Despite substantial progress in understanding the genetic basis for differences in
morphology, physiology, and behavior, many phenotypes of interest are difficult to study with …

Gene expression data for Archaeplastida are accumulating exponentially, with more than
300 000 RNA-sequencing (RNA-seq) experiments available for hundreds of species. The …

OrthoList, a compendium of Caenorhabditis elegans genes with human orthologs compiled
in 2011 by a meta-analysis of four orthology-prediction methods, has been a popular tool for …

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 …

The Brassicaceae family comprises c. 4000 species including economically important crops
and the model plant Arabidopsis thaliana. Despite their importance, the relationships among …

To gain insight into how mammalian gene expression is controlled by rapidly evolving
regulatory elements, we jointly analysed promoter and enhancer activity with downstream …

The origin and evolution of cell types has emerged as a key topic in evolutionary biology.
Driven by rapidly accumulating single-cell datasets, recent attempts to infer cell type …

Benthic diatoms are the main primary producers in shallow freshwater and coastal
environments, fulfilling important ecological functions such as nutrient cycling and sediment …

Motivation The computational prediction of gene function is a key step in making full use of
newly sequenced genomes. Function is generally predicted by transferring annotations from …

Hundreds of cell types form the vertebrate brain but it is largely unknown how similar cellular
repertoires are between or within species or how cell-type diversity evolves. To examine cell …