AIMC Topic: Genetic Variation

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A machine learning model to determine the accuracy of variant calls in capture-based next generation sequencing.

BMC genomics Apr 17, 2018
BACKGROUND: Next generation sequencing (NGS) has become a common technology for clinical genetic tests. The quality of NGS calls varies widely and is influenced by features like reference sequence characteristics, read depth, and mapping accuracy. Wi...
Models, Statistical Genetic Variation High-Throughput Nucleotide Sequencing Base Sequence Machine Learning
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Selection plays the hand it was dealt: evidence that human adaptation commonly targets standing genetic variation.

Genome biology Aug 1, 2017
Using a powerful machine learning approach, a recent study of human genomes has revealed widespread footprints of recent positive selection on standing genetic variation.
Genetic Variation Genome, Human Selection, Genetic Linkage Disequilibrium Humans Machine Learning Models, Genetic Biological Evolution Sequence Analysis, DNA Adaptation, Biological Genetics, Population
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Imbalance-Aware Machine Learning for Predicting Rare and Common Disease-Associated Non-Coding Variants.

Scientific reports Jun 7, 2017
Disease and trait-associated variants represent a tiny minority of all known genetic variation, and therefore there is necessarily an imbalance between the small set of available disease-associated and the much larger set of non-deleterious genomic v...
Reproducibility of Results Genome-Wide Association Study Genetic Predisposition to Disease Models, Genetic Humans Mutation Machine Learning Genetic Variation Software RNA, Untranslated Algorithms
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Multiple Trait Covariance Association Test Identifies Gene Ontology Categories Associated with Chill Coma Recovery Time in Drosophila melanogaster.

Scientific reports May 25, 2017
The genomic best linear unbiased prediction (GBLUP) model has proven to be useful for prediction of complex traits as well as estimation of population genetic parameters. Improved inference and prediction accuracy of GBLUP may be achieved by identify...
Algorithms Computer Simulation Genetic Variation Drosophila melanogaster Gene Ontology Quantitative Trait Loci Animals Genome-Wide Association Study Models, Statistical Models, Biological Quantitative Trait, Heritable Inheritance Patterns Coma
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SNooPer: a machine learning-based method for somatic variant identification from low-pass next-generation sequencing.

BMC genomics Nov 14, 2016
BACKGROUND: Next-generation sequencing (NGS) allows unbiased, in-depth interrogation of cancer genomes. Many somatic variant callers have been developed yet accurate ascertainment of somatic variants remains a considerable challenge as evidenced by t...
Workflow Genetic Variation Polymorphism, Single Nucleotide High-Throughput Nucleotide Sequencing Web Browser Machine Learning Computational Biology Software Mutation Algorithms Reproducibility of Results
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WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning.

PLoS computational biology Nov 3, 2016
The rapid advancement of technology in genomics and targeted genetic manipulation has made comparative biology an increasingly prominent strategy to model human disease processes. Predicting orthology relationships between species is a vital componen...
Sequence Homology, Amino Acid Genetic Speciation Genetic Variation High-Throughput Nucleotide Sequencing Pattern Recognition, Automated Humans Machine Learning Software Algorithms Animals Evolution, Molecular Proteins
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Development of neuro-fuzzy model to explore gene-nutrient interactions modulating warfarin dose requirement.

Pharmacogenomics Jul 27, 2016
AIM: To investigate the influence of alterations in vitamin K (K1, K2 and K3) in modulating warfarin dose requirement.
Humans Female Aged Young Adult Adult Male Middle Aged Asian People Genetic Variation Vitamin K Polymorphism, Genetic Fuzzy Logic Adolescent Models, Neurological Child Anticoagulants Genotype Warfarin
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Machine Learning Based Classification of Microsatellite Variation: An Effective Approach for Phylogeographic Characterization of Olive Populations.

PloS one Nov 24, 2015
Finding efficient analytical techniques is overwhelmingly turning into a bottleneck for the effectiveness of large biological data. Machine learning offers a novel and powerful tool to advance classification and modeling solutions in molecular biolog...
Microsatellite Repeats Phylogeography Alleles Genotype Machine Learning Olea Iran Computational Biology Geography Algorithms Genetic Variation DNA, Plant Decision Trees Reproducibility of Results Genes, Plant Bayes Theorem
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Prioritizing Clinically Relevant Copy Number Variation from Genetic Interactions and Gene Function Data.

PloS one Oct 5, 2015
It is becoming increasingly necessary to develop computerized methods for identifying the few disease-causing variants from hundreds discovered in each individual patient. This problem is especially relevant for Copy Number Variants (CNVs), which can...
Gene Regulatory Networks Genetic Predisposition to Disease Genetic Association Studies Models, Genetic Genetic Diseases, Inborn Gene Ontology Causality Humans Oligonucleotide Array Sequence Analysis Mutation Congenital Abnormalities Genetic Variation Gene Dosage Developmental Disabilities
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Model-Based Multifactor Dimensionality Reduction for Rare Variant Association Analysis.

Human heredity Jul 28, 2015
Genome-wide association studies have revealed a vast amount of common loci associated to human complex diseases. Still, a large proportion of heritability remains unexplained. The extent to which rare genetic variants (RVs) are able to explain a rele...
Models, Genetic Genetic Variation Multifactor Dimensionality Reduction Chromosomes, Human, Pair 4 Humans Genome-Wide Association Study
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