Phantom epistasis in genomic selection: on the predictive ability of epistatic models

MF Schrauf, JWR Martini, H Simianer… - G3: Genes …, 2020 - academic.oup.com
Genomic selection uses whole-genome marker models to predict phenotypes or genetic
values for complex traits. Some of these models fit interaction terms between markers, and …

Efficient algorithms for calculating epistatic genomic relationship matrices

Y Jiang, JC Reif - Genetics, 2020 - academic.oup.com
The genomic relationship matrix plays a key role in the analysis of genetic diversity, genomic
prediction, and genome-wide association studies. The epistatic genomic relationship matrix …

[HTML][HTML] On the approximation of interaction effect models by Hadamard powers of the additive genomic relationship

JWR Martini, FH Toledo, J Crossa - Theoretical population biology, 2020 - Elsevier
Whole genome epistasis models with interactions between different loci can be
approximated by genomic relationship models based on Hadamard powers of the additive …

Accounting for epistasis improves genomic prediction of phenotypes with univariate and bivariate models across environments

E Vojgani, T Pook, JWR Martini, AC Hölker… - Theoretical and Applied …, 2021 - Springer
Abstract Key Message The accuracy of genomic prediction of phenotypes can be increased
by including the top-ranked pairwise SNP interactions into the prediction model. Abstract We …

On Hadamard and Kronecker products in covariance structures for genotype× environment interaction

JWR Martini, J Crossa, FH Toledo… - The Plant …, 2020 - Wiley Online Library
When including genotype× environment interactions (G× E) in genomic prediction models,
Hadamard or Kronecker products have been used to model the covariance structure of …

Incorporating omics data in genomic prediction

JWR Martini, N Gao, J Crossa - … Prediction of Complex Traits: Methods and …, 2022 - Springer
In this chapter, we discuss the motivation for integrating other types of omics data into
genomic prediction methods. We give an overview of literature investigating the …

MIDESP: mutual information-based detection of epistatic SNP pairs for qualitative and quantitative phenotypes

F Heinrich, F Ramzan, A Rajavel, AO Schmitt, M Gültas - Biology, 2021 - mdpi.com
Simple Summary The interactions between SNPs, which are known as epistasis, can
strongly influence the phenotype. Their detection is still a challenge, which is made even …

[PDF][PDF] Exploring and exploiting genetic variation for balancing short-and long-term genetic gains in plant breeding

D Vanavermaete - 2021 - imec-publications.be
ir. David M. Vanavermaete Page 1 Department of Data Analysis and Mathematical Modelling
Exploring and exploiting genetic variation for balancing short- and long-term genetic gains in …

[PDF][PDF] Accounting for Epistasis in Genomic Phenotype Prediction

E Vojgani - 2021 - ediss.uni-goettingen.de
Wide availability of genomic data has had a considerable impact on plant and animal
breeding programs which enables the study of genotypes and their relationships with …

[PDF][PDF] Sparse Partial Least Square Correspondence Analysis (SPLA-CA): Applications to Genetics and Behavioral Studies

JC Yu - 2021 - utd-ir.tdl.org
Most research questions in modern cognitive neuroscience relate two sets of variables
collected from the same observations (eg, participants). A popular multivariate method for …