Transcription factors are key cellular components that control gene expression: their
activities determine how cells function and respond to the environment. Currently, there is …

The hypothesis that differences in gene regulation have an important role in speciation and
adaptation is more than 40 years old. With the advent of new sequencing technologies, we …

Noncoding DNA is central to our understanding of human gene regulation and complex
diseases,, and measuring the evolutionary sequence constraint can establish the functional …

Abstract Changes in gene expression are thought to underlie many of the phenotypic
differences between species. However, large-scale analyses of gene expression evolution …

A substantial amount of phenotypic diversity results from changes in gene expression levels
and patterns. Understanding how the transcriptome evolves is therefore a key priority in …

Genome instability has long been implicated as the main causal factor in aging. Somatic
cells are continuously exposed to various sources of DNA damage, from reactive oxygen …

Motivation: Microarray data must be background corrected to remove the effects of non-
specific binding or spatial heterogeneity across the array, but this practice typically causes …

Genome-wide scans for positively selected genes (PSGs) in mammals have provided insight
into the dynamics of genome evolution, the genetic basis of differences between species …

Regulatory variation influencing gene expression is a key contributor to phenotypic diversity,
both within and between species. Unfortunately, RNA degrades too rapidly to be recovered …

Gene expression changes may underlie much of phenotypic evolution. The development of
high-throughput RNA sequencing protocols has opened the door to unprecedented large …