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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)
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)
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)
A major challenge in systems biology is to understand how complex and highly connected metabolic networks are organized. The structure of these networks is investigated here by identifying sets of metabolites that have a similar biosynthetic potential. We measure the biosynthetic potential of a particular compound by determining all metabolites than can be(More)
Non-linear correlations based on mutual information are evaluated to measure statistical dependencies among data points measured from metabolism in two dimensional space. While the Pearson correlation coefficient is only rigorously applicable to characterize strictly linear correlations with Gaussian noise, the mutual information coefficient is more(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)
MOTIVATION Network-centered studies in systems biology attempt to integrate the topological properties of biological networks with experimental data in order to make predictions and posit hypotheses. For any topology-based prediction, it is necessary to first assess the significance of the analyzed property in a biologically meaningful context. Therefore,(More)
Cooperation between organisms of different species is a widely observed phenomenon in biology, ranging from large scale systems such as whole ecosystems to more direct interactions like symbiotic relationships. In the present work, we explore inter-species cooperations on the level of metabolic networks. For our analysis, we extract 447 organism specific(More)