The Maximum Similarity Partitioning Problem and its Application in the Transcriptome Reconstruction and Quantification Problem

  • Alex Z. ZaccaronEmail author
  • Said S. Adi
  • Carlos H. A. Higa
  • Eloi Araujo
  • Burton H. Bluhm
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9155)


Reconstruct and quantify the RNA molecules in a cell at a given moment is an important problem in molecular biology that allows one to know which genes are being expressed and at which intensity level. Such problem is known as Transcriptome Reconstruction and Quantification Problem (TRQP). Although several approaches were already designed that solve the TRQP, none of them model it as a combinatorial optimization problem. In order to narrow this gap, we present here a new combinatorial optimization problem called Maximum Similarity Partitioning Problem (MSPP) that models the TRQP. In addition, we prove that the MSPP is NP-complete in the strong sense and present a greedy heuristic for it.


Partition Similarity Transcriptome Reconstruction and quantification 


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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Alex Z. Zaccaron
    • 1
    Email author
  • Said S. Adi
    • 1
  • Carlos H. A. Higa
    • 1
  • Eloi Araujo
    • 1
  • Burton H. Bluhm
    • 2
  1. 1.Faculdade de ComputaçãoUniversidade Federal de Mato Grosso do SulCampo GrandeBrazil
  2. 2.Plant Pathology DepartmentUniversity of ArkansasFayettevilleUSA

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