Our research interests are in
- Mathematical and computational modelling
- Molecular systems biology
- Metabolic and regulatory networks
- Constraint-based methods
- Discrete and hybrid dynamical systems
The group "Mathematics in Life Sciences" of Alexander Bockmayr is working on mathematical and computational methods for molecular systems biology [SYS, Chapter A2]. The main topics of interest are metabolic and regulatory 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.
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 [CYA1], [CYA2].