Tutorial on DNA Computing and Graph Transformation

  • Tero Harju
  • Ion Petre
  • Grzegorz Rozenberg
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3256)


DNA computing, or more generally molecular computing, is an exciting research area at the intersection of mathematics, computer science and molecular biology. Research in DNA computing can be roughly divided in two streams: DNA computing in vitro and in vivo. The former is concerned with building (specialized) DNA-based computers in test tubes, while the latter is concerned with implementing some computational components in living cells, as well as with studying the computational processes taking place in the living cells.

In this tutorial, we shall discuss the computational nature of an intricate DNA processing taking place in single cell organisms called ciliates, in the process of gene assembly. We shall discuss the role of graph transformations in modelling and studying gene assembly process. In particular, we demonstrate that graph transformations provide a suitable level of abstraction, and useful technical tools for studying gene assembly. On the other hand, the gene assembly process inspires a new computing paradigm, computing by folding and recombination, which induces novel questions and challenges for research on graph transformation. For details, we refer to the recent monograph [1].


Graph Transformation Gene Assembly Single Cell Organism Molecular Computing Legal String 
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  1. 1.
    Ehrenfeucht, A., Harju, T., Petre, I., Prescott, D.M., Rozenberg, G.: Computation in Living Cell. In: Gene Assembly in Ciliates, xviii + 201 pages. Springer, Heidelberg (2004)Google Scholar
  2. 2.
    Ehrenfeucht, A., Prescott, D.M., Rozenberg, G.: Computational aspects of gene (un)scrambling in ciliates. In: Landwerber, L., Winfree, E. (eds.) Evolution as Computation, pp. 45–86. Springer, Heidelberg (2000)Google Scholar
  3. 3.
    Prescott, D.M., Ehrenfeucht, A., Rozenberg, G.: Molecular operations for DNA processing in hypotrichous ciliates. Europ. J. Protistology 37, 241–260 (2001)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Tero Harju
    • 1
  • Ion Petre
    • 2
  • Grzegorz Rozenberg
    • 3
  1. 1.Department of MathematicsUniversity of TurkuTurkuFinland
  2. 2.Department of Computer ScienceÅbo Academi UniversityTurkuFinland
  3. 3.Leiden Institute for Advanced Computer ScienceLeiden UniversityLeidenThe Netherlands

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