title: Direct calculation of minimal cut sets involving a specific reaction knock-out.
abstract: The concept of Minimal Cut Sets (MCSs) is used in metabolic network modeling to describe minimal groups of reactions or genes whose simultaneous deletion eliminates the capability of the network to perform a specific task. Previous work showed that MCSs where closely related to Elementary Flux Modes (EFMs) in a particular dual problem, opening up the possibility to use the tools developed for computing EFMs to compute MCSs. Until recently, however, there existed no method to compute an EFM with some specific characteristic, meaning that, in the case of MCSs, the only strategy to obtain them was to enumerate them using, for example, the standard K-shortest EFMs algorithm.
  
  
  
  In this work, we adapt the recently developed theory to compute EFMs satisfying several constraints to the calculation of MCSs involving a specific reaction knock-out. Importantly, we emphasize that not all the EFMs in the dual problem correspond to real MCSs, and propose a new formulation capable of correctly identifying the MCS wanted. Furthermore, this formulation brings interesting insights about the relationship between the primal and the dual problem of the MCS computation.
  
  
  
  A Matlab-Cplex implementation of the proposed algorithm is available as a supplementary material
  
  
  
  fplanes@ceit.es
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: CEIT and Tecnun, University of Navarra, San Sebastián 20018, Spain.
authors.forename: Luis
authors.initials: L
authors.lastname: Tobalina
authors.affiliation: CEIT and Tecnun, University of Navarra, San Sebastián 20018, Spain.
authors.forename: Jon
authors.initials: J
authors.lastname: Pey
authors.affiliation: CEIT and Tecnun, University of Navarra, San Sebastián 20018, Spain.
authors.forename: Francisco J
authors.initials: FJ
authors.lastname: Planes
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D004926:Escherichia coli / Q000378:metabolism; D006801:Humans; D064688:Metabolic Flux Analysis / Q000379:methods*; D053858:Metabolic Networks and Pathways