Tutorial on DNA Computing and Graph Transformation - Computational Nature of Gene Assembly in Ciliates

  • Tero Harju
  • Ion Petre
  • Grzegorz Rozenberg
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2505)


DNA computing, or more generally molecular computing, is a novel exciting area of research at the intersection of mathematics, computer science and molecular biology. The area of DNA computing studies the use of biomolecules for the purpose of computing (in vitro or in vivo). Molecular biologists assists here computer scientists in their attempt to replace or to complement the silicon-based computers by DNA-based computers. The hardware for such computations consists of biomolecules ( bioware).


Graph Transformation Gene Assembly Single Cell Organism Legal String Hypotrichous Ciliate 
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  1. 1.
    Adleman, L., Molecular Computation of Solutions to Combinatorial Problems, Science, Vol. 266, 11 November 1994, pp. 1021–1023.Google Scholar
  2. 2.
    Ehrenfeucht, A., Harju, T., Petre, I., Prescott, D. M., and Rozenberg, G., Formal systems for gene assembly in ciliates, Theoret. Comput. Sci., to appear.Google Scholar
  3. 3.
    Ehrenfeucht, A., Petre, I., Prescott, D. M., and Rozenberg, G., Universal and simple operations for gene assembly in ciliates, to appear in Words, Sequences, Languages: Where computer science, biology and linguistics come across, Mitrana, V., Martin-Vide, C. (eds.) (2000).Google Scholar
  4. 4.
    Ehrenfeucht, A., Petre, I., Prescott, D. M., and Rozenberg, G., String and graph reduction systems for gene assembly in ciliates, Math. Structures Comput. Sci. 12 (2002), 113–134.zbMATHCrossRefMathSciNetGoogle Scholar
  5. 5.
    Ehrenfeucht, A., Prescott, D. M., and Rozenberg, G., Computational aspects of gene (un)scrambling in ciliates. In Evolution as Computation, Landwerber, L., Winfree, E. (eds.), 45–86, Springer Verlag, Berlin, Heidelberg, 2000.Google Scholar
  6. 6.
    Prescott, D. M., The evolutionary scrambling and developmental unscabling of germlike genes in hypotrichous ciliates, Nucl. Acids Res. 27 (1999), 1243–1250.CrossRefGoogle Scholar
  7. 7.
    Prescott, D. M., Ehrenfeucht, A., and Rozenberg, G., Molecular operations for DNA processing in hypotrichous ciliates, European Journal of Protistology, to appear.Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2002

Authors and Affiliations

  • Tero Harju
    • 1
  • Ion Petre
    • 2
  • Grzegorz Rozenberg
    • 3
    • 4
  1. 1.Department of MathematicsUniversity of TurkuTurkuFinland
  2. 2.Department of Computer ScienceÅbo Academi UniversityTurkuFinland
  3. 3.Leiden Institute for Advanced Computer ScienceLeiden UniversityCA Leidenthe Netherlands
  4. 4.Department of Computer ScienceUniversity of Colorado at BoulderBoulderUSA

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