AIMC Topic: Genome-Wide Association Study

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RegVar: Tissue-specific Prioritization of Non-coding Regulatory Variants.

Genomics, proteomics & bioinformatics Dec 29, 2021
Non-coding genomic variants constitute the majority of trait-associated genome variations; however, the identification of functional non-coding variants is still a challenge in human genetics, and a method for systematically assessing the impact of r...
Neural Networks, Computer Genome-Wide Association Study Genomics Polymorphism, Single Nucleotide Humans
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Deep learning enables genetic analysis of the human thoracic aorta.

Nature genetics Nov 26, 2021
Enlargement or aneurysm of the aorta predisposes to dissection, an important cause of sudden death. We trained a deep learning model to evaluate the dimensions of the ascending and descending thoracic aorta in 4.6 million cardiac magnetic resonance i...
Adult Male Middle Aged Transcriptome Humans Female Aged Magnetic Resonance Imaging Aorta, Thoracic Biological Variation, Population Deep Learning Quantitative Trait Loci Genome-Wide Association Study Aortic Aneurysm Image Processing, Computer-Assisted
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Personalized Cell Therapy for Patients with Peripheral Arterial Diseases in the Context of Genetic Alterations: Artificial Intelligence-Based Responder and Non-Responder Prediction.

Cells Nov 23, 2021
Stem/progenitor cell transplantation is a potential novel therapeutic strategy to induce angiogenesis in ischemic tissue, which can prevent major amputation in patients with advanced peripheral artery disease (PAD). Thus, clinicians can use cell ther...
Transcriptome Genome-Wide Association Study Peripheral Arterial Disease Whole Genome Sequencing Artificial Intelligence Precision Medicine Risk Factors Cell- and Tissue-Based Therapy Humans
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Leveraging machine learning essentiality predictions and chemogenomic interactions to identify antifungal targets.

Nature communications Nov 11, 2021
Fungal pathogens pose a global threat to human health, with Candida albicans among the leading killers. Systematic analysis of essential genes provides a powerful strategy to discover potential antifungal targets. Here, we build a machine learning mo...
Systems Biology Machine Learning Genome-Wide Association Study Candida albicans Antifungal Agents Kinetochores
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Deep Learning of the Retina Enables Phenome- and Genome-Wide Analyses of the Microvasculature.

Circulation Nov 8, 2021
BACKGROUND: The microvasculature, the smallest blood vessels in the body, has key roles in maintenance of organ health and tumorigenesis. The retinal fundus is a window for human in vivo noninvasive assessment of the microvasculature. Large-scale com...
Middle Aged Deep Learning Genome-Wide Association Study Genomics Humans Female Male Mendelian Randomization Analysis Retina Microvessels
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Predicting physiological aging rates from a range of quantitative traits using machine learning.

Aging Oct 29, 2021
It is widely thought that individuals age at different rates. A method that measures "physiological age" or physiological aging rate independent of chronological age could therefore help elucidate mechanisms of aging and inform an individual's risk o...
Models, Biological Neuroticism Longitudinal Studies DNA Methylation Pulse Wave Analysis Aged Aged, 80 and over Young Adult Adult Machine Learning Male Algorithms Humans Aging Phenotype Female Middle Aged Genome-Wide Association Study
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Spatial rank-based multifactor dimensionality reduction to detect gene-gene interactions for multivariate phenotypes.

BMC bioinformatics Oct 4, 2021
BACKGROUND: Identifying interaction effects between genes is one of the main tasks of genome-wide association studies aiming to shed light on the biological mechanisms underlying complex diseases. Multifactor dimensionality reduction (MDR) is a popul...
Computer Simulation Genome-Wide Association Study Polymorphism, Single Nucleotide Models, Genetic Epistasis, Genetic Multifactor Dimensionality Reduction Algorithms Phenotype
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LightGBM: accelerated genomically designed crop breeding through ensemble learning.

Genome biology Sep 20, 2021
LightGBM is an ensemble model of decision trees for classification and regression prediction. We demonstrate its utility in genomic selection-assisted breeding with a large dataset of inbred and hybrid maize lines. LightGBM exhibits superior performa...
Crops, Agricultural Plant Breeding Genomics Machine Learning Polymorphism, Single Nucleotide Software Decision Trees Genome-Wide Association Study Zea mays
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Genetic dissection of complex traits using hierarchical biological knowledge.

PLoS computational biology Sep 17, 2021
Despite the growing constellation of genetic loci linked to common traits, these loci have yet to account for most heritable variation, and most act through poorly understood mechanisms. Recent machine learning (ML) systems have used hierarchical bio...
Metabolic Networks and Pathways Neural Networks, Computer Copper Benomyl Machine Learning Mutation Nucleotidyltransferases Gene Ontology Phenotype Glucose Glycine Computational Biology Hydroxyurea Knowledge Bases Genome-Wide Association Study Systems Biology Polymorphism, Single Nucleotide Saccharomyces cerevisiae Chromosome Mapping Models, Genetic Multifactorial Inheritance
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ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation.

PLoS computational biology Sep 7, 2021
Regulatory elements control gene expression through transcription initiation (promoters) and by enhancing transcription at distant regions (enhancers). Accurate identification of regulatory elements is fundamental for annotating genomes and understan...
Mutation Gene Expression Regulation Genome, Human Promoter Regions, Genetic Molecular Sequence Annotation Enhancer Elements, Genetic Genes, Reporter Deep Learning Genome-Wide Association Study Computational Biology Models, Genetic Regulatory Sequences, Nucleic Acid Humans Transcription Initiation, Genetic
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