Marco J. L. de Groot

TL;DR: Overproduction of XKIA did not reduce the size of the intracellular arabitol and xylitol pools, and therefore had no effect on expression of genes encoding xylan and arabinan degrading enzymes nor on the activity of the enzymes of the catabolic pathway, which supports the suggestion that l-arabitol may be the specific low molecular mass inducer of the genes involved inArabinan degradation.

TL;DR: It is proposed that the araA and araB mutations are localized in positive-acting components of the regulatory system involved in the expression of the arabinanase-encoding genes and the genes encoding the L-arabinose catabolic pathway.

TL;DR: This work systematically search for conserved pathways in two species, quantify their similarities, and focus on the variations between them, and presents an efficient framework, Metabolic Pathway Alignment and Scoring (M-PAS), for identifying and ranking conserved metabolic pathways.

TL;DR: A novel algorithm is proposed that significantly reduces computation time for finding large MCSs, compared to a number of state-of-the-art approaches, and is demonstrated in an application predicting the transcriptional response of breast cancer cell lines to different drug-like compounds.

TL;DR: A comparative analysis of metabolic reaction networks between different species is introduced and a clear framework for matching metabolic pathways is presented, and a scoring scheme which combines enzyme functional similarity with protein sequence similarity is proposed.