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Research

Our research interests are in

  • Mathematical and computational modelling
  • Molecular systems biology
  • Constraint-based methods
  • Discrete and hybrid dynamical systems
  • Metabolic and regulatory networks

The group "Mathematics in Life Sciences" of Alexander Bockmayr is working on mathematical and computational methods for molecular systems biology [SYS]. The main topics of interest are metabolic and regulatory networks.

    Regulatory Networks
   

Metabolic Networks  

Special emphasis is on constraint-based methods, i.e., reasoning with constraints, where each constraint represents a piece of partial information on the structure or dynamics of the network under study.
The mathematical background of the group lies in discrete mathematics and optimisation, constraint/integer programming, and computational logic.

Regarding constraint-based analysis of metabolic networks, the group has recently developed new algorithms for flux coupling analysis [FCA] , flux variability analysis in the presence of thermodynamic constraints [tFVA] , elementary mode computation [EFM], flux module identification [MOD 1], [MOD 2] , and single or double knock-out [KO] simulations in a lattice-theoretic framework [LAT] .

In the field of regulatory networks, the group is developing graph-theoretic methods and algorithms to elucidate the relationship between the structure and dynamics of regulatory network models in the context of the discrete modelling formalism of R. Thomas [REG 1] , [REG 2] , [REG 3] , [REG 4] .

Currently, the main focus of the group is on integrated modelling of metabolism and gene regulation. A dynamic optimisation framework has been developed that allows predicting the temporal regulation of gene expression from an optimality principle [DYN] . Among others, this has been applied to study the diurnal dynamics of phototrophic metabolism in cyanobacteria [CYA] .