On the use of the Pearson correlation coefficient for model evaluation in genome-wide prediction

P Waldmann - Frontiers in genetics, 2019 - frontiersin.org
The large number of markers in genome-wide prediction demands the use of methods with
regularization and model comparison based on some hold-out test prediction error measure …

Training set optimization of genomic prediction by means of EthAcc

B Mangin, R Rincent, CE Rabier, L Moreau… - PLoS …, 2019 - journals.plos.org
Genomic prediction is a useful tool for plant and animal breeding programs and is starting to
be used to predict human diseases as well. A shortcoming that slows down the genomic …

Evaluation of approaches for estimating the accuracy of genomic prediction in plant breeding

SB Ould Estaghvirou, JO Ogutu, T Schulz-Streeck… - BMC genomics, 2013 - Springer
Background In genomic prediction, an important measure of accuracy is the correlation
between the predicted and the true breeding values. Direct computation of this quantity for …

Systematic bias of correlation coefficient may explain negative accuracy of genomic prediction

Y Zhou, MI Vales, A Wang, Z Zhang - Briefings in bioinformatics, 2017 - academic.oup.com
Accuracy of genomic prediction is commonly calculated as the Pearson correlation
coefficient between the predicted and observed phenotypes in the inference population by …

Genome-enabled prediction methods based on machine learning

EL Reinoso-Peláez, D Gianola… - Genomic prediction of …, 2022 - Springer
Growth of artificial intelligence and machine learning (ML) methodology has been explosive
in recent years. In this class of procedures, computers get knowledge from sets of …

Controlling the overfitting of heritability in genomic selection through cross validation

Z Jia - Scientific reports, 2017 - nature.com
In genomic selection (GS), all the markers across the entire genome are used to conduct
marker-assisted selection such that each quantitative trait locus of complex trait is in linkage …

Genome-wide prediction of discrete traits using Bayesian regressions and machine learning

O González-Recio, S Forni - Genetics Selection Evolution, 2011 - Springer
Background Genomic selection has gained much attention and the main goal is to increase
the predictive accuracy and the genetic gain in livestock using dense marker information …

Design of training populations for selective phenotyping in genomic prediction

D Akdemir, J Isidro-Sánchez - Scientific reports, 2019 - nature.com
Phenotyping is the current bottleneck in plant breeding, especially because next-generation
sequencing has decreased genotyping cost more than 100.000 fold in the last 20 years …

Do feature selection methods for selecting environmental covariables enhance genomic prediction accuracy?

OA Montesinos-López, L Crespo-Herrera… - Frontiers in …, 2023 - frontiersin.org
Genomic selection (GS) is transforming plant and animal breeding, but its practical
implementation for complex traits and multi-environmental trials remains challenging. To …

Genome-wide prediction using Bayesian additive regression trees

P Waldmann - Genetics Selection Evolution, 2016 - Springer
Background The goal of genome-wide prediction (GWP) is to predict phenotypes based on
marker genotypes, often obtained through single nucleotide polymorphism (SNP) chips. The …