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Optimizing clinico-genomic disease prediction across ancestries: a machine learning strategy with Pareto improvement
BackgroundAccurate prediction of an individual’s predisposition to diseases is vital for preventive medicine and early intervention. Various...
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Weighted kernels improve multi-environment genomic prediction
Crucial to variety improvement programs is the reliable and accurate prediction of genotype’s performance across environments. However, due to the...
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Multibreed genomic prediction using summary statistics and a breed-origin-of-alleles approach
Because of an increasing interest in crossbreeding between dairy breeds in dairy cattle herds, farmers are requesting breeding values for crossbred...
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Enhancing prediction accuracy of coronary artery disease through machine learning-driven genomic variant selection
Machine learning (ML) methods are increasingly becoming crucial in genome-wide association studies for identifying key genetic variants or SNPs that...
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Leveraging functional genomic annotations and genome coverage to improve polygenic prediction of complex traits within and between ancestries
We develop a method, SBayesRC, that integrates genome-wide association study (GWAS) summary statistics with functional genomic annotations to improve...
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First large-scale genomic prediction in the honey bee
Genomic selection has increased genetic gain in several livestock species, but due to the complicated genetics and reproduction biology not yet in...
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Performance of Bayesian and BLUP alphabets for genomic prediction: analysis, comparison and results
We evaluated the performances of three BLUP and five Bayesian methods for genomic prediction by using nine actual and 54 simulated datasets. The...
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Genomic prediction of cotton fibre quality and yield traits using Bayesian regression methods
Genomic selection or genomic prediction (GP) has increasingly become an important molecular breeding technology for crop improvement. GP aims to...
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Unsupervised representation learning on high-dimensional clinical data improves genomic discovery and prediction
Although high-dimensional clinical data (HDCD) are increasingly available in biobank-scale datasets, their use for genetic discovery remains...
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Including dominance effects in the prediction model through locus-specific weights on heterozygous genotypes can greatly improve genomic predictive abilities
The dominance effect is considered to be a key factor affecting complex traits. However, previous studies have shown that the improvement of the...
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Multi-generation genomic prediction of maize yield using parametric and non-parametric sparse selection indices
Genomic prediction models are often calibrated using multi-generation data. Over time, as data accumulates, training data sets become increasingly...
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Molecular genomic and epigenomic characteristics related to aspirin and clopidogrel resistance
BackgroundMediators, genomic and epigenomic characteristics involving in metabolism of arachidonic acid by cyclooxygenase (COX) and lipoxygenase...
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Screening Host Genomic Data for Wolbachia Infections
Less than a decade ago, the production of Wolbachia genomic assemblies was tedious, time-consuming, and expensive. The production of Wolbachia...
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Investigating the Performance of Frequentist and Bayesian Techniques in Genomic Evaluation
The genomic evaluation process relies on the assumption of linkage disequilibrium between dense single-nucleotide polymorphism (SNP) markers at the...
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Gene based markers improve precision of genome-wide association studies and accuracy of genomic predictions in rice breeding
It is hypothesized that the genome-wide genic markers may increase the prediction accuracy of genomic selection for quantitative traits. To test this...
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Oncogenic Genomic Changes in Cancer
A common cause of all cancers leads us to a common definition. This definition is mutation. Cancer cells tend to constantly resist irregularity under...
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Integrating environmental gradients into breeding: application of genomic reactions norms in a perennial species
Global warming threatens the productivity of forest plantations. We propose here the integration of environmental information into a genomic...
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Clinically conserved genomic subtypes of gastric adenocarcinoma
Gastric adenocarcinoma (GAC) is a lethal disease characterized by genomic and clinical heterogeneity. By integrating 8 previously established genomic...
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A guide for kernel generalized regression methods for genomic-enabled prediction
The primary objective of this paper is to provide a guide on implementing Bayesian generalized kernel regression methods for genomic prediction in...