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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 M. Maniadi, Ioannis G. Tollis
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Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites
Biotechnology Journal, 2017AbstractReaction atom mappings track the positional changes of all of the atoms between the substrates and the products as they undergo the biochemical transformation. However, information on atom transitions in the context of metabolic pathways is not widely available in the literature. The understanding of metabolic pathways at the atomic level is of
Noushin, Hadadi +3 more
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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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Nature Biotechnology, 2000
A set of linear pathways often does not capture the full range of behaviors of a metabolic network. The concept of 'elementary flux modes' provides a mathematical tool to define and comprehensively describe all metabolic routes that are both stoichiometrically and thermodynamically feasible for a group of enzymes.
Schuster, Stefan +2 more
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A set of linear pathways often does not capture the full range of behaviors of a metabolic network. The concept of 'elementary flux modes' provides a mathematical tool to define and comprehensively describe all metabolic routes that are both stoichiometrically and thermodynamically feasible for a group of enzymes.
Schuster, Stefan +2 more
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METABOLIC PATHWAY ALIGNMENT (M-PAL) REVEALS DIVERSITY AND ALTERNATIVES IN CONSERVED NETWORKS
Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 2007We introduce a comparative analysis of metabolic reaction networks between different species. Our method systematically investigates full metabolic networks of multiple species at the same time, with the goal of identifying highly similar yet non-identical pathways which execute the same metabolic function, i.e.
YUNLEI LI +3 more
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Design of Pathway-Level Bioprocess Monitoring and Control Strategies Supported by Metabolic Networks
2012In this chapter we explore the basic tools for the design of bioprocess monitoring, optimization, and control algorithms that incorporate a priori knowledge of metabolic networks. The main advantage is that this ultimately enables the targeting of intracellular control variables such as metabolic reactions or metabolic pathways directly linked with ...
Inês A, Isidro +5 more
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Visualising Metabolic Pathways and Networks: Past, Present, Future
2021Falk Schreiber +3 more
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Bile acids and the gut microbiota: metabolic interactions and impacts on disease
Nature Reviews Microbiology, 2022Stephanie Collins, Andrew D Patterson
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