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Pleiotropy, epistasis and the genetic architecture of quantitative traits
Pleiotropy (whereby one genetic polymorphism affects multiple traits) and epistasis (whereby non-linear interactions between genetic polymorphisms...
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A complete chromosome substitution map** panel reveals genome-wide epistasis in Arabidopsis
Chromosome substitution lines (CSLs) are tentatively supreme resources to investigate non-allelic genetic interactions. However, the difficulty of...
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Epistasis Methods and Protocols
This volume explores methods and protocols for detecting epistasis from genetic data. Chapters provide methods and protocols demonstrating approaches...
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NRN1 epistasis with BDNF and CACNA1C: mediation effects on symptom severity through neuroanatomical changes in schizophrenia
The expression of Neuritin-1 ( NRN1 ), a neurotrophic factor crucial for neurodevelopment and synaptic plasticity, is enhanced by the Brain Derived...
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Analyzing High-Order Epistasis from Genotype-Phenotype Maps Using ‘Epistasis’ Package
Epistasis is the phenomenon about the interactions between genes, leading to complex phenotypic effects. The interactions between three or more...
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Epistasis-Based Feature Selection Algorithm
Variable selection is an important procedure to select relevant features from large datasets in optimization problems. The use of epistasis concepts...
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Epistasis Detection Based on Epi-GTBN
Epistasis detection is a hot topic in bioinformatics due to its relevance to the detection of specific phenotypic traits and gene–gene interactions....
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W-Test for Genetic Epistasis Testing
The genetic epistasis effect has been widely acknowledged as an essential contributor to genetic variation in complex diseases. In this chapter, we...
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Brief Survey on Machine Learning in Epistasis
In biology, the term “epistasis” indicates the effect of the interaction of a gene with another gene. A gene can interact with an independently...
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Simulating Evolution in Asexual Populations with Epistasis
I show how to use OncoSimulR, software for forward-time genetic simulations, to simulate evolution of asexual populations in the presence of...
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Epistasis Analysis: Classification Through Machine Learning Methods
Complex disease is different from Mendelian disorders. Its development usually involves the interaction of multiple genes or the interaction between...
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Protocol for Epistasis Detection with Machine Learning Using GenEpi Package
To develop medical treatments and prevention, the association between disease and genetic variants needs to be identified. The main goal of...
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The Combined Analysis of Pleiotropy and Epistasis (CAPE)
Epistasis, or gene–gene interaction, contributes substantially to trait variation in organisms ranging from yeast to humans, and modeling epistasis...
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Two-Stage Testing for Epistasis: Screening and Verification
Undiscovered gene-to-gene interaction (epistasis) is a possible explanation for the “missing heritability” of complex traits and diseases. On a...
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A Belief Degree–Associated Fuzzy Multifactor Dimensionality Reduction Framework for Epistasis Detection
Epistasis is a challenge in prediction, classification, and suspicion of human genetic diseases. Many technologies, methods, and tools have been...
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Genome-wide epistasis analysis for Alzheimer’s disease and implications for genetic risk prediction
BackgroundSingle-nucleotide polymorphisms (SNPs) identified by genome-wide association studies only explain part of the heritability of Alzheimer’s...
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Using C-JAMP to Investigate Epistasis and Pleiotropy
Unraveling the complex biological mechanisms underlying human health and disease is a great challenge. With genomic data, many aspects can be...
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Evidence of genetic epistasis in autoimmune diabetes susceptibility revealed by mouse congenic sublines
Susceptibility to autoimmune diabetes is a complex genetic trait. Linkage analyses exploiting the NOD mouse, which spontaneously develops autoimmune...
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SNPInt-GPU: Tool for Epistasis Testing with Multiple Methods and GPU Acceleration
We present SNPInt-GPU, a software providing several methods for statistical epistasis testing. SNPInt-GPU supports GPU acceleration using the Nvidia...
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Phenotype Prediction Under Epistasis
Reliable methods of phenotype prediction from genomic data play an increasingly important role in many areas of plant and animal breeding. Thus,...