TY - JOUR 
A1 - Hidalgo Céspedes, José Francisco
AU - Egea Larrosa, José Alberto
AU - Guil Asensio, Francisco de Asís
AU - García Carrasco, José Manuel
T1 - Improving the EFMs quality by augmenting their representativeness in LP methods
Y1 - 2018
SN - 1752-0509
UR - http://hdl.handle.net/10317/7776
AB - Background
Although cellular metabolism has been widely studied, its fully comprehension is still a challenge. A main tool for this study is the analysis of meaningful pieces of knowledge called modes and, in particular, specially interesting classes of modes such as pathways and Elementary Flux Modes (EFMs). Its study often has to deal with issues such as the appearance of infeasibilities or the difficulty of finding representative enough sets of modes that are free of repetitions. Mode extraction methods usually incorporate strategies devoted to mitigate this phenomena but they still get a high ratio of repetitions in the set of solutions.

Results
This paper presents a proposal to improve the representativeness of the full set of metabolic reactions in the set of computed modes by penalizing the eventual high frequency of occurrence of some reactions during the extraction. This strategy can be applied to any linear programming based extraction existent method.

Conclusions
Our strategy enhances the quality of a set of extracted EFMs favouring the presence of every reaction in it and improving the efficiency by mitigating the occurrence of repeated solutions. The new proposed strategy can complement other EFMs extraction methods based on linear programming. The obtained solutions are more likely to be diverse using less computing effort and improving the efficiency of the extraction.
KW - Matemática Aplicada
KW - Metabolic networks
KW - Pathways and EFMs
KW - Representativeness and quality
KW - Flux modes
KW - Linear programming
KW - Systems biology
KW - 12 Matemáticas
LA - eng
PB - BMC
ER -