05.05.2020

Automatic linking from genome to the reactome

Manuel Dienert's approach for the automatic inference of gene-protein reaction rules

Manuel Dienert successfully defended his bachelor's thesis. Therein, he dealt with the question of how gene-protein reaction rules (GPRs) for systems biological models of any organism can be automatically derived. GPRs link genes with reactions and thus enable metabolic analyses on the genome level. This includes, for example, the prediction of possible phenotypes after gene knockouts.
The developed approach automatically derives GPRs for a part of the reactions of tested models. For this purpose, Mr. Dienert uses annotated genomes and links the genes to reactions of the model using EC numbers with which reactions and genes are often annotated. The method was implemented in Java™️ using the library JSBML.
The results provided by his work provide a valuable starting point for model reconstructions in future projects.