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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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Homomorphisms of Multisource Trees into Networks with Applications to Metabolic Pathways
2007 IEEE 7th International Symposium on BioInformatics and BioEngineering, 2007Network mapping is a convenient tool for comparing and exploring biological networks; it can be used for predicting unknown pathways, fast and meaningful searching of databases, and potentially establishing evolutionary relations. Unfortunately, existing tools for mapping paths into general networks (PathBlast) or trees into tree networks allowing gaps
Qiong Cheng +2 more
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Text Mining for Metabolic Pathways, Signaling Cascades, and Protein Networks
Science's STKE, 2005The complexity of the information stored in databases and publications on metabolic and signaling pathways, the high throughput of experimental data, and the growing number of publications make it imperative to provide systems to help the researcher navigate through these interrelated information resources.
Hoffmann, Robert +5 more
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Biotechnology and Bioengineering, 2004
AbstractCentral carbon metabolism of the yeast Saccharomyces cerevisiae was analyzed using metabolic pathway analysis tools. Elementary flux modes for three substrates (glucose, galactose, and ethanol) were determined using the catabolic reactions occurring in yeast.
Tunahan, Cakir +2 more
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AbstractCentral carbon metabolism of the yeast Saccharomyces cerevisiae was analyzed using metabolic pathway analysis tools. Elementary flux modes for three substrates (glucose, galactose, and ethanol) were determined using the catabolic reactions occurring in yeast.
Tunahan, Cakir +2 more
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gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota
Nature Biotechnology, 2023Victoria Pascal Andreu +2 more
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