Physical separation of DNA according to Royal Road fitness

Proceedings of the 1999 Congress on Evolutionary Computation, CEC 1999

Volumn 2, Issue , 1999, Pages 1011-1016

  Wood, David Harlan ^a   Chen, Junghuei ^b  

^a University of Delaware   (United States)

^b UNIVERSITY OF DELAWARE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CALCULATIONS; HEALTH; ROADS AND STREETS; SEPARATION;

DNA STRANDS; LABORATORY METHODS; LABORATORY OPERATIONS; PHYSICAL SEPARATION;

DNA;

EID: 84901419246     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CEC.1999.782534     Document Type: Conference Paper

References (41)

1. Thomas Back, Joost N. Kok, and Grzegorz Rozenberg. Evolutionary computation as a paradigm for DNA-based computing. In Laura Landweber, Erik Winfree, Richard Lipton, and Stephan Freeland, editors, Preliminary Proceedings DIMACS Workshop on Evolution as Computation, pages 67-88, DIMACS, Piscataway NJ, January 1999. Available on request from DIMACS. Paper found at URL: http://www.wi. LeidenUniv. nl/~joost.
2. Eric B. Baum. DNA sequences useful for computation. In Landweber and Lipton [22].
3. Junghuei Chen, Eugene Antipov, Bertrand Lemieux, Walter Cedefio, and David Harlan Wood. DNA computing implementing genetic algorithms. In Laura Landweber, Erik Winfree, Richard Lipton, and Stephan Freeland, editors, Preliminary Proceedings DIMACS Workshop on Evolution as Computation, pages 39-49, DIMACS, Piscataway NJ, January 1999. Available on request from DIMACS. Paper found at URL: http://www.cis.udel.edu/"wood/papers/DIMACS-99.ps.
4. H. C. Crick, J. S. Griffith, and L. E. Orgel. Codes without commas. Proceedings of the National Academy of Sciences USA, 43:416-121, 1957.
5. James P. Crutchfield and Erik van Nimwegen. Optimizing epochal evolutionary search: Populationsize independent theory. SFI Working Paper 98-06-046, 1998, 18 pages. Paper found at URL: http://www.santafe.edu/projects/ evca/evabstracts.html.
6. James P. Crutchfield and Erik van Nimwegen. Optimizing epochal evolutionary search: Populationsize dependent theory. SFI Working Paper 98-10-090, 1998, 18 pages. Paper found at URL: http://www.santafe.edu/projects/ evca/evabstracts.html.
7. James P. Crutchfield and Erik van Nimwegen. The evolutionary unfolding of complexity. In Laura Landweber, Erik Winfree, Richard Lipton, and Stephan Freeland, editors, Proceedings of the DIMACS Workshop on Evolution as Computation, New York, 1999, to appear. Springer-Verlag.
8. J. H. M. Dassen. A bibliography of molecular computation and splicing systems. HTML in: http://www.wi. LeidenUniv. nl/jdassen/dna.html, Bib-TeX source: http://www.wi. LeidenUniv. nl/jdassen/dna.bib. This bibliography is also hooked into http://liinwww.ira.uka.de/bibliography/, The Collection of Computer Science Bibliographies.
9. R. Deaton, Max H. Garzon, R. C. Murphy, Donald R. Franceschetti, and Jr. S. E. Stevens. Genetic search of reliable encodings for DNA based computation. In First Conference on Genetic Programming, Stanford University, 1996.
10. R. Deaton, R. C. Murphy, J. A. Rose, Max H. Garzon, Donald R. Franceschetti, and S. E. Stevens Jr. A DNA based implementation of an evolutionary search for good encodings for DNA computation. In IEEE International Conference on Evolutionary Computation, pages 267-271, Indianapolis, Illinois, April 13-16, 1997.
11. R. Deaton, R. C. Murphy, M. Garzon, D. R. Franceschetti, and S. E. Stevens, Jr. Good encodings forDNA-based solutions to combinatorial problems. In Landweber and Lipton [22].
12. R. Deaton, R. C. Murphy, M. Garzon, D. R. Franceschetti, and S. E. Stevens, Jr. Good encodings for DNA-based solutions to combinatorial problems. In Landweber and Lipton [22].
13. Alan Dove. From bits to bases: Computing with DNA. Nature Biotechnology, 16(9):830-832, September 1998.
14. Tino GramB, Stephan Bornholdt, Michael GramB, Melanie Mitchell, and Thomas Pellizzari. Nonstandard Computation. Wiley-VCH, Weinheim, 1998.
15. Rachel Green, Andrew D. Ellington, David P. Bartel, and Jack W. Szostak. In vitro genetic analysis: Selection and amplification of rare functional nucleic acids. Methods, 2:75-86, 1991.
16. Alexander J. Hartemink, David K. Gifford, and Julia Khodor. Automated constraint-based nucleotide sequence selection for dna computation. In Harvey Rubin and David Harlan Wood, editors, Preliminary Proceedings of the Fourth Annual Workshop on DNA Based Computers, held at the University of Pennsylvania, June 15-19, 1998. University of Pennsylvania, 1998.
17. B. H. Jiggs. Recent results on comma-free codes. Canadian Journal of Mathematics, 15:178-187, 1963.
18. Peter Kaplan, Guillermo Cecchi, and Albert Libchaber. DNA based molecular computation: Template-template interactions in PCR. In Landweber and Lipton [22].
19. Peter D. Kaplan, Guillermo Cecchi, and Albert Libchaber. Molecular computation: Adleman's experiment repeated. Technical report, NEC Research Institute, 1995.
20. Peter D. Kaplan, Guillermo Cecchi, and Albert Libchaber. DNA based molecular computation: templatetemplate interactions in PCR. In Landweber and Lipton [22].
21. Laura Landweber, Richard Lipton, Andrew Ellington, and Robert Dorit, editors. DIMACS Nucleic Selection, DIMACS, Piscataway NJ, March 1998. Abstracts only. Available on request from DIMACS. URL: http://dimacs.rutgers.edu/ Workshops/NucleicAcid.
22. Laura F. Landweber and Richard J. Lipton, editors. DNA Based Computers II: DIMACS Workshop, June 10-12, 1996, volume 44 of DIMACS series in discrete mathematics and theoretical computer science, Providence, 1998. American Mathematical Society.
23. L. S. Lerman, K. Silverstein, and E. Grinfeld. Searching for gene defects by denaturing gradient gel electrophoresis. Trends in Biochemical Sciences, 172(3):89-93, 1992.
24. Carlo C. Maley. DNA computation: Theory, practice, and prospects. Evolutionary Computation, 6(3):201-229, 1998.
25. M. Mitchell, S. Forrest, and J. H. Holland. The royal road for genetic algorithms: Fitness landscapes and GA performance. In F. V. Varela and P. Bourgine, editors, Proceedings of the First European Conference on Artificial Life, pages 245-254, Paris, France, 1991. MIT Press.
26. Robert Pool. Forget silicon, try DNA. New Scientist, 151(2038):26-31, July 13, 1996.
27. D. L. Robertson and F. G. Joyce. Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature, 344(6265):467-168, March 29, 1990.
28. D. D. Shoemaker, D. A. Lashkari, D. Morris, M. Mittmann, and R. W. Davis. Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nature Genetics, 14:450-456, 1996.
29. Gerhard Steger. Thermal denaturation of doublestranded nucleic acids: Prediction of temperatures critical for gradient gel electrophoresis and polymerase chain reaction. Nucleic Acids Research, 22(14):2760-2768, July 25, 1994. On line server is found at the URL: http://www.biophys.uniduesseldorf.de/ POLAND/poland.html.
30. Willem P. C. Stemmer. DNA shuffling by random fragmentation and reassembly: In vitro recombination for molecular evolution. Proceedings of the National Academy of Science, U. S. A., 91:389-391, 1994.
31. Willem P. C. Stemmer. Rapid evolution of a protein by DNA shuffling. Nature, 370:389-391, 1994.
32. Willem P. C. Stemmer. The evolution of molecular computation. Science, 270:1510-1510, December 1, 1995.
33. Willem P. C. Stemmer. Sexual PCR and assembly PCR. In Robert M. Meyers, editor, The Encyclopedia of Molecular Biology and Molecular Medicine, volume 5, pages 447-57. VCH, New York, 1996.
34. Jack W. Szostak. In vitro genetics. Trends in Biochemical Sciences, 172(3):89-93, 1992.
35. H. J. Thiesen and C. Bach. Target detection assay (TDA) - A versatile procedure to determine DNA-binding sites as demonstrated on SP1 protein. Nucleic Acids Research, 18(11):3203-3209, 1990.
36. C. Tuerk and L. Gold. Systematic evolution of ligands by exponential enrichment - RNA ligands to bacteriophage-T4 DNA-polymerase. Science, 249(4968):505-510, August 3, 1990.
37. Erik van Nimwegen, James P. Crutchfield, and Melanie Mitchell. Finite populations induce metastability in evolutionary search. Physics Letters A, 229(3):144-150, May 12 1997.
38. Erik van Nimwegen, James P. Crutchfield, and Melanie Mitchell. Statistical dynamics of the Royal Road genetic algorithm. Theoretical Computer Science, to Appear.
39. Roy Williams. Data powers of ten. Web page at http://www.ccsf.cal tech.edu/~roy/dataquan.
40. David Harlan Wood. Applying error correcting codes to DNA coding. In Harvey Rubin and David Harlan Wood, editors, Preliminary Proceedings of the Fourth Annual Workshop on DNA Based Computers, held at the University of Pennsylvania, June 15-19, 1998, pages 109-110. University of Pennsylvania, 1998. (unrefereed extended abstract).
41. David Harlan Wood, Junghuei Chen, Eugene Antipov, Walter Cedefio, and Bertrand Lemieux. A DNA implementation of the Max Is problem. In Wolfgang Banzhaf, A. E. Eiben, Max H. Garzon, Vasant Honavar, Mark Jakiela, and Robert E. Smith, editors, GECCO-99: Proceedings of the Genetic and Evolutionary Computation Conference, July 13-17, 1999, Orlando, Florida USA., San Francisco, 1999. Morgan Kaufman.