ReviewEpigenomics2015
Base resolution methylome profiling: considerations in platform selection, data preprocessing and analysis.
Review in Epigenomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
62 citing papers in PubMed.
- Adherence to Mediterranean diet is associated with methylation changes in inflammation-related genes in peripheral blood cells.Journal of physiology and biochemistry · 2016Trial
- Cell-free DNA methylation profiling reveals injury types and severities in swine rotational and contusional models of traumatic brain injury.Acta neuropathologica communications · 2026Article
- Genome-wide methylation detection and episignature analysis using PacBio long-read sequencing.Genome medicine · 2026Article
- Emerging liquid biopsy markers in thyroid cancer: from isolation technologies to clinical translation.Frontiers in endocrinology · 2026Review
- The hidden Markov model and its applications in bioinformatics analysis.Genes & diseases · 2026Review
- PoreMeth2 for decoding the evolution of methylome alterations with nanopore sequencing.Genome research · 2025Article
- Methylome Profiling of a Deuterostome Invertebrate Using Oxford Nanopore Technology (ONT).Molecular ecology resources · 2025Article
- Genome-wide profiling of unmodified DNA using methyltransferase-directed tagging and enrichment.Cell reports methods · 2025Article
- Robust molecular subgrouping and reference-free aneuploidy detection in medulloblastoma using low-depth whole genome bisulfite sequencing.Acta neuropathologica communications · 2025Article
- Next-generation sequencing in cancer diagnosis and treatment: clinical applications and future directions.Discover oncology · 2025Review
- EpiAge: a next-generation sequencing-basedAging · 2025Article
- Comparison of enzymatic and bisulfite-based methods for sequencing-based cell-free DNA methylation profiling.Frontiers in epigenetics and epigenomics · 2025Article
- Genomic context determines the effect of DNA methylation on gene expression in the gut epithelium of Atlantic salmon (Epigenetics · 2024Article
- Circulating tumor DNA methylation detection as biomarker and its application in tumor liquid biopsy: advances and challenges.MedComm · 2024Review
- Discovery and Validation of Methylation Signatures in Circulating Cell-Free DNA for the Detection of Colorectal Cancer.Biomolecules · 2024Article
- Whole-genome bisulfite sequencing identifies stage- and subtype-specific DNA methylation signatures in pancreatic cancer.iScience · 2024Article
- Mutations in human DNA methyltransferase DNMT1 induce specific genome-wide epigenomic and transcriptomic changes in neurodevelopment.Human molecular genetics · 2023Article
- High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of chemoresistance in leukemias.Communications biology · 2023Article
- A Clinician's Guide to Bioinformatics for Next-Generation Sequencing.Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer · 2023Review
- Simultaneous detection of DNA variation and methylation at HLA class II locus and immune gene promoters using targeted SureSelect Methyl-Sequencing.Frontiers in immunology · 2023Article
2 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.
Funding
Abstract
Bisulfite treatment-based methylation microarray (mainly Illumina 450K Infinium array) and next-generation sequencing (reduced representation bisulfite sequencing, Agilent SureSelect Human Methyl-Seq, NimbleGen SeqCap Epi CpGiant or whole-genome bisulfite sequencing) are commonly used for base resolution DNA methylome research. Although multiple tools and methods have been developed and used for the data preprocessing and analysis, confusions remains for these platforms including how and whether the 450k array should be normalized; which platform should be used to better fit researchers' needs; and which statistical models would be more appropriate for differential methylation analysis. This review presents the commonly used platforms and compares the pros and cons of each in methylome profiling. We then discuss approaches to study design, data normalization, bias correction and model selection for differentially methylated individual CpGs and regions.
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What OpenQuestion holds
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.