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Genetic Algorithm Combined with a Local Search Method for Identifying Susceptibility Genes Cover

Genetic Algorithm Combined with a Local Search Method for Identifying Susceptibility Genes

Open Access
|Jun 2016

References

  1. [1] A. D Roses, A. M. Saunders, Y. Huang, J. Strum, K. H. Weisgraber, and R. W. Mahley, Complex disease-associated pharmacogenetics: drug efficacy, drug safety, and confirmation of a pathogenetic hypothesis (Alzheimer’s disease), Pharmacogenomics Journal, vol. 7, pp. 10-28, Feb 2007.10.1038/sj.tpj.650039716770341
  2. [2] R. Sanjuan and M. R. Nebot, A Network Model for the Correlation between Epistasis and Genomic Complexity, PLos One, vol. 3, pp. e2663, Jul 2008.10.1371/journal.pone.0002663248127918648534
  3. [3] C. H. Yang, L. Y. Chuang, Y. H. Cheng, Y. D. Lin, C. L. Wang, C. H. Wen, et al., Single nucleotide polymorphism barcoding to evaluate oral cancer risk using odds ratio-based genetic algorithms, Kaohsiung Journal of Medical Sciences, vol. 28, pp. 362-368, Jul 2012.10.1016/j.kjms.2012.02.00222726897
  4. [4] J. B. Chen, Y. H. Yang, W. C. Lee, C. W. Liou, T. K. Lin, Y. H. Chung, et al., Sequence-based polymorphisms in the mitochondrial D-Loop and potential SNP predictors for chronic dialysis, PLoS One, vol. 7, pp. e41125, Jul 2012.10.1371/journal.pone.0041125339981222815937
  5. [5] C. Y. Yen, S. Y. Liu, C. H. Chen, H. F. Tseng, L. Y. Chuang, C. H. Yang, et al., Combinational polymorphisms of four DNA repair genes XRCC1, XRCC2, XRCC3, and XRCC4 and their association with oral cancer in Taiwan, Journal of Oral Pathology & Medicine, vol. 37, pp. 271-277, May 2008.10.1111/j.1600-0714.2007.00608.x18410587
  6. [6] J. H. Moore, A global view of epistasis, Nature Genetics, vol. 37, pp. 13-14, Jan 2005.10.1038/ng0105-1315624016
  7. [7] J. H. Moore, F.W. Asselbergs, and S. M.Williams, Bioinformatics challenges for genome-wide association studies, Bioinformatics, vol. 26, pp. 445-455, Feb 15 2010.10.1093/bioinformatics/btp713282068020053841
  8. [8] S. Purcell, B. Neale, K. Todd-Brown, L. Thomas, M. A. R. Ferreira, D. Bender, et al., PLINK: A tool set for whole-genome association and populationbased linkage analyses, American Journal of Human Genetics, vol. 81, pp. 559-575, Sep 2007.10.1086/519795195083817701901
  9. [9] X. A. Wan, C. Yang, Q. A. Yang, H. Xue, X. D. Fan, N. L. S. Tang, et al., BOOST: A fast approach to detecting gene-gene interactions in genome-wide case-control studies, American Journal of Human Genetics, vol. 87, pp. 325-340, Sep 2010.10.1016/j.ajhg.2010.07.021293333720817139
  10. [10] C. S. Greene, B. C. White, and J. H. Moore, Ant colony optimization for genome-wide genetic analysis, in Ant Colony Optimization and Swarm Intelligence, ed: Springer, pp. 37-47, 2008.10.1007/978-3-540-87527-7_4
  11. [11] L. Y. Chuang, H. Y. Lane, Y. D. Lin, M. T. Lin, C. H. Yang, and H. W. Chang, Identification of SNP barcode biomarkers for genes associated with facial emotion perception using particle swarm optimization algorithm, Annals of General Psychiatry, vol. 13, pp. 15, May 2014.10.1186/1744-859X-13-15405022024955105
  12. [12] S. J. Wu, L. Y. Chuang, Y. D. Lin, W. H. Ho, F. T. Chiang, C. H. Yang, et al., Particle swarm optimization algorithm for analyzing SNP-SNP interaction of renin-angiotensin system genes against hypertension, Molecular Biology Reports, vol. 40, pp. 4227-4233, Jul 2013.
  13. [13] J. B. Chen, L. Y. Chuang, Y. D. Lin, C. W. Liou, T. K. Lin, W. C. Lee, et al., Genetic algorithmgenerated SNP barcodes of the mitochondrial Dloop for chronic dialysis susceptibility, Mitochondrial DNA, vol. 25, pp. 231-237, Jun 2014.10.3109/19401736.2013.79651323777414
  14. [14] W. C. Chang, Y. Y. Fang, H. W. Chang, L. Y. Chuang, Y. D. Lin, M. F. Hou, et al., “Identifying association model for single-nucleotide polymorphisms of ORAI1 gene for breast cancer,” Cancer Cell International, vol. 14, pp. 29, Mar 2014.10.1186/1475-2867-14-29399422724685237
  15. [15] J. H. Holland, Adaptation in natural and artificial systems: An introductory analysis with applications to biology, control, and artificial intelligence: U Michigan Press, 1975.
  16. [16] L. P. Li, C. R. Weinberg, T. A. Darden, and L. G. Pedersen, Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method, Bioinformatics, vol. 17, pp. 1131-1142, Dec 2001.
  17. [17] C. H. Yang, Y. H. Cheng, L. Y. Chuang, and H. W. Chang, Confronting two-pair primer design for enzyme-free SNP genotyping based on a genetic algorithm, BMC Bioinformatics, vol. 11, pp. 509, Oct 2010.10.1186/1471-2105-11-509296468320942913
  18. [18] E. H. Aarts and J. K. Lenstra, Local search in combinatorial optimization: Princeton University Press, 2003.10.1515/9780691187563
  19. [19] G. Moslehi and M. Mahnam, A Pareto approach to multi-objective flexible job-shop scheduling problem using particle swarm optimization and local search, International Journal of Production Economics, vol. 129, pp. 14-22, Jan 2011.10.1016/j.ijpe.2010.08.004
  20. [20] B. Y. Qu, J. J. Liang, and P. N. Suganthan, Niching particle swarm optimization with local search for multi-modal optimization, Information Sciences, vol. 197, pp. 131-143, Aug 2012.10.1016/j.ins.2012.02.011
  21. [21] Wan W, Birch JB: An Improved Hybrid Genetic Algorithm with a New Local Search Procedure. Journal of Applied Mathematics 2013, vol. 2013, Article ID 103591, Aug 2013.
  22. [22] J. H. Moore, L. W. Hahn, M. D. Ritchie, T. A. Thornton, and B. C. White, Application of genetic algorithms to the discovery of complex models for simulation studies in human genetics, in Proceedings of the Genetic and Evolutionary Computation Conference/GECCO. Genetic and Evolutionary Computation Conference, 2002, pp. 1150.
  23. [23] W. N. Frankel and N. J. Schork, Who’s afraid of epistasis?, Nature genetics, vol. 14, pp. 371-373, 1996.10.1038/ng1296-3718944011
  24. [24] J. H. Moore, L. W. Hahn, M. D. Ritchie, T. A. Thornton, and B. C. White, Routine discovery of complex genetic models using genetic algorithms, Applied Soft Computing, vol. 4, pp. 79-86, Feb 2004.10.1016/j.asoc.2003.08.003295295720948983
  25. [25] R. J. Urbanowicz, J. Kiralis, N. A. Sinnott- Armstrong, T. Heberling, J. M. Fisher, and J. H. Moore, GAMETES: a fast, direct algorithm for generating pure, strict, epistatic models with random architectures, Biodata Mining, vol. 5, pp. 16, Oct 2012.10.1186/1756-0381-5-16360510823025260
  26. [26] A. Mousa, M. El-Shorbagy, and W. Abd-El- Wahed, Local search based hybrid particle swarm optimization algorithm for multiobjective optimization, Swarm and Evolutionary Computation, vol. 3, pp. 1-14, Apr 2012.10.1016/j.swevo.2011.11.005
  27. [27] H. Derbel, B. Jarboui, S. Hanafi, and H. Chabchoub, Genetic algorithm with iterated local search for solving a location-routing problem, Expert Systems with Applications, vol. 39, pp. 2865-2871, Feb 2012.
Language: English
Page range: 203 - 212
Published on: Jun 10, 2016
Published by: SAN University
In partnership with: Paradigm Publishing Services
Publication frequency: 4 issues per year

© 2016 Cheng-Hong Yang, Sin-Hua Moi, Yu-Da Lin, Li-Yeh Chuang, published by SAN University
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.