Rational engineering of biological systems is an inherently complex process due to their
evolved nature. Metabolic engineering emerged and developed over the past 20 years as a …

Untargeted metabolomics makes it possible to identify compounds that undergo significant
changes in concentration in different experimental conditions. The resulting metabolomic …

Genome-scale metabolic reconstructions have proven to be valuable resources in
enhancing our understanding of metabolic networks as they encapsulate all known …

Next-generation sequencing has paved the way for the reconstruction of genome-scale
metabolic networks as a powerful tool for understanding metabolic circuits in any organism …

Motivation: Finding novel or non-standard metabolic pathways, possibly spanning multiple
species, has important applications in fields such as metabolic engineering, metabolic …

Background A central problem in computational metabolic modelling is how to find
biochemically plausible pathways between metabolites in a metabolic network. Two …

We present an elaborate framework for formally modelling pathways in chemical reaction
networks on a mechanistic level. Networks are modelled mathematically as directed multi …

Motivation: In recent years, several methods have been proposed for determining metabolic
pathways in an automated way based on network topology. The aim of this work is to …

We present MetaRoute, an efficient search algorithm based on atom mapping rules and path
weighting schemes that returns relevant or textbook-like routes between a source and a …

Metabolic databases contain information about thousands of small molecules and reactions,
which can be represented as networks. In the context of metabolic reconstruction, pathways …