigenetics · 2024Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The arrival of the Infinium DNA methylation BeadChips for mice and other nonhuman mammalian species has outpaced the development of the informatics that supports their use for epigenetics study in model organisms. Here, we present informatics infrastructure and methods to allow easy DNA methylation analysis on multiple species, including domesticated animals and inbred laboratory mice (in SeSAMe version 1.16.0+). First, we developed a data-driven analysis pipeline covering species inference, genome-specific data preprocessing and regression modeling. We targeted genomes of 310 species and 37 inbred mouse strains and showed that genome-specific preprocessing prevents artifacts and yields more accurate measurements than generic pipelines. Second, we uncovered the dynamics of the epigenome evolution in different genomic territories and tissue types through comparative analysis. We identified a catalog of inbred mouse strain-specific methylation differences, some of which are linked to the strains' immune, metabolic and neurological phenotypes. By streamlining DNA methylation array analysis for undesigned genomes, our methods extend epigenome research to broad species contexts.
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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.