ArticleBMC bioinformatics2016
ampliMethProfiler: a pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite sequenced amplicons.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- DNA methylation patterns re-establish during clonal expansion restoring cell-to-cell epialleles heterogeneity.Biology direct · 2026Article
- Detection of Brain-Derived Cell-Free DNA in Plasma.Diagnostics (Basel, Switzerland) · 2024Article
- Methylation haplotypes of the insulin gene promoter in children and adolescents with type 1 diabetes: Can a dimensionality reduction approach predict the disease?Experimental and therapeutic medicine · 2023Article
- Evaluation of DNA Methylation Profiles of LINE-1, Alu and Ribosomal DNA Repeats in Human Cell Lines Exposed to Radiofrequency Radiation.International journal of molecular sciences · 2023Article
- Quadrato Motor Training (QMT) is associated with DNA methylation changes at DNA repeats: A pilot study.PloS one · 2023Article
- MC profiling: a novel approach to analyze DNA methylation heterogeneity in genome-wide bisulfite sequencing data.NAR genomics and bioinformatics · 2022Article
- Epigenetic remodelling of Fxyd1 promoters in developing heart and brain tissues.Scientific reports · 2022Article
- A novel workflow for the qualitative analysis of DNA methylation data.Computational and structural biotechnology journal · 2022Article
- Effects of the Mediterranean Diet during pregnancy on the onset of allergy in at risk children: A study protocol of a multi-center, randomized- controlled, parallel groups, prospective trial (the PREMEDI study).Frontiers in nutrition · 2022Article
- DNA Methylation Analysis of Ribosomal DNA in Adults With Down Syndrome.Frontiers in genetics · 2022Article
- Ten Years of EWAS.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2021Review
- MethPanel: a parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection.Bioinformatics (Oxford, England) · 2021Article
- Epigenome Chaos: Stochastic and Deterministic DNA Methylation Events Drive Cancer Evolution.Cancers · 2021Review
- DNA Methylation Profiles ofBiomolecules · 2021Article
- Tracing and tracking epiallele families in complex DNA populations.NAR genomics and bioinformatics · 2020Article
- Insulin gene promoter methylation status in Greek children and adolescents with Type 1 Diabetes.Biomedical reports · 2020Article
- Modeling DNA Methylation Profiles through a Dynamic Equilibrium between Methylation and Demethylation.Biomolecules · 2020Article
- Article
- Selective demethylation of two CpG sites causes postnatal activation of the Dao gene and consequent removal of D-serine within the mouse cerebellum.Clinical epigenetics · 2019Article
- TheCancers · 2019Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCpG sites in an individual molecule may exist in a binary state (methylated or unmethylated) and each individual DNA molecule, containing a certain number of CpGs, is a combination of these states defining an epihaplotype. Classic quantification based approaches to study DNA methylation are intrinsically unable to fully represent the complexity of the underlying methylation substrate. Epihaplotype based approaches, on the other hand, allow methylation profiles of cell populations to be studied at the single molecule level. For such investigations, next-generation sequencing techniques can be used, both for quantitative and for epihaplotype analysis. Currently available tools for methylation analysis lack output formats that explicitly report CpG methylation profiles at the single molecule level and that have suited statistical tools for their interpretation.
resultsHere we present ampliMethProfiler, a python-based pipeline for the extraction and statistical epihaplotype analysis of amplicons from targeted deep bisulfite sequencing of multiple DNA regions.
conclusionsampliMethProfiler tool provides an easy and user friendly way to extract and analyze the epihaplotype composition of reads from targeted bisulfite sequencing experiments. ampliMethProfiler is written in python language and requires a local installation of BLAST and (optionally) QIIME tools. It can be run on Linux and OS X platforms. The software is open source and freely available at http://amplimethprofiler.sourceforge.net .
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