TY - JOUR
T1 - Metabolic pathways in the post-genome era
AU - Papin, Jason A.
AU - Price, Nathan D.
AU - Wiback, Sharon J.
AU - Fell, David A.
AU - Palsson, Bernhard O.
N1 - Funding Information:
We acknowledge the support of the National Science Foundation (BES 01–20363), the National Institutes of Health (GM 57089) and the Whitaker Foundation (Graduate Research Fellowship to JP). We also thank Timothy Allen, Derren Barken, Natalie Duarte, Steve Fong and Thuy Vo for critical readings of the article.
PY - 2003/5/1
Y1 - 2003/5/1
N2 - Metabolic pathways are a central paradigm in biology. Historically, they have been defined on the basis of their step-by-step discovery. However, the genome-scale metabolic networks now being reconstructed from annotation of genome sequences demand new network-based definitions of pathways to facilitate analysis of their capabilities and functions, such as metabolic versatility and robustness, and optimal growth rates. This demand has led to the development of a new mathematically based analysis of complex, metabolic networks that enumerates all their unique pathways that take into account all requirements for cofactors and byproducts. Applications include the design of engineered biological systems, the generation of testable hypotheses regarding network structure and function, and the elucidation of properties that can not be described by simple descriptions of individual components (such as product yield, network robustness, correlated reactions and predictions of minimal media). Recently, these properties have also been studied in genome-scale networks. Thus, network-based pathways are emerging as an important paradigm for analysis of biological systems.
AB - Metabolic pathways are a central paradigm in biology. Historically, they have been defined on the basis of their step-by-step discovery. However, the genome-scale metabolic networks now being reconstructed from annotation of genome sequences demand new network-based definitions of pathways to facilitate analysis of their capabilities and functions, such as metabolic versatility and robustness, and optimal growth rates. This demand has led to the development of a new mathematically based analysis of complex, metabolic networks that enumerates all their unique pathways that take into account all requirements for cofactors and byproducts. Applications include the design of engineered biological systems, the generation of testable hypotheses regarding network structure and function, and the elucidation of properties that can not be described by simple descriptions of individual components (such as product yield, network robustness, correlated reactions and predictions of minimal media). Recently, these properties have also been studied in genome-scale networks. Thus, network-based pathways are emerging as an important paradigm for analysis of biological systems.
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U2 - 10.1016/S0968-0004(03)00064-1
DO - 10.1016/S0968-0004(03)00064-1
M3 - Review article
C2 - 12765837
AN - SCOPUS:0037727678
SN - 0968-0004
VL - 28
SP - 250
EP - 258
JO - Trends in biochemical sciences
JF - Trends in biochemical sciences
IS - 5
ER -