• Asia-pacific Journal of Multimedia Services Convergent with Art, Humanities, and Sociology
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• v.8 no.4
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• pp.251-258
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• 2018

In mathematics and computer science, an optimization problem is the problem of finding the best solution from feasible ones. In the context of genetic algorithm, the difficulty of an optimization problem can be explained in terms of problem epistasis. In biology, epistasis means that the phenotype of a gene is suppressed by one or more genes, but in an evolutionary algorithm it means the interaction between genes. In this paper, we experimentally show that problem epistasis and the performance of genetic algorithm are closely related. We compared problem epistasis (One-Max, Royal Road, and NK-Landscape) using a framework that quantifies problem epistasis based on Shannon's information theory, and could show that problem becomes more difficult as problem epistasis grows. In the case that a genetic algorithm finds the optimal solution, performance is compared through the number of generations, otherwise through the ratio of the fitness of the optimal solution to that of the best solution.

• BMB Reports
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• v.42 no.9
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• pp.617-622
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• 2009

We investigated the genetic associations of ischemic stroke by identifying epistasis of its heterogeneous subtypes such as small vessel occlusion (SVO) and large artery atherosclerosis (LAA). Epistasis was analyzed with 24 genes in 207 controls and 271 patients (SVO = 110, LAA = 95) using multifactor dimensionality reduction and entropy decomposition. The multifactor dimensionality reduction analysis with any of 1- to 4-locus models showed no significant association with LAA (P > 0.05). The analysis of SVO, however, revealed a significant association in the best 3-locus model with P10L of TGF-$\beta{1}$, C1013T of SPP1, and R485K of F5 (testing balanced accuracy = 63.17%, P < 0.05). Subsequent entropy analysis also revealed that such heterogeneity was present and quite a large entropy was estimated among the 3 loci for SVO (5.43%), but only a relatively small entropy was estimated for LAA (1.81%). This suggests that the synergistic epistasis model might contribute specifically to the pathogenetsis of SVO, which implies a different etiopathogenesis of the ischemic stroke subtypes.

• Genomics & Informatics
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• v.12 no.4
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• pp.216-224
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• 2014

Gastritis is a common but a serious disease with a potential risk of developing carcinoma. Helicobacter pylori infection is reported as the most common cause of gastritis, but other genetic and genomic factors exist, especially single-nucleotide polymorphisms (SNPs). Association studies between SNPs and gastritis disease are important, but results on epistatic interactions from multiple SNPs are rarely found in previous genome-wide association (GWA) studies. In this study, we performed computational GWA case-control studies for gastritis in Korea Associated Resource (KARE) data. By transforming the resulting SNP epistasis network into a gene-gene epistasis network, we also identified potential gene-gene interaction factors that affect the susceptibility to gastritis.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.11
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• pp.1511-1514
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• 2012

Epistasis that may explain a large portion of the phenotypic variation for complex economic traits of animals has been ignored in many genetic association studies. A Baysian method was introduced to draw inferences about multilocus genotypic effects based on their marginal posterior distributions by a Gibbs sampler. A simulation study was conducted to provide statistical powers under various unbalanced designs by using this method. Data were simulated by combined designs of number of loci, within genotype variance, and sample size in unbalanced designs with or without null combined genotype cells. Mean empirical statistical power was estimated for testing posterior mean estimate of combined genotype effect. A practical example for obtaining empirical statistical power estimates with a given sample size was provided under unbalanced designs. The empirical statistical powers would be useful for determining an optimal design when interactive associations of multiple loci with complex phenotypes were examined.

• Journal of KIISE:Software and Applications
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• v.33 no.4
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• pp.440-448
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• 2006

Self-Organizing Map (SOM) is an unsupervised learning neural network and it is used for preserving the structural relationships in the data without prior knowledge. SOM has been applied in the study of complex problems such as vector quantization, combinatorial optimization, and pattern recognition. This paper proposes a new usage of SOM as a tool for schema transformation hoping to achieve more efficient genetic process. Every offspring is transformed into an isomorphic neural network with more desirable shape for genetic search. This helps genes with strong epistasis to stay close together in the chromosome. Experimental results showed considerable improvement over previous results.

• Journal of the Korean Society of Tobacco Science
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• v.14 no.2
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• pp.116-125
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• 1992

This experiment was conducted to examine characteristics of agronomic characters and estimate of gene effect for several mutant characters. The genetic populations were derived from cross between 83H-5 and Hicks. There were significant difference for plant height, stlk height, leaf shape and bacterial wilt disease index except leaf number, leaf length, and what is more, F3 variance is more than Bl and B2 generation from cross 83H-5 X Hicks. Gene actions for stalk height and bacterial wilt disease were estimated by 3-parameter, and by 6- parameter model for all characters except above two characters but stalk height and bacterial wilt disease index are not significant in the additive and dominance effects. Dominant$\times$dominant epitasis for plant height, dominant and dominant$\times$dominant epistasis for leaf length, additive and additive$\times$additive and dominant$\times$dominant epistasis for leaf width, and additive and additive$\times$dominant epistasis for days to flower were appeared significant in gene action.

• Korean Journal of Environmental Biology
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• v.26 no.4
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• pp.377-384
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• 2008

A cell is the product of a long period of evolution and can be represented as an optimized system (homeostasis). Stimuli from the outside environment are received by sensory apparatus on the surface of the cell and transferred through complicated pathways and eventually regulate gene expression. These signals affect cell physiology, growth, and development, and the interaction among genes in the signal transduction pathway is a critical part of the regulation. In this study, the interactions of deletion mutants and overexpression of the extracopies of the genes were used to understand their relationships to each other. Also, green fluorescent protein (GFP reporter gene) was fused to the regulatory genes to elucidate their interactions. Cooverexpression of the two genes in extracopy plasmids suggested that patS acts at the downstream of hetR in the regulatory network. The experiments using gfp fusion in different genetic background cells also indicated the epistasis relationships between the two genes. A model describing the regulatory network that controls cell development is presented.

• Journal of the Korean Institute of Intelligent Systems
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• v.15 no.6
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• pp.661-667
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• 2005

In this paper, we propose a new hybrid genetic algorithm for sequential ordering problem (SOP). In the proposed genetic algorithm, the Voronoi quantized crossover (VQX) is used as a crossover operator and the path-preserving 3-Opt is used as a local search heuristic. VQX is a crossotver operator that uses the epistasis information of given problem instance. Since it is a crossover proposed originally for the traveling salesman problem (TSP), its application to SOP requires considerable modification. In this study, we appropriately modify VQX for SOP, and develop three algorithms, required in the modified VQX, named Feasible solution Generation Algorithm, Precedence Cycle Decomposition Algorithm, and Genic Distance Assignment Method. The results of the tests on SOP instances obtained from TSPLIB and ZIB-MP-Testdata show that the proposed genetic algorithm outperforms other genetic algorithms in stability and solution quality.

• The Transactions of The Korean Institute of Electrical Engineers
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• v.57 no.9
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• pp.1636-1641
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• 2008

In this study, we introduce a new approach to Parallel Genetic Algorithms (PGA) which combines AHFCGA with crossover operator. As to crossover operators, we use three types of the crossover operators such as modified simple crossover(MSX), arithmetic crossover(AX), and Unimodal Normal Distribution Crossover(UNDX) for real coding. The AHFC model is given as an extended and adaptive version of HFC for parameter optimization. The migration topology of AHFC is composed of sub-populations(demes), the admission threshold levels, and admission buffer for the deme of each threshold level through succesive evolution process. In particular, UNDX is mean-centric crossover operator using multiple parents, and generates offsprings obeying a normal distribution around the center of parents. By using test functions having multimodality and/or epistasis, which are commonly used in the study of function parameter optimization, Experimental results show that AHFCGA can produce more preferable output performance result when compared to HFCGA and RCGA.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.1
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• pp.124-130
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• 2009

Estimating genetic interaction effects in animal genomics would be one of the most challenging studies because the phenotypic variation for economically important traits might be largely explained by interaction effects among multiple nucleotide sequence variants under various environmental exposures. Genetic improvement of economic animals would be expected by understanding multi-locus genetic interaction effects associated with economic traits. Most analyses in animal breeding and genetics, however, have excluded the possibility of genetic interaction effects in their analytical models. This review discusses a historical estimation of the genetic interaction and difficulties in analyzing the interaction effects. Furthermore, two recently developed methods for assessing genetic interactions are introduced to animal genomics. One is the restricted partition method, as a nonparametric grouping-based approach, that iteratively utilizes grouping of genotypes with the smallest difference into a new group, and the other is the Bayesian method that draws inferences about the genetic interaction effects based on their marginal posterior distributions and attains the marginalization of the joint posterior distribution through Gibbs sampling as a Markov chain Monte Carlo. Further developing appropriate and efficient methods for assessing genetic interactions would be urgent to achieve accurate understanding of genetic architecture for complex traits of economic animals.