Dear Colleagues,

The computational systems biology of cellular metabolism has grown into a rich field. Models are based on genome-scale stoichiometric descriptions of metabolic networks, but recent efforts are moving away from only modeling the metabolic network. Metabolism and expression (ME) models take, for instance, the synthesis reactions of all individual macromolecular components of the cell into account, such as of each mRNA and protein, leading to enormous models with much greater predictive accuracy. Other models consider reduced descriptions of metabolism and cellular growth to understand how particular constraints, such as limited biosynthetic machinery and protein-accessible volumes, influence cellular growth and how cells would be predicted to change their protein expression across conditions if they are maximizing their growth rate. Novel methods for optimal metabolic regulation are also being pioneered; in order to figure out how protein expression can be optimized in time, when particular cellular objective are optimized, such as total biomass formation within some time window or period of particular environmental conditions, such as circadian rhythm.

To help the biologists evaluate the specific characteristics of these modeling approaches, we think that it is helpful for the field to have a Special Issue of Metabolites dedicated to novel computational and theoretical methods in the systems biology of metabolism.

Topics that we deem relevant for this review collections are:

1. Principles and illustrations of ME models;
2. Physicochemical constraints and optimization of whole cell models;
3. Optimality and metabolic regulation;
4. Novel theoretical results related to metabolic regulation.

Prof. Dr. Frank J. Bruggeman
Prof. Dr. Steffen Waldherr
Prof. Dr. Radhakrishnan Mahadevan
Guest Editors

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