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.