### Citations

5963 |
Classification and Regression Trees
- Breiman, Friedman, et al.
- 1984
(Show Context)
Citation Context ...to identify important p-way interactions, GPAS is able to detect such interactions using only the n variables as inputs. For a comparison of GPAS with further tree-based discrimination methods, CART (=-=Breiman et al., 1984-=-), bagging (Breiman, 1996) and Random Forests (Breiman, 2001) are applied to the GENICA data set, where the parameters of the latter two procedures are optimized over several values. (In both bagging ... |

3732 |
Genetic programming: on the programming of computers by means of natural selection.
- Koza
- 1992
(Show Context)
Citation Context ... called GPAS (Genetic Programming for Association Studies) employs multi-valued logic, and attempts to detect DNFs associated with the response directly. To search for such DNFs, genetic programming (=-=Koza, 1993-=-) is used. Genetic programming naturally provides not a single best model, but a set of models (called individuals) that fit almost equally well, which is an advantage in the analysis of genotype data... |

3648 | Bagging predictors
- Breiman
- 1996
(Show Context)
Citation Context ... with the lowest misclassification rate (for a given length), is used, or an ensemble of models is considered either by averaging over a set consisting of the best individuals or by applying bagging (=-=Breiman, 1996-=-) to GPAS. 2.4 GPAS To summarize, we propose the following specialized genetic programming algorithm called GPAS for the analysis of genotype data. ALGORITHM (GPAS). (1) Create an initial random popul... |

3610 | Random forests
- Breiman
(Show Context)
Citation Context ...ch interactions using only the n variables as inputs. For a comparison of GPAS with further tree-based discrimination methods, CART (Breiman et al., 1984), bagging (Breiman, 1996) and Random Forests (=-=Breiman, 2001-=-) are applied to the GENICA data set, where the parameters of the latter two procedures are optimized over several values. (In both bagging and Random Forests, different numbers of trees are considere... |

2481 | Significance analysis of microarrays applied to the ionizing radiation responses - Tusher, 1L, et al. |

557 | A comparison of Bayesian methods for haplotype reconstruction from population genotype data
- Stephens, Donnelly
- 2003
(Show Context)
Citation Context ...hisms such as microsatellites or to haplotypes. However, GPAS currently is not able to take into account the uncertainties that show up if the haplotypes are estimated using procedures such as PHASE (=-=Stephens and Donelly, 2003-=-). Furthermore, the design of GPAS is flexible: by default, the set of literals is composed of all possible values for any of the variables and their corresponding complements. It is, however, possibl... |

428 | Genetic Programming - An Introduction: on the Automatic Evolution of Computer Programs and Its Applications. - Banzhaf, Nordin, et al. - 1998 |

154 | Genome-wide strategies for detecting multiple loci that influence complex diseases. - Marchini, Donnelly, et al. - 2005 |

141 | C.: Introduction to Algorithms, 2nd edn - Cormen, Leiserson, et al. - 2001 |

111 | Multifactordimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer,” - Ritchie, Hahn, et al. - 2001 |

95 | A Perspective on Epistasis: Limits of Models Displaying no Main Effect - Culverhouse, Suarez, et al. - 2002 |

91 | Mathematical multi-locus approaches to localizing complex human trait genes. - Hoh, Ott - 2003 |

80 | Statistical methods in cancer research. The analysis of case-control studies - Breslow, Day - 1980 |

76 | Logic Regression. - Ruczinski, Kooperberg, et al. - 2003 |

62 |
Identifying interacting SNPs using Monte Carlo logic regression,”
- Kooperberg, Ruczinski
- 2005
(Show Context)
Citation Context ...data (Kooperberg et al., 2001; Ruczinski et al., 2004; Schwender, 2007; Witte and Fijal, 2001). Moreover, logic regression can be employed for detecting interactions and quantifying their importance (=-=Kooperberg and Ruczinski, 2005-=-; Schwender and Ickstadt, 2007). For an application of logic regression to genotype data, each SNP needs to be coded by (at least) two dummy variables, as logic regression can only handle binary predi... |

44 | Identification of SNP interactions using logic regression,”
- Schwender, Ickstadt
- 2008
(Show Context)
Citation Context ...uczinski et al., 2004; Schwender, 2007; Witte and Fijal, 2001). Moreover, logic regression can be employed for detecting interactions and quantifying their importance (Kooperberg and Ruczinski, 2005; =-=Schwender and Ickstadt, 2007-=-). For an application of logic regression to genotype data, each SNP needs to be coded by (at least) two dummy variables, as logic regression can only handle binary predictors, but SNPs can take three... |

43 | Screening large-scale association study data: exploiting interactions using random forests - Lunetta - 2004 |

33 | Association studies for finding cancer-susceptibility genetic variants,” - Pharoah, Dunning, et al. - 2004 |

17 | Sequence analysis using logic regression. - Kooperberg - 2001 |

16 |
Metabolic Susceptibility Genes as Cancer Risk Factors: Time for a Reassessment
- Garte
- 2001
(Show Context)
Citation Context ...ypically only have a slight to moderate effect—in particular, when considering complex diseases such as sporadic breast cancer—the focus is on the detection of interactions (Culverhouse et al., 2002; =-=Garte, 2001-=-). The search for such interacting SNPs is additionally impeded by the facts that the interactions are usually of a high order, and that they are explanatory for relatively small subgroups of the pati... |

14 | Exploring Interactions in High-Dimensional Genomic Data: An Overview of Logic Regression, with Applications - Ruczinski, Kooperberg, et al. - 2004 |

13 | The Challenge for Genetic Epidemiologists: How to Analyze Large Numbers of SNPs in Relation to Complex Diseases. BioMed Central Genetics - Heidema, Boer, et al. - 2006 |

13 | ERCC2 Genotypes and a Corresponding Haplotype are Linked with Breast Cancer Risk in a German Population - Justenhoven, Hamann, et al. - 2004 |

10 |
Modifying Microarray Analysis Methods for Categorical Data
- Schwender
- 2005
(Show Context)
Citation Context ...he number of variables has to be reduced to a size that these approaches can handle. We therefore use the Significance Analysis of Microarrays (SAM; Tusher et al., 2001) adapted for categorical data (=-=Schwender, 2005-=-) to reduce the number of SNPs from 121 774 to 157, where this subset of SNPs exhibits an estimated FDR (False Discovery Rate) of 0.069. All discrimination methods are then applied to this subset of S... |

10 |
Introduction: Analysis of Sequence Data and Population Structure. Genetic Epidemiology
- Witte, Fijal
- 2001
(Show Context)
Citation Context ...ons with other regression or discrimination approaches, logic regression has shown a good performance in its application to SNP data (Kooperberg et al., 2001; Ruczinski et al., 2004; Schwender, 2007; =-=Witte and Fijal, 2001-=-). Moreover, logic regression can be employed for detecting interactions and quantifying their importance (Kooperberg and Ruczinski, 2005; Schwender and Ickstadt, 2007). For an application of logic re... |

5 | Exploring SNP-SNP interactions and colon cancer risk using polymorphism interaction analysis,” - Goodman, Mechanic, et al. - 2006 |

3 | Statistical Analysis of Genotype and Gene Expression Data
- Schwender
- 2007
(Show Context)
Citation Context ... several comparisons with other regression or discrimination approaches, logic regression has shown a good performance in its application to SNP data (Kooperberg et al., 2001; Ruczinski et al., 2004; =-=Schwender, 2007-=-; Witte and Fijal, 2001). Moreover, logic regression can be employed for detecting interactions and quantifying their importance (Kooperberg and Ruczinski, 2005; Schwender and Ickstadt, 2007). For an ... |

2 | Multiple testing for SNP-SNP interactions: A flexible asymptotic framework - Boulesteix, Strobl, et al. - 2007 |