Literature DB >> 25504286

Genetic data simulators and their applications: an overview.

Bo Peng1, Huann-Sheng Chen, Leah E Mechanic, Ben Racine, John Clarke, Elizabeth Gillanders, Eric J Feuer.   

Abstract

Computer simulations have played an indispensable role in the development and applications of statistical models and methods for genetic studies across multiple disciplines. The need to simulate complex evolutionary scenarios and pseudo-datasets for various studies has fueled the development of dozens of computer programs with varying reliability, performance, and application areas. To help researchers compare and choose the most appropriate simulators for their studies, we have created the genetic simulation resources (GSR) website, which allows authors of simulation software to register their applications and describe them with more than 160 defined attributes. This article summarizes the properties of 93 simulators currently registered at GSR and provides an overview of the development and applications of genetic simulators. Unlike other review articles that address technical issues or compare simulators for particular application areas, we focus on software development, maintenance, and features of simulators, often from a historical perspective. Publications that cite these simulators are used to summarize both the applications of genetic simulations and the utilization of simulators.
© 2014 WILEY PERIODICALS, INC.

Entities:  

Keywords:  genetic simulation; genetic simulation resources; software

Mesh:

Year:  2014        PMID: 25504286      PMCID: PMC4804465          DOI: 10.1002/gepi.21876

Source DB:  PubMed          Journal:  Genet Epidemiol        ISSN: 0741-0395            Impact factor:   2.135


  52 in total

1.  Transmission-ratio distortion and allele sharing in affected sib pairs: a new linkage statistic with reduced bias, with application to chromosome 6q25.3.

Authors:  Mathieu Lemire; Nicole M Roslin; Catherine Laprise; Thomas J Hudson; Kenneth Morgan
Journal:  Am J Hum Genet       Date:  2004-08-20       Impact factor: 11.025

Review 2.  An overview of population genetic data simulation.

Authors:  Xiguo Yuan; David J Miller; Junying Zhang; David Herrington; Yue Wang
Journal:  J Comput Biol       Date:  2011-12-09       Impact factor: 1.479

3.  SimPed: a simulation program to generate haplotype and genotype data for pedigree structures.

Authors:  Suzanne M Leal; Kai Yan; Bertram Müller-Myhsok
Journal:  Hum Hered       Date:  2005-10-13       Impact factor: 0.444

4.  Rose: generating sequence families.

Authors:  J Stoye; D Evers; F Meyer
Journal:  Bioinformatics       Date:  1998       Impact factor: 6.937

Review 5.  Genome simulation approaches for synthesizing in silico datasets for human genomics.

Authors:  Marylyn D Ritchie; William S Bush
Journal:  Adv Genet       Date:  2010       Impact factor: 1.944

6.  Chromosome-based method for rapid computer simulation in human genetic linkage analysis.

Authors:  J D Terwilliger; M Speer; J Ott
Journal:  Genet Epidemiol       Date:  1993       Impact factor: 2.135

7.  Simulation of genes and genomes forward in time.

Authors:  Antonio Carvajal-Rodríguez
Journal:  Curr Genomics       Date:  2010-03       Impact factor: 2.236

8.  EggLib: processing, analysis and simulation tools for population genetics and genomics.

Authors:  Stéphane De Mita; Mathieu Siol
Journal:  BMC Genet       Date:  2012-04-11       Impact factor: 2.797

9.  An integrated map of genetic variation from 1,092 human genomes.

Authors:  Goncalo R Abecasis; Adam Auton; Lisa D Brooks; Mark A DePristo; Richard M Durbin; Robert E Handsaker; Hyun Min Kang; Gabor T Marth; Gil A McVean
Journal:  Nature       Date:  2012-11-01       Impact factor: 49.962

10.  Fregene: simulation of realistic sequence-level data in populations and ascertained samples.

Authors:  Marc Chadeau-Hyam; Clive J Hoggart; Paul F O'Reilly; John C Whittaker; Maria De Iorio; David J Balding
Journal:  BMC Bioinformatics       Date:  2008-09-08       Impact factor: 3.169

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  11 in total

1.  Genetic Simulation Resources and the GSR Certification Program.

Authors:  Bo Peng; Man Chong Leong; Huann-Sheng Chen; Melissa Rotunno; Katy R Brignole; John Clarke; Leah E Mechanic
Journal:  Bioinformatics       Date:  2019-02-15       Impact factor: 6.937

2.  Genetic simulation tools for post-genome wide association studies of complex diseases.

Authors:  Huann-Sheng Chen; Carolyn M Hutter; Leah E Mechanic; Elizabeth M Gillanders; Eric J Feuer; Christopher I Amos; Vineet Bafna; Elizabeth R Hauser; Ryan D Hernandez; Chun Li; David A Liberles; Kimberly McAllister; Jason H Moore; Dina N Paltoo; George J Papanicolaou; Bo Peng; Marylyn D Ritchie; Gabriel Rosenfeld; John S Witte
Journal:  Genet Epidemiol       Date:  2014-11-04       Impact factor: 2.135

3.  Population genetic simulations of complex phenotypes with implications for rare variant association tests.

Authors:  Lawrence H Uricchio; Raul Torres; John S Witte; Ryan D Hernandez
Journal:  Genet Epidemiol       Date:  2014-11-21       Impact factor: 2.135

4.  Efficient ancestry and mutation simulation with msprime 1.0.

Authors:  Franz Baumdicker; Gertjan Bisschop; Daniel Goldstein; Graham Gower; Aaron P Ragsdale; Georgia Tsambos; Sha Zhu; Bjarki Eldon; E Castedo Ellerman; Jared G Galloway; Ariella L Gladstein; Gregor Gorjanc; Bing Guo; Ben Jeffery; Warren W Kretzschumar; Konrad Lohse; Michael Matschiner; Dominic Nelson; Nathaniel S Pope; Consuelo D Quinto-Cortés; Murillo F Rodrigues; Kumar Saunack; Thibaut Sellinger; Kevin Thornton; Hugo van Kemenade; Anthony W Wohns; Yan Wong; Simon Gravel; Andrew D Kern; Jere Koskela; Peter L Ralph; Jerome Kelleher
Journal:  Genetics       Date:  2022-03-03       Impact factor: 4.402

5.  GESDB: a platform of simulation resources for genetic epidemiology studies.

Authors:  Po-Ju Yao; Ren-Hua Chung
Journal:  Database (Oxford)       Date:  2016-05-30       Impact factor: 3.451

6.  Analysis validation has been neglected in the Age of Reproducibility.

Authors:  Kathleen E Lotterhos; Jason H Moore; Ann E Stapleton
Journal:  PLoS Biol       Date:  2018-12-10       Impact factor: 8.029

7.  SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination.

Authors:  Abbas Jariani; Christopher Warth; Koen Deforche; Pieter Libin; Alexei J Drummond; Andrew Rambaut; Frederick A Matsen Iv; Kristof Theys
Journal:  Virus Evol       Date:  2019-03-08

8.  isqg: A Binary Framework for in Silico Quantitative Genetics.

Authors:  Fernando H Toledo; Paulino Pérez-Rodríguez; José Crossa; Juan Burgueño
Journal:  G3 (Bethesda)       Date:  2019-08-08       Impact factor: 3.154

9.  Simulation of Chordate Intron Evolution Using Randomly Generated and Mutated Base Sequences.

Authors:  Guang-Dong Wang; Yong Wang; Zhen Zeng; Jun-Ming Mao; Qin-Liu He; Qin Yao; Ke-Ping Chen
Journal:  Evol Bioinform Online       Date:  2020-01-29       Impact factor: 1.625

Review 10.  Review: Balancing Selection for Deleterious Alleles in Livestock.

Authors:  Martijn F L Derks; Marije Steensma
Journal:  Front Genet       Date:  2021-12-03       Impact factor: 4.599

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