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.

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