Comparison of network-based pathway analysis methods.

By Jason A. Papin, J. Stelling, Nathan D. Price, Steffen Klamt, S. Schuster, Bernhard O. Palsson. Trends in Biotechnology, 2004

397 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1116dc9cfd98b7e2dd8cdfa4e628e3ffb0f8f363

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Citations in the corpus

Robustness of Cellular Functions (2004, neutral): “son, B.O. (2004). Comparison of network-based pathway analysis”
Computational prediction of human metabolic pathways from the complete human genome (2004, methodology): “Additional methods for prediction of metabolic pathways include methods that infer 'extreme pathways' and 'elementary modes' from flux-balance models of reaction networks [29], which have been applied to the human mito-chondrion [30].”
Applications of genome-scale metabolic reconstructions (2009, background): “Another class of constraint-based approaches, termed pathway analysis methods, enables an accounting of all possible flux pathways in a given network, and have been used to examine network properties such as flexibility and variability of flux distributions”
Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods (2012, background): “Two such unbiased approaches, elementary flux mode (EFM) analysis and extreme pathway (ExPa) analysis, globally characterize allowable phenotypes and have been reviewed and compared previously 17–19 .”
Flux balance analysis of biological systems: applications and challenges (2009, methodology): “Methods such as elementary flux mode analysis [47] and extreme pathway analysis [48] have been in vogue for analysing large metabolic networks and have been reviewed elsewhere [49].”
Introduction to systems biology. (2007, background): “Most noticeably are small world organization [57, 58], modularity [59, 60], motifs [61–63], fl ux balance analysis, extreme pathway and elementary mode analysis [6, 64–67].”
Genome-scale models of bacterial metabolism: reconstruction and applications (2008, background): “These notions differ only slightly in their mathematical formulation (Klamt & Stelling, 2003; Papin et al ., 2004): the main idea is to determine the set of elementary and independent metabolic routes that can occur in the metabolic model.”