HIBLUP: an integration of statistical models on the BLUP framework for efficient genetic evaluation using big genomic data

L Yin, H Zhang, Z Tang, D Yin, Y Fu, X Yuan… - Nucleic acids …, 2023 - academic.oup.com
Human diseases and agricultural traits can be predicted by modeling a genetic random
polygenic effect in linear mixed models. To estimate variance components and predict …

Single-step genomic evaluations from theory to practice: using SNP chips and sequence data in BLUPF90

D Lourenco, A Legarra, S Tsuruta, Y Masuda, I Aguilar… - Genes, 2020 - mdpi.com
Single-step genomic evaluation became a standard procedure in livestock breeding, and
the main reason is the ability to combine all pedigree, phenotypes, and genotypes available …

Predicted residual error sum of squares of mixed models: an application for genomic prediction

S Xu - G3: Genes, Genomes, Genetics, 2017 - academic.oup.com
Genomic prediction is a statistical method to predict phenotypes of polygenic traits using
high-throughput genomic data. Most diseases and behaviors in humans and animals are …

Enhancing genome-enabled prediction by bagging genomic BLUP

D Gianola, KA Weigel, N Krämer, A Stella, CC Schön - PLoS One, 2014 - journals.plos.org
We examined whether or not the predictive ability of genomic best linear unbiased
prediction (GBLUP) could be improved via a resampling method used in machine learning …

A Bayesian method and its variational approximation for prediction of genomic breeding values in multiple traits

T Hayashi, H Iwata - BMC bioinformatics, 2013 - Springer
Background Genomic selection is an effective tool for animal and plant breeding, allowing
effective individual selection without phenotypic records through the prediction of genomic …

Expanding the BLUP alphabet for genomic prediction adaptable to the genetic architectures of complex traits

J Wang, Z Zhou, Z Zhang, H Li, D Liu, Q Zhang… - Heredity, 2018 - nature.com
Improvement of statistical methods is crucial for realizing the potential of increasingly dense
genetic markers. Bayesian methods treat all markers as random effects, exhibit an …

Genomic BLUP decoded: a look into the black box of genomic prediction

D Habier, RL Fernando, DJ Garrick - Genetics, 2013 - academic.oup.com
Genomic best linear unbiased prediction (BLUP) is a statistical method that uses
relationships between individuals calculated from single-nucleotide polymorphisms (SNPs) …

The impact of genetic architecture on genome-wide evaluation methods

HD Daetwyler, R Pong-Wong, B Villanueva… - Genetics, 2010 - academic.oup.com
The rapid increase in high-throughput single-nucleotide polymorphism data has led to a
great interest in applying genome-wide evaluation methods to identify an individual's …

GAPIT version 2: an enhanced integrated tool for genomic association and prediction

Y Tang, X Liu, J Wang, M Li, Q Wang, F Tian… - The plant …, 2016 - Wiley Online Library
Most human diseases and agriculturally important traits are complex. Dissecting their
genetic architecture requires continued development of innovative and powerful statistical …

Predicting genetic values: a kernel-based best linear unbiased prediction with genomic data

U Ober, M Erbe, N Long, E Porcu, M Schlather… - Genetics, 2011 - academic.oup.com
Genomic data provide a valuable source of information for modeling covariance structures,
allowing a more accurate prediction of total genetic values (GVs). We apply the kriging …