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Analysis of the pathway structure of metabolic networks
Journal of Biotechnology, 1999Metabolic networks comprise a multitude of enzymatic reactions carrying out various functions related to cell growth and product formation. Although such reactions are occasionally organized into biochemical pathways, a formal procedure is desired to identify the independent pathways in a bioreaction network and the degree of engagement of each ...
Brian D. Follstad +2 more
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Metabolite-Enzyme Coevolution: From Single Enzymes to Metabolic Pathways and Networks.
Annual Review of Biochemistry, 2018How individual enzymes evolved is relatively well understood. However, individual enzymes rarely confer a physiological advantage on their own. Judging by its current state, the emergence of metabolism seemingly demanded the simultaneous emergence of ...
Lianet Noda-García +2 more
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Neural Networks for Modeling Metabolic Pathways
2021Metabolic pathways are enzyme-catalyzed reactions that can be described by the Michaelis-Menten equation. The inherent problem with Michaelis-Menten kinetics is that the model is not reversible. Reverse catalysis, which is common in metabolic pathways, can be better described by Cell Communication Protocol© which offers a Self-Organizing Map (SOM) for ...
Christoph Gille +7 more
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Fluxes through plant metabolic networks: measurements, predictions, insights and challenges.
Biochemical Journal, 2015Although the flows of material through metabolic networks are central to cell function, they are not easy to measure other than at the level of inputs and outputs.
N. Kruger, R. Ratcliffe
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From Metabolic Reactions to Networks and Pathways
2011Enzymatic reactions form a hypergraph structure and their translation into a graph structure accompanies an information loss. This chapter introduces well-known topological transformations from metabolic reactions to a graph, and discusses their advantages and disadvantages. Also discussed is the legitimacy of defining cofactors or currency metabolites,
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Finding Feasible Pathways in Metabolic Networks
2005Recent small-world studies of the global structure of metabolic networks have been based on the shortest-path distance. In this paper, we propose new distance measures that are based on the structure of feasible metabolic pathways between metabolites.
Juho Rousu +3 more
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Parallel extreme pathway computation for metabolic networks
Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004., 2004We parallelized the serial extreme pathways algorithm presented by Schilling et al., in J. Theor. Biol. 203 (2000) using the message passing interface (MPI). The parallel algorithm exhibits super-linear scalability because the number of independence tests performed decreases as the number of MPI nodes increases.
J. Varner, Kwok Ko, Lie-Quan Lee
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Green pathways: Metabolic network analysis of plant systems
Metabolic Engineering, 2016Metabolic engineering of plants with enhanced crop yield and value-added compositional traits is particularly challenging as they probably exhibit the highest metabolic network complexity of all living organisms. Therefore, approaches of plant metabolic network analysis, which can provide systems-level understanding of plant physiology, appear valuable
Lisa Maria Dersch +2 more
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Gene Networks Validation based on Metabolic Pathways
2011 IEEE 11th International Conference on Bioinformatics and Bioengineering, 2011In the last few years, DNA microarray technology has attained a very important role in biological and biomedical research. It enables analyzing the relations among thousands of genes simultaneously, generating huge amounts of data. The gene networks represent, in a graph data structure, genes or gene products and the functional relationships between ...
Norberto Díaz-Díaz +2 more
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Combinatorial complexity of pathway analysis in metabolic networks.
Molecular biology reports, 2002Elementary flux mode analysis is a promising approach for a pathway-oriented perspective of metabolic networks. However, in larger networks it is hampered by the combinatorial explosion of possible routes. In this work we give some estimations on the combinatorial complexity including theoretical upper bounds for the number of elementary flux modes in ...
Jörg Stelling, Steffen Klamt
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