AIMC Topic: Genome-Wide Association Study

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Predicting physiological aging rates from a range of quantitative traits using machine learning.

Aging
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...

Spatial rank-based multifactor dimensionality reduction to detect gene-gene interactions for multivariate phenotypes.

BMC bioinformatics
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...

LightGBM: accelerated genomically designed crop breeding through ensemble learning.

Genome biology
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...

Genetic dissection of complex traits using hierarchical biological knowledge.

PLoS computational biology
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...

ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation.

PLoS computational biology
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...

The "GEnomics of Musculo Skeletal Traits TranslatiOnal NEtwork": Origins, Rationale, Organization, and Prospects.

Frontiers in endocrinology
Musculoskeletal research has been enriched in the past ten years with a great wealth of new discoveries arising from genome wide association studies (GWAS). In addition to the novel factors identified by GWAS, the advent of whole-genome and whole-exo...

Prioritization of disease genes from GWAS using ensemble-based positive-unlabeled learning.

European journal of human genetics : EJHG
A primary challenge in understanding disease biology from genome-wide association studies (GWAS) arises from the inability to directly implicate causal genes from association data. Integration of multiple-omics data sources potentially provides impor...

Prioritizing and characterizing functionally relevant genes across human tissues.

PLoS computational biology
Knowledge of genes that are critical to a tissue's function remains difficult to ascertain and presents a major bottleneck toward a mechanistic understanding of genotype-phenotype links. Here, we present the first machine learning model-FUGUE-combini...

Use of Deep-Learning Genomics to Discriminate Healthy Individuals from Those with Alzheimer's Disease or Mild Cognitive Impairment.

Behavioural neurology
OBJECTIVES: Alzheimer's disease (AD) is the most prevalent neurodegenerative disorder and the most common form of dementia in the elderly. Certain genes have been identified as important clinical risk factors for AD, and technological advances in gen...

An artificial neural network approach integrating plasma proteomics and genetic data identifies PLXNA4 as a new susceptibility locus for pulmonary embolism.

Scientific reports
Venous thromboembolism is the third common cardiovascular disease and is composed of two entities, deep vein thrombosis (DVT) and its potential fatal form, pulmonary embolism (PE). While PE is observed in ~ 40% of patients with documented DVT, there ...