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Original Articles

A Case Study in Experimental Design Applied to Genetic Algorithms with Applications to DNA Sequence Assembly

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Pages 369-396 | Published online: 14 Aug 2013

  • BohachevskyJohnson, and Stein, (1986)] BohachevskyI. O., JohnsonM. E., and SteinM. L.. Generalized simulated annealing for function optimization. Technometrics, 28:209–217.
  • BohachevskyJohnson, and Stein, (1992)] BohachevskyI. O., JohnsonM. E., and SteinM. L.. Stochastic optimization and the gambler's ruin problem. Journal of Computational and Graphical Statistics, l(4):367–384.
  • BohachevskyJohnson, and Stein, (1995)] BohachevskyI. O., JohnsonM. E., and SteinM. L.. Simulated annealing and generalizations. In KalivarJ. H., editor, Adaptation of Simulation Annealing to Chemical Optimization, pages 3–24. Elsevier, AmsterdamThe Netherlands.
  • BurksParsons, and Engle, (1994)] BurksC., ParsonsR. J., and EngleM. L.. Integration of competing ancillary assertions in genome assembly. In Proceedings of the Second International Conference on Intelligent Systems in Molecular Biology, pages 62–69. AAAI Press, Menlo Park, CaliforniaUSA.
  • Carlsson, Darnfors, Olofsson, and Bjursell, (1986)] CarlssonP., DarnforsC., OlofssonS.-O., and BjursellG.. Analysis of the human apolipoprotein B gene; complete structure of the B-74 region. Gene, 49:29–51.
  • Churchill, Burks, Eggert, Engle, and Waterman, (1993)] ChurchillG., BurksC., EggertM., EngleM. L., and WatermanM. S.. Assembling DNA sequence fragments by shuffling and simulated annealing. Technical report, Los Alamos National Laboratory.
  • CollinsEglese, and Golden, (1988)] CollinsN. E., EgleseR. W., and GoldenB. L.. Simulated annealing – an annotated bibliography. American Journal of Mathematical and Management Sciences, 8:209–307.
  • Forrest, (1993)] ForrestS.. Genetic algorithms: Principles of natural selection applied to computation. Science, 261:872–878.
  • Goldberg, (1989)] GoldbergD. E.. Genetic Algorithms in Search, Optimization, and Machine Learning. Addison Wesley Publishing Company, Reading, MassachusettsUSA.
  • Goldstein and Waterman, (1987)] GoldsteinL. and WatermanM. S.. Mapping DNA by stochastic relaxation. Advances in Applied Mathematics, 8:194–207.
  • Grefenstette, (1984)] GrefenstetteJohn J.. Genesis: A system for using genetic search procedures. In Proceedings of a Conference on Intelligent Systems and Machines, pages 161–165, Rochester, MinnesotaUSA.
  • Holland, (1975)] HollandJ. H.. Adaptation in Natural and Artificial Systems. The University of Michigan Press, Ann Arbor, MichiganUSA.
  • Holland, (1995)] HollandJ. H.. Hidden Order: How Adaptation Builds Complexity. Addison Wesley, Reading, MassachusettsUSA.
  • Howe and Ward, (1989)] HoweC. M. and WardE. S., editors. Nucleic Acids Sequencing: A Practical Approach. The Practical Approach Series. IRL Press at Oxford University Press, OxfordEngland.
  • Hunkapiller, Kaiser, Koop, and Hood, (1991)] HunkapillerT., KaiserR. J., KoopB. F., and HoodL.. Large-scale and automated DNA sequence determination. Science, 254:59–67.
  • Johnson (1988)] JohnsonM. E., editor. Simulated Annealing (SA) and Optimization: Modern Algorithms with VLSI, Optimal Design and Missile Defense Applications. Volume 17, American Series in Mathematical and Management Sciences. American Sciences Press, Columbus, OhioUSA.
  • Kececioglu and Myers, (1995)] KececiogluJ. D. and MyersE. W.. Combinatorial algorithms for dna sequence assembly. Algorithmica, 13 (1/2):7–51.
  • Myers (1994)] An alternative formulation of sequence assembly. DIMACS Workshop on Combinatorial Methods for DNA Mapping and Sequencing.
  • ParsonsForrest, and Burks, (1995)] ParsonsR. J., ForrestS., and BurksC.. Genetic algorithms, operators and DNA fragment assembly. Machine Learning, 21 (1/2): 11–33.
  • Sanger, Coulson, Hill, and Petersen, (1982)] SangerF., CoulsonA. R., HillD. F., and PetersenG. B.. Nucleotide sequence of bacteriophage lambda DNA. Journal of Molecular Biology, 162:729–773.
  • SetoKoop, and Hood, (1993)] SetoD., KoopB. F., and HoodL.. An experimentally-derived data set constructed for testing large-scale DNA sequence assembly algorithms. Genomics, 15 (3):673–673.
  • Starkweather, McDaniel, Mathias, Whitley, and Whitley, (1991)] StarkweatherT., McDanielS., MathiasK., WhitleyD., and WhitleyC.. A comparison of genetic sequencing operators. In 4th International Conference on Genetic Algorithms, pages 69–76.
  • Waterman, (1995)] WatermanM. S.. Introduction to Computational Biology: Maps, Sequences and Genomes. Interdisciplinary Statistics Series. Chapman and Hall, LondonEngland.
  • Whitley and Yoo, (1995)] WhitleyD. and YooN.. Modeling simple genetic algorithms for permutation problems. In Foundations of Genetic Algorithms 3. Morgan Kaufman, San Mateo, CaliforniaUSA.

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