Albert J. Vilella
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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: 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: The 2006 NESCent Phyloinformatics Hackathon: A Field Report
The 2006 NESCent Phyloinformatics Hackathon: A Field Report Open
In December, 2006, a group of 26 software developers from some of the most widely used life science programming toolkits and phylogenetic software projects converged on Durham, North Carolina, for a Phyloinformatics Hackathon, an intense f…
View article: ewels/MultiQC: MultiQC Version 1.4
ewels/MultiQC: MultiQC Version 1.4 Open
A slightly earlier-than-expected release due to a new problem with dependency packages that is breaking MultiQC installations since 2018-01-11. New Modules: Sargasso Parses output from Sargasso - a tool to separate mixed-species RNA-seq re…
View article: scientificomputing/Montage v1.4
scientificomputing/Montage v1.4 Open
First release of Montage
View article: ncRNA orthologies in the vertebrate lineage
ncRNA orthologies in the vertebrate lineage Open
Annotation of orthologous and paralogous genes is necessary for many aspects of evolutionary analysis. Methods to infer these homology relationships have traditionally focused on protein-coding genes and evolutionary models used by these m…
View article: Ensembl comparative genomics resources
Ensembl comparative genomics resources Open
Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and ot…