A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks

By S. Schuster, David A. Fell, Thomas Dandekar. Nature Biotechnology, 2000

1,003 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/62ad844617809a7fe8e5dbe99a3524745ad0365a

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In Materials Chemistry

In Molecular Biology

Citations in the corpus

A methodology for the structural and functional analysis of signaling and regulatory networks (2006, methodology): “Therefore, it may seem reasonable to compute elementary modes, which typically represent pathways in reaction networks with mass flow [25].”
Structural and functional analysis of cellular networks with CellNetAnalyzer (2007, neutral): “In particular EM analysis has become a standard tool in metabolic network analysis [14,5].”
Functional cartography of complex metabolic networks (2005, background): “have reported on the impossibility of obtaining elementary flux mode”
Exploring the diversity of complex metabolic networks (2005, neutral): “Computational approaches for this problem involve the use of artificial intelligence methods (Mavrovouniotis et al., 1992), stoichiometric analysis (Price et al., 2003; Schuster et al., 2000) and graph network analysis (Arita, 2000; Jeong et al., 2000).”
Minimal cut sets in biochemical reaction networks (2004, methodology): “This check is analogous to the one used for calculating elementary modes (cf. Schuster et al., 2000).”
Using graph theory to analyze biological networks (2011, methodology): “Methods to detect such motifs have been applied on network pathways analysis [44,45,47,48], one example being flux mode analysis [48].”
Flux coupling analysis of genome-scale metabolic network reconstructions. (2004, methodology): “Following this spirit, several frameworks for examining structural and topological network properties based on convex analysis have been developed and demonstrated for small-scale metabolic representations (∼100 reactions) to identify extreme pathways (Schilling et al. 2000) or elementary modes (Sch”
Analyzing and modeling real-world phenomena with complex networks: a survey of applications (2007, background): “The structures of a metabolic network are organized in a modular, hierarchical fashion [385].”
Evolutionary programming as a platform for in silico metabolic engineering (2005, background): “Because of the large number of reactions occurring in cellular metabolism, the dimensions of the solution space (or the number of feasible metabolic phenotypes) defined by genome-scale models [10,11] is very large.”
Use of network analysis of metabolic systems in bioengineering (2002, methodology): “pdf, where several errata in [34] have been corrected).”
Metabolomics – the link between genotypes and phenotypes (2004, background): “In a series of related papers, Pfeiffer et al. (1999), Schuster (1999) and Schuster et al. (1999, 2000) described the concept of elementary flux mode.”