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We designed a web server for the analysis of biosynthetic capacities of metabolic networks. The implementation is based on the network expansion algorithm and the concept of scopes. For a given network and predefined external resources, called the seed metabolites, the scope is defined as the set of products which the network is in principle able to(More)
For a given metabolic network, we address the problem of determining the minimum cardinality set of substrate compounds necessary for synthesizing a set of target metabolites, called the inverse scope problem. We define three variants of the inverse scope problem whose solutions may indicate minimal nutritional requirements that must be met to ensure(More)
In many plants, starch is synthesized during the day and degraded during the night to avoid carbohydrate starvation in darkness. The circadian clock participates in a dynamic adjustment of starch turnover to changing environmental condition through unknown mechanisms. We used mathematical modelling to explore the possible scenarios for the control of starch(More)
The ability of an organism to survive depends on its capability to adapt to external conditions. In addition to metabolic versatility and efficient replication, reliable signal transduction is essential. As signaling systems are under permanent evolutionary pressure one may assume that their structure reflects certain functional properties. However, despite(More)
Methods are developed for structural analysis of metabolic networks expanding in size. Expansion proceeds in consecutive generations in which new reactions are attached to the network produced in the previous stage. Different rules are applied resulting in various modes of expansion. Expansion is performed on the set of glycolytic reactions as well as on a(More)
A vital quest in biology is comprehensible visualization and interpretation of correlation relationships on a genome scale. Such relationships may be represented in the form of networks, which usually require disassembly into smaller manageable units, or clusters, to facilitate interpretation. Several graph-clustering algorithms that may be used to(More)
We compare a large number of organisms with respect to their metabolic network functions. We measure such functions in terms of the synthesizing capacity of a network when it is provided with a few small chemical substances as external resources. We call this measure the scope and show that it is generally robust against structural alterations of the(More)
Under natural conditions, plants are exposed to rapidly changing light intensities. To acclimate to such fluctuations, plants have evolved adaptive mechanisms that optimally exploit available light energy and simultaneously minimise damage of the photosynthetic apparatus through excess light. An important mechanism is the dissipation of excess excitation(More)
Glycans comprise ubiquitous and essential biopolymers, which usually occur as highly diverse mixtures. The myriad different structures are generated by a limited number of carbohydrate-active enzymes (CAZymes), which are unusual in that they catalyze multiple reactions by being relatively unspecific with respect to substrate size. Existing experimental and(More)
The concept of scopes is applied to analyse large metabolic networks. Scopes are defined as sets of metabolites that can be synthesised by a metabolic network when it is provided with given seeds (Sets of initial metabolic compounds). Thus, scopes represent synthesising capacities of the seeds in the network. A hierarchy is discussed in the sense that(More)