Bjoern Usadel

TL;DR: Timmomatic is developed as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data and is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested.

TL;DR: This article found that starch is an integrator of the overall metabolic response in Arabidopsis, and they hypothesized that this reflects variation in a regulatory network that balances growth with the carbon supply and identified two genes (myo-inositol-1-phosphate synthase, a Kelch-domain protein) whose transcripts correlate with biomass.

TL;DR: Examples from the literature, wherein co-expression has been used to corroborate and discover various aspects of plant biology are presented, and statistical issues including how normalization of gene expression data can influence co- expression results are discussed.

TL;DR: Rapid diurnal changes in transcript levels are integrated over time to generate quasi-stable changes across large sectors of metabolism, which implies that correlations between metabolites and transcripts are due to regulation of gene expression by metabolites, rather than metabolites being changed as a consequence of a change in gene expression.

TL;DR: The PlaNet platform enables comparative analysis of genome-wide coexpression networks across seven plant species, thus enabling prediction of gene function and elucidation of the identity of functional homologs, and can swiftly infer similar coexpressed network vicinities within and across species.