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Volumn 3, Issue 1, 2013, Pages

Improved branch and bound algorithm for detecting SNP-SNP interactions in breast cancer

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EID: 84896354885     PISSN: None     EISSN: 20439113     Source Type: Journal    
DOI: 10.1186/2043-9113-3-4     Document Type: Article
Times cited : (14)

References (37)
  • 1
    • 67349166946 scopus 로고    scopus 로고
    • Detecting gene-gene interactions that underlie human diseases
    • 2872761, 19434077
    • Cordell HJ. Detecting gene-gene interactions that underlie human diseases. Nat Rev Genet 2009, 10(6):392-404. 2872761, 19434077.
    • (2009) Nat Rev Genet , vol.10 , Issue.6 , pp. 392-404
    • Cordell, H.J.1
  • 2
    • 64549155302 scopus 로고    scopus 로고
    • Combinational polymorphisms of seven CXCL12-related genes are protective against breast cancer in Taiwan
    • 10.1089/omi.2008.0050, 19196101
    • Lin GT, Tseng HF, Yang CH, Hou MF, Chuang LY, Tai HT, Tai MH, Cheng YH, Wen CH, Liu CS. Combinational polymorphisms of seven CXCL12-related genes are protective against breast cancer in Taiwan. OMICS 2009, 13(2):165-172. 10.1089/omi.2008.0050, 19196101.
    • (2009) OMICS , vol.13 , Issue.2 , pp. 165-172
    • Lin, G.T.1    Tseng, H.F.2    Yang, C.H.3    Hou, M.F.4    Chuang, L.Y.5    Tai, H.T.6    Tai, M.H.7    Cheng, Y.H.8    Wen, C.H.9    Liu, C.S.10
  • 3
    • 54149088214 scopus 로고    scopus 로고
    • Epistasis-the essential role of gene interactions in the structure and evolution of genetic systems
    • 10.1038/nrg2452, 2689140, 18852697
    • Phillips PC. Epistasis-the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet 2008, 9(11):855-867. 10.1038/nrg2452, 2689140, 18852697.
    • (2008) Nat Rev Genet , vol.9 , Issue.11 , pp. 855-867
    • Phillips, P.C.1
  • 4
    • 77956395423 scopus 로고    scopus 로고
    • BOOST: A fast approach to detecting gene-gene interactions in genome-wide case-control studies
    • 10.1016/j.ajhg.2010.07.021, 2933337, 20817139
    • Wan X, Yang C, Yang Q, Xue H, Fan X, Tang NLS, Yu W. BOOST: A fast approach to detecting gene-gene interactions in genome-wide case-control studies. Am J Hum Genet 2010, 87:325-340. 10.1016/j.ajhg.2010.07.021, 2933337, 20817139.
    • (2010) Am J Hum Genet , vol.87 , pp. 325-340
    • Wan, X.1    Yang, C.2    Yang, Q.3    Xue, H.4    Fan, X.5    Tang, N.L.S.6    Yu, W.7
  • 5
    • 80052880887 scopus 로고    scopus 로고
    • Methods for identifying SNP interactions: a review on variations of logic regression, random forest and bayesian logistic regression
    • Chen CCM, Schwender H, Keith J, Nunkesser R, Mengersen K, Macrossan P. Methods for identifying SNP interactions: a review on variations of logic regression, random forest and bayesian logistic regression. IEEE/ACM Trans Comput Biol Bioinform 2011, 8(6):1580-1591.
    • (2011) IEEE/ACM Trans Comput Biol Bioinform , vol.8 , Issue.6 , pp. 1580-1591
    • Chen, C.C.M.1    Schwender, H.2    Keith, J.3    Nunkesser, R.4    Mengersen, K.5    Macrossan, P.6
  • 6
    • 37249085147 scopus 로고    scopus 로고
    • Identification of SNP interactions using logic regression
    • Schwender H, Ickstadt K. Identification of SNP interactions using logic regression. Biostatistics 2008, 9(1):187-198.
    • (2008) Biostatistics , vol.9 , Issue.1 , pp. 187-198
    • Schwender, H.1    Ickstadt, K.2
  • 7
    • 0037433052 scopus 로고    scopus 로고
    • Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions
    • 10.1093/bioinformatics/btf869, 12584123
    • Hahn LW, Ritchie MD, Moore JH. Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions. Bioinformatics 2003, 19(3):376. 10.1093/bioinformatics/btf869, 12584123.
    • (2003) Bioinformatics , vol.19 , Issue.3 , pp. 376
    • Hahn, L.W.1    Ritchie, M.D.2    Moore, J.H.3
  • 8
    • 42949084703 scopus 로고    scopus 로고
    • Polymorphism interaction analysis (PIA): a method for investigating complex gene-gene interactions
    • Mechanic LE, Luke BT, Goodman JE, Chanock SJ, Harris CC. Polymorphism interaction analysis (PIA): a method for investigating complex gene-gene interactions. BMC Bioinforma 2008, 9(1):146.
    • (2008) BMC Bioinforma , vol.9 , Issue.1 , pp. 146
    • Mechanic, L.E.1    Luke, B.T.2    Goodman, J.E.3    Chanock, S.J.4    Harris, C.C.5
  • 9
    • 65849422663 scopus 로고    scopus 로고
    • Bayesian variable and model selection methods for genetic association studies
    • 10.1002/gepi.20353, 18618760
    • Fridley BL. Bayesian variable and model selection methods for genetic association studies. Genet Epidemiol 2009, 33(1):27-37. 10.1002/gepi.20353, 18618760.
    • (2009) Genet Epidemiol , vol.33 , Issue.1 , pp. 27-37
    • Fridley, B.L.1
  • 10
    • 75249087515 scopus 로고    scopus 로고
    • Predictive rule inference for epistatic interaction detection in genome-wide association studies
    • 10.1093/bioinformatics/btp622, 19880365
    • Wan X, Yang C, Yang Q, Xue H, Tang NLS, Yu WC. Predictive rule inference for epistatic interaction detection in genome-wide association studies. Bioinformatics 2010, 26(1):30-37. 10.1093/bioinformatics/btp622, 19880365.
    • (2010) Bioinformatics , vol.26 , Issue.1 , pp. 30-37
    • Wan, X.1    Yang, C.2    Yang, Q.3    Xue, H.4    Tang, N.L.S.5    Yu, W.C.6
  • 11
    • 77954485448 scopus 로고    scopus 로고
    • On safari to random jungle: a fast implementation of random forests for high-dimensional data
    • 10.1093/bioinformatics/btq257, 2894507, 20505004
    • Schwarz DF, Konig IR, Ziegler A. On safari to random jungle: a fast implementation of random forests for high-dimensional data. Bioinformatics 2010, 26(14):1752. 10.1093/bioinformatics/btq257, 2894507, 20505004.
    • (2010) Bioinformatics , vol.26 , Issue.14 , pp. 1752
    • Schwarz, D.F.1    Konig, I.R.2    Ziegler, A.3
  • 12
    • 40349093248 scopus 로고    scopus 로고
    • Odds ratio-based genetic algorithms for generating SNP barcodes of genotypes to predict disease susceptibility
    • 10.1089/omi.2007.0036, 18266556
    • Chang HW, Chuang LY, Ho CH, Chang PL, Yang CH. Odds ratio-based genetic algorithms for generating SNP barcodes of genotypes to predict disease susceptibility. OMICS 2008, 12(1):71-81. 10.1089/omi.2007.0036, 18266556.
    • (2008) OMICS , vol.12 , Issue.1 , pp. 71-81
    • Chang, H.W.1    Chuang, L.Y.2    Ho, C.H.3    Chang, P.L.4    Yang, C.H.5
  • 14
    • 76849095353 scopus 로고    scopus 로고
    • Gene function prediction with gene interaction networks: a context graph kernel approach
    • Li X, Chen H, Li J, Zhang Z. Gene function prediction with gene interaction networks: a context graph kernel approach. IEEE Trans Inf Technol Biomed 2010, 14(1):119-128.
    • (2010) IEEE Trans Inf Technol Biomed , vol.14 , Issue.1 , pp. 119-128
    • Li, X.1    Chen, H.2    Li, J.3    Zhang, Z.4
  • 15
    • 84861833559 scopus 로고    scopus 로고
    • Chaotic particle swarm optimization for detecting SNP-SNP interactions for CXCL12-related genes in breast cancer prevention
    • 10.1097/CEJ.0b013e32834e31f6, 22127289
    • Chuang LY, Chang HW, Lin MC, Yang CH. Chaotic particle swarm optimization for detecting SNP-SNP interactions for CXCL12-related genes in breast cancer prevention. Eur J Cancer Prev 2012, 21(4):336-342. 10.1097/CEJ.0b013e32834e31f6, 22127289.
    • (2012) Eur J Cancer Prev , vol.21 , Issue.4 , pp. 336-342
    • Chuang, L.Y.1    Chang, H.W.2    Lin, M.C.3    Yang, C.H.4
  • 16
    • 84862059143 scopus 로고    scopus 로고
    • An improved PSO algorithm for generating protective SNP barcodes in breast cancer
    • 10.1371/journal.pone.0037018, 3356401, 22623973
    • Chuang LY, Lin YD, Chang HW, Yang CH. An improved PSO algorithm for generating protective SNP barcodes in breast cancer. PLoS One 2012, 7(5):e37018. 10.1371/journal.pone.0037018, 3356401, 22623973.
    • (2012) PLoS One , vol.7 , Issue.5
    • Chuang, L.Y.1    Lin, Y.D.2    Chang, H.W.3    Yang, C.H.4
  • 17
    • 33847059518 scopus 로고    scopus 로고
    • Detection of gene x gene interactions in genome-wide association studies of human population data
    • 10.1159/000099179, 17283436
    • Musani SK, Shriner D, Liu NJ, Feng R, Coffey CS, Yi NJ, Tiwari HK, Allison DB. Detection of gene x gene interactions in genome-wide association studies of human population data. Hum Hered 2007, 63(2):67-84. 10.1159/000099179, 17283436.
    • (2007) Hum Hered , vol.63 , Issue.2 , pp. 67-84
    • Musani, S.K.1    Shriner, D.2    Liu, N.J.3    Feng, R.4    Coffey, C.S.5    Yi, N.J.6    Tiwari, H.K.7    Allison, D.B.8
  • 18
    • 85007745189 scopus 로고    scopus 로고
    • Statistics notes: the odds ratio
    • Bland JM, Altman DG. Statistics notes: the odds ratio. Br Med J 2000, 320(7247):1468.
    • (2000) Br Med J , vol.320 , Issue.7247 , pp. 1468
    • Bland, J.M.1    Altman, D.G.2
  • 19
    • 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. Odds ratio based multifactor-dimensionality reduction method for detecting gene-gene interactions. Bioinformatics 2006, 23(1):71.
    • (2006) Bioinformatics , vol.23 , Issue.1 , pp. 71
    • Chung, Y.1    Lee, S.Y.2    Elston, R.C.3    Park, T.4
  • 20
    • 84864004527 scopus 로고    scopus 로고
    • Sequence-based polymorphisms in the mitochondrial D-loop and potential SNP predictors for chronic dialysis
    • 10.1371/journal.pone.0041125, 3399812, 22815937
    • Chen JB, Yang YH, Lee WC, Liou CW, Lin TK, Chung YH, Chuang LY, Yang CH, Chang HW. Sequence-based polymorphisms in the mitochondrial D-loop and potential SNP predictors for chronic dialysis. PLoS One 2012, 7(7):e41125. 10.1371/journal.pone.0041125, 3399812, 22815937.
    • (2012) PLoS One , vol.7 , Issue.7
    • Chen, J.B.1    Yang, Y.H.2    Lee, W.C.3    Liou, C.W.4    Lin, T.K.5    Chung, Y.H.6    Chuang, L.Y.7    Yang, C.H.8    Chang, H.W.9
  • 21
    • 73249122912 scopus 로고    scopus 로고
    • Polymorphisms in the xenobiotic transporter multidrug resistance 1(MDR 1) and interaction with meat intake in relation to risk of colorectal cancer in a danish prospective case-cohort study
    • 10.1186/1471-2407-9-407, 2797527, 19930591
    • Andersen V, Ostergaard M, Christensen J, Overvad K, Tjonneland A, Vogel U. Polymorphisms in the xenobiotic transporter multidrug resistance 1(MDR 1) and interaction with meat intake in relation to risk of colorectal cancer in a danish prospective case-cohort study. BMC Cancer 2009, 9(1):407. 10.1186/1471-2407-9-407, 2797527, 19930591.
    • (2009) BMC Cancer , vol.9 , Issue.1 , pp. 407
    • Andersen, V.1    Ostergaard, M.2    Christensen, J.3    Overvad, K.4    Tjonneland, A.5    Vogel, U.6
  • 22
    • 79957442050 scopus 로고    scopus 로고
    • MDM2 SNP309, gene-gene interaction, and tumor susceptibility: an updated meta-analysis
    • 10.1186/1471-2407-11-208, 3115916, 21619694
    • Wan Y, Wu W, Yin Z, Guan P, Zhou B. MDM2 SNP309, gene-gene interaction, and tumor susceptibility: an updated meta-analysis. BMC Cancer 2011, 11(1):208. 10.1186/1471-2407-11-208, 3115916, 21619694.
    • (2011) BMC Cancer , vol.11 , Issue.1 , pp. 208
    • Wan, Y.1    Wu, W.2    Yin, Z.3    Guan, P.4    Zhou, B.5
  • 23
    • 33644854273 scopus 로고    scopus 로고
    • Exploring SNP SNP interactions and colon cancer risk using polymorphism interaction analysis
    • 10.1002/ijc.21523, 1451415, 16217767
    • Goodman JE, Mechanic LE, Luke BT, Ambs S, Chanock S, Harris CC. Exploring SNP SNP interactions and colon cancer risk using polymorphism interaction analysis. Int J Cancer 2006, 118(7):1790-1797. 10.1002/ijc.21523, 1451415, 16217767.
    • (2006) Int J Cancer , vol.118 , Issue.7 , pp. 1790-1797
    • Goodman, J.E.1    Mechanic, L.E.2    Luke, B.T.3    Ambs, S.4    Chanock, S.5    Harris, C.C.6
  • 24
    • 3042521641 scopus 로고    scopus 로고
    • Deficient host-bacteria interactions in inflammatory bowel disease? The toll-like receptor (TLR)-4 Asp299gly polymorphism is associated with Crohn's disease and ulcerative colitis
    • 10.1136/gut.2003.030205, 1774122, 15194649
    • Franchimont D, Vermeire S, El Housni H, Pierik M, Van Steen K, Gustot T, Quertinmont E, Abramowicz M, Van Gossum A, Deviere J. Deficient host-bacteria interactions in inflammatory bowel disease? The toll-like receptor (TLR)-4 Asp299gly polymorphism is associated with Crohn's disease and ulcerative colitis. Gut 2004, 53(7):987. 10.1136/gut.2003.030205, 1774122, 15194649.
    • (2004) Gut , vol.53 , Issue.7 , pp. 987
    • Franchimont, D.1    Vermeire, S.2    El Housni, H.3    Pierik, M.4    Van Steen, K.5    Gustot, T.6    Quertinmont, E.7    Abramowicz, M.8    Van Gossum, A.9    Deviere, J.10
  • 25
    • 68949196784 scopus 로고    scopus 로고
    • The role of TNF genetic variants and the interaction with cigarette smoking for gastric cancer risk: a nested case-control study
    • 10.1186/1471-2407-9-238, 2725140, 19615068
    • Yang JJ, Ko KP, Cho LY, Shin A, Gwack J, Chang SH, Shin HR, Yoo KY, Kang D, Park SK. The role of TNF genetic variants and the interaction with cigarette smoking for gastric cancer risk: a nested case-control study. BMC Cancer 2009, 9:238. 10.1186/1471-2407-9-238, 2725140, 19615068.
    • (2009) BMC Cancer , vol.9 , pp. 238
    • Yang, J.J.1    Ko, K.P.2    Cho, L.Y.3    Shin, A.4    Gwack, J.5    Chang, S.H.6    Shin, H.R.7    Yoo, K.Y.8    Kang, D.9    Park, S.K.10
  • 26
    • 33744937046 scopus 로고    scopus 로고
    • Machine learning for detecting gene-gene interactions: a review
    • 10.2165/00822942-200605020-00002, 3244050, 16722772
    • McKinney BA, Reif DM, Ritchie MD, Moore JH. Machine learning for detecting gene-gene interactions: a review. Appl Bioinformatics 2006, 5(2):77-88. 10.2165/00822942-200605020-00002, 3244050, 16722772.
    • (2006) Appl Bioinformatics , vol.5 , Issue.2 , pp. 77-88
    • McKinney, B.A.1    Reif, D.M.2    Ritchie, M.D.3    Moore, J.H.4
  • 27
    • 68149144254 scopus 로고    scopus 로고
    • Novel generating protective single nucleotide polymorphism barcode for breast cancer using particle swarm optimization
    • 10.1016/j.canep.2009.07.001, 19679063
    • Yang CH, Chang HW, Cheng YH, Chuang LY. Novel generating protective single nucleotide polymorphism barcode for breast cancer using particle swarm optimization. Cancer Epidemiol 2009, 33(2):147-154. 10.1016/j.canep.2009.07.001, 19679063.
    • (2009) Cancer Epidemiol , vol.33 , Issue.2 , pp. 147-154
    • Yang, C.H.1    Chang, H.W.2    Cheng, Y.H.3    Chuang, L.Y.4
  • 28
    • 3042527351 scopus 로고    scopus 로고
    • Fast branch & bound algorithms for optimal feature selection
    • 10.1109/TPAMI.2004.28, 18579948
    • Somol P, Pudil P, Kittler J. Fast branch & bound algorithms for optimal feature selection. IEEE Trans Pattern Anal Mach Intell 2004, 26(7):900-912. 10.1109/TPAMI.2004.28, 18579948.
    • (2004) IEEE Trans Pattern Anal Mach Intell , vol.26 , Issue.7 , pp. 900-912
    • Somol, P.1    Pudil, P.2    Kittler, J.3
  • 29
    • 0017535866 scopus 로고
    • A branch and bound algorithm for feature subset selection
    • Narendra PM, Fukunaga K. A branch and bound algorithm for feature subset selection. IEEE Trans Comput 1977, 100(9):917-922.
    • (1977) IEEE Trans Comput , vol.100 , Issue.9 , pp. 917-922
    • Narendra, P.M.1    Fukunaga, K.2
  • 30
    • 0038329332 scopus 로고    scopus 로고
    • An improved branch and bound algorithm for feature selection
    • Chen X. An improved branch and bound algorithm for feature selection. Pattern Recognit Lett 2003, 24(12):1925-1933.
    • (2003) Pattern Recognit Lett , vol.24 , Issue.12 , pp. 1925-1933
    • Chen, X.1
  • 31
    • 46249123633 scopus 로고    scopus 로고
    • A maximum common substructure-based algorithm for searching and predicting drug-like compounds
    • 10.1093/bioinformatics/btn186, 2718661, 18586736
    • Cao Y, Jiang T, Girke T. A maximum common substructure-based algorithm for searching and predicting drug-like compounds. Bioinformatics 2008, 24(13):i366. 10.1093/bioinformatics/btn186, 2718661, 18586736.
    • (2008) Bioinformatics , vol.24 , Issue.13
    • Cao, Y.1    Jiang, T.2    Girke, T.3
  • 32
    • 46249128543 scopus 로고    scopus 로고
    • Identifying functional modules in protein-protein interaction networks: an integrated exact approach
    • 10.1093/bioinformatics/btn161, 2718639, 18586718
    • Dittrich MT, Klau GW, Rosenwald A, Dandekar T, Muller T. Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics 2008, 24(13):i223. 10.1093/bioinformatics/btn161, 2718639, 18586718.
    • (2008) Bioinformatics , vol.24 , Issue.13
    • Dittrich, M.T.1    Klau, G.W.2    Rosenwald, A.3    Dandekar, T.4    Muller, T.5
  • 33
    • 34548659932 scopus 로고    scopus 로고
    • A recursive branch-and-bound algorithm for the rectangular guillotine strip packing problem
    • Cui Y, Yang Y, Cheng X, Song P. A recursive branch-and-bound algorithm for the rectangular guillotine strip packing problem. Comput Oper Res 2008, 35(4):1281-1291.
    • (2008) Comput Oper Res , vol.35 , Issue.4 , pp. 1281-1291
    • Cui, Y.1    Yang, Y.2    Cheng, X.3    Song, P.4
  • 34
    • 60649085547 scopus 로고    scopus 로고
    • Sequencing surgical cases in a day-care environment: an exact branch-and-price approach
    • Cardoen B, Demeulemeester E, Belin J. Sequencing surgical cases in a day-care environment: an exact branch-and-price approach. Comput Oper Res 2009, 36(9):2660-2669.
    • (2009) Comput Oper Res , vol.36 , Issue.9 , pp. 2660-2669
    • Cardoen, B.1    Demeulemeester, E.2    Belin, J.3
  • 35
    • 0037242377 scopus 로고    scopus 로고
    • Absence of epistasis for grain yield in elite maize hybrids
    • Hinze LL, Lamkey KR. Absence of epistasis for grain yield in elite maize hybrids. Crop Sci 2003, 43(1):46-56.
    • (2003) Crop Sci , vol.43 , Issue.1 , pp. 46-56
    • Hinze, L.L.1    Lamkey, K.R.2
  • 36
    • 60849106351 scopus 로고    scopus 로고
    • Breast biopsy patterns and outcomes in surveillance, epidemiology, and end results-medicare data
    • 10.1002/cncr.24085, 3291169, 19152430
    • Friese CR, Neville BA, Edge SB, Hassett MJ, Earle CC. Breast biopsy patterns and outcomes in surveillance, epidemiology, and end results-medicare data. Cancer 2009, 115(4):716-724. 10.1002/cncr.24085, 3291169, 19152430.
    • (2009) Cancer , vol.115 , Issue.4 , pp. 716-724
    • Friese, C.R.1    Neville, B.A.2    Edge, S.B.3    Hassett, M.J.4    Earle, C.C.5
  • 37
    • 84950756067 scopus 로고
    • Computing an exact confidence interval for the common odds ratio in several 2 x 2 contingency tables
    • Mehta CR, Patel NR, Gray R. Computing an exact confidence interval for the common odds ratio in several 2 x 2 contingency tables. J Am Stat Assoc 1985, 80(392):969-973.
    • (1985) J Am Stat Assoc , vol.80 , Issue.392 , pp. 969-973
    • Mehta, C.R.1    Patel, N.R.2    Gray, R.3


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