Formal systems for gene assembly in ciliates

Theoretical Computer Science

Volumn 292, Issue 1, 2003, Pages 199-219

  Ehrenfeucht, Andrzej ^a   Harju, Tero ^b   Petre, Ion ^b,c   Prescott, David M ^d   Rozenberg, Grzegorz ^a,e  

^a University of Colorado at Boulder   (United States)

^b UNIVERSITY OF TURKU   (Finland)

^c TURKU CENTRE FOR COMPUTER SCIENCE   (Finland)

^d UNIVERSITY OF COLORADO   (United States)

^e LEIDEN UNIVERSITY   (Netherlands)

Author keywords

Ciliates; DNA computing; Gene assembly; Graph rewriting; Overlap graphs; Reduction systems; String rewriting

Indexed keywords

COMPUTATIONAL METHODS; DATA STRUCTURES; DNA; GENES; GRAPH THEORY;

STRING REWRITING;

COMPUTER SCIENCE;

EID: 0037427767     PISSN: 03043975     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0304-3975(01)00223-7     Document Type: Article

References (13)

1. Bouchet A. Graphic presentations of isotropic systems. J. Combin. Theory Ser B. 45:1988;58-76.
2. Bouchet A. Circle graph obstructions. J. Combin. Theory Ser B. 60:1994;107-144.
3. Condon A., Rozenberg G. Proc. 6th Internat. Meeting on DNA Based Computers, Lecture Notes in Computer Science. 2000;Springer, Berlin.
4. Ehrenfeucht A., Petre I., Prescott D.M., Rozenberg G. Universal and simple operations for gene assembly in ciliates. Martin-Vide C., Mitrana V. Where Mathematics, Computer Science, Linguistics and Biology Meet. 2001;329-342 Kluwer Academic Publishers, Dordrecht/Boston.
5. A. Ehrenfeucht, I. Petre, D.M. Prescott, G. Rozenberg, String and graph reduction systems for gene assembly in ciliates, to appear in Math. Struct. in Comput. Sci., 2001.
6. Ehrenfeucht A., Prescott D.M., Rozenberg G. Computational aspects of gene (un)scrambling in ciliates. Landweber L., Winfree E. Evolution as Computation. 2000;45-86 Springer, Berlin.
7. Gasse E. A proof of a circle graph characterization. Discrete Math. 173:1997;277-283.
8. Golumbic M.C. Algorithmic Graph Theory and Perfect Graphs. 1980;Academic Press, New York.
9. L.F. Landweber, L. Kari, The evolution of cellular computing: nature's solution to a computational problem, Proc. 4th DIMACS Meeting on DNA Based Computers, Philadelphia, 1998, pp. 3-15.
10. L.F. Landweber, L. Kari, Universal molecular computation in ciliates, in: L. Landweber, E. Winfree, (Eds.), Evolution as Computation, Springer Verlag. Berlin, Heidelberg, to appear, 2001.
11. Paun G., Rozenberg G., Salomaa A. DNA Computing. 1998;Springer, Berlin.
12. D.M. Prescott, A. Ehrenfeucht, G. Rozenberg, Molecular operations for DNA processing in hypotrichous ciliates, Manuscript, 1999.
13. W.D. Smith, DNA computers in vitro and vivo, Proc. 1st DIMACS Meeting on DNA Based Computers, Princeton, 1995, pp. 121-186.