Evaluating the different combinatorial constraints in DNA computing based on minimum free energy

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Volumn 65, Issue 2, 2011, Pages 291-308

  Zhang, Qiang ^a   Wang, Bin ^a,b   Wei, Xiaopeng ^a,b  

^a DALIAN UNIVERSITY   (China)

^b DALIAN UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79959620911     PISSN: 03406253     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (36)

1. L. Adleman, Molecular computation of solution to combinatorial problems, Science 266 (1994) 1021-1024. (Pubitemid 24373714)
2. C. T. Celland, V. Risca, C. Bancroft, Hiding messages in DNA microdots, Nature 399 (1999) 533-534. (Pubitemid 129623051)
3. A. Dietrich, W. Been, Memory and DNA, J. Theor. Biol. 208 (2001) 145-149. (Pubitemid 32099417)
4. E. B. Baum, DNA sequences useful for computation, Proceedings of 2nd DIMACS Workshop on DNA Based Computers 1996, pp. 122-127.
5. R. Deaton, R. C. Murphy, J. A. Rose, M. Garzón, D. R. Franceschetti, S. E. Jr. Stevens, A DNA based implementation of an evolutionary search for good encodings for DNA computation, Proceedings of the 1997 IEEE International Conference on Evolutionary Computation, 1997, pp. 267-272.
6. R. Deaton, Franceschetti, M. Garzón, A. J. Rose, R. C. Murphy, S. E. J. Stevens, Information transfer through hybridization reaction in DNA based computing, Proceedings of the Second Annual Conference, California, 1997, pp. 463-471.
7. D. H. Wood, Applying error correcting codes to DNA computing, 4th DIMACS workshop on DNA based computers, Pennsylvania, 1998, pp. 109-110.
8. A. J. Hartemink, D. K. Gifford, Thermodynamics simulation of deoxyoligonucleotide hybridize for DNA computation, 3rd DIMACS meeting on DNA based computers, Pennsylvania, 1997, pp. 23-25.
9. A. Hartemink, D. K. Gifford, J. Khodor, Automated constraint-based nucleotide sequence selection for DNA computation, 4th DIMACS workshop on DNA based computers, Pennsylvania, 1998, pp. 287-297.
10. S. Y. Shin, D. Min, Evolutionary sequence generation for reliable DNA computing, Evolutionary Computation, 2002. CEC'02. Proceedings of the 2002 Congress on.
11. S. Y. Shin, I. H. Lee, D. Kim, B. T. Zhang, Multi-objective evolutionary optimization of DNA sequences for reliable DNA computing, IEEE Transac. Evolution. Comput. 9 (2005) 143-158. (Pubitemid 40573248)
12. W. B. Liu, S. D. Wang, L. Gao J. Xu, DNA sequence design based on template strategy, J. Chem. Inf. Comput. Sci.43 (2003) 2014-2018.
13. B. Wang, Q. Zhang, R. Zhang, Design of DNA sequence based on improved genetic algorithm, Lecture Notes in Computer Science LNCS 5226, 2008, pp. 9-14.
14. X. C. Zhang, Y. F. Wang, G. Z. Cui, Y. Niu, J. Xu, Application of a novel IWO to the design of encoding sequences for DNA computing, Comput. Math. Appl. 57(2009)2001-2008.
15. R. Zhang, Q. Zhang, B. Wang, Improved particle swarm optimization algorithm for designing DNA codewords, Inter. Interdise. J. 12 (2009) 497-505.
16. A. Marathe, A. Condon, R. Com, On combinatorial DNA word design, J. Comput. Biol. 18 (2001) 201-220.
17. T. G. Bogdanova, A. E. Brouwer, S. N. Kapralov, P. R. J. Ostergard, Error-correcting codes over an alphabet of four elements, Des. Cod. Crypt. 23 (2001)333-342.
18. B. Paolo, L. Anne, M. Vincenzo, M. Victor, Superposition based on Watson-Crick-like complementarity, Theor. Comput. Sys. 39 (2006) 503-524.
19. D. C. Tulpan, H. Hoos, A. Condon, Stochastic local search algorithms for DNA word design, Lecture Notes in Computer Science, DNA 8, LNCS 2568, 2002, pp. 229-241.
20. Y. M. Chee, S. Ling, Improved lower bounds for constant GC-content DNA codes, IEEE Trans. Inf. Theor. 54 (2008) 391-394.
21. D. C. Tulpan, H. Hoos, Hybrid randomized neighborhoods improve stochastic local search for DNA code design, Proc. Advances in Artificial Intelligence, 16th Conference of the Canadian Society for Computational Studies of Intelligence, Lecture Notes in Computer Science LNCS 2671, 2003, pp. 418-433.
22. S. Kawashimo, H. Ono, K. Sadakane, M. Yamashita, DNA sequence design by dynamic neighborhood searches, Lecture Notes in Computer Science, DNA 12, LNCS4287, 2006, pp. 157-171.
23. R. Montemanni, D. H. Smith, Construction of constant GC-content DNA codes via a variable neighborhood search algorithm, J. Math. Model. Algor. 7 (2008)311-326.
24. Q. Zhang, B. Wang, R. Zhang, C. X. Xu, Genetic algorithm-based design for DNA sequences sets, Chinese J. Comput. 31 (2008) 2193-2199.
25. R. Zhang, Q. Zhang, B. Wang, DNA sequence sets design by particle swarm optimization algorithm, Inter. J. Innov. Comput. Inf. Control 5 (2009) 2249-2255.
26. O. D. King, Bounds for DNA codes with constant GC-content, Elec. J. Comb. 10 (2003) R33: 1-13.
27. P. Gaborit, O. D. King, Linear constructions for DNA codes, Theor. Comput. 334(2005)99-113. (Pubitemid 40467296)
28. S. Kawashimo, H. Ono, K. Sadakane, M. Yamashita, Dynamic neighborhood searches for thermodynamically designing DNA sequence, Lecture Notes Comput. Sci. DNA 13, LNCS4848, 2008, pp. 130-139.
29. M. Andronescu, Z. Zhang, A. Condon, Secondary structure prediction of interacting RNA molecules, J. Molec. Biol. 345 (2005) 987-1001. (Pubitemid 40092219)
30. D. C. Tulpan, M. Andronescu, S. B. Chang, M. R. Shortreed, A. Condon, H. H. Hoos, L. M. Smith, Thermodynamically based DNA strand design, Nucleic Acids Res. 33 (2005) 4951-4964. (Pubitemid 41418894)
31. M. Garzon, V. Phan, S. Roy, A. Neel, In search of optimal codes for DNA computing, Lecture Notes Computer Science, LNCS4287, 2006, pp. 143-156.
32. S. Kawashimo, Y. K. Ng, H. Ono, K. Sadakane, M. Yamashita. Speeding up local-search type algorithms for designing DNA sequences under thermodynamical constraints, Lecture Notes Computer Science, DNA 14, LNCS5347, 2009, pp. 168-178.
33. M. Garzon, R. Deaton, L. F. Nino, S. E. Stevens, M. Wittner, Genome encoding for DNA computing, Proc. Third Genetic Programming Conf, Madison, 1998, pp. 684-690.
34. Q. Zhang, B. Wang, Designing DNA • sequences satisfy combinational constraints, J. Comput. Theor. Nanosci. in press.
35. B. Wang, Q. Zhang, R. Zhang, C. X. Xu, Improved lower bounds of DNA coding, J. Comput. Theor. Nanosci. 7 (2010) 638-641.
36. M. R. Shortreed, S. B. Chang, D. G. Hong, M. Phillips, B. Campion, D. C. Tulpan, M. Andronescu, A. Condon, H. H. Hoos, L. M. Smith. A thermodynamic approach to designing structure-free combinatorial DNA word sets, Nucleic Acids Res. 33 (2005) 4965-4977. (Pubitemid 41418895)