Nicolas J. Walker
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View article: Simultaneous sequencing of genetic and epigenetic bases in DNA
Simultaneous sequencing of genetic and epigenetic bases in DNA Open
DNA comprises molecular information stored in genetic and epigenetic bases, both of which are vital to our understanding of biology. Most DNA sequencing approaches address either genetics or epigenetics and thus capture incomplete informat…
View article: 3D genome organization links non-coding disease-associated variants to genes
3D genome organization links non-coding disease-associated variants to genes Open
Genome sequencing has revealed over 300 million genetic variations in human populations. Over 90% of variants are single nucleotide polymorphisms (SNPs), the remainder include short deletions or insertions, and small numbers of structural …
View article: Hydroxymethylation profile of cell-free DNA is a biomarker for early colorectal cancer
Hydroxymethylation profile of cell-free DNA is a biomarker for early colorectal cancer Open
Early detection of cancer will improve survival rates. The blood biomarker 5-hydroxymethylcytosine has been shown to discriminate cancer. In a large covariate-controlled study of over two thousand individual blood samples, we created, test…
View article: Accurate simultaneous sequencing of genetic and epigenetic bases in DNA
Accurate simultaneous sequencing of genetic and epigenetic bases in DNA Open
DNA comprises molecular information stored via genetic bases (G, C, T, A) and also epigenetic bases, principally 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Both genetic and epigenetic information are vital to our understand…
View article: Hydroxymethylation profile of cell free DNA is a biomarker for early colorectal cancer
Hydroxymethylation profile of cell free DNA is a biomarker for early colorectal cancer Open
Early detection of colorectal cancer (CRC) will improve survival rates. We created a classifier to detect CRC, based on 5-hydroxymethylcytosine levels in cell free DNA isolated from blood samples of 2198 individuals. Our classifier discrim…
View article: Methylation and expression data for whole-genome human imprinting study
Methylation and expression data for whole-genome human imprinting study Open
Supplementary data for Zink et al. , "Insights into Imprinting from Parent-of-Origin Phased Methylomes and Transcriptomes", Nature Genetics (2018)We combined whole genome oxidative bisulfite sequencing of 285 people and allele-specific RNA…
View article: Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet
Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet Open
Transcription factors bind DNA in specific sequence contexts. In addition to distinguishing one nucleobase from another, some transcription factors can distinguish between unmodified and modified bases. Current models of transcription fact…