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Volumn 844, Issue , 2014, Pages 153-187

Systems analysis of high-throughput data

Author keywords

Genomics; High throughput data; Machine learning; Microarrays; Network models; NGS; Sequencing; Statistical analysis

Indexed keywords

ARTICLE; CELL INTERACTION; CLASS DISCOVERY; CLASSIFIER; DATA ANALYSIS; EIGENGENE; ENRICHMENT ANALYSIS; GENE CLUSTER; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOMICS; HIGH THROUGHPUT SCREENING; HIGH THROUGHPUT SEQUENCING; HUMAN; MACHINE LEARNING; MICROARRAY ANALYSIS; NEAREST SHRUNKEN CENTROID; NETWORK INFERENCE; NETWORK STATISTIC; NEXT GENERATION SEQUENCING; NONLINEAR DIMENSION REDUCTION; PARTITION DECOUPLING METHOD; PATHWAY ANALYSIS; PRINCIPAL COMPONENT ANALYSIS; PROTEOMICS; RANDOM FOREST; SINGLE NUCLEOTIDE POLYMORPHISM; SYSTEM ANALYSIS; SYSTEMS BIOLOGY; TRANSCRIPTOMICS; ANIMAL; CLUSTER ANALYSIS; GENETICS; METHODOLOGY; PROCEDURES; SIGNAL TRANSDUCTION; STATISTICAL ANALYSIS; STATISTICS AND NUMERICAL DATA;

EID: 84916219351     PISSN: 00652598     EISSN: 22148019     Source Type: Book Series    
DOI: 10.1007/978-1-4939-2095-2_8     Document Type: Article
Times cited : (22)

References (131)
  • 1
    • 33747168764 scopus 로고    scopus 로고
    • Cost-effectiveness of pharmacogenomics in clinical practice: A case study of thiopurine methyltransferase genotyping in acute lymphoblastic leukemia in Europe
    • van den Akker-van Marle ME, Gurwitz D, Detmar SB, Enzing CM, Hopkins MM, de Mesa EG, Ibarreta D. Cost-effectiveness of pharmacogenomics in clinical practice: a case study of thiopurine methyltransferase genotyping in acute lymphoblastic leukemia in Europe. Pharmacogenomics. 2006;7(5):783-92.
    • (2006) Pharmacogenomics , vol.7 , Issue.5 , pp. 783-792
    • Van Den Akker-Van Marle, M.E.1    Gurwitz, D.2    Detmar, S.B.3    Enzing, C.M.4    Hopkins, M.M.5    De Mesa, E.G.6    Ibarreta, D.7
  • 4
    • 0003509805 scopus 로고
    • Modern theories of development: An introduction to theoretical biology
    • Woodger JH, Oxford University Press, (originally published 1928)
    • Von Bertalanffy L: Modern theories of development: an introduction to theoretical biology. In: Woodger JH, transl. Oxford University Press; 1933 (originally published 1928).
    • (1933) Transl
    • Von Bertalanffy, L.1
  • 6
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • Bolstad BM, Irizarry RA, Åstrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003;19(2):185-93.
    • (2003) Bioinformatics , vol.19 , Issue.2 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Åstrand, M.3    Speed, T.P.4
  • 8
    • 79956314887 scopus 로고    scopus 로고
    • Genotype and snp calling from next-generation sequencing data
    • Nielsen R, Paul JS, Albrechtsen A, Song YS. Genotype and snp calling from next-generation sequencing data. Nat Rev Genet. 2011;12(6):443-51.
    • (2011) Nat Rev Genet , vol.12 , Issue.6 , pp. 443-451
    • Nielsen, R.1    Paul, J.S.2    Albrechtsen, A.3    Song, Y.S.4
  • 9
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies the next generation
    • Metzker ML. Sequencing technologies the next generation. Nat Rev Genet. 200911(1): 31-46.
    • (2009) Nat Rev Genet , vol.11 , Issue.1 , pp. 31-46
    • Metzker, M.L.1
  • 15
    • 33846978784 scopus 로고    scopus 로고
    • Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting
    • Dupuy A, Simon RM. Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting. J Natl Cancer Inst. 2007;99(2):147-57.
    • (2007) J Natl Cancer Inst , vol.99 , Issue.2 , pp. 147-157
    • Dupuy, A.1    Simon, R.M.2
  • 16
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B. 1995; pp. 289-300.
    • (1995) J R Stat Soc B , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 17
    • 0035733108 scopus 로고    scopus 로고
    • The control of the false discovery rate in multiple testing under dependency
    • Benjamini Y, Yekutieli, D. The control of the false discovery rate in multiple testing under dependency. Ann Stat. 2001; pp. 1165-88.
    • (2001) Ann Stat , pp. 1165-1188
    • Benjamini, Y.1    Yekutieli, D.2
  • 18
    • 66349103652 scopus 로고    scopus 로고
    • Rapid and accurate multiple testing correction and power estimation for millions of correlated markers
    • Han, B., Kang, H.M., Eskin, E.: Rapid and accurate multiple testing correction and power estimation for millions of correlated markers. PLoS Genet. 2009;5(4):e1000,456.
    • (2009) Plos Genet , vol.5 , Issue.4
    • Han, B.1    Kang, H.M.2    Eskin, E.3
  • 19
    • 0036500834 scopus 로고    scopus 로고
    • Reverse engineering of biological complexity
    • Csete ME, Doyle JC. Reverse engineering of biological complexity. Science 2002;295(5560), 1664-9.
    • (2002) Science , vol.295 , Issue.5560 , pp. 1664-1669
    • Csete, M.E.1    Doyle, J.C.2
  • 20
    • 0035923604 scopus 로고    scopus 로고
    • Degeneracy and complexity in biological systems
    • Edelman GM, Gally JA. Degeneracy and complexity in biological systems. Proc Natl Acad Sci. 2001;98(24):13763-8.
    • (2001) Proc Natl Acad Sci , vol.98 , Issue.24 , pp. 13763-13768
    • Edelman, G.M.1    Gally, J.A.2
  • 21
    • 28644449917 scopus 로고    scopus 로고
    • How does gene expression clustering work?
    • D’haeseleer P. How does gene expression clustering work? Nat Biotechnol. 2005;23(12): 1499-501.
    • (2005) Nat Biotechnol , vol.23 , Issue.12 , pp. 1499-1501
    • D’Haeseleer, P.1
  • 22
    • 0037342510 scopus 로고    scopus 로고
    • Comparisons and validation of statistical clustering techniques for microarray gene expression data
    • Datta S, Datta, S. Comparisons and validation of statistical clustering techniques for microarray gene expression data. Bioinformatics. 2003;19(4):459-66.
    • (2003) Bioinformatics , vol.19 , Issue.4 , pp. 459-466
    • Datta, S.1    Datta, S.2
  • 23
    • 0032441150 scopus 로고    scopus 로고
    • Cluster analysis and display of genome-wide expression patterns
    • Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci. 1998;95(25):14863-8.
    • (1998) Proc Natl Acad Sci , vol.95 , Issue.25 , pp. 14863-14868
    • Eisen, M.B.1    Spellman, P.T.2    Brown, P.O.3    Botstein, D.4
  • 25
    • 84899013108 scopus 로고    scopus 로고
    • On spectral clustering: Analysis and an algorithm
    • Ng A, Jordan M, Weiss Y. On spectral clustering: analysis and an algorithm. Adv Neur Inf Process Syst. 2002;2, 849-56.
    • (2002) Adv Neur Inf Process Syst , vol.2 , pp. 849-856
    • Ng, A.1    Jordan, M.2    Weiss, Y.3
  • 26
    • 58549089495 scopus 로고    scopus 로고
    • Topological structures in the equities market network
    • Leibon G, Pauls S, Rockmore D, Savell R. Topological structures in the equities market network. Proc Natl Acad Sci. 2008;105(52):20589-594.
    • (2008) Proc Natl Acad Sci , vol.105 , Issue.52 , pp. 20589-20594
    • Leibon, G.1    Pauls, S.2    Rockmore, D.3    Savell, R.4
  • 28
    • 34548583274 scopus 로고    scopus 로고
    • A tutorial on spectral clustering
    • von Luxburg U. A tutorial on spectral clustering. Stat Comput. 2007;17(4):395-416.
    • (2007) Stat Comput , vol.17 , Issue.4 , pp. 395-416
    • Von Luxburg, U.1
  • 29
    • 70349193395 scopus 로고    scopus 로고
    • Simultaneous class discovery and classification of microarray data using spectral analysis
    • Qiu P, Plevritis SK. Simultaneous class discovery and classification of microarray data using spectral analysis. J Comput Biol. 2009;16:935-44.
    • (2009) J Comput Biol , vol.16 , pp. 935-944
    • Qiu, P.1    Plevritis, S.K.2
  • 30
    • 84855175268 scopus 로고    scopus 로고
    • Partition decoupling for multi-gene analysis of gene expression profiling data
    • Braun R, Leibon G, Pauls S, Rockmore D. Partition decoupling for multi-gene analysis of gene expression profiling data. BMC Bioinformatics. 2011;12(497).
    • (2011) BMC Bioinformatics , vol.12 , Issue.497
    • Braun, R.1    Leibon, G.2    Pauls, S.3    Rockmore, D.4
  • 31
    • 18744364197 scopus 로고    scopus 로고
    • Detecting clusters of different geometrical shapes in microarray gene expression data
    • Kim D, Lee K, Lee D. Detecting clusters of different geometrical shapes in microarray gene expression data. Bioinformatics 2005;21(9):1927-34.
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 1927-1934
    • Kim, D.1    Lee, K.2    Lee, D.3
  • 32
    • 77956492136 scopus 로고    scopus 로고
    • Simple and flexible classification of gene expression microarrays via swirls and ripples
    • Baker S. Simple and flexible classification of gene expression microarrays via swirls and ripples. BMC Bioinformat. 2010;11(1):452
    • (2010) BMC Bioinformat , vol.11 , Issue.1
    • Baker, S.1
  • 33
    • 22844453564 scopus 로고    scopus 로고
    • MCLUST: Software for model-based cluster analysis
    • Fraley C, Raftery A. MCLUST: Software for model-based cluster analysis. J. Classification 1999;16(2):297-306.
    • (1999) J. Classification , vol.16 , Issue.2 , pp. 297-306
    • Fraley, C.1    Raftery, A.2
  • 34
    • 10044254422 scopus 로고    scopus 로고
    • How many clusters? An information-theoretic perspective
    • Still S, Bialek W. How many clusters? An information-theoretic perspective. Neural Comput. 2004;16(12):2483-506.
    • (2004) Neural Comput , vol.16 , Issue.12 , pp. 2483-2506
    • Still, S.1    Bialek, W.2
  • 35
    • 0035532141 scopus 로고    scopus 로고
    • Estimating the number of clusters in a data set via the gap statistic
    • Tibshirani R, Walther G, Hastie T. Estimating the number of clusters in a data set via the gap statistic. J R Stat Soc B. 2002;63(2):411-23.
    • (2002) J R Stat Soc B , vol.63 , Issue.2 , pp. 411-423
    • Tibshirani, R.1    Walther, G.2    Hastie, T.3
  • 36
    • 0038724494 scopus 로고    scopus 로고
    • Consensus clustering: A resampling-based method for class discovery and visualization of gene expression microarray data
    • Monti S, Tamayo P, Mesirov J, Golub T. Consensus clustering: a resampling-based method for class discovery and visualization of gene expression microarray data. Mach Learn. 2003;52 (1-2):91-118.
    • (2003) Mach Learn , vol.52 , Issue.1-2 , pp. 91-118
    • Monti, S.1    Tamayo, P.2    Mesirov, J.3    Golub, T.4
  • 37
    • 20144382754 scopus 로고    scopus 로고
    • Molecular profiling of diffuse large b-cell lymphoma identifies robust subtypes including one characterized by host inflammatory response
    • Monti S, Savage KJ, Kutok JL, Feuerhake F, Kurtin P, Mihm, M, Wu B, Pasqualucci L, Neuberg D, Aguiar RC, et al. Molecular profiling of diffuse large b-cell lymphoma identifies robust subtypes including one characterized by host inflammatory response. Blood. 2005;105(5):1851-61.
    • (2005) Blood , vol.105 , Issue.5 , pp. 1851-1861
    • Monti, S.1    Savage, K.J.2    Kutok, J.L.3    Feuerhake, F.4    Kurtin, P.5    Mihm, M.6    Wu, B.7    Pasqualucci, L.8    Neuberg, D.9    Aguiar, R.C.10
  • 41
    • 0034730140 scopus 로고    scopus 로고
    • Singular value decomposition for genome-wide expression data processing and modeling
    • Alter O, Brown PO, Botstein D. Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci. 2000;97(18):10101-6.
    • (2000) Proc Natl Acad Sci , vol.97 , Issue.18 , pp. 10101-10106
    • Alter, O.1    Brown, P.O.2    Botstein, D.3
  • 42
    • 84864751449 scopus 로고    scopus 로고
    • Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway
    • McIsaac RS, Petti AA, Bussemaker HJ, Botstein D. Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway. Mol Biol Cell 2012;23(15):2993-3007.
    • (2012) Mol Biol Cell , vol.23 , Issue.15 , pp. 2993-3007
    • McIsaac, R.S.1    Petti, A.A.2    Bussemaker, H.J.3    Botstein, D.4
  • 43
    • 77955502318 scopus 로고    scopus 로고
    • Modeling reveals bistability and low-pass filtering in the network module determining blood stem cell fate
    • Narula J, Smith AM, Gottgens B, Igoshin OA. Modeling reveals bistability and low-pass filtering in the network module determining blood stem cell fate. PLoS Comput Biol. 2010;6(5):e1000771.
    • (2010) Plos Comput Biol , vol.6 , Issue.5
    • Narula, J.1    Smith, A.M.2    Gottgens, B.3    Igoshin, O.A.4
  • 46
    • 0042863923 scopus 로고    scopus 로고
    • Analysis of gene expression data using self-organizing maps
    • Törönen P, Kolehmainen M, Wong G, Castrén E. Analysis of gene expression data using self-organizing maps. FEBS Lett. 1999;451(2):142-6.
    • (1999) FEBS Lett , vol.451 , Issue.2 , pp. 142-146
    • Törönen, P.1    Kolehmainen, M.2    Wong, G.3    Castrén, E.4
  • 47
    • 0033027794 scopus 로고    scopus 로고
    • Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation
    • Tamayo P, Slonim D, Mesirov J, Zhu Q, E Dmitrovsky SK, Lander ES, Golub TR. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci. 1999;96(6):2907-12.
    • (1999) Proc Natl Acad Sci , vol.96 , Issue.6 , pp. 2907-2912
    • Tamayo, P.1    Slonim, D.2    Mesirov, J.3    Zhu, Q.4    E Dmitrovsky, S.K.5    Lander, E.S.6    Golub, T.R.7
  • 54
    • 84861123691 scopus 로고    scopus 로고
    • Ten years of pathway analysis: Current approaches and outstanding challenges
    • Khatri P, Sirota M, Butte AJ. Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol. 2012;8(2):e1002375.
    • (2012) Plos Comput Biol , vol.8 , Issue.2
    • Khatri, P.1    Sirota, M.2    Butte, A.J.3
  • 56
    • 33847324900 scopus 로고    scopus 로고
    • Extensions to gene set enrichment
    • Jiang Z, Gentleman R. Extensions to gene set enrichment. Bioinformatics. 2007;23(3): 306-13.
    • (2007) Bioinformatics , vol.23 , Issue.3 , pp. 306-313
    • Jiang, Z.1    Gentleman, R.2
  • 57
    • 34249663294 scopus 로고    scopus 로고
    • Analyzing gene expression data in terms of gene sets: Methodological issues
    • Goeman JJ, Bühlmann P. Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics. 2007;23(8):980-7.
    • (2007) Bioinformatics , vol.23 , Issue.8 , pp. 980-987
    • Goeman, J.J.1    Bühlmann, P.2
  • 59
    • 1642317557 scopus 로고    scopus 로고
    • Gene expression profile of adult t-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival
    • Chiaretti S, Li X, Gentleman R, Vitale A, Vignetti M, Mandelli F, Ritz J, Foa R. Gene expression profile of adult t-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival. Blood. 2004;103(7):2771-8.
    • (2004) Blood , vol.103 , Issue.7 , pp. 2771-2778
    • Chiaretti, S.1    Li, X.2    Gentleman, R.3    Vitale, A.4    Vignetti, M.5    Mandelli, F.6    Ritz, J.7    Foa, R.8
  • 60
    • 78149422057 scopus 로고    scopus 로고
    • Deconvoluting post-transplant immunity: Cell subset-specific mapping reveals pathways for activation and expansion of memory t, monocytes and b cells
    • Grigoryev YA, Kurian SM, Avnur Z, Borie D, Deng J, Campbell D, Sung J, Nikolcheva T, Quinn A, Schulman H, et al. Deconvoluting post-transplant immunity: cell subset-specific mapping reveals pathways for activation and expansion of memory t, monocytes and b cells. PloS One. 2010;5(10):e13,358.
    • (2010) Plos One , vol.5 , Issue.10
    • Grigoryev, Y.A.1    Kurian, S.M.2    Avnur, Z.3    Borie, D.4    Deng, J.5    Campbell, D.6    Sung, J.7    Nikolcheva, T.8    Quinn, A.9    Schulman, H.10
  • 61
    • 63549098588 scopus 로고    scopus 로고
    • Identification of differential gene pathways with principal component analysis
    • Ma S, Kosorok MR. Identification of differential gene pathways with principal component analysis. Bioinformatics. 2009;25(7):882-9.
    • (2009) Bioinformatics , vol.25 , Issue.7 , pp. 882-889
    • Ma, S.1    Kosorok, M.R.2
  • 62
    • 58149301302 scopus 로고    scopus 로고
    • Identifying differential correlation in gene/pathway combinations
    • Braun R, Cope L, Parmigiani G. Identifying differential correlation in gene/pathway combinations. BMC Bioinformatics. 2008;9:488.
    • (2008) BMC Bioinformatics , vol.9
    • Braun, R.1    Cope, L.2    Parmigiani, G.3
  • 63
    • 2342533421 scopus 로고    scopus 로고
    • Class prediction by nearest shrunken centroids, with applications to dna microarrays
    • Tibshirani R, Hastie T, Narasimhan B, Chu G. Class prediction by nearest shrunken centroids, with applications to dna microarrays. Stat Sci. 2003;104-17.
    • (2003) Stat Sci , pp. 104-117
    • Tibshirani, R.1    Hastie, T.2    Narasimhan, B.3    Chu, G.4
  • 66
    • 13144306071 scopus 로고    scopus 로고
    • Genome-wide association studies for common diseases and complex traits
    • Hirschhorn JN, Daly MJ. Genome-wide association studies for common diseases and complex traits. Nat Rev Genet. 2005;6(2):95-108.
    • (2005) Nat Rev Genet , vol.6 , Issue.2 , pp. 95-108
    • Hirschhorn, J.N.1    Daly, M.J.2
  • 69
    • 68649101805 scopus 로고    scopus 로고
    • Common vs. Rare allele hypotheses for complex diseases
    • Schork N, Murray S, Frazer K, Topol E. Common vs. rare allele hypotheses for complex diseases. Current Opin Genet Dev. 2009;19(3):212-9.
    • (2009) Current Opin Genet Dev , vol.19 , Issue.3 , pp. 212-219
    • Schork, N.1    Murray, S.2    Frazer, K.3    Topol, E.4
  • 70
    • 77949497074 scopus 로고    scopus 로고
    • Bioinformatics challenges for genome-wide association studies
    • Moore J, Asselbergs F, Williams S. Bioinformatics challenges for genome-wide association studies. Bioinformatics. 2010;26(4):445.
    • (2010) Bioinformatics , vol.26 , Issue.4
    • Moore, J.1    Asselbergs, F.2    Williams, S.3
  • 71
    • 66849097781 scopus 로고    scopus 로고
    • Failure to replicate a genetic association may provide important clues about genetic architecture
    • Greene C, Penrod N, Williams S, Moore J. Failure to replicate a genetic association may provide important clues about genetic architecture. PLoS One. 2009;4(6):e5639.
    • (2009) Plos One , vol.4 , Issue.6
    • Greene, C.1    Penrod, N.2    Williams, S.3    Moore, J.4
  • 72
    • 0345411335 scopus 로고    scopus 로고
    • The ubiquitous nature of epistasis in determining susceptibility to common human diseases
    • Moore J. The ubiquitous nature of epistasis in determining susceptibility to common human diseases. Hum Hered. 2003;56(1-3):73-82.
    • (2003) Hum Hered , vol.56 , Issue.1-3 , pp. 73-82
    • Moore, J.1
  • 73
    • 62849096643 scopus 로고    scopus 로고
    • Shadows of complexity: What biological networks reveal about epistasis and pleiotropy
    • Tyler A, Asselbergs F, Williams S, Moore J. Shadows of complexity: what biological networks reveal about epistasis and pleiotropy. BioEssays. 2009;31(2):220-7.
    • (2009) Bioessays , vol.31 , Issue.2 , pp. 220-227
    • Tyler, A.1    Asselbergs, F.2    Williams, S.3    Moore, J.4
  • 74
    • 77958486255 scopus 로고    scopus 로고
    • Statistical methods for pathway analysis of genome-wide data for association with complex genetic traits
    • Holmans P. Statistical methods for pathway analysis of genome-wide data for association with complex genetic traits. Adv Genet. 2010;72:141.
    • (2010) Adv Genet , vol.72
    • Holmans, P.1
  • 75
    • 78549251736 scopus 로고    scopus 로고
    • Analysing biological pathways in genome-wide association studies
    • Wang K, Li M, Hakonarson H. Analysing biological pathways in genome-wide association studies. Nat Rev Genet. 2010;11(12):843-54.
    • (2010) Nat Rev Genet , vol.11 , Issue.12 , pp. 843-854
    • Wang, K.1    Li, M.2    Hakonarson, H.3
  • 76
    • 36249029788 scopus 로고    scopus 로고
    • Pathway-based approaches for analysis of genomewide association studies
    • Wang K, Li M, Bucan M. Pathway-based approaches for analysis of genomewide association studies. Am J Hum Genet. 2007;81(6):1278.
    • (2007) Am J Hum Genet , vol.81 , Issue.6
    • Wang, K.1    Li, M.2    Bucan, M.3
  • 77
    • 56649097558 scopus 로고    scopus 로고
    • GSEA-SNP: Applying gene set enrichment analysis to SNP data from genome-wide association studies
    • Holden M, Deng S, Wojnowski L, Kulle B. GSEA-SNP: applying gene set enrichment analysis to SNP data from genome-wide association studies. Bioinformatics. 2008;24(23):2784-5.
    • (2008) Bioinformatics , vol.24 , Issue.23 , pp. 2784-2785
    • Holden, M.1    Deng, S.2    Wojnowski, L.3    Kulle, B.4
  • 78
    • 33645230600 scopus 로고    scopus 로고
    • Multifactor dimensionality reduction: An analysis strategy for modelling and detecting gene-gene interactions in human genetics and pharmacogenomics studies
    • Motsinger A, Ritchie M. Multifactor dimensionality reduction: an analysis strategy for modelling and detecting gene-gene interactions in human genetics and pharmacogenomics studies. Hum Genomics. 2006;2(5):318-28.
    • (2006) Hum Genomics , vol.2 , Issue.5 , pp. 318-328
    • Motsinger, A.1    Ritchie, M.2
  • 79
    • 33745599582 scopus 로고    scopus 로고
    • A flexible computational framework for detecting, characterizing, and interpreting statistical patterns of epistasis in genetic studies of human disease susceptibility
    • Moore J, Gilbert J, Tsai C, Chiang F, Holden T, Barney N, White B.A flexible computational framework for detecting, characterizing, and interpreting statistical patterns of epistasis in genetic studies of human disease susceptibility. J Theor Biol. 2006;241(2):252-61.
    • (2006) J Theor Biol , vol.241 , Issue.2 , pp. 252-261
    • Moore, J.1    Gilbert, J.2    Tsai, C.3    Chiang, F.4    Holden, T.5    Barney, N.6    White, B.7
  • 80
    • 67349166946 scopus 로고    scopus 로고
    • Detecting gene-gene interactions that underlie human diseases
    • Cordell H. Detecting gene-gene interactions that underlie human diseases. Nat Rev Genet. 2009;10(6):392-404.
    • (2009) Nat Rev Genet , vol.10 , Issue.6 , pp. 392-404
    • Cordell, H.1
  • 81
    • 77949614812 scopus 로고    scopus 로고
    • Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic als
    • Greene C, Sinnott-Armstrong N, Himmelstein D, Park P, Moore J, Harris B. Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic als. Bioinformatics. 2010;26(5):694.
    • (2010) Bioinformatics , vol.26 , Issue.5
    • Greene, C.1    Sinnott-Armstrong, N.2    Himmelstein, D.3    Park, P.4    Moore, J.5    Harris, B.6
  • 84
    • 42249088310 scopus 로고    scopus 로고
    • Genome-wide analysis of epistasis using multifactor dimensionality reduction: Feature selection and construction in the domain of human genetics
    • Moore J. Genome-wide analysis of epistasis using multifactor dimensionality reduction: feature selection and construction in the domain of human genetics. Knowledge Discovery and Data Mining: Challenges and Realities with RealWorld Data; 2007. pp. 17-30.
    • (2007) Knowledge Discovery and Data Mining: Challenges and Realities with Realworld Data , pp. 17-30
    • Moore, J.1
  • 85
    • 69449088874 scopus 로고    scopus 로고
    • Spatially Uniform ReliefF (SURF) for computationally-efficient filtering of gene-gene interactions
    • Greene C, Penrod N, Kiralis J, Moore J. Spatially Uniform ReliefF (SURF) for computationally-efficient filtering of gene-gene interactions. BioData Mining. 2009;2:5.
    • (2009) Biodata Mining , vol.2
    • Greene, C.1    Penrod, N.2    Kiralis, J.3    Moore, J.4
  • 87
    • 73449120797 scopus 로고    scopus 로고
    • Needles in the haystack: Identifying individuals present in pooled genomic data
    • Braun R, Rowe W, Schaefer C, Zhang J, Buetow K. Needles in the haystack: Identifying individuals present in pooled genomic data. PLoS Genet. 2009;5(10):e1000668.
    • (2009) Plos Genet , vol.5 , Issue.10
    • Braun, R.1    Rowe, W.2    Schaefer, C.3    Zhang, J.4    Buetow, K.5
  • 88
    • 73449105071 scopus 로고    scopus 로고
    • The limits of individual identification from sample allele frequencies: Theory and statistical analysis
    • Visscher PM, Hill WG. The limits of individual identification from sample allele frequencies: theory and statistical analysis. PLoS Genet. 2009;5(10):e1000628.
    • (2009) Plos Genet , vol.5 , Issue.10
    • Visscher, P.M.1    Hill, W.G.2
  • 89
    • 79959814530 scopus 로고    scopus 로고
    • Pathways of Distinction Analysis: A new technique for multi-SNP ana lysis of GWAS data
    • Braun R, Buetow K. Pathways of Distinction Analysis: a new technique for multi-SNP ana lysis of GWAS data. PLoS Genet. 2011;7(6):e1002101.
    • (2011) Plos Genet , vol.7 , Issue.6
    • Braun, R.1    Buetow, K.2
  • 90
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman L. Random forests. Machine Learn. 2001;45(1):5-32.
    • (2001) Machine Learn , vol.45 , Issue.1 , pp. 5-32
    • Breiman, L.1
  • 92
    • 30644464444 scopus 로고    scopus 로고
    • Gene selection and classification of microarray data using random forest
    • Díaz-Uriarte R, De Andres SA. Gene selection and classification of microarray data using random forest. BMC Bioinformatics. 2006;7(1):3.
    • (2006) BMC Bioinformatics , vol.7 , Issue.1
    • Díaz-Uriarte, R.1    De Andres, S.A.2
  • 93
    • 12344294601 scopus 로고    scopus 로고
    • Bagboosting for tumor classification with gene expression data
    • Dettling M. Bagboosting for tumor classification with gene expression data. Bioinformatics. 2004;20(18):3583-93.
    • (2004) Bioinformatics , vol.20 , Issue.18 , pp. 3583-3593
    • Dettling, M.1
  • 94
    • 10444280144 scopus 로고    scopus 로고
    • An extensive comparison of recent classification tools applied to microarray data
    • Lee JW, Lee JB, Park M, Song SH. An extensive comparison of recent classification tools applied to microarray data. Comput Stat Data Anal. 2005;48(4):869-85.
    • (2005) Comput Stat Data Anal , vol.48 , Issue.4 , pp. 869-885
    • Lee, J.W.1    Lee, J.B.2    Park, M.3    Song, S.H.4
  • 95
    • 47049105891 scopus 로고    scopus 로고
    • Discovery of agents that eradicate leukemia stem cells using an in silico screen of public gene expression data
    • Hassane DC, Guzman ML, Corbett C, Li X, Abboud R, Young F, Liesveld JL, Carroll M, Jordan CT. Discovery of agents that eradicate leukemia stem cells using an in silico screen of public gene expression data. Blood. 2008;111(12):5654-62.
    • (2008) Blood , vol.111 , Issue.12 , pp. 5654-5662
    • Hassane, D.C.1    Guzman, M.L.2    Corbett, C.3    Li, X.4    Abboud, R.5    Young, F.6    Liesveld, J.L.7    Carroll, M.8    Jordan, C.T.9
  • 96
    • 52449099461 scopus 로고    scopus 로고
    • Genomic variation in myeloma: Design, content, and initial application of the bank on a cure snp panel to detect associations with progression-free survival
    • Van Ness B, Ramos C, Haznadar M, Hoering A, Haessler J, Crowley J, Jacobus S, Oken M, Rajkumar V, Greipp P, et al. Genomic variation in myeloma: design, content, and initial application of the bank on a cure snp panel to detect associations with progression-free survival. BMC Med. 2008;6(1):26.
    • (2008) BMC Med , vol.6 , Issue.1
    • Van Ness, B.1    Ramos, C.2    Haznadar, M.3    Hoering, A.4    Haessler, J.5    Crowley, J.6    Jacobus, S.7    Oken, M.8    Rajkumar, V.9    Greipp, P.10
  • 97
    • 84916243051 scopus 로고    scopus 로고
    • Elucidating the regulatory mechanisms of transcription factor activity in hematopoietic stem cell differentiation
    • Ackermann M, Sikora-Wohlfeld W, Beyer A. Elucidating the regulatory mechanisms of transcription factor activity in hematopoietic stem cell differentiation. In: Saxon Biotechnology Symposium; 2011. p. 79.
    • (2011) Saxon Biotechnology Symposium
    • Ackermann, M.1    Sikora-Wohlfeld, W.2    Beyer, A.3
  • 100
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell’s functional organization
    • Barabasi AL, Oltvai ZN. Network biology: understanding the cell’s functional organization. Nat Rev Genet. 2004;5(2):101-13.
    • (2004) Nat Rev Genet , vol.5 , Issue.2 , pp. 101-113
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 101
    • 0034609791 scopus 로고    scopus 로고
    • The large-scale organization of metabolic networks
    • Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL. The large-scale organization of metabolic networks. Nature. 2000;407(6804):651-4.
    • (2000) Nature , vol.407 , Issue.6804 , pp. 651-654
    • Jeong, H.1    Tombor, B.2    Albert, R.3    Oltvai, Z.N.4    Barabasi, A.L.5
  • 102
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • Jeong H, Mason SP, Barabasi AL, Oltvai ZN. Lethality and centrality in protein networks. Nature. 2001;411(6833):41-2.
    • (2001) Nature , vol.411 , Issue.6833 , pp. 41-42
    • Jeong, H.1    Mason, S.P.2    Barabasi, A.L.3    Oltvai, Z.N.4
  • 104
    • 34248593385 scopus 로고    scopus 로고
    • Gene expression network analysis and applications to immunology
    • Nacu S, Critchley-Thorne R, Lee P, Holmes S. Gene expression network analysis and applications to immunology. Bioinformatics. 2007;23(7):850-8.
    • (2007) Bioinformatics , vol.23 , Issue.7 , pp. 850-858
    • Nacu, S.1    Critchley-Thorne, R.2    Lee, P.3    Holmes, S.4
  • 105
    • 46249128543 scopus 로고    scopus 로고
    • Identifying functional modules in protein-protein interaction networks: An integrated exact approach
    • Dittrich MT, Klau GW, Rosenwald A, Dandekar T, Müller T. Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics. 2008;24(13):i223-31.
    • (2008) Bioinformatics , vol.24 , Issue.13
    • Dittrich, M.T.1    Klau, G.W.2    Rosenwald, A.3    Dandekar, T.4    Müller, T.5
  • 106
    • 77951972600 scopus 로고    scopus 로고
    • Bionet: An r-package for the functional analysis of biological networks
    • Beisser D, Klau GW, Dandekar T, Müller T, Dittrich MT. Bionet: an r-package for the functional analysis of biological networks. Bioinformatics. 2010;26(8):1129-30.
    • (2010) Bioinformatics , vol.26 , Issue.8 , pp. 1129-1130
    • Beisser, D.1    Klau, G.W.2    Dandekar, T.3    Müller, T.4    Dittrich, M.T.5
  • 107
    • 37849022459 scopus 로고    scopus 로고
    • Identification of key processes underlying cancer phenotypes using biologic pathway analysis
    • Efroni S, Schaefer CF, Buetow KH. Identification of key processes underlying cancer phenotypes using biologic pathway analysis. PLoS One. 2007;2(5):e425.
    • (2007) Plos One , vol.2 , Issue.5
    • Efroni, S.1    Schaefer, C.F.2    Buetow, K.H.3
  • 108
    • 14644430468 scopus 로고    scopus 로고
    • Calculating the statistical significance of changes in pathway activity from gene expression data
    • Jörg R, Jochen M, Thomas L, et al. Calculating the statistical significance of changes in pathway activity from gene expression data. Stat Appl Genet Mol Biol. 2004;3(1):1-31.
    • (2004) Stat Appl Genet Mol Biol , vol.3 , Issue.1 , pp. 1-31
    • Jörg, R.1    Jochen, M.2    Thomas, L.3
  • 114
    • 14844286390 scopus 로고    scopus 로고
    • Reverse-engineering transcription control networks
    • Gardner T, Faith J. Reverse-engineering transcription control networks. Phys Life Rev. 2005;2(1):65-88.
    • (2005) Phys Life Rev , vol.2 , Issue.1 , pp. 65-88
    • Gardner, T.1    Faith, J.2
  • 115
    • 59949086432 scopus 로고    scopus 로고
    • Minet: An R/Bioconductor package for inferring large transcriptional networks using mutual information
    • Meyer P, Lafitte F, Bontempi G. minet: An R/Bioconductor package for inferring large transcriptional networks using mutual information. BMC Bioinformatics. 2008;9(1):461.
    • (2008) BMC Bioinformatics , vol.9 , Issue.1
    • Meyer, P.1    Lafitte, F.2    Bontempi, G.3
  • 116
    • 0036683181 scopus 로고    scopus 로고
    • Linking the genes: Inferring quantitative gene networks from microarray data
    • de la Fuente A, Brazhnik P, Mendes P. Linking the genes: inferring quantitative gene networks from microarray data. TRENDS Genet. 2002;18(8);395-8.
    • (2002) TRENDS Genet , vol.18 , Issue.8 , pp. 395-398
    • De La Fuente, A.1    Brazhnik, P.2    Mendes, P.3
  • 117
    • 0038048325 scopus 로고    scopus 로고
    • Inferring genetic networks and identifying compound mode of action via expression profiling
    • Gardner T, di Bernardo, D, Lorenz D, Collins J: Inferring genetic networks and identifying compound mode of action via expression profiling. Sci Signal. 2003;301(5629):102.
    • (2003) Sci Signal , vol.301 , Issue.5629
    • Gardner, T.1    Di Bernardo, D.2    Lorenz, D.3    Collins, J.4
  • 118
    • 15944367731 scopus 로고    scopus 로고
    • Reconstructing biological networks using conditional correlation analysis
    • Rice J, Tu Y, Stolovitzky G. Reconstructing biological networks using conditional correlation analysis. Bioinformatics. 21(6):765-73.
    • Bioinformatics , vol.21 , Issue.6 , pp. 765-773
    • Rice, J.1    Tu, Y.2    Stolovitzky, G.3
  • 120
    • 77954484005 scopus 로고    scopus 로고
    • Revealing differences in gene network inference algorithms on the network level by ensemble methods
    • Altay G, Emmert-Streib F: Revealing differences in gene network inference algorithms on the network level by ensemble methods. Bioinformatics. 2010;26(14):1738-44.
    • (2010) Bioinformatics , vol.26 , Issue.14 , pp. 1738-1744
    • Altay, G.1    Emmert-Streib, F.2
  • 121
    • 34249080596 scopus 로고    scopus 로고
    • Theoretical analysis of epigenetic cell memory by nucleosome modification
    • Dodd IB, Micheelsen MA, Sneppen K, Thon G. Theoretical analysis of epigenetic cell memory by nucleosome modification. Cell. 2007;129(4):813-22.
    • (2007) Cell , vol.129 , Issue.4 , pp. 813-822
    • Dodd, I.B.1    Micheelsen, M.A.2    Sneppen, K.3    Thon, G.4
  • 122
    • 38049125593 scopus 로고    scopus 로고
    • Epigenetic chromatin silencing: Bistability and front propagation
    • Sedighi M, Sengupta AM. Epigenetic chromatin silencing: bistability and front propagation. Phys Biol. 2007;4(4):246-55.
    • (2007) Phys Biol , vol.4 , Issue.4 , pp. 246-255
    • Sedighi, M.1    Sengupta, A.M.2
  • 123
    • 71449125977 scopus 로고    scopus 로고
    • Forcing cells to change lineages
    • Graf T, Enver T. Forcing cells to change lineages. Nature. 2009;462:(7273):587-94.
    • (2009) Nature , vol.462 , Issue.7273 , pp. 587-594
    • Graf, T.1    Enver, T.2
  • 124
    • 28944444652 scopus 로고    scopus 로고
    • Differential coexpression analysis using microarray data and its application to human cancer
    • Choi JK, Yu U, Yoo OJ, Kim S. Differential coexpression analysis using microarray data and its application to human cancer. Bioinformatics. 2005;21(24):4348-55.
    • (2005) Bioinformatics , vol.21 , Issue.24 , pp. 4348-4355
    • Choi, J.K.1    Yu, U.2    Yoo, O.J.3    Kim, S.4
  • 126
    • 34548058037 scopus 로고    scopus 로고
    • Searching for differentially expressed gene combinations
    • Dettling M, Gabrielson E, Parmigiani G. Searching for differentially expressed gene combinations. Genome Biol. 2005;6:R88.
    • (2005) Genome Biol , vol.6
    • Dettling, M.1    Gabrielson, E.2    Parmigiani, G.3


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