4.4 Article

A rarefaction approach for measuring population differences in rare and common variation

Related references

Note: Only part of the references are listed.
Article Biology

Apportioning archaic variants among modern populations

Kelsey E. Witt et al.

Summary: The distribution of archaic ancestry in Eurasian populations shows distinct patterns at the individual- and population-levels, indicating different demographic and archaic admixture events. South Asians have more population-unique archaic alleles, while Europeans have more Neanderthal ancestry than East Asians.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2022)

Article Biochemistry & Molecular Biology

High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

Marta Byrska-Bishop et al.

Summary: The 1000 Genomes Project is the largest open resource of whole-genome sequencing data, and a new high-coverage WGS 1kGP resource has been released, improving the sensitivity and accuracy of variant calls and making it more valuable for association studies.
Article Multidisciplinary Sciences

Counter the weaponization of genetics research by extremists

Jedidiah Carlson et al.

NATURE (2022)

Article Genetics & Heredity

Visualizing population structure with variational autoencoders

C. J. Battey et al.

Summary: The study investigates the utility of variational autoencoders (VAEs) in visualizing population genetic variation, showing that VAEs preserve global geometry better than popular methods like t-SNE and UMAP. The implementation of popvae tool generates latent embeddings that capture subtle aspects of population structure.

G3-GENES GENOMES GENETICS (2021)

Article Biochemistry & Molecular Biology

Genetic Landscapes Reveal How Human Genetic Diversity Aligns with Geography

Benjamin M. Peter et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Biochemistry & Molecular Biology

Network-based hierarchical population structure analysis for large genomic data sets

Gili Greenbaum et al.

GENOME RESEARCH (2019)

Article Genetics & Heredity

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

Alex Diaz-Papkovich et al.

PLOS GENETICS (2019)

Review Genetics & Heredity

A genomic perspective on HLA evolution

Diogo Meyer et al.

IMMUNOGENETICS (2018)

Article Biochemical Research Methods

Visualizing the geography of genetic variants

Joseph H. Marcus et al.

BIOINFORMATICS (2017)

Article Genetics & Heredity

Visualizing spatial population structure with estimated effective migration surfaces

Desislava Petkova et al.

NATURE GENETICS (2016)

Article Multidisciplinary Sciences

A global reference for human genetic variation

David M. Altshuler et al.

NATURE (2015)

Article Genetics & Heredity

Mapping Bias Overestimates Reference Allele Frequencies at the HLA Genes in the 1000 Genomes Project Phase I Data

Debora Y. C. Brandt et al.

G3-GENES GENOMES GENETICS (2015)

Article Genetics & Heredity

Haploscope: A Tool for the Graphical Display of Haplotype Structure in Populations

F. Anthony San Lucas et al.

GENETIC EPIDEMIOLOGY (2012)

Article Genetics & Heredity

Identifying Candidate Causal Variants Via Trans-Population Fine-Mapping

Yik-Ying Teo et al.

GENETIC EPIDEMIOLOGY (2010)

Article Multidisciplinary Sciences

Integrating common and rare genetic variation in diverse human populations

David M. Altshuler et al.

NATURE (2010)

Article Biochemistry & Molecular Biology

Signals of recent positive selection in a worldwide sample of human populations

Joseph K. Pickrell et al.

GENOME RESEARCH (2009)

Article Biochemical Research Methods

ADZE: a rarefaction approach for counting alleles private to combinations of populations

Zachary A. Szpiech et al.

BIOINFORMATICS (2008)

Article Multidisciplinary Sciences

Genotype, haplotype and copy-number variation in worldwide human populations

Mattias Jakobsson et al.

NATURE (2008)

Article Genetics & Heredity

A worldwide survey of haplotype variation and linkage disequilibrium in the human genome

Donald F. Conrad et al.

NATURE GENETICS (2006)

Article Biodiversity Conservation

Counting alleles with rarefaction: Private alleles and hierarchical sampling designs

ST Kalinowski

CONSERVATION GENETICS (2004)

Article Multidisciplinary Sciences

Genetic structure of human populations

NA Rosenberg et al.

SCIENCE (2002)