EpiSIM: simulation of multiple epistasis, linkage disequilibrium patterns and haplotype blocks for genome-wide interaction analysis

Barrett JC, Fry B, Maller J, Daly MJ (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21:263–265

Cancare F, Marin A, Sciuto D (2011) Dedicated hardware accelerators for the epistatic analysis of human genetic data. International Conference on Embedded Computer Systems:102–109

Carvajal-Rodriguez A (2008) Simulation of genomes: a review. Curr Genomics 9:155–159

Carvajal-Rodriguez A (2010) Simulation of genes and genomes forward in time. Curr Genomics 11:58–61

Chen GK, Marjoram P, Wall JD (2009a) Fast and flexible simulation of DNA sequence data. Genome Res 19:136–142

Chen L, Yu G, Miller DJ, Song L, Langefeld C, Herrington D, Liu Y, Wang Y (2009b) A ground truth based comparative study on detecting epistatic SNPs. IEEE Internat Confer Bioinform Biomed Workshop:26–31

Culverhouse R, Suarez BK, Lin J, Reich T (2002) A perspective on epistasis: limits of models displaying no main effect. Am J Hum Genet 70:461–471

Gunther T, Gawenda I, Schmid KJ (2011) Phenosim: a software to simulate phenotypes for testing in genome-wide association studies. BMC Bioinformatics 12:265

Herold C, Steffens M, Brockschmidt FF, Baur MP, Becker T (2009) INTERSNP: genome-wide interaction analysis guided by a priori information. Bioinformatics 25:3275–3281

Hoban S, Bertorelle G, Gaggiotti OE (2012) Computer simulations: tools for population and evolutionary genetics. Nat Rev Genet 13:110–122

Jenkins PA, Griffiths RC (2011) Inference from samples of DNA sequences using a two-locus model. J Comput Biol 18:109–127

Li J, Chen Y (2008) Generating samples for association studies based on HapMap data. BMC Bioinformatics 9:44

Liang L, Zollner S, Abecasis GR (2007) GENOME: a rapid coalescent-based whole genome simulator. Bioinformatics 23:1565–1567

Maher B (2008) Personal genomes: the case of the missing heritability. Nature 456:18–21

Mailund T, Schierup MH, Pedersen CN, Mechlenborg PJ, Madsen JN, Schauser L (2005) CoaSim: a flexible environment for simulating genetic data under coalescent models. BMC Bioinformatics 6:252

Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A et al (2009) Finding the missing heritability of complex diseases. Nature 461:747–753

Miller DJ, Zhang Y, Yu G, Liu Y, Chen L, Langefeld CD, Herrington D, Wang Y (2009) An algorithm for learning maximum entropy probability models of disease risk that efficiently searches and sparingly encodes multilocus genomic interactions. Bioinformatics 25:2478–2485

Moore JH, Williams SM (2005) Traversing the conceptual divide between biological and statistical epistasis: systems biology and a more modern synthesis. BioEssays 27:637–646

Neuenschwander S, Hospital F, Guillaume F, Goudet J (2008) quantiNemo: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation. Bioinformatics 24:1552–1553

Pattaro C, Ruczinski I, Fallin DM, Parmigiani G (2008) Haplotype block partitioning as a tool for dimensionality reduction in SNP association studies. BMC Genomics 9:405

Peng B, Amos CI (2010) Forward-time simulation of realistic samples for genome-wide association studies. BMC Bioinformatics 11:442

Peng B, Kimmel M (2005) simuPOP: a forward-time population genetics simulation environment. Bioinformatics 21:3686–3687

Posada D, Wiuf C (2003) Simulating haplotype blocks in the human genome. Bioinformatics 19:289–290

Ritchie MD, Hahn LW, Roodi N, Bailey LR, Dupont WD, Parl FF, Moore JH (2001) Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. Am J Hum Genet 69:138–147

Scott MD, Alison AM, Digna RV, Scott MW, Marylyn DR (2006) Data simulation software for whole-genome association and other studies in human genetics. Pacific Symposium on Biocomputing:499–510

Shang J, Zhang J, Sun Y, Liu D, Ye D, Yin Y (2011) Performance analysis of novel methods for detecting epistasis. BMC Bioinformatics 12:475

Shang J, Zhang J, Lei X, Zhang Y, Chen B (2012) Incorporating heuristic information into ant colony optimization for epistasis detection. Genes Genomics 34:271–278

Tang W, Wu X, Jiang R, Li Y (2009) Epistatic module detection for case-control studies: a Bayesian model with a Gibbs sampling strategy. PLoS Genet 5:e1000464

VanLiere JM, Rosenberg NA (2008) Mathematical properties of the r2 measure of linkage disequilibrium. Theor Popul Biol 74:130–137

Wan X, Yang C, Yang Q, Xue H, Fan X, Tang NL, Yu W (2010a) BOOST: a fast approach to detecting gene–gene interactions in genome-wide case-control studies. Am J Hum Genet 87:325–340

Wan X, Yang C, Yang Q, Xue H, Tang NL, Yu W (2010b) Predictive rule inference for epistatic interaction detection in genome-wide association studies. Bioinformatics 26:30–37

Wang Y, Liu X, Robbins K, Rekaya R (2010) AntEpiSeeker: detecting epistatic interactions for case-control studies using a two-stage ant colony optimization algorithm. BMC Res Notes 3:117

Wright FA, Huang H, Guan X, Gamiel K, Jeffries C, Barry WT, de Villena FP, Sullivan PF, Wilhelmsen KC, Zou F (2007) Simulating association studies: a data-based resampling method for candidate regions or whole genome scans. Bioinformatics 23:2581–2588

Yuan X, Zhang J, Wang Y (2011) Simulating linkage disequilibrium structures in a human population for SNP association studies. Biochem Genet 49:395–409

Yuan X, Miller DJ, Zhang J, Herrington D, Wang Y (2012) An overview of population genetic data simulation. J Comput Biol 19:42–54

Zhang Y, Liu JS (2007) Bayesian inference of epistatic interactions in case-control studies. Nat Genet 39:1167–1173

Zhang F, Liu J, Chen J, Deng HW (2008) HAPSIMU: a genetic simulation platform for population-based association studies. BMC Bioinformatics 9:331

Zhang X, Huang S, Zou F, Wang W (2010) TEAM: efficient two-locus epistasis tests in human genome-wide association study. Bioinformatics 26:i217–i227