path finding methods accounting for stoichiometry in metabolic networks路径搜索方法占了化学计量学在代谢网络.pdfVIP

Pey et al. Genome Biology 2011, 12:R49 /2011/12/5/R49 METHOD Open Access Path finding methods accounting for stoichiometry in metabolic networks 1 1 2* 1* Jon Pey , Joaquín Prada , John E Beasley and Francisco J Planes Abstract Graph-based methods have been widely used for the analysis of biological networks. Their application to metabolic networks has been much discussed, in particular noting that an important weakness in such methods is that reaction stoichiometry is neglected. In this study, we show that reaction stoichiometry can be incorporated into path-finding approaches via mixed-integer linear programming. This major advance at the modeling level results in improved prediction of topological and functional properties in metabolic networks. Background definition of connectivity is debatable, however, particu- The use of graph theory in the analysis of biological net- larly when it is claimed that such a path is a competent works has been extensive in the past decade [1]. Particu- metabolic pathway, as recently discussed [25-27]. In this larly, in metabolic networks different relevant topics context, the major criticism raised as to path-finding have been examined using the rich variety of graph-the- methods is that they neglect reaction stoichiometry and oretic concepts, ranging from topological properties there is, therefore, no guarantee that any path found can [2-5], evolutionary analysis [6-8], pathway analysis operate in sustained steady-state. [9-13], transcriptional regulation [14-16], functional The steady-state conditi