Abstract
This paper gives a short survey, and a reading grid, of results about the coding problem of molecular design.
This work has been funded by European MolCoNet Project.
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References
Arita, M., Kobayashi, S.: DNA sequence design using templates. New Generation Computing 20, 263 (2002)
Baum, E.B.: DNA sequences useful for computation. In: Proc. 2nd DIMACS Workshop on DNA Based Computers (June 1996)
Ben-Dor, A., Karp, R., Schwikowski, B., Yakhini, Z.: Universal DNA tag systems: a combinatorial design scheme. J. Computational Biology 7(3/4) (2000)
Brenneman, A., Condon, A.E.: Strand design for bio-molecular computation. Theoretical Computer Science 287(1), 39 (2002)
Deaton, R., Chen, J., Bi, H., Garzon, M., Rubin, H., Wood, D.H.: A PCR-based protocol for in vitro selection of non-crosshybridizing oligonucleotides. In: Proc. 8th DIMACS Workshop on DNA Based Computers (June 2002)
Deaton, R., Chen, J., Bi, H., Rose, J.: A software tool for generating noncrosshybridizing libraries of DNA oligonucleotides. In: Proc. 8th DIMACS Workshop on DNA Based Computers (June 2002)
Deaton, R., Garzon, M., Murphy, R.C., Rose, J.A., Franceschetti, D.R., Stevens Jr., S.E.: Genetic search of reliable encodings for DNA-based computation, Late breaking papers at the Genetic Programming conference, Stanford University (July 1996)
Deaton, R., Murphy, R.C., Garzon, M., Franceschetti, D.R., Stevens Jr., S.E.: Good encodings for DNA-based solutions to combinatorial problems. In: Proc. 2nd DIMACS Workshop on DNA Based Computers (June 1996)
Feldkamp, U., Banzhaf, W., Rahue, H.: A DNA sequence compiler. In: Proc. 6th International Meeting on DNA Based Computers (2000)
Feldkamp, U., Saghafi, S., Banzhaf, W., Rahue, H.: DNASequenceGenerator: a program for the construction of DNA sequences. In: Proc. 7th International Meeting on DNA Based Computers (2001)
Frutos, A.G., Liu, Q., Thiel, A.J., Sanner, A.W., Condon, A.E., Smith, L.M., Corn, R.M.: Demonstration of a word strategy for DNA computing on surfaces. Nucleic Acid Research 25(23) (1997)
Garzon, M., Deaton, R., Neathery, P., Murphy, R.C., Franceschetti, D.R., Stevens Jr., S.E.: On the encoding problem for DNA computing. In: Proc. 3rd DIMACS Workshop on DNA Based Computers (1997)
Hartemik, A.J., Gifford, D.K., Khodor, J.: Automated constraint-based nucleotide sequence selection for DNA computation. In: Proc. 4th DIMACS Workshop on DNA Based Computers (June 1998)
Head, T.: Relativised code concepts and multi-tube DNA dictionaries (2002) (submitted)
Heitsch, C.E., Condon, A.E., Hoos, H.H.: From RNA secondary structure to coding theory: a combinatorial approach. In: Proc. 8th DIMACS Workshop on DNA Based Computers (June 2002)
Hofacker, I.L., Fontana, W., Stadler, P.F., Bonhoffer, S., Tacker, M., Schuster, P.: Fast folding and comparison of RNA secondary structures. In: Montashefte f. Chemie, vol. 125 (1994)
Hussini, S., Kari, L., Konstantinidis, S.: Coding properties of DNA languages. Theoretical Computer Science 290, 1557 (2003)
Kaderali, L., Schliep, A.: An algorithm to select target specific probes for DNA chips, to be published by Bioinformatics (2002)
Kari, L., Kitto, R., Thierrin, G.: Codes, involutions and DNA encoding. In: Brauer, W., Ehrig, H., Karhumäki, J., Salomaa, A. (eds.) Formal and Natural Computing. LNCS, vol. 2300, p. 376. Springer, Heidelberg (2002)
Kim, D., Shin, S.-Y., Lee, I.-H., Zhang, B.-T.: NACST/Seq: a sequence design system with multiobjective optimization. In: Proc. 8th DIMACS Workshop on DNA Based Computers (June 2002)
Kobayashi, S., Kondo, T., Arita, M.: On template method for DNA sequence design. In: Proc. 8th DIMACS Workshop on DNA Based Computers (June 2002)
Marathe, A., Condon, A.E., Corn, R.M.: On combinatorial DNA word design. J. Computational Biology 8(3) (2001)
Reif, J.H., LaBean, T.H.: Computationally inspired biotechnologies: improved DNA synthesis and associative search using error-correcting codes and vector-quantization. In: Proc. 6th DIMACS Workshop on DNA Based Computers (June 2000)
Rose, J.A., Deaton, R., Garzon, M., Murphy, R.C., Franceschetti, D.R., Stevens Jr., S.E.: The effect of uniform melting temperatures on the efficiency of DNA computing. In: Proc. 3rd DIMACS Workshop on DNA Based Computers (1997)
Rose, J.A., Deaton, R.J., Hagiya, M., Suyama, A.: The fidelity of the Tag- Antitag system. In: Proc. 7th International Meeting on DNA Based Computers (2001)
Seeman, N.C.: De novo design of sequences for nucleic acid structural engineering. J. Biomolecular Structure and Dynamics 8(3) (1990)
Tulpan, D., Hoos, H., Condon, A.: Stochastic local search algorithms for DNA word design. In: Proc. 8th DIMACS Workshop on DNA Based Computers (June 2002)
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Mauri, G., Ferretti, C. (2004). Word Design for Molecular Computing: A Survey. In: Chen, J., Reif, J. (eds) DNA Computing. DNA 2003. Lecture Notes in Computer Science, vol 2943. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-24628-2_5
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DOI: https://doi.org/10.1007/978-3-540-24628-2_5
Publisher Name: Springer, Berlin, Heidelberg
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