title: Identification of metabolic pathways using pathfinding approaches: a systematic review.
abstract: Metabolic pathways have become increasingly available for various microorganisms. Such pathways have spurred the development of a wide array of computational tools, in particular, mathematical pathfinding approaches. This article can facilitate the understanding of computational analysis of metabolic pathways in genomics. Moreover, stoichiometric and pathfinding approaches in metabolic pathway analysis are discussed. Three major types of studies are elaborated: stoichiometric identification models, pathway-based graph analysis and pathfinding approaches in cellular metabolism. Furthermore, evaluation of the outcomes of the pathways with mathematical benchmarking metrics is provided. This review would lead to better comprehension of metabolism behaviors in living cells, in terms of computed pathfinding approaches.
authors.affiliation: MaGIC-X (Media and Games Innovation Centre of Excellence), UTM-IRDA Digital Media Centre, Universiti Teknologi Malaysia, Johor Bahru, Malaysia.
authors.forename: Zeyad
authors.initials: Z
authors.lastname: Abd Algfoor
authors.affiliation: MaGIC-X (Media and Games Innovation Centre of Excellence), UTM-IRDA Digital Media Centre, Universiti Teknologi Malaysia, Johor Bahru, Malaysia.
authors.forename: Mohd
authors.initials: M
authors.lastname: Shahrizal Sunar
authors.affiliation: Boston University School of Medicine, Boston Medical Center, Boston, MA, USA.|Duke Global Health Institute, Duke University, Durham, NC, USA.|Global Health Program, Duke Kunshan University, Jiangsu, China.
authors.forename: Afnizanfaizal
authors.initials: A
authors.lastname: Abdullah
authors.affiliation: Department of Computer Science, Liverpool John Moores University, Liverpool, UK.
authors.forename: Hoshang
authors.initials: H
authors.lastname: Kolivand
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D053858:Metabolic Networks and Pathways; D008962:Models, Theoretical; D015398:Signal Transduction; D012984:Software
keywords: graph methods; identification; metabolic pathways; pathfinding algorithms; stoichiometric approaches