AIMC Topic: Gene Frequency

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Serum vitamin D deficiency and vitamin D receptor gene polymorphism are associated with increased risk of cardiovascular disease in a Chinese rural population.

Nutrition research (New York, N.Y.)
Several studies have reported a conflicting association between vitamin D deficiency, vitamin D receptor (VDR) polymorphism, and the risk of cardiovascular disease (CVD). We hypothesized that serum 25(OH)D concentrations and single nucleotide polymor...

Prediction of opioid dose in cancer pain patients using genetic profiling: not yet an option with support vector machine learning.

BMC research notes
OBJECTIVE: Use of opioids for pain management has increased over the past decade; however, inadequate analgesic response is common. Genetic variability may be related to opioid efficacy, but due to the many possible combinations and variables, statis...

Multiobjective differential evolution-based multifactor dimensionality reduction for detecting gene-gene interactions.

Scientific reports
Epistasis within disease-related genes (gene-gene interactions) was determined through contingency table measures based on multifactor dimensionality reduction (MDR) using single-nucleotide polymorphisms (SNPs). Most MDR-based methods use the single ...

Assessing and comparison of different machine learning methods in parent-offspring trios for genotype imputation.

Journal of theoretical biology
Genotype imputation is an important tool for prediction of unknown genotypes for both unrelated individuals and parent-offspring trios. Several imputation methods are available and can either employ universal machine learning methods, or deploy algor...

Machine learning approach for pooled DNA sample calibration.

BMC bioinformatics
BACKGROUND: Despite ongoing reduction in genotyping costs, genomic studies involving large numbers of species with low economic value (such as Black Tiger prawns) remain cost prohibitive. In this scenario DNA pooling is an attractive option to reduce...

An efficiency analysis of high-order combinations of gene-gene interactions using multifactor-dimensionality reduction.

BMC genomics
BACKGROUND: Multifactor dimensionality reduction (MDR) is widely used to analyze interactions of genes to determine the complex relationship between diseases and polymorphisms in humans. However, the astronomical number of high-order combinations mak...

De novo transcriptome assembly of pummelo and molecular marker development.

PloS one
Pummelo (Citrus grandis) is an important fruit crop worldwide because of its nutritional value. To accelerate the pummelo breeding program, it is essential to obtain extensive genetic information and develop relative molecular markers. Here, we obtai...

Methylomes Reveal Recent Evolutionary Changes in Populations of Two Plant Species.

Genome biology and evolution
Plant DNA methylation changes occur hundreds to thousands of times faster than DNA mutations and can be transmitted transgenerationally, making them useful for studying population-scale patterns in clonal or selfing species. However, a state-of-the-a...

Scalable CNN-based classification of selective sweeps using derived allele frequencies.

Bioinformatics (Oxford, England)
MOTIVATION: Selective sweeps can successfully be distinguished from neutral genetic data using summary statistics and likelihood-based methods that analyze single nucleotide polymorphisms (SNPs). However, these methods are sensitive to confounding fa...