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Mod/Resc Parsimony Inference

  • Igor Nor
  • Danny Hermelin
  • Sylvain Charlat
  • Jan Engelstadter
  • Max Reuter
  • Olivier Duron
  • Marie-France Sagot
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6129)

Abstract

We address in this paper a new computational biology problem that aims at understanding a mechanism that could potentially be used to genetically manipulate natural insect populations infected by inherited, intra-cellular parasitic bacteria. In this problem, that we denote by Mod/Resc Parsimony Inference, we are given a boolean matrix and the goal is to find two other boolean matrices with a minimum number of columns such that an appropriately defined operation on these matrices gives back the input. We show that this is formally equivalent to the Bipartite Biclique Edge Cover problem and derive some complexity results for our problem using this equivalence. We provide a new, fixed-parameter tractability approach for solving both that slightly improves upon a previously published algorithm for the Bipartite Biclique Edge Cover. Finally, we present experimental results where we applied some of our techniques to a real-life data set.

Keywords

Computational biology biclique edge covering bipartite graph boolean matrix NP-completeness graph theory fixed-parameter tractability kernelization 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Igor Nor
    • 1
    • 2
  • Danny Hermelin
    • 3
  • Sylvain Charlat
    • 1
  • Jan Engelstadter
    • 4
  • Max Reuter
    • 5
  • Olivier Duron
    • 6
  • Marie-France Sagot
    • 1
    • 2
  1. 1.Université de Lyon, F-69000, Lyon, Université Lyon 1, CNRS, UMR5558 
  2. 2.Bamboo TeamINRIA Grenoble Rhône-AlpesFrance
  3. 3.Max Planck Institute for InformaticsSaarbrückenGermany
  4. 4.Institute of Integrative BiologyETH ZurichSwitzerland
  5. 5.University College LondonUK
  6. 6.Institute of Evolutionary SciencesCNRS - University of Montpellier IIFrance

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