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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 ...
T W, Simpson +2 more
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Pathway knockout and redundancy in metabolic networks
Journal of Theoretical Biology, 2011The robustness and stability of complex cellular networks is often attributed to the redundancy of components, including genes, enzymes and pathways. Estimation of redundancy is still an open question in systems biology. Current theoretical tools to measure redundancy have various strengths and shortcomings in providing a comprehensive description of ...
Yong, Min +5 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 ...
Klamt, S. ; https://orcid.org/0000-0003-2563-7561 +1 more
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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.
Esa Pitkänen +3 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 ...
Meir Israelowitz +7 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 ...
Francisco Gómez-Vela +2 more
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Predicting Metabolic Pathways by Sub-network Extraction
2011Various methods result in groups of functionally related genes obtained from genomes (operons, regulons, syntheny groups, and phylogenetic profiles), transcriptomes (co-expression groups) and proteomes (modules of interacting proteins). When such groups contain two or more enzyme-coding genes, graph analysis methods can be applied to extract a ...
Faust, Karoline, van Helden, Jacques
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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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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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Analysis and visualization of metabolic pathways and networks: A hypegraph approach
IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI), 2014Metabolic pathways are series of chemical reactions occurring in a cell. Various graph-based models are used to represent metabolic data. However, diverse problems may arise from adopting these models. A more accurate modeling framework can be offered by hypergraphs.
Evaggelia Maniadi, Ioannis G. Tollis
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