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Enumerating Chemical Organisations in Consistent Metabolic Networks: Complexity and Algorithms

  • Paulo Vieira Milreu
  • Vicente Acuña
  • Etienne Birmelé
  • Pierluigi Crescenzi
  • Alberto Marchetti-Spaccamela
  • Marie-France Sagot
  • Leen Stougie
  • Vincent Lacroix
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6293)

Abstract

The structural analysis of metabolic networks aims both at understanding the function and the evolution of metabolism. While it is commonly admitted that metabolism is modular, the identification of metabolic modules remains an open topic. Several definitions of what is a module have been proposed. We focus here on the notion of chemical organisations, i.e. sets of molecules which are closed and self-maintaining. We show that finding a reactive organisation is NP-hard even if the network is flux-consistent and that the hardness comes from blocking cycles. We then propose new algorithms for enumerating chemical organisations that are theoretically more efficient than existing approaches.

Keywords

Directed Graph Metabolic Network Elementary Mode Directed Cycle White Vertex 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Paulo Vieira Milreu
    • 1
    • 2
  • Vicente Acuña
    • 1
    • 2
  • Etienne Birmelé
    • 3
  • Pierluigi Crescenzi
    • 4
  • Alberto Marchetti-Spaccamela
    • 5
  • Marie-France Sagot
    • 1
    • 2
  • Leen Stougie
    • 6
  • Vincent Lacroix
    • 1
    • 2
  1. 1.Laboratoire de Biométrie et Biologie EvolutiveUniversité de Lyon, F-69000 Lyon, Université Lyon 1, CNRS, UMR5558VilleurbanneFrance
  2. 2.INRIA Rhône-AlpesMontbonnot Saint-MartinFrance
  3. 3.Lab. Statistique et Génome, CNRS UMR8071 INRA1152Université d’ÉvryFrance
  4. 4.Dipartimento di Sistemi e InformaticaUniversità di FirenzeFirenzeItaly
  5. 5.Sapienza University of RomeItaly
  6. 6.VU University and CWIAmsterdamThe Netherlands

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