Profiling genome-wide DNA methylation
DNA methylation is an epigenetic modification that plays an important role in regulating
gene expression and therefore a broad range of biological processes and diseases. DNA …
gene expression and therefore a broad range of biological processes and diseases. DNA …
Analysing and interpreting DNA methylation data
C Bock - Nature Reviews Genetics, 2012 - nature.com
DNA methylation is an epigenetic mark that has suspected regulatory roles in a broad range
of biological processes and diseases. The technology is now available for studying DNA …
of biological processes and diseases. The technology is now available for studying DNA …
BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data
Background DNA methylation is an important epigenetic modification involved in many
biological processes. Bisulfite treatment coupled with high-throughput sequencing provides …
biological processes. Bisulfite treatment coupled with high-throughput sequencing provides …
Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values
BS Pedersen, DA Schwartz, IV Yang… - Bioinformatics, 2012 - academic.oup.com
comb-p is a command-line tool and a python library that manipulates BED files of possibly
irregularly spaced P-values and (1) calculates auto-correlation,(2) combines adjacent P …
irregularly spaced P-values and (1) calculates auto-correlation,(2) combines adjacent P …
DNA methylome analysis using short bisulfite sequencing data
Bisulfite conversion of genomic DNA combined with next-generation sequencing (BS-seq) is
widely used to measure the methylation state of a whole genome, the methylome, at single …
widely used to measure the methylation state of a whole genome, the methylome, at single …
[HTML][HTML] Strategies for analyzing bisulfite sequencing data
DNA methylation is one of the main epigenetic modifications in the eukaryotic genome; it
has been shown to play a role in cell-type specific regulation of gene expression, and …
has been shown to play a role in cell-type specific regulation of gene expression, and …
Fast and accurate alignment of long bisulfite-seq reads
BS Pedersen, K Eyring, S De, IV Yang… - arXiv preprint arXiv …, 2014 - arxiv.org
Longer sequencing reads, with at least 200 bases per template are now common. While
traditional aligners have adopted new strategies to improve the mapping of longer reads …
traditional aligners have adopted new strategies to improve the mapping of longer reads …
Epigenetic control of gene regulation during development and disease: A view from the retina
Complex biological processes, such as organogenesis and homeostasis, are stringently
regulated by genetic programs that are fine-tuned by epigenetic factors to establish cell fates …
regulated by genetic programs that are fine-tuned by epigenetic factors to establish cell fates …
[HTML][HTML] Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR
Cytosine methylation is an important DNA epigenetic modification. In vertebrates,
methylation occurs at CpG sites, which are dinucleotides where a cytosine is immediately …
methylation occurs at CpG sites, which are dinucleotides where a cytosine is immediately …
Base resolution methylome profiling: considerations in platform selection, data preprocessing and analysis
Bisulfite treatment-based methylation microarray (mainly Illumina 450K Infinium array) and
next-generation sequencing (reduced representation bisulfite sequencing, Agilent …
next-generation sequencing (reduced representation bisulfite sequencing, Agilent …