Related papers: Flux networks in metabolic graphs
Networks of biochemical reactions, like cellular metabolic networks, are kept in non-equilibrium steady states by the exchange fluxes connecting them to the environment. In most cases, feasible flux configurations can be derived from…
The metabolic network plays a crucial role in regulating bacterial metabolism and growth, but it is subject to inherent molecular stochasticity. Previous studies have utilized flux balance analysis and the maximum entropy method to predict…
Identifying a small molecule from its mass spectrum is the primary open problem in computational metabolomics. This is typically cast as information retrieval: an unknown spectrum is matched against spectra predicted computationally from a…
Flows in networks (or graphs) play a significant role in numerous computer vision tasks. The scalar-valued edges in these graphs often lead to a loss of information and thereby to limitations in terms of expressiveness. For example,…
Modeling and optimization of metabolic networks has been one of the hottest topics in computational systems biology within recent years. However, the complexity and uncertainty of these networks in addition to the lack of necessary data has…
We have created a genome-scale network reconstruction of Escherichia coli metabolism. Existing reconstructions were improved in terms of annotation standards, to facilitate their subsequent use in dynamic modelling. The resultant network is…
The metabolic network of a living cell involves several hundreds or thousands of interconnected biochemical reactions. Previous research has shown that under realistic conditions only a fraction of these reactions is concurrently active in…
Systems of dynamical interactions between competing species can be used to model many complex systems, and can be mathematically described by {\em random} networks. Understanding how patterns of activity arise in such systems is important…
We investigate the distribution of flavonoids, a major category of plant secondary metabolites, across species. Flavonoids are known to show high species specificity, and were once considered as chemical markers for understanding adaptive…
Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…
Many computational chemistry and molecular simulation workflows can be expressed as graphs. This abstraction is useful to modularize and potentially reuse existing components, as well as provide parallelization and ease reproducibility.…
Bipartite graphs have received some attention in the study of social networks and of biological mutualistic systems. A generalization of a previous model is presented, that evolves the topology of the graph in order to optimally account for…
In a cell or microorganism the processes that generate mass, energy, information transfer, and cell fate specification are seamlessly integrated through a complex network of various cellular constituents and reactions. However, despite the…
Graph transformation formalisms have proven to be suitable tools for the modelling of chemical reactions. They are well established in theoretical studies and increasingly also in practical applications in chemistry. The latter is made…
Mapping network flows provides insight into the organization of networks, but even though many real-networks are bipartite, no method for mapping flows takes advantage of the bipartite structure. What do we miss by discarding this…
Metabolic pathways are fundamental maps in biochemistry that detail how molecules are transformed through various reactions. The complexity of metabolic network, where a single compound can play a part in multiple pathways, poses a…
Life and functioning of higher organisms depends on the continuous supply of metabolites to tissues and organs. What are the requirements on the transport network pervading a tissue to provide a uniform supply of nutrients, minerals, or…
As metabolomics datasets are becoming larger and more complex, there is an increasing need for model-based data integration and analysis to optimally leverage these data. Dynamical models of metabolism allow for the integration of…
As a granular material is compressed, the particles and forces within the system arrange to form complex heterogeneous structures. Force chains are a prime example and are thought to constrain bulk properties such as mechanical stability…
Gene function prediction from microarray data is a first step toward better understanding the machinery of the cell from relatively cheap and easy-to-produce data. In this paper we investigate whether the knowledge of many metabolic…