On the representativeness and stability of a set of EFMs

Guil Asensio, Francisco; Hidalgo Céspedes, José Francisco; García Carrasco, José Manuel

Publication:
On the representativeness and stability of a set of EFMs

dc.contributor.author	Guil Asensio, Francisco
dc.contributor.author	Hidalgo Céspedes, José Francisco
dc.contributor.author	García Carrasco, José Manuel
dc.contributor.department	Ingeniería y Tecnología de Computadores
dc.date.accessioned	2024-02-08T12:17:35Z
dc.date.available	2024-02-08T12:17:35Z
dc.date.issued	2023-05-30
dc.description	©2023. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/ This document is the Published, version of a Published Work that appeared in final form in Bioinformatics. To access the final edited and published work see https://doi.org/10.1093/bioinformatics/btad356	es
dc.description.abstract	Motivation: Elementary flux modes are a well-known tool for analyzing metabolic networks. The whole set of elementary flux modes (EFMs) cannot be computed in most genome-scale networks due to their large cardinality. Therefore, different methods have been proposed to compute a smaller subset of EFMs that can be used for studying the structure of the network. These latter methods pose the problem of studying the representativeness of the calculated subset. In this article, we present a methodology to tackle this problem. Results: We have introduced the concept of stability for a particular network parameter and its relation to the representativeness of the EFM extraction method studied. We have also defined several metrics to study and compare the EFM biases. We have applied these techniques to compare the relative behavior of previously proposed methods in two case studies. Furthermore, we have presented a new method for the EFM computation (PiEFM), which is more stable (less biased) than previous ones, has suitable representativeness measures, and exhibits better variability in the extracted EFMs	es
dc.format	application/pdf	es
dc.format.extent	10	es
dc.identifier.citation	Bioinformatics, 2023, 39(6), btad356
dc.identifier.doi	https://doi.org/10.1093/bioinformatics/btad356
dc.identifier.issn	1367-4811
dc.identifier.uri	http://hdl.handle.net/10201/139003
dc.language	eng	es
dc.publisher	Oxford Academic	es
dc.relation	This work has been partially funded by the AEI (State Research Agency, Spain), and the ERDF (European Regional Development Fund, EU) under the Contract No. RTI2018-098156-B-C53. Additionally, this work has been partially funded by Campus de Excelencia Internacional de Ambito Regional (CEIR) Campus Mare Nostrum (CMN).	es
dc.rights	info:eu-repo/semantics/openAccess	es
dc.rights	Attribution-NonCommercial-NoDerivatives 4.0 Internacional	*
dc.rights.uri	http://creativecommons.org/licenses/by-nc-nd/4.0/	*
dc.title	On the representativeness and stability of a set of EFMs	es
dc.type	info:eu-repo/semantics/article	es
dspace.entity.type	Publication	es