Dear Colleagues,

The last two decades of systems biology research have propelled the construction of large-scale models of metabolism in diverse organisms across all kingdoms of life. These models formalize the description of the entirety of characterized biochemical reactions in a biological system across different organizational scales (e.g., pathways, organelles, cell types, and interconnected organs). The development of these medium- and large-scale metabolic model backbones have been coupled with development of computational approaches that allow for inferring genotype–phenotype relationships, characterizing the effect of particular environments and cellular contexts on the traits of interest. These methodological advances go hand-in-hand with headway in technologies for high-throughput profiling of cellular components. Altogether, integrative data-driven large-scale modeling has provide the possibility to posit hypotheses about metabolic functions and to test their validity in particular scenarios.

Yet, despite these advances, there is still the need to develop methods that can provide testable predictions by integrating large-scale models with measurable read-outs (e.g., protein abundance, metabolite content). These methods should allow for augmenting the structural backbone of the metabolic models with additional information about: (i) the type of kinetic law governing the reaction rates, (ii) constraints concerning feasible parameter values for the respective kinetic, and (iii) thermodynamic feasibility of reactions. They should also be coupled with appropriate approaches for model selection based on steady-state and time-resolved data from multiple experimental scenarios. Therefore, this Special Issue of Metabolites will be dedicated to publishing current advances on medium- and large-scale metabolic network modeling that address these pressing challenges by providing case studies of hypotheses that can be tested by integration of data from modern metabolomics technologies.

Dr. Zoran Nikoloski
Dr. Georg Basler
Guest Editors

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• metabolic network
• constraint-based modeling
• reaction kinetic
• thermodynamic constraints
• model selection
• multi-view data
• regulation of reaction rates
• metabolomics data
• network robustness and plasticity

• Metabolic Network Models in Metabolites (10 articles)