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Genetic Association Studies

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Discovering genotype-phenotype relationships with machine learning and the Visual Physiology Opsin Database (VPOD).

GigaScience
BACKGROUND: Predicting phenotypes from genetic variation is foundational for fields as diverse as bioengineering and global change biology, highlighting the importance of efficient methods to predict gene functions. Linking genetic changes to phenoty...

Predicting miRNA-disease associations using an ensemble learning framework with resampling method.

Briefings in bioinformatics
MOTIVATION: Accumulating evidences have indicated that microRNA (miRNA) plays a crucial role in the pathogenesis and progression of various complex diseases. Inferring disease-associated miRNAs is significant to explore the etiology, diagnosis and tr...

Protocol for Epistasis Detection with Machine Learning Using GenEpi Package.

Methods in molecular biology (Clifton, N.J.)
To develop medical treatments and prevention, the association between disease and genetic variants needs to be identified. The main goal of genome-wide association study (GWAS) is to discover the underlying reason for vulnerability to disease and uti...

Machine learning demonstrates that somatic mutations imprint invariant morphologic features in myelodysplastic syndromes.

Blood
Morphologic interpretation is the standard in diagnosing myelodysplastic syndrome (MDS), but it has limitations, such as varying reliability in pathologic evaluation and lack of integration with genetic data. Somatic events shape morphologic features...

Mantis-ml: Disease-Agnostic Gene Prioritization from High-Throughput Genomic Screens by Stochastic Semi-supervised Learning.

American journal of human genetics
Access to large-scale genomics datasets has increased the utility of hypothesis-free genome-wide analyses. However, gene signals are often insufficiently powered to reach experiment-wide significance, triggering a process of laborious triaging of gen...

Multi-dimensional machine learning approaches for fruit shape phenotyping in strawberry.

GigaScience
BACKGROUND: Shape is a critical element of the visual appeal of strawberry fruit and is influenced by both genetic and non-genetic determinants. Current fruit phenotyping approaches for external characteristics in strawberry often rely on the human e...

ES-MDA: Enhanced Similarity-based MiRNA-Disease Association.

Current protein & peptide science
Accumulating evidence demonstrate that miRNAs can be treated as critical biomarkers in various complex human diseases. Thus, the identifications on potential miRNA-disease associations have become a hotpot for providing better understanding of diseas...

EHAI: Enhanced Human Microbe-Disease Association Identification.

Current protein & peptide science
Recently, an increasing number of biological and clinical reports have demonstrated that imbalance of microbial community has the ability to play important roles among several complex diseases concerning human health. Having a good knowledge of disco...