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Volumn 112, Issue 6, 2014, Pages 666-674

Cuckoo search epistasis: A new method for exploring significant genetic interactions

Author keywords

cuckoo search; dimensionality reduction; epistatic interactions; single nucleotide polymorphism

Indexed keywords

DATA SET; DISEASE; EPISTASIS; GENETIC ALGORITHM; GENETIC STRUCTURE; POLYMORPHISM;

EID: 84901048237     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2014.4     Document Type: Article
Times cited : (47)

References (55)
  • 1
    • 57749172222 scopus 로고
    • A mathematical theory of adaptive control processes
    • Bellman R, Kalaba R (1959). A mathematical theory of adaptive control processes. Proc Natl Acad Sci USA 45: 1288-1290.
    • (1959) Proc Natl Acad Sci USA , vol.45 , pp. 1288-1290
    • Bellman, R.1    Kalaba, R.2
  • 2
    • 61949417042 scopus 로고    scopus 로고
    • Biofilter: A knowledge-integration system for the multi-locus analysis of genome-wide association studies
    • Bush WS, Dudek SM, Ritchie MD (2009). Biofilter: a knowledge-integration system for the multi-locus analysis of genome-wide association studies. Pac Symp Biocomput 368-379.
    • (2009) Pac Symp Biocomput , pp. 368-379
    • Bush, W.S.1    Dudek, S.M.2    Ritchie, M.D.3
  • 3
    • 44949257101 scopus 로고    scopus 로고
    • Alternative contingency table measuresimprove the power and detection of multifactor dimensionality reduction
    • Bush WS, Edwards TL, Dudek SM, McKinney BA, Ritchie MD (2007). Alternative contingency table measuresimprove the power and detection of multifactor dimensionality reduction. BMC Bioinformatics 9: 238.
    • (2007) BMC Bioinformatics , vol.9 , pp. 238
    • Bush, W.S.1    Edwards, T.L.2    Dudek, S.M.3    McKinney, B.A.4    Ritchie, M.D.5
  • 5
    • 33845903040 scopus 로고    scopus 로고
    • Odds ratio based multifactor-dimensionality reduction method for detecting gene-gene interactions
    • Chung Y, Lee SY, Elston RC, Park T (2007). Odds ratio based multifactor-dimensionality reduction method for detecting gene-gene interactions. Bioinformatics 23: 71-76.
    • (2007) Bioinformatics , vol.23 , pp. 71-76
    • Chung, Y.1    Lee, S.Y.2    Elston, R.C.3    Park, T.4
  • 7
    • 34047272692 scopus 로고    scopus 로고
    • A high-density whole-genome association study reveals that APOE is the major susceptibility gene for sporadic late-onset Alzheimer;s disease
    • Coon KD, Myers AJ, Craig DW, Webster JA, Pearson JV, Lince DH et al. (2007). A high-density whole-genome association study reveals that APOE is the major susceptibility gene for sporadic late-onset Alzheimer;s disease. J Clin Psychiatry 68: 613.
    • (2007) J Clin Psychiatry , vol.68 , pp. 613
    • Coon, K.D.1    Myers, A.J.2    Craig, D.W.3    Webster, J.A.4    Pearson, J.V.5    Lince, D.H.6
  • 8
    • 34249832377 scopus 로고
    • A Bayesian method for the induction of probabilistic networks from data
    • Cooper G, Herskovits E (1992). A Bayesian method for the induction of probabilistic networks from data. Mach Learn 9: 309-347.
    • (1992) Mach Learn , vol.9 , pp. 309-347
    • Cooper, G.1    Herskovits, E.2
  • 9
    • 67349166946 scopus 로고    scopus 로고
    • Genome-wide association studies: Detecting gene-gene interactions that underlie human diseases
    • Cordell HJ (2009). Genome-wide association studies: detecting gene-gene interactions that underlie human diseases. Nat Rev Genet 10: 392-404.
    • (2009) Nat Rev Genet , vol.10 , pp. 392-404
    • Cordell, H.J.1
  • 10
  • 12
    • 38049078695 scopus 로고    scopus 로고
    • Multistage designs in the genomic era: Providing balance in complex disease studies
    • Dube MP, Schmidt S, Hauser E (2007). Multistage designs in the genomic era: providing balance in complex disease studies. Genet Epidemiol 31(Suppl 1): S1-S6.
    • (2007) Genet Epidemiol , vol.31 , Issue.SUPPL. 1
    • Dube, M.P.1    Schmidt, S.2    Hauser, E.3
  • 13
    • 77249127732 scopus 로고    scopus 로고
    • Powerful Bayesian gene-gene interaction analysis
    • Ferreira T, Donnelly P, Marchini J (2007). Powerful Bayesian gene-gene interaction analysis. Am J Hum Genet 81(Suppl): 32.
    • (2007) Am J Hum Genet , vol.81 , Issue.SUPPL. , pp. 32
    • Ferreira, T.1    Donnelly, P.2    Marchini, J.3
  • 15
    • 51349122031 scopus 로고    scopus 로고
    • A method for detecting epistasis in geneome-wide studies using casecontrol multi locus association analysis
    • Gayan J, González-Pérez A, Bermudo F, Sáez ME, Royo JL, Quintas A et al. (2008). A method for detecting epistasis in geneome-wide studies using casecontrol multi locus association analysis. BMC Genomics 9: 360.
    • (2008) BMC Genomics , vol.9 , pp. 360
    • Gayan, J.1    González-Pérez, A.2    Bermudo, F.3    Sáez, M.E.4    Royo, J.L.5    Quintas, A.6
  • 16
    • 84901057542 scopus 로고    scopus 로고
    • A robust multifactor dimensionality reduction method for detecting gene-gene interactions with application to the genetic analysis of bladder cancer susceptibility
    • Gui J, Andrew AS, Andrews P, Nelson HM, Kelsey KT, Karagas MR et al. (2007). A robust multifactor dimensionality reduction method for detecting gene-gene interactions with application to the genetic analysis of bladder cancer susceptibility. Ann Hum Genet 23: 71-76.
    • (2007) Ann Hum Genet , vol.23 , pp. 71-76
    • Gui, J.1    Andrew, A.S.2    Andrews, P.3    Nelson, H.M.4    Kelsey, K.T.5    Karagas, M.R.6
  • 18
    • 79959918492 scopus 로고    scopus 로고
    • Evolving hard problems: Generating human genetics datasets with a complex etiology
    • Himmelstein DS, Greene CS, Moore JH (2011). Evolving hard problems: generating human genetics datasets with a complex etiology. Bio Data Mining 4: 21.
    • (2011) Bio Data Mining , vol.4 , pp. 21
    • Himmelstein, D.S.1    Greene, C.S.2    Moore, J.H.3
  • 19
    • 70350469056 scopus 로고    scopus 로고
    • The complexity of cell signaling and the need for a new mechanics
    • Hlavacek W, Faeder J (2009). The complexity of cell signaling and the need for a new mechanics. Sciences 2: pe46.
    • (2009) Sciences , vol.2
    • Hlavacek, W.1    Faeder, J.2
  • 20
    • 67651222400 scopus 로고    scopus 로고
    • A flexible and accurate genotype imputation method for the next generation of genome-wide association studies
    • Howie BN, Donnelly P, Marchini J (2009). A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 5: e1000529.
    • (2009) PLoS Genet , vol.5
    • Howie, B.N.1    Donnelly, P.2    Marchini, J.3
  • 21
    • 25444528447 scopus 로고    scopus 로고
    • Feature selection and classification for microarray data analysis: Evolutionary methods for identifying predictive genes
    • Jirapech-Umpai T, Aitken S (2005). Feature selection and classification for microarray data analysis: evolutionary methods for identifying predictive genes. BMC Bioinfor-matics 6: 146.
    • (2005) BMC Bioinfor-matics , vol.6 , pp. 146
    • Jirapech-Umpai, T.1    Aitken, S.2
  • 22
    • 66249147910 scopus 로고    scopus 로고
    • Allelic-based gene-gene interaction associated with quantitative traits
    • Jung J, Sun B, Kwon D, Koller DL, Foroud TM (2009). Allelic-based gene-gene interaction associated with quantitative traits. Genet Epidemiol 33: 332-343.
    • (2009) Genet Epidemiol , vol.33 , pp. 332-343
    • Jung, J.1    Sun, B.2    Kwon, D.3    Koller, D.L.4    Foroud, T.M.5
  • 24
    • 35748972938 scopus 로고    scopus 로고
    • Log-linear model-based multifactor dimensionality reduction method to detect gene-gene interactions
    • Lee SY, Chung Y, Elston RC, Kim Y, Park T (2007). Log-linear model-based multifactor dimensionality reduction method to detect gene-gene interactions. Bioinformatics 23:19 2589-2595.
    • (2007) Bioinformatics , vol.23 , Issue.19 , pp. 2589-2595
    • Lee, S.Y.1    Chung, Y.2    Elston, R.C.3    Kim, Y.4    Park, T.5
  • 25
    • 0036139278 scopus 로고    scopus 로고
    • Gene selection for sample classification based on gene expression data: Study of sensitivity to choice of parameters of the GA/KNN method
    • Li L, Weinberg C, Darden T, Pedersen L (2001). Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method. Bioinformatics 17: 1131-1142.
    • (2001) Bioinformatics , vol.17 , pp. 1131-1142
    • Li, L.1    Weinberg, C.2    Darden, T.3    Pedersen, L.4
  • 26
    • 38349038412 scopus 로고    scopus 로고
    • Candidate single nucleotide polymorphisms from a genome wide association study of Alzheimer disease
    • Li H, Wetten S, Li L, St Jean PL, Upmanyu R, Surh L et al. (2008a). Candidate single nucleotide polymorphisms from a genome wide association study of Alzheimer disease. Arch Neurol 65: 45-53.
    • (2008) Arch Neurol , vol.65 , pp. 45-53
    • Li, H.1    Wetten, S.2    Li, L.3    St Jean, P.L.4    Upmanyu, R.5    Surh, L.6
  • 27
    • 57349087128 scopus 로고    scopus 로고
    • Mixture model approach in gene x gene interaction for binary phenotype
    • Li L, Yu M, Jason RD, Shen C, Azzouz F, McLeod HL et al. (2008b). Mixture model approach in gene x gene interaction for binary phenotype. J Biopharm Stat 18: 1150-1177.
    • (2008) J Biopharm Stat , vol.18 , pp. 1150-1177
    • Li, L.1    Yu, M.2    Jason, R.D.3    Shen, C.4    Azzouz, F.5    McLeod, H.L.6
  • 28
    • 70349885499 scopus 로고    scopus 로고
    • An algorithm for learning maximum entropy probability models of disease risk that efficiently searches and sparingly encodes multilocus genomic interactions
    • Miller DJ, Zhang Y, Yu G, Liu Y, Chen L, Langefeld CD et al. (2009). An algorithm for learning maximum entropy probability models of disease risk that efficiently searches and sparingly encodes multilocus genomic interactions. Bioin formatics 25: 2478-2485.
    • (2009) Bioin Formatics , vol.25 , pp. 2478-2485
    • Miller, D.J.1    Zhang, Y.2    Yu, G.3    Liu, Y.4    Chen, L.5    Langefeld, C.D.6
  • 29
    • 77949497074 scopus 로고    scopus 로고
    • Bioinformatics challenges for genome-wide association studies
    • Moore JH, Asselbergs FW, Wiliams SM (2010). Bioinformatics challenges for genome-wide association studies. Bioinformatics 26: 445-455.
    • (2010) Bioinformatics , vol.26 , pp. 445-455
    • Moore, J.H.1    Asselbergs, F.W.2    Wiliams, S.M.3
  • 31
    • 69449084184 scopus 로고    scopus 로고
    • Identification of gene-gene interactions in the presence of missing data using the multifactor dimensionality reduction method
    • Namkung J, Elston R, Yang J, Park T (2009). Identification of gene-gene interactions in the presence of missing data using the multifactor dimensionality reduction method. Genet Epidemiol 33: 646-656.
    • (2009) Genet Epidemiol , vol.33 , pp. 646-656
    • Namkung, J.1    Elston, R.2    Yang, J.3    Park, T.4
  • 32
    • 0037245772 scopus 로고    scopus 로고
    • Genetic algorithms applied to multi-class prediction for the analysis of gene expressiondata
    • Ooi C, Tan P (2003). Genetic algorithms applied to multi-class prediction for the analysis of gene expressiondata. Bioinformatics 19: 3744.
    • (2003) Bioinformatics , vol.19 , pp. 3744
    • Ooi, C.1    Tan, P.2
  • 34
    • 37249080278 scopus 로고    scopus 로고
    • Penalized logistic regression for detecting gene interactions
    • Park MY, Hastie T (2008). Penalized logistic regression for detecting gene interactions. Biostatistics 9: 30-50.
    • (2008) Biostatistics , vol.9 , pp. 30-50
    • Park, M.Y.1    Hastie, T.2
  • 35
  • 37
    • 0034973569 scopus 로고    scopus 로고
    • Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer
    • Ritchie MD, Hahn LW, Roodi N, Bailey LR, Dupont WD et al. (2001). Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. Am J Hum Genet 69: 138-147.
    • (2001) Am J Hum Genet , vol.69 , pp. 138-147
    • Ritchie, M.D.1    Hahn, L.W.2    Roodi, N.3    Bailey, L.R.4    Dupont, W.D.5
  • 38
    • 35748932917 scopus 로고    scopus 로고
    • A review of feature selection techniques in bioinformatics
    • Saeys Y, Inza I, Larranaga P (2007). A review of feature selection techniques in bioinformatics. Bioinformatics 23: 2507-2517.
    • (2007) Bioinformatics , vol.23 , pp. 2507-2517
    • Saeys, Y.1    Inza, I.2    Larranaga, P.3
  • 39
    • 4043081192 scopus 로고    scopus 로고
    • Data mining and genetic algorithm based gene/SNP selection
    • Shah SC, Kusiak A (2004). Data mining and genetic algorithm based gene/SNP selection. Artif Intell Med 31:183-196.
    • (2004) Artif Intell Med , vol.31 , pp. 183-196
    • Shah, S.C.1    Kusiak, A.2
  • 40
    • 77954646488 scopus 로고    scopus 로고
    • Analysis of genome-wide association study (GWAS) data looking for replicating signals in Alzheimer's disease (AD)
    • Shi H, Medway C, Bullock J, Brown K, Kalsheker N, Morgan K (2010). Analysis of genome-wide association study (GWAS) data looking for replicating signals in Alzheimer's disease (AD). Int J Mol Epidemiol Genet 1:1 53-66.
    • (2010) Int J Mol Epidemiol Genet , vol.1 , Issue.1 , pp. 53-66
    • Shi, H.1    Medway, C.2    Bullock, J.3    Brown, K.4    Kalsheker, N.5    Morgan, K.6
  • 41
    • 79958840472 scopus 로고    scopus 로고
    • Travelling the world of gene-gene interactions
    • Steen KV (2011). Travelling the world of gene-gene interactions. Briefings Bioinform 10: 1-19.
    • (2011) Briefings Bioinform , vol.10 , pp. 1-19
    • Steen, K.V.1
  • 42
    • 34247338434 scopus 로고    scopus 로고
    • A balanced accuracy function for epistasis modeling in imbalanced datasets using multifactor dimensionality reduction
    • Velez DR, White BC, Motsinger AA, Bush WS, Ritchie MD, Williams SM et al. (2007). A balanced accuracy function for epistasis modeling in imbalanced datasets using multifactor dimensionality reduction. Genet Epidemiol 31:4 306-315.
    • (2007) Genet Epidemiol , vol.31 , Issue.4 , pp. 306-315
    • Velez, D.R.1    White, B.C.2    Motsinger, A.A.3    Bush, W.S.4    Ritchie, M.D.5    Williams, S.M.6
  • 43
    • 79953790148 scopus 로고    scopus 로고
    • A Bayesian method for identifying genetic interactions
    • Visweswaran S, Wong AL, Barmada MM (2009). A Bayesian method for identifying genetic interactions. AMIA 2009: 673-677.
    • (2009) AMIA , vol.2009 , pp. 673-677
    • Visweswaran, S.1    Wong, A.L.2    Barmada, M.M.3
  • 44
    • 80051982682 scopus 로고    scopus 로고
    • Modified cuckoo search: A new gradient free optimisation algorithm
    • Walton S, Hassan O, Morgan K, Brown MR (2011). Modified cuckoo search: a new gradient free optimisation algorithm. Chaos Solitons Fractals 44:9 710-718.
    • (2011) Chaos Solitons Fractals , vol.44 , Issue.9 , pp. 710-718
    • Walton, S.1    Hassan, O.2    Morgan, K.3    Brown, M.R.4
  • 45
    • 65849377200 scopus 로고    scopus 로고
    • A partial least square approach for modeling gene-gene and gene-environment interactions when multiple markers are genotyped
    • Wang T (2009). A partial least square approach for modeling gene-gene and gene-environment interactions when multiple markers are genotyped. Genet Epidemiol 33: 644-651.
    • (2009) Genet Epidemiol , vol.33 , pp. 644-651
    • Wang, T.1
  • 46
    • 0033515888 scopus 로고    scopus 로고
    • Complexity in biological signaling systems
    • Weng G, Bhalla U, Iyengar R (1999). Complexity in biological signaling systems. Science 284: 92-96.
    • (1999) Science , vol.284 , pp. 92-96
    • Weng, G.1    Bhalla, U.2    Iyengar, R.3
  • 47
    • 62549115747 scopus 로고    scopus 로고
    • Genome-wide association analysis by lasso penalized logistic regression
    • Wu TT., Chen YF, Hastie T, Sobel E, Lange K (2009). Genome-wide association analysis by lasso penalized logistic regression. Bioinformatics 25: 714-721.
    • (2009) Bioinformatics , vol.25 , pp. 714-721
    • Wu, T.T.1    Chen, Y.F.2    Hastie, T.3    Sobel, E.4    Lange, K.5
  • 48
    • 77958048688 scopus 로고    scopus 로고
    • A genetic ensemble approach for gene-gene interaction identification
    • Yang P, Ho JW, Zomaya A, Zhou BB (2010). A genetic ensemble approach for gene-gene interaction identification. BMC Bioinformatics 11: 524.
    • (2010) BMC Bioinformatics , vol.11 , pp. 524
    • Yang, P.1    Ho, J.W.2    Zomaya, A.3    Zhou, B.B.4
  • 51
    • 77952894198 scopus 로고    scopus 로고
    • A multi-filter enhanced genetic ensemble system for gene selection and sample classification of microarray data
    • Yang, Zhou BB, Zhang Z, Zomaya AY (2010). A multi-filter enhanced genetic ensemble system for gene selection and sample classification of microarray data. BMC Bioinformatics 11(Suppl 1): S5.
    • (2010) BMC Bioinformatics , vol.11 , Issue.SUPPL. 1
    • Yang Zhou, B.B.1    Zhang, Z.2    Zomaya, A.Y.3
  • 52
    • 34548352849 scopus 로고    scopus 로고
    • Bayesian inference of epistatic interactions in case-control studies
    • Zhang Y, Liu JS (2007). Bayesian inference of epistatic interactions in case-control studies. Nat Genet 39: 1167-1173.
    • (2007) Nat Genet , vol.39 , pp. 1167-1173
    • Zhang, Y.1    Liu, J.S.2
  • 53
    • 22144459429 scopus 로고    scopus 로고
    • A penalized maximum likelihood method for estimating epistatic effects of QTL
    • Zhang YM, Xu S (2005). A penalized maximum likelihood method for estimating epistatic effects of QTL. Heredity 95: 96-104.
    • (2005) Heredity , vol.95 , pp. 96-104
    • Zhang, Y.M.1    Xu, S.2
  • 54
    • 71549138167 scopus 로고    scopus 로고
    • An ensemble of classifiers with genetic algorithm based feature selection
    • Zhang Z, Yang P (2008). An ensemble of classifiers with genetic algorithm based feature selection. IEEE Intelligent Informatics Bulletin 9: 18-24.
    • (2008) IEEE Intelligent Informatics Bulletin , vol.9 , pp. 18-24
    • Zhang, Z.1    Yang, P.2
  • 55
    • 33751074962 scopus 로고    scopus 로고
    • Test for interaction between two unlinked loci
    • Zhao J, Xiong M (2006). Test for interaction between two unlinked loci. Am J Hum Genet 79: 831-845.
    • (2006) Am J Hum Genet , vol.79 , pp. 831-845
    • Zhao, J.1    Xiong, M.2


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