Review of processing and analysis methods for DNA methylation array data
The promise of epigenome-wide association studies and cancer-specific somatic DNA
methylation changes in improving our understanding of cancer, coupled with the decreasing …
methylation changes in improving our understanding of cancer, coupled with the decreasing …
SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions
We report a new class of artifacts in DNA methylation measurements from Illumina
HumanMethylation450 and MethylationEPIC arrays. These artifacts reflect failed …
HumanMethylation450 and MethylationEPIC arrays. These artifacts reflect failed …
Comprehensive analysis of DNA methylation data with RnBeads
RnBeads is a software tool for large-scale analysis and interpretation of DNA methylation
data, providing a user-friendly analysis workflow that yields detailed hypertext reports …
data, providing a user-friendly analysis workflow that yields detailed hypertext reports …
Bioinformatics tools for genome-wide epigenetic research
VE Angarica, A Del Sol - Neuroepigenomics in Aging and Disease, 2017 - Springer
Epigenetics play a central role in the regulation of many important cellular processes, and
dysregulations at the epigenetic level could be the source of serious pathologies, such as …
dysregulations at the epigenetic level could be the source of serious pathologies, such as …
[HTML][HTML] Epigenetic-aging-signature to determine age in different tissues
CM Koch, W Wagner - Aging (Albany NY), 2011 - ncbi.nlm.nih.gov
All tissues of the organism are affected by aging. This process is associated with epigenetic
modifications such as methylation changes at specific cytosine residues in the DNA (CpG …
modifications such as methylation changes at specific cytosine residues in the DNA (CpG …
CancerDetector: ultrasensitive and non-invasive cancer detection at the resolution of individual reads using cell-free DNA methylation sequencing data
The detection of tumor-derived cell-free DNA in plasma is one of the most promising
directions in cancer diagnosis. The major challenge in such an approach is how to identify …
directions in cancer diagnosis. The major challenge in such an approach is how to identify …
IMA: an R package for high-throughput analysis of Illumina's 450K Infinium methylation data
The Illumina Infinium HumanMethylation450 BeadChip is a newly designed high-density
microarray for quantifying the methylation level of over 450 000 CpG sites within human …
microarray for quantifying the methylation level of over 450 000 CpG sites within human …
Detection of significantly differentially methylated regions in targeted bisulfite sequencing data
Motivation: Bisulfite sequencing is currently the gold standard to obtain genome-wide DNA
methylation profiles in eukaryotes. In contrast to the rapid development of appropriate pre …
methylation profiles in eukaryotes. In contrast to the rapid development of appropriate pre …
Estimating and accounting for tumor purity in the analysis of DNA methylation data from cancer studies
We present a set of statistical methods for the analysis of DNA methylation microarray data,
which account for tumor purity. These methods are an extension of our previously developed …
which account for tumor purity. These methods are an extension of our previously developed …
Differential DNA Methylation in Umbilical Cord Blood of Infants Exposed to Low Levels of Arsenic in Utero
DC Koestler, M Avissar-Whiting… - Environmental …, 2013 - ehp.niehs.nih.gov
Background: There is increasing epidemiologic evidence that arsenic exposure in utero,
even at low levels found throughout much of the world, is associated with adverse …
even at low levels found throughout much of the world, is associated with adverse …