Genomic prediction in animals and plants: simulation of data, validation, reporting, and benchmarking

HD Daetwyler, MPL Calus, R Pong-Wong… - Genetics, 2013 - academic.oup.com
The genomic prediction of phenotypes and breeding values in animals and plants has
developed rapidly into its own research field. Results of genomic prediction studies are often …

An overview of SNP interactions in genome-wide association studies

P Li, M Guo, C Wang, X Liu, Q Zou - Briefings in functional …, 2015 - academic.oup.com
With the recent explosion in high-throughput genotyping technology, the amount and quality
of single-nucleotide polymorphism (SNP) data has increased exponentially. Therefore, the …

A review on methods for detecting SNP interactions in high-dimensional genomic data

S Uppu, A Krishna, RP Gopalan - IEEE/ACM transactions on …, 2016 - ieeexplore.ieee.org
In this era of genome-wide association studies (GWAS), the quest for understanding the
genetic architecture of complex diseases is rapidly increasing more than ever before. The …

Accounting for population stratification in practice: a comparison of the main strategies dedicated to genome-wide association studies

M Bouaziz, C Ambroise, M Guedj - PloS one, 2011 - journals.plos.org
Genome-Wide Association Studies are powerful tools to detect genetic variants associated
with diseases. Their results have, however, been questioned, in part because of the bias …

Fast and accurate shared segment detection and relatedness estimation in un-phased genetic data via TRUFFLE

A Dimitromanolakis, AD Paterson, L Sun - The American Journal of Human …, 2019 - cell.com
Relationship estimation and segment detection between individuals is an important aspect
of disease gene mapping. Existing methods are either tailored for computational efficiency …

sim1000G: a user-friendly genetic variant simulator in R for unrelated individuals and family-based designs

A Dimitromanolakis, J Xu, A Krol, L Briollais - BMC bioinformatics, 2019 - Springer
Background Simulation of genetic variants data is frequently required for the evaluation of
statistical methods in the fields of human and animal genetics. Although a number of high …

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

J Shang, J Zhang, X Lei, W Zhao, Y Dong - Genes & Genomics, 2013 - Springer
Epistasis is a ubiquitous phenomenon in genetics, and is considered to be one of the main
factors in current efforts to detect missing heritability for complex diseases. Simulation is a …

A review: simulation tools for genome-wide interaction studies

J Shang, A Xu, M Bi, Y Zhang, F Li… - Briefings in Functional …, 2024 - academic.oup.com
Genome-wide association study (GWAS) is essential for investigating the genetic basis of
complex diseases; nevertheless, it usually ignores the interaction of multiple single …

Inferring coancestry in population samples in the presence of linkage disequilibrium

MD Brown, CG Glazner, C Zheng, EA Thompson - Genetics, 2012 - academic.oup.com
In both pedigree linkage studies and in population-based association studies there has
been much interest in the use of modern dense genetic marker data to infer segments of …

Hardware-accelerated simulation-based inference of stochastic epidemiology models for COVID-19

S Kulkarni, MM Krell, S Nabarro, CA Moritz - ACM Journal on Emerging …, 2022 - dl.acm.org
Epidemiology models are central to understanding and controlling large-scale pandemics.
Several epidemiology models require simulation-based inference such as Approximate …