AIMC Topic: Genetics, Population

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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.
Adaptation, Biological Genetics, Population Genetic Variation Genome, Human Linkage Disequilibrium Biological Evolution Selection, Genetic Models, Genetic Sequence Analysis, DNA Humans Machine Learning
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Deep Learning for Population Genetic Inference.

PLoS computational biology Mar 28, 2016
Given genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce a novel likelihood-free inference framework by applying deep learning,...
Machine Learning Genomics Models, Genetic Animals Drosophila melanogaster Genetics, Population
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S/HIC: Robust Identification of Soft and Hard Sweeps Using Machine Learning.

PLoS genetics Mar 15, 2016
Detecting the targets of adaptive natural selection from whole genome sequencing data is a central problem for population genetics. However, to date most methods have shown sub-optimal performance under realistic demographic scenarios. Moreover, over...
Genome, Human Selection, Genetic Chromosomes, Human, Pair 18 Genetic Drift Genetics, Population Humans Machine Learning Haplotypes
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Inference and Analysis of Population Structure Using Genetic Data and Network Theory.

Genetics Feb 17, 2016
Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based app...
Genetics, Population Models, Genetic Cluster Analysis Neural Networks, Computer Algorithms Humans
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Hierarchical boosting: a machine-learning framework to detect and classify hard selective sweeps in human populations.

Bioinformatics (Oxford, England) Aug 26, 2015
MOTIVATION: Detecting positive selection in genomic regions is a recurrent topic in natural population genetic studies. However, there is little consistency among the regions detected in several genome-wide scans using different tests and/or populati...
Humans Polymorphism, Genetic Machine Learning Genetics, Population Demography Selection, Genetic Genomics
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Artificial neural networks reveal efficiency in genetic value prediction.

Genetics and molecular research : GMR Jun 18, 2015
The objective of this study was to evaluate the efficiency of artificial neural networks (ANNs) for predicting genetic value in experiments carried out in randomized blocks. Sixteen scenarios were simulated with different values of heritability (10, ...
Animals Genotype Genetics, Population Computer Simulation Breeding Neural Networks, Computer Plants Reproducibility of Results Inheritance Patterns Phenotype Selection, Genetic
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Deep learning insights into distinct patterns of polygenic adaptation across human populations.

Nucleic acids research Dec 11, 2024
Response to spatiotemporal variation in selection gradients resulted in signatures of polygenic adaptation in human genomes. We introduce RAISING, a two-stage deep learning framework that optimizes neural network architecture through hyperparameter t...
Deep Learning Genomics Models, Genetic Neural Networks, Computer Phylogeny Adaptation, Physiological Humans Multifactorial Inheritance Genetics, Population Genome, Human Selection, Genetic
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Tree Sequences as a General-Purpose Tool for Population Genetic Inference.

Molecular biology and evolution Nov 1, 2024
As population genetic data increase in size, new methods have been developed to store genetic information in efficient ways, such as tree sequences. These data structures are computationally and storage efficient but are not interchangeable with exis...
Neural Networks, Computer Phylogeny Genetics, Population
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Using Runs of Homozygosity and Machine Learning to Disentangle Sources of Inbreeding and Infer Self-Fertilization Rates.

Genome biology and evolution Jul 3, 2024
Runs of homozygosity (ROHs) are indicative of elevated homozygosity and inbreeding due to mating of closely related individuals. Self-fertilization can be a major source of inbreeding which elevates genome-wide homozygosity and thus should also creat...
Machine Learning Animals Self-Fertilization Genetics, Population Inbreeding Models, Genetic Homozygote
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Computationally Efficient Demographic History Inference from Allele Frequencies with Supervised Machine Learning.

Molecular biology and evolution May 3, 2024
Inferring past demographic history of natural populations from genomic data is of central concern in many studies across research fields. Previously, our group had developed dadi, a widely used demographic history inference method based on the allele...
Humans Neural Networks, Computer Models, Genetic Genetics, Population Supervised Machine Learning Gene Frequency
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