Theoretical Methods for Metabolic Modeling and Design

We develop various mathematical approaches to analyze cellular networks. One particular focus is theoretical and compu­ta­tio­nal methods for the analysis and targeted modification of metabolic networks based on stoichiometric and constraint-based modeling approaches:

• Analysis of solution spaces arising in stoichiometric modeling and flux balance analysis of metabolic networks.
• Theory of elementary flux modes and of elementary flux vectors for metabolic pathway analysis.
• Theory of minimal cut sets for targeted (re)design of metabolic networks.
• Theory of growth-coupled product synthesis.
• Thermodynamic constraints in metabolic pathway analysis and design.
• Efficient inclusion of enzyme constraints in constraint-based metabolic models.
• Methods for reduction of genome-scale metabolic networks to core models.
• Methods for constraint-based modeling and design of microbial communities.

We have also been developing various tools and methods for qualitative and semi-quantitative modeling of signaling and regulatory networks based on interaction graphs, logical networks, and logic-based ODEs and used them to analyze large-scale mammalian signaling networks.