Ralf Zimmer

TL;DR: A comprehensive blind assessment of over 30 network inference methods on Escherichia coli, Staphylococcus aureus, Saccharomyces cerevisiae and in silico microarray data defines the performance, data requirements and inherent biases of different inference approaches, and provides guidelines for algorithm application and development.

TL;DR: RelEx, an approach for relation extraction from free text based on natural language preprocessing producing dependency parse trees and applying a small number of simple rules to these trees, is developed.

TL;DR: An improved approach to separate total cellular RNA into newly transcribed and preexisting RNA following 10-15 min of metabolic labeling is developed and a previously undisclosed highly connected network of short-lived transcripts selectively down-regulated by IFNgamma is identified.

TL;DR: Overexpression of NSP1 and infection with live SARS-CoV strongly increased signalling through the Calcineurin/NFAT pathway and enhanced the induction of interleukin 2, compatible with late-stage immunopathogenicity and long-term cytokine dysregulation as observed in severe SARS cases.

TL;DR: The resulting clusters are easily interpretable in terms of the biochemical network and the gene expression data and suggest that the method is able to automatically identify processes that are relevant under the measured conditions.