DNA strand generation for DNA computing by using a multi-objective differential evolution algorithm

BioSystems

Volumn 116, Issue 1, 2014, Pages 49-64

  Chaves González, José M ^a   Vega Rodríguez, Miguel A ^a  

^a UNIVERSITY OF EXTREMADURA   (Spain)

Author keywords

Differential evolution with Pareto tournaments; DNA sequence design; Multiobjective optimization

Indexed keywords

DNA; DOUBLE STRANDED DNA;

COMPARATIVE STUDY; DNA; EVOLUTION; GENETIC ALGORITHM; NANOTECHNOLOGY; SORTING;

ARTICLE; BASE PAIRING; DIFFERENTIAL EVOLUTION; DNA LIBRARY; DNA SEQUENCE; DNA STRAND; EVOLUTION; EVOLUTIONARY ALGORITHM; GENETIC ALGORITHM; HYBRIDIZATION;

DIFFERENTIAL EVOLUTION WITH PARETO TOURNAMENTS; DNA SEQUENCE DESIGN; MULTIOBJECTIVE OPTIMIZATION;

ALGORITHMS; BASE SEQUENCE; COMPUTERS, MOLECULAR; DNA; EVOLUTION, MOLECULAR; MODELS, THEORETICAL;

EID: 84891717223     PISSN: 03032647     EISSN: 18728324     Source Type: Journal    
DOI: 10.1016/j.biosystems.2013.12.005     Document Type: Article

References (63)

1. Abbass H., Sarker R., Newton C. PDE: a Pareto-frontier differential evolution approach for multi-objective optimization problems. Proceedings of the 2001 Congress on Evolutionary Computation (CEC 2001), vol. 2 2001, 971-978.
2. Adleman L.M. Molecular computation of solutions to combinatorial problems. Science 1994, 266:1021-1024.
3. Arita M., Kobayashi S. DNA sequence design using templates. New Gen. Comput. 2002, 20:263-277.
4. Arita M., Nishikawa A., Hagiya M., Komiya K., Gouzu H., Sakamoto K. Improving sequence design for DNA computing. Proceedings of the Genetic and Evolutionary Computation Conference (GECCO) 2000, 875-882.
5. Brenneman A., Condon A.E. Strand design for biomolecular computation. Theor. Comput. Sci. 2002, 287:39-58.
6. Chaves-Gonzalez J.M., Vega-Rodriguez M.A. DNA sequence design for reliable DNA computing by using a multiobjective approach. Proceedings of 13th IEEE International Symposium on Computational Intelligence and Informatics 2013, 73-78.
7. Chaves-Gonzalez J.M., Vega-Rodriguez M.A., Granado-Criado J.M. A multiobjective swarm intelligence approach based on artificial bee colony for reliable DNA sequence design. Eng. Appl. Artif. Intell. 2013, 26(9):2045-2057.
8. Coello C.A., Van Veldhuizen D.A., Lamont G.B. Evolutionary Algorithms for Solving Multi-Objective Problems, Genetic Algorithms and Evolutionary Computation 2002, Springer, NY, USA.
9. Cui G., Li X. The optimization of DNA encodings based on modified PSO/GA algorithm. Proceedings of International Conference on Computer Design and Applications 2010, 609-614.
10. Deaton R., Chen J., Bi H., Garzon M., Rubin H., Wood D.H. A PCR-based protocol for in vitro selection of noncrosshybridizing olgionucleotides. Proceedings of 8th International Workshop on DNA-Based Computers 2002, 196-204.
11. Deaton R., Chen J., Bi H., Rose J.A. A software tool for generating noncrosshybridization libraries of DNA oligonucleotides. Proceedings of 8th International Workshop on DNA Based Computers 2002, 252-261.
12. Deaton R., Garzon M., Murphy R.C., Rose J.A., Franceschetti D.R., Stevens S.E. Reliability and efficiency of a DNA-based computation. Phys. Rev. Lett. 1998, 80(2):417-420.
13. Deaton R., Murphy R.C., Garzon M., Franceschetti D.R., Stevens S.E. Good encodings for DNA-based solutions to combinatorial problems. Proceedings of 2nd Annual Meeting on DNA Based Computation 1996, 247-258.
14. Deb K. Multi-Objective Optimization Using Evolutionary Algorithms 2001, John Wiley & Sons, Chichester, West Sussex, England.
15. Deb K., Pratap A., Agarwal S., Meyarivan T. A fast elitist multi-objective genetic algorithm: NSGA-II. IEEE Trans. Evol. Comput. 2002, 6:182-197.
16. Elbaz J., Lioubashevski O., Wang F., Remacle F., Levine R.D., Willner I. DNA computing circuits using libraries of DNAzyme subunits. Nat. Nanotechnol. 2010, 5:417-422.
17. Faulhammer D., Cukras A.R., Lipton R.J., Landweber L.F. Molecular computation: RNA solutions to chess problems. Proc. Natl. Acad. Sci. U.S.A. 2000, 97:1385-1389.
18. Feldkamp U., Saghafi S., Banzhaf W., Rauhe H. DNA sequence generator - a program for the construction of DNA sequences. Proceedings of 7th International Workshop on DNA Based Computers 2001, 179-188.
19. Fogel G.B., Porto V.W., Varga G., Dow E.R., Craven A.M., Powers D.M., Harlow H.B., Su E.W., Onyia J.E., Su C. Evolutionary computation for discovery of composite transcription factor binding sites. Nucleic Acids Res. 2008, 36(21):pe142.
20. Frutos G., Thiel A.J., Condon A.E., Smith L.M., Corn R.M. DNA computing at surfaces: four base mismatch word design. Proceedings of 3rd DIMACS Workshop on DNA Based Computers 1997, 238.
21. Gansauge M-T., Meyer M. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat. Protoc. 2013, 8:737-748.
22. Garzon M.H., Deaton R.J. Codeword design and information encoding in DNA ensembles. Nat. Comput. 2004, 3:253-292.
23. Garzon M.H., Deaton R.J. Biomolecular computing and programming. IEEE Trans. Evol. Comput. 1999, 3:236-250.
24. Hartemink J., Gifford D.K., Khodor J. Automated constraint based nucleotide sequence selection for DNA computation. Proceedings of 4th DIMACS Workshop on DNA Based Computers 1998, 227-235.
25. Heitsch E., Condon A.E., Hoos H.H. From RNA secondary structure to coding theory: a combinatorial approach. Proceedings of 8th International Workshop on DNA Based Computers 2002, 215-228.
26. Hongyan Z., Xiyu L. Improved genetic algorithm for designing DNA sequences. Proceedings of 2nd International Symposium on Electronic Commerce and Security 2009, 514-518.
27. Ibrahim Z., Khalid N.K., Buyamin S., Ibrahim I., Mukred J.A.A., Yusof Z.M., Mohamad M.S., Mokhtar N., Saaid M.F.M., Engelbrecht A. DNA sequence design for DNA computation based on binary particle swarm optimization. Int. J. Innov. Comput. Inf. Control 2012, 8(5B):3441-3450.
28. Jaszkiewicz A. On the performance of multiple-objective genetic local search on the 0/1 knapsack problem - a comparative experiment. IEEE Trans. Evol. Comput. 2002, 8(4):402-412.
29. Khalid N.K., Kurniawan T.B., Ibrahim Z., Yusof Z.M., Khalid M., Engelbrecht A.P. A model to optimize DNA sequences based on particle swarm optimization. Proceedings of 2nd Asia International Conference on Modeling & Simulation 2008, 534-539.
30. Knowles J., Corne D. The Pareto archived evolution strategy: a new baseline algorithm for Pareto multiobjective optimization. Proceedings of Congress on Evolutionary Computation (CEC) 1999, 98-105.
31. Kukkonen S., Lampinen J. GDE3: the third evolution step of generalized differential evolution. Proceedings of the 2005 Congress on Evolutionary Computation (CEC 2005), vol. 1 2005, 443-450.
32. Kurniawan T.B., Khalid N.K., Ibrahim Z., Khalid M., Middendorf M. Evaluation of ordering methods for DNA sequence design based on ant colony system. Proceedings of 2nd Asia International Conference on Modeling & Simulation 2008, 905-910.
33. Kurniawan T.B., Khalid N.K., Ibrahim Z., Abidin M.S.Z., Khalid M. Sequence design for direct-proportional length-based DNA computing using population-based ant colony optimization. Proceedings of ICROS-SICE International Joint Conference 2009, 1486-1491.
34. Lee J.Y., Shin S.-Y., Park T.H., Zhang B.-T. Solving traveling salesman problems with DNA molecules encoding numerical values. BioSystems 2004, 78:39-47.
35. Lindman H.R. Analysis of Variance in Complex Experimental Designs 1974, Erlbaum. Ed. Freeman & Co., San Francisco, CA, USA.
36. Liu W., Wang S., Gao L., Zhang F., Xu J. DNA sequence design based on template strategy. J. Chem. Inf. Comput. Sci. 2003, 43:2014-2018.
37. Madavan N.K. Multiobjective optimization using a Pareto differential evolution approach. Proceedings of the 2002 Congress on Evolutionary Computation (CEC 2002), vol. 2 2002, 1145-1150.
38. Marathe A., Condon A.E., Corn R.M. On combinatorial DNA word design. Proceedings of 5th DIMACS Workshop on DNA Based Computers 1999, 75-89.
39. Mustaza S.M., Abidin A.F.Z., Ibrahim Z., Shamsudin M.A., Husain A.R., Mukred J.A.A. A modified computational model of ant colony system in DNA sequence design. Proceedings of IEEE Student Conference on Research and Development (SCOReD) 2011, 169-173.
40. Ouyang Q., Kaplan P.D., Liu S., Libchaber A. DNA solution of the maximal clique problem. Science 1997, 278:446-449.
41. Penchovsky R., Ackermann J. DNA library design for molecular computation. J. Comput. Biol. 2003, 10(2):215-229.
42. Price K., Storn R. Differential evolution - a simple evolution strategy for fast optimization. Dr. Dobb's J. 1997, 22(4):18-24.
43. Robic T., Filipic B. DEMO: differential evolution for multiobjective optimization. Proceedings of the 3rd International Conference on Evolutionary Multi-Criterion Optimization (EMO 2005). Springer LNCS, vol. 3410 2005, 520-533.
44. Ruben J., Freeland S.J., Landweber L. PUNCH: an evolutionary algorithm for optimizing bit set selection. Proceedings of 7th International Workshop on DNA Based Computers 2001, 260-270.
45. Sakamoto K., Gouzu H., Komiya K., Kiga D., Yokoyama S., Yokomori T., Hagiya M. Molecular computation by DNA hairpin formation. Science 2000, 288:1223-1226.
46. Santa Lucia J. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. U.S.A. 1998, 95:1460-1465.
47. Sheskin J. Handbook of Parametric and Nonparametric Statistical Procedures 2011, Chapman & Hall/CRC Press, New York. 5th ed.
48. Shin S.H., Kim D.M., Lee I.H., Zhang B.T. Evolutionary sequence generation for reliable DNA computing. Proceedings of Congress on Evolutionary Computation (CEC) 2002, 79-84.
49. Shin S.H., Lee I.H., Kim D.M., Zhang B.T. Multiobjective evolutionary optimization of DNA sequences for reliable DNA computing. IEEE Trans. Evol. Comput. 2005, 9(2):143-158.
50. Tanaka F., Nakatsugawa M., Yamamoto M., Shiba T., Ohuchi A. Toward a general-purpose sequence design system in DNA computing. Proceedings of Congress on Evolutionary Computation (CEC) 2002, 73-78.
51. Tanaka F., Nakatsugawa M., Yamamoto M., Shiba T., Ohuchi A. Developing support system for sequence design in DNA computing. Proceedings of 7th International Workshop on DNA Based Computers 2001, 340-349.
52. Wang Y., Cai Z., Guo G., Zhou Y. Multiobjective optimization and hybrid evolutionary algorithm to solve constrained optimization problems. IEEE Trans. Syst. Man Cybern. B: Cybern. 2007, 37(3):560-575.
53. Wang Y., Shen Y., Zhang X., Cui G. DNA codewords design using the improved NSGA-II algorithms. Proceedings of 4th International Conference on Bio-Inspired Computing 2009, 48-52.
54. Wetmur J.G. DNA probes: applications of the principles of nucleic acid hybridization. Crit. Rev. Biochem. Mol. Biol. 1991, 26:227-259.
55. Xiao J., Cheng Z. DNA sequences optimization based on gravitational search algorithm for reliable DNA computing. Proceedings of Sixth International Conference on Bio-Inspired Computing 2011, 103-107.
56. Xu C., Zhang Q., Wang B., Zhang R. Research on the DNA sequence design based on GA/PSO algorithms. Proceedings of 2nd International Conference on Bioinformatics and Biomedicine Engineering 2008, 816-819.
57. Xue F., Sanderson A.C., Graves R.J. Pareto-based multi-objective differential evolution. Proceedings of the 2003 Congress on Evolutionary Computation (CEC 2003), vol. 2 2003, 862-869.
58. Zhang B.T., Shin S.Y. Molecular algorithms for efficient and reliable DNA computing. Proceedings of Gen. Program 1998, 735-742.
59. Zhang Q., Li H. MOEA/D: a multiobjective evolutionary algorithm based on decomposition. IEEE Trans. Evol. Comput. 2007, 11:712-731.
60. Zhang Q., Wang B., Wei X., Fang X., Zhou C. DNA word set design based on minimum free energy. IEEE Trans. Nanobiosci. 2010, 9(4):273-277.
61. Zitzler E., Deb K., Thiele L. Comparison of multiobjective evolutionary algorithms: empirical results. Evol. Comput. 2000, 8(2):173-195.
62. Zitzler E., Künzli S. Indicator-based selection in multiobjective search. Proceedings of 8th International Conference on Parallel Problem Solving from Nature (PPSN VIII) 2004, 832-842.
63. Zaharie D. A comparative analysis of crossover variants in differential evolution. Proceedings of the International Multiconference on Computer Science and Information Technology 2007, 171-181.