Genome Simulation

Advances in Genetics - Tập 72 - Trang 1-24 - 2010
Marylyn D. Ritchie1,2,3, William S. Bush1,3
1Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA
2Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA.
3Department of Biomedical Informatics Vanderbilt University, Nashville, Tennessee, USA

Tài liệu tham khảo

Balloux, 2001, EASYPOP (version 1.7): A computer program for population genetics simulations, J. Hered., 92, 301, 10.1093/jhered/92.3.301 Bass, 1993, Pedigree generation for analysis of genetic linkage and association, Pac. Symp. Biocomput., 2004, 93 Boehnke, 1986, Estimating the power of a proposed linkage study: A practical computer simulation approach, Am. J. Hum. Genet., 39, 513 Boehnke, 1997 Carvajal-Rodriguez, 2008, GENOMEPOP: A program to simulate genomes in populations, BMC Bioinform., 9, 223, 10.1186/1471-2105-9-223 Chen, 2009, Fast and flexible simulation of DNA sequence data, Genome Res., 19, 136, 10.1101/gr.083634.108 Cook, 2004, Tree and spline based association analysis of gene–gene interaction models for ischemic stroke, Stat. Med., 23, 1439, 10.1002/sim.1749 Cristianini, 2000 Culverhouse, 2002, A perspective on epistasis: Limits of models displaying no main effect, Am. J. Hum. Genet., 70, 461, 10.1086/338759 Culverhouse, 2004, Detecting epistatic interactions contributing to quantitative traits, Genet. Epidemiol., 27, 141, 10.1002/gepi.20006 Dudek, 2006, Data simulation software for whole-genome association and other studies in human genetics, Pac. Symp. Biocomput., 499, 10.1142/9789812701626_0046 Durrant, 2004, Linkage disequilibrium mapping via cladistic analysis of single-nucleotide polymorphism haplotypes, Am. J. Hum. Genet., 75, 35, 10.1086/422174 Edwards, 2008, Generating linkage disequilibrium patterns in data simulations using genomeSIMLA, Lect. Notes Comput. Sci., 4973, 24, 10.1007/978-3-540-78757-0_3 Edwards, 2009, Exploring the performance of multifactor dimensionality reduction in large scale SNP studies and in the presence of genetic heterogeneity among epistatic disease models, Hum. Hered., 67, 183, 10.1159/000181157 Ewing, 2010, MSMS: A coalescent simulation program including recombination, demographic structure and selection at a single locus, Bioinformatics, 26, 2064, 10.1093/bioinformatics/btq322 Frazer, 2007, A second generation human haplotype map of over 3.1 million SNPs, Nature, 449, 851, 10.1038/nature06258 Hahn, 2003, Multifactor dimensionality reduction software for detecting gene–gene and gene–environment interactions, Bioinformatics, 19, 376, 10.1093/bioinformatics/btf869 Hastie, 2001 Hey, 2005 Hoggart, 2007, Sequence-level population simulations over large genomic regions, Genetics, 177, 1725, 10.1534/genetics.106.069088 Hudson, 2002, Generating samples under a Wright–Fisher neutral model of genetic variation, Bioinformatics, 18, 337, 10.1093/bioinformatics/18.2.337 Kaufman, 1990 Kingman, 1982, The coalescent, Stochastic Processes Appl., 13, 235, 10.1016/0304-4149(82)90011-4 Kooperberg, 2001, Sequence analysis using logic regression, Genet. Epidemiol., 21, S626, 10.1002/gepi.2001.21.s1.s626 Li, 2008, Generating samples for association studies based on HapMap data, BMC Bioinform., 9, 44, 10.1186/1471-2105-9-44 Li, 2008, GWAsimulator: A rapid whole-genome simulation program, Bioinformatics, 24, 140, 10.1093/bioinformatics/btm549 Liang, 2007, GENOME: A rapid coalescent-based whole genome simulator, Bioinformatics, 23, 1565, 10.1093/bioinformatics/btm138 Mailund, 2005, CoaSim: A flexible environment for simulating genetic data under coalescent models, BMC Bioinform., 6, 252, 10.1186/1471-2105-6-252 Marchini, 2005, Genome-wide strategies for detecting multiple loci that influence complex diseases, Nat. Genet., 37, 413, 10.1038/ng1537 Marjoram, 2006, Fast “coalescent” simulation, BMC Genet., 7, 16, 10.1186/1471-2156-7-16 Moore, 2004, Routine discovery of high-order epistasis models for computational studies in human genetics, Appl. Soft Comput., 4, 79, 10.1016/j.asoc.2003.08.003 Motsinger, 2007, Novel methods for detecting epistasis in pharmacogenomics studies, Pharmacogenomics, 1229, 10.2217/14622416.8.9.1229 Nelson, 2001, A combinatorial partitioning approach to identify multilocus genotypic partitions that predict quantitative trait variation, Genome Res., 10.1101/gr.172901 Ott, 1989, Computer-simulation methods in human linkage analysis, Proc. Natl Acad. Sci. USA, 86, 4175, 10.1073/pnas.86.11.4175 Peng, 2005, simuPOP: A forward-time population genetics simulation environment, Bioinformatics, 10.1093/bioinformatics/bti584 Peng, 2007, Forward-time simulations of human populations with complex diseases, PLoS Genet., 3, e47, 10.1371/journal.pgen.0030047 Ploughman, 1989, Estimating the power of a proposed linkage study for a complex genetic trait, Am. J. Hum. Genet., 44, 543 Richards, 1959, A flexible growth function for empirical use, J. Exp. Bot., 10, 290, 10.1093/jxb/10.2.290 Ripley, 1996 Ritchie, 2001, Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer, Am. J. Hum. Genet., 69, 138, 10.1086/321276 Ritchie, 2003, Power of multifactor dimensionality reduction for detecting gene–gene interactions in the presence of genotyping error, missing data, phenocopy, and genetic heterogeneity, Genet. Epidemiol., 24, 150, 10.1002/gepi.10218 Schmidt, 2004, Extension of the SIMLA package for generating pedigrees with complex inheritance patterns: Environmental covariates, gene–gene and gene–environment interaction, Stat. Appl. Genet. Mol. Biol., 2005 Schmidt, 2004, Extension of the SIMLA package for generating pedigrees with complex inheritance patterns: Environmental covariates, gene–gene and gene–environment interaction, Stat. Appl. Genet. Mol. Biol., 2005 Spencer, 2004, SelSim: A program to simulate population genetic data with natural selection and recombination, Bioinformatics, 20, 3673, 10.1093/bioinformatics/bth417 Terwilliger, 1994 Terwilliger, 1993, Chromosome-based method for rapid computer simulation in human genetic linkage analysis, Genet. Epidemiol., 10, 217, 10.1002/gepi.1370100402 Weeks, 1990, SLINK: A general simulation paorgram for linkage analysis, Am. J. Hum. Genet., 47, A204 Wille, 2003, Sum statistics for the joint detection of multiple disease loci in case–control association studies with SNP markers, Genet. Epidemiol., 25, 350, 10.1002/gepi.10263 Wolfram, 1994 Wright, 2007, Simulating association studies: A data-based resampling method for candidate regions or whole genome scans, Bioinformatics, 23, 2581, 10.1093/bioinformatics/btm386 Wright, 2007, Simulating association studies: A data-based resampling method for candidate regions or whole genome scans, Bioinformatics, 23, 2581, 10.1093/bioinformatics/btm386 Zhang, 2008, HAPSIMU: A genetic simulation platform for population-based association studies, BMC Bioinform., 9, 331, 10.1186/1471-2105-9-331 Zhu, 2004, Classification of gene microarrays by penalized logistic regression, Biostatistics, 5, 427, 10.1093/biostatistics/kxg046