AIMC Topic: Linkage Disequilibrium

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Improving genomic prediction accuracy for meat tenderness in Nellore cattle using artificial neural networks.

Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie Feb 5, 2020
The goal of this study was to compare the predictive performance of artificial neural networks (ANNs) with Bayesian ridge regression, Bayesian Lasso, Bayes A, Bayes B and Bayes Cπ in estimating genomic breeding values for meat tenderness in Nellore c...
Quantitative Trait, Heritable Pedigree Genome Linkage Disequilibrium Chromosomes Bayes Theorem Meat Gene Frequency Breeding Neural Networks, Computer Animals Cattle Genomics Polymorphism, Single Nucleotide Genotype
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Ensemble of machine learning algorithms using the stacked generalization approach to estimate the warfarin dose.

PloS one Oct 19, 2018
Warfarin dosing remains challenging due to narrow therapeutic index and highly individual variability. Incorrect warfarin dosing is associated with devastating adverse events. Remarkable efforts have been made to develop the machine learning based wa...
Medical Errors Pharmacogenetics Vitamin K Epoxide Reductases Humans Cohort Studies Polymorphism, Single Nucleotide Machine Learning Genotype Algorithms Aged Databases, Factual Aged, 80 and over Anticoagulants Female Male Drug Administration Schedule Warfarin Multivariate Analysis Thrombosis Middle Aged International Cooperation Hemorrhage Linkage Disequilibrium
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An unsupervised machine learning method for discovering patient clusters based on genetic signatures.

Journal of biomedical informatics Jul 29, 2018
INTRODUCTION: Many chronic disorders have genomic etiology, disease progression, clinical presentation, and response to treatment that vary on a patient-to-patient basis. Such variability creates a need to identify characteristics within patient popu...
Computational Biology Databases, Genetic Cluster Analysis Unsupervised Machine Learning Gene Ontology Linkage Disequilibrium Precision Medicine Genome-Wide Association Study Gene Regulatory Networks Polymorphism, Single Nucleotide Humans Algorithms
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Selection plays the hand it was dealt: evidence that human adaptation commonly targets standing genetic variation.

Genome biology Aug 1, 2017
Using a powerful machine learning approach, a recent study of human genomes has revealed widespread footprints of recent positive selection on standing genetic variation.
Biological Evolution Adaptation, Biological Genetic Variation Genetics, Population Genome, Human Humans Selection, Genetic Machine Learning Linkage Disequilibrium Models, Genetic Sequence Analysis, DNA
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Methylomes Reveal Recent Evolutionary Changes in Populations of Two Plant Species.

Genome biology and evolution May 30, 2025
Plant DNA methylation changes occur hundreds to thousands of times faster than DNA mutations and can be transmitted transgenerationally, making them useful for studying population-scale patterns in clonal or selfing species. However, a state-of-the-a...
Polymorphism, Single Nucleotide Genome, Plant Linkage Disequilibrium Arabidopsis DNA Methylation Brachypodium Evolution, Molecular Epigenome Gene Frequency
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DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome.

Bioinformatics (Oxford, England) Dec 13, 2022
MOTIVATION: Understanding the functional consequence of genetic variants, especially the non-coding ones, is important but particularly challenging. Genome-wide association studies (GWAS) or quantitative trait locus analyses may be subject to limited...
Polymorphism, Single Nucleotide Quantitative Trait Loci Linkage Disequilibrium Humans Deep Learning Genome-Wide Association Study Genomics
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Deep learning model reveals potential risk genes for ADHD, especially Ephrin receptor gene EPHA5.

Briefings in bioinformatics Nov 5, 2021
Attention deficit hyperactivity disorder (ADHD) is a common neurodevelopmental disorder. Although genome-wide association studies (GWAS) identify the risk ADHD-associated variants and genes with significant P-values, they may neglect the combined eff...
Polymorphism, Single Nucleotide Computational Biology Deep Learning Area Under Curve Quantitative Trait Loci Humans Gene Ontology Genome-Wide Association Study Linkage Disequilibrium Biomarkers ROC Curve Attention Deficit Disorder with Hyperactivity Genetic Predisposition to Disease Receptor, EphA5
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Revisiting genome-wide association studies from statistical modelling to machine learning.

Briefings in bioinformatics Jul 20, 2021
Over the last decade, genome-wide association studies (GWAS) have discovered thousands of genetic variants underlying complex human diseases and agriculturally important traits. These findings have been utilized to dissect the biological basis of dis...
Genome-Wide Association Study Polymorphism, Single Nucleotide Models, Genetic Models, Statistical Humans Machine Learning Epistasis, Genetic Linkage Disequilibrium
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Predicting regulatory variants using a dense epigenomic mapped CNN model elucidated the molecular basis of trait-tissue associations.

Nucleic acids research Jan 11, 2021
Assessing the causal tissues of human complex diseases is important for the prioritization of trait-associated genetic variants. Yet, the biological underpinnings of trait-associated variants are extremely difficult to infer due to statistical noise ...
Molecular Sequence Annotation Binding Sites Linkage Disequilibrium Genetic Diseases, Inborn Causality Epigenome Datasets as Topic Organ Specificity Chromatin Immunoprecipitation Histone Code Humans Deep Learning Genome-Wide Association Study Polymorphism, Single Nucleotide Epigenomics Models, Genetic Transcription Factors
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TAGOOS: genome-wide supervised learning of non-coding loci associated to complex phenotypes.

Nucleic acids research Aug 22, 2019
Genome-wide association studies (GWAS) associate single nucleotide polymorphisms (SNPs) to complex phenotypes. Most human SNPs fall in non-coding regions and are likely regulatory SNPs, but linkage disequilibrium (LD) blocks make it difficult to dist...
Humans Phenotype Linkage Disequilibrium Regulatory Sequences, Nucleic Acid Internet Genome-Wide Association Study Supervised Machine Learning Genetic Predisposition to Disease Gene Expression Regulation Polymorphism, Single Nucleotide Quantitative Trait Loci Computational Biology
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