Bioconductor is an open-source, open-development software project for the analysis and
comprehension of high-throughput data in genomics and molecular biology. The project …

Abstract Motivation: The recently released Infinium HumanMethylation450 array (the
'450k'array) provides a high-throughput assay to quantify DNA methylation (DNAm) at∼ 450 …

To gain insight into how genomic information is translated into cellular and developmental
programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) …

High-throughput sequencing technologies, such as the Illumina Genome Analyzer, are
powerful new tools for investigating a wide range of biological and medical questions …

Tumor heterogeneity is a major barrier to effective cancer diagnosis and treatment. We
recently identified cancer-specific differentially DNA-methylated regions (cDMRs) in colon …

Background: It is well known that the time from conception to early childhood has importance
for health conditions that reach into later stages of life. Recent research supports this view …

Generation of cDNA using random hexamer priming induces biases in the nucleotide
composition at the beginning of transcriptome sequencing reads from the Illumina Genome …

We propose an extension to quantile normalization that removes unwanted technical
variation using control probes. We adapt our algorithm, functional normalization, to the …

DNA methylation is an important epigenetic modification involved in gene regulation, which
can now be measured using whole-genome bisulfite sequencing. However, cost, complexity …

The ability to measure gene expression on a genome-wide scale is one of the most
promising accomplishments in molecular biology. Microarrays, the technology that first …