Methods in molecular biology (Clifton, N.J.)
Jan 1, 2021
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...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2021
We report a step-by-step protocol to use pysster, a TensorFlow-based package for building deep neural networks on a broad range of epistatic sequences such as DNA, RNA, or annotated secondary structure sequences. Pysster provides users comprehensive ...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2021
In biology, the term "epistasis" indicates the effect of the interaction of a gene with another gene. A gene can interact with an independently sorted gene, located far away on the chromosome or on an entirely different chromosome, and this interacti...
MOTIVATION: Detecting epistatic interactions in genome-wide association studies (GWAS) is a computational challenge. Such huge numbers of single-nucleotide polymorphism (SNP) combinations limit the some of the powerful algorithms to be applied to det...
MOTIVATION: Gene-gene interaction (GGI) is one of the most popular approaches for finding and explaining the missing heritability of common complex traits in genome-wide association studies. The multifactor dimensionality reduction (MDR) method has b...
MOTIVATION: Much of the biological knowledge accumulated over the last decades is stored in different databases governed by various organizations and institutes. Integrating and connecting these vast knowledge repositories is an extremely useful meth...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2015
Here we introduce artificial intelligence (AI) methodology for detecting and characterizing epistasis in genetic association studies. The ultimate goal of our AI strategy is to analyze genome-wide genetics data as a human would using sources of exper...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2015
Here we introduce the multifactor dimensionality reduction (MDR) methodology and software package for detecting and characterizing epistasis in genetic association studies. We provide a general overview of the method and then highlight some of the ke...
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