Modes and cuts in metabolic networks: complexity and algorithms

Bio Systems
Vicente AcuñaLeen Stougie

Abstract

Constraint-based approaches recently brought new insight into our understanding of metabolism. By making very simple assumptions such as that the system is at steady-state and some reactions are irreversible, and without requiring kinetic parameters, general properties of the system can be derived. A central concept in this methodology is the notion of an elementary mode (EM for short) which represents a minimal functional subsystem. The computation of EMs still forms a limiting step in metabolic studies and several algorithms have been proposed to address this problem leading to increasingly faster methods. However, although a theoretical upper bound on the number of elementary modes that a network may possess has been established, surprisingly, the complexity of this problem has never been systematically studied. In this paper, we give a systematic overview of the complexity of optimisation problems related to modes. We first establish results regarding network consistency. Most consistency problems are easy, i.e., they can be solved in polynomial time. We then establish the complexity of finding and counting elementary modes. We show in particular that finding one elementary mode is easy but that this task becomes hard when ...Continue Reading

References

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Citations

Mar 12, 2013·Bio Systems·Dimitrije Jevremović, Daniel Boley
Oct 2, 2009·Bioinformatics·Luis F de FigueiredoFrancisco J Planes
Aug 19, 2011·BMC Bioinformatics·Sangaalofa T Clark, Wynand S Verwoerd
Jun 7, 2011·BMC Systems Biology·Kuhn IpDesmond S Lun
May 30, 2009·PLoS Computational Biology·Steffen KlamtFabian Theis
Jan 24, 2014·PLoS Computational Biology·Nikos VlassisThomas Sauter
Dec 26, 2015·Metabolic Engineering·Lisa Maria DerschChristoph Wittmann
Nov 8, 2011·Parallel Computing·Dimitrije JevremovićDaniel Boley
Feb 15, 2011·Bio Systems·Steffen Klamt, Axel von Kamp
Jun 16, 2010·Journal of Bioscience and Bioengineering·Quanyu Zhao, Hiroyuki Kurata
Dec 8, 2009·Bio Systems·Vicente AcuñaLeen Stougie
Jun 22, 2013·Biotechnology Journal·Jürgen ZanghelliniChristian Jungreuthmayer
Jul 11, 2012·The FEBS Journal·Juliane GebauerChristoph Kaleta
Sep 12, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Laszlo David, Alexander Bockmayr
Feb 18, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Ehsan UllahSoha Hassoun
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Nov 21, 2019·Briefings in Bioinformatics·Ehsan UllahSoha Hassoun
Dec 3, 2020·Metabolites·Francisco GuilJosé M García

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