Visualizing population structure with variational autoencoders

Predicting the landscape of recombination using deep learning

(2020) Jeffrey R Adrion et al.   MOLECULAR BIOLOGY AND EVOLUTION

scVAE: Variational auto-encoders for single-cell gene expression data

(2020) Christopher Heje Grønbech et al.   BIOINFORMATICS

Evolution of the insecticide target Rdl in African Anopheles is driven by interspecific and interkaryotypic introgression

(2020) Xavier Grau-Bové et al.   MOLECULAR BIOLOGY AND EVOLUTION

Insights into human genetic variation and population history from 929 diverse genomes

(2020) Anders Bergström et al.   SCIENCE

A community-maintained standard library of population genetic models

(2020) Jeffrey R Adrion et al.   eLife

Polygenic adaptation on height is overestimated due to uncorrected stratification in genome-wide association studies

(2019) Mashaal Sohail et al.   eLife

Reduced signal for polygenic adaptation of height in UK Biobank

(2019) Jeremy J Berg et al.   eLife

Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America

(2019) Pavel Flegontov et al.   NATURE

A demonstration of unsupervised machine learning in species delimitation

(2019) Shahan Derkarabetian et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Ancient Rome: A genetic crossroads of Europe and the Mediterranean

(2019) Margaret L. Antonio et al.   SCIENCE

UMAP reveals cryptic population structure and phenotype heterogeneity in large genomic cohorts

(2019) Alex Diaz-Papkovich et al.   PLoS Genetics

Reconstructing the Deep Population History of Central and South America

(2018) Cosimo Posth et al.   CELL

Local PCA Shows How the Effect of Population Structure Differs Along the Genome

(2018) Han Li et al.   GENETICS

The Unreasonable Effectiveness of Convolutional Neural Networks in Population Genetic Inference

(2018) Lex Flagel et al.   MOLECULAR BIOLOGY AND EVOLUTION

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

VASC: Dimension Reduction and Visualization of Single-cell RNA-seq Data by Deep Variational Autoencoder

(2018) Dongfang Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Genetic diversity of the African malaria vector Anopheles gambiae

(2017) Alistair Miles et al.   NATURE

The Anopheles gambiae 2La chromosome inversion is associated with susceptibility to Plasmodium falciparum in Africa

(2017) Michelle M Riehle et al.   eLife

Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes

(2016) Jerome Kelleher et al.   PLoS Computational Biology

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Visualizing spatial population structure with estimated effective migration surfaces

(2015) Desislava Petkova et al.   NATURE GENETICS

Principal component analysis with missing values: a comparative survey of methods

(2014) Stéphane Dray et al.   PLANT ECOLOGY

Differential confounding of rare and common variants in spatially structured populations

(2012) Iain Mathieson et al.   NATURE GENETICS

Investigation of Inversion Polymorphisms in the Human Genome Using Principal Components Analysis

(2012) Jianzhong Ma et al.   PLoS One

Genetics in geographically structured populations: defining, estimating and interpreting FST

(2009) Kent E. Holsinger et al.   NATURE REVIEWS GENETICS

A Genealogical Interpretation of Principal Components Analysis

(2009) Gil McVean   PLoS Genetics

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS

Interpreting principal component analyses of spatial population genetic variation

(2008) John Novembre et al.   NATURE GENETICS