Anthony Bolger

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: RobiNA is an integrated solution that consolidates all steps of RNA-Seq-based differential gene-expression analysis in one user-friendly cross-platform application featuring a rich graphical user interface and supports quality checking, flexible filtering and statistical analysis of differential gene expression based on state of the art biostatistical methods developed in the R/Bioconductor projects.

TL;DR: A high-quality genome assembly of the parents of the IL population of S. pennellii is described, defining candidate genes for stress tolerance and providing evidence that transposable elements had a role in the evolution of these traits.

TL;DR: High-throughput sequencing is used to identify changes in DNA sequence and gene expression that differentiate cultivated tomato and its wild relatives and identifies hundreds of candidate genes that have evolved new protein sequences or have changed expression levels in response to natural selection in wild tomato relatives.

TL;DR: A redesigned and significantly enhanced MapMan4 framework is presented, together with a revised version of the associated online Mercator annotation tool, providing protein annotations for all embryophytes with a comparably high quality.