title: Advances in network-based metabolic pathway analysis and gene expression data integration.
abstract: With the emergence of metabolic networks, novel mathematical pathway concepts were introduced in the past decade, aiming to go beyond canonical maps. However, the use of network-based pathways to interpret 'omics' data has been limited owing to the fact that their computation has, until very recently, been infeasible in large (genome-scale) metabolic networks. In this review article, we describe the progress made in the past few years in the field of network-based metabolic pathway analysis. In particular, we review in detail novel optimization techniques to compute elementary flux modes, an important pathway concept in this field. In addition, we summarize approaches for the integration of metabolic pathways with gene expression data, discussing recent advances using network-based pathway concepts.
authors.forename: Alberto
authors.initials: A
authors.lastname: Rezola
authors.forename: Jon
authors.initials: J
authors.lastname: Pey
authors.forename: Luis
authors.initials: L
authors.lastname: Tobalina
authors.forename: Ángel
authors.initials: Á
authors.lastname: Rubio
authors.forename: John E
authors.initials: JE
authors.lastname: Beasley
authors.forename: Francisco J
authors.initials: FJ
authors.lastname: Planes
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000706:statistics & numerical data; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D012984:Software
keywords: constraint-based modelling; elementary flux modes; gene expression data; genome-scale metabolic networks; network-based metabolic pathway analysis