Shrinking the Metabolic Solution Space Using Experimental Datasets

Shrinking the Metabolic Solution Space Using Experimental Datasets

Constraint-based models of metabolism have been used in a variety of studies on drug discovery, metabolic engineering, evolution, and multi-species interactions. These genome-scale models can be generated for any sequenced organism since their main parameters (i.e., reaction stoichiometry) are highly conserved. Their relatively low parameter requirement makes these models easy to develop; howev...

Shrinking the Search Space for Clustered Planarity

A clustered graph is a graph augmented with a hierarchical inclusion structure over its vertices, and arises very naturally in multiple application areas. While it is long known that planarity—i.e., drawability without edge crossings—of graphs can be tested in polynomial (linear) time, the complexity for the clustered case is still unknown. In this paper, we present a new graph theoretic reduct...

The solution space of metabolic networks: producibility, robustness and fluctuations

Flux analysis is a class of constraint-based approaches to the study of biochemical reaction networks: they are based on determining the reaction flux configurations compatible with given stoichiometric and thermodynamic constraints. One of its main areas of application is the study of cellular metabolic networks. We briefly and selectively review the main approaches to this problem and then, b...

Experimental Datasets

Physiologically Shrinking the Solution Space of a Saccharomyces cerevisiae Genome-Scale Model Suggests the Role of the Metabolic Network in Shaping Gene Expression Noise

Sampling the solution space of genome-scale models is generally conducted to determine the feasible region for metabolic flux distribution. Because the region for actual metabolic states resides only in a small fraction of the entire space, it is necessary to shrink the solution space to improve the predictive power of a model. A common strategy is to constrain models by integrating extra datas...