Detalle Publicación


TreeEFM: calculating elementary flux modes using linear optimization in a tree-based algorithm

Autores: Pey Pérez, Jon; Villar, J.; Tobalina, L.; Rezola Urquía, Alberto; Garcia, J.; Beasley, J.; Planes Pedreño, Francisco Javier
Título de la revista: BIOINFORMATICS
ISSN: 1367-4803
Volumen: 31
Número: 6
Páginas: 897 - 904
Fecha de publicación: 2015
Motivation: Elementary flux modes (EFMs) analysis constitutes a fundamental tool in systems biology. However, the efficient calculation of EFMs in genome-scale metabolic networks (GSMNs) is still a challenge. We present a novel algorithm that uses a linear programming-based tree search and efficiently enumerates a subset of EFMs in GSMNs. Results: Our approach is compared with the EFMEvolver approach, demonstrating a significant improvement in computation time. We also validate the usefulness of our new approach by studying the acetate overflow metabolism in the Escherichia coli bacteria. To do so, we computed 1 million EFMs for each energetic amino acid and then analysed the relevance of each energetic amino acid based on gene/protein expression data and the obtained EFMs. We found good agreement between previous experiments and the conclusions reached using EFMs. Finally, we also analysed the performance of our approach when applied to large GSMNs.