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List of works by Joshua M. Akey

(P1) Technology Development in a Multidisciplinary Center

A Grand Challenge in Evolutionary and Population Genetics: New Paradigms for Exploring the Past and Charting the Future in the Post-Genomic era ⬇️

scientific article published on July 21, 2011

A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome

scientific article published on 11 October 2016

A flexible method for estimating the fraction of fitness influencing mutations from large sequencing data sets

scientific article

A genome-wide in vitro bacterial-infection screen reveals human variation in the host response associated with inflammatory disease

scientific article (publication date: August 2009)

A high-resolution integrated map of copy number polymorphisms within and between breeds of the modern domesticated dog

scientific article

A map of human wanderlust

scientific article published in Nature

A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data

scientific article

Adaptive evolution in humans revealed by the negative correlation between the polymorphism and fixation phases of evolution

scholarly article

Adaptive evolution of the FADS gene cluster within Africa

scientific article

An expansive human regulatory lexicon encoded in transcription factor footprints

scientific article

Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

scientific article published on 28 November 2012

Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture

scientific article published on 9 March 2018

Archaic Hominin Admixture Facilitated Adaptation to Out-of-Africa Environments.

scientific article

Assaying DNA methylation based on high-throughput melting curve approaches

scientific article (publication date: October 2002)

Characteristics of neutral and deleterious protein-coding variation among individuals and populations

scientific article published on October 2014

Clusters of adaptive evolution in the human genome

scientific article published on 9 September 2011

Complex history of admixture between modern humans and Neandertals

scientific article

Comprehensive identification and analysis of human accelerated regulatory DNA

scientific article

Constructing genomic maps of positive selection in humans: where do we go from here?

scientific article published on May 2009

Copy number variation in the domestic dog.

scientific article published on 04 December 2011

Correction: Telomere Length as a Quantitative Trait: Genome-Wide Survey and Genetic Mapping of Telomere Length-Control Genes in Yeast.

scientific article published on 30 June 2006

Detecting Sources of Transcriptional Heterogeneity in Large-Scale RNA-Seq Data Sets

scientific article

Developmental fate and cellular maturity encoded in human regulatory DNA landscapes

scientific article published on August 2013

Distribution of recombination crossovers and the origin of haplotype blocks: the interplay of population history, recombination, and mutation

scientific article published on 15 October 2002

Editorial overview: Evolutionary genomics - from molecular mechanisms to phenotypes to populations

scientific article published on 01 June 2020

Editorial overview: Genetics of human origin: New horizons in human population genetics

scientific article published on 23 November 2016

Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility

scientific article published on 03 August 2016

Erratum: Corrigendum: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

scientific article published in Nature

Estimates of continental ancestry vary widely among individuals with the same mtDNA haplogroup.

scientific article

Estimators of the human effective sex ratio detect sex biases on different timescales

scientific article

Evolution and genetic architecture of chromatin accessibility and function in yeast

scientific article

Evolution of DNAaseI Hypersensitive Sites in MHC Regulatory Regions of Primates.

scientific article published on 18 April 2018

Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers

scientific article (publication date: 3 August 2012)

Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia

scientific article published in Science

Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals.

scientific article published on 17 March 2016

Exonic transcription factor binding directs codon choice and affects protein evolution

scientific article published on December 2013

Exploring signatures of positive selection in pigmentation candidate genes in populations of East Asian ancestry.

scientific article

Fine-scale patterns of population stratification confound rare variant association tests

scientific article

Fitting background-selection predictions to levels of nucleotide variation and divergence along the human autosomes

scientific article

Functional genetic screen of human diversity reveals that a methionine salvage enzyme regulates inflammatory cell death

scientific article

Gene-expression variation within and among human populations

scientific article published on 11 January 2007

Genetic architecture of quantitative traits and complex diseases.

scientific article

Genome wide association identifies PPFIA1 as a candidate gene for acute lung injury risk following major trauma

scientific article

Genome-wide insights into the patterns and determinants of fine-scale population structure in humans

scientific article

Genome-wide scans for loci under selection in humans

scientific article

Genomic insights into positive selection

scientific article published on 30 June 2006

Genomic signatures of positive selection in humans and the limits of outlier approaches

scientific article

Global and disease-associated genetic variation in the human Fanconi anemia gene family

scientific article

Global genetic variation at nine short tandem repeat loci and implications on forensic genetics

scientific article

Great ape genetic diversity and population history

scientific article published on 03 July 2013

Heritable variation of mRNA decay rates in yeast

scientific article

Highly punctuated patterns of population structure on the X chromosome and implications for African evolutionary history

scientific article

Human Diversity in a Cell Surface Receptor that Inhibits Autophagy.

scientific article published on 21 June 2016

Human RECQ Helicase Pathogenic Variants, Population Variation and "Missing" Diseases

scientific article published on 17 November 2016

Human evolution: genomic gifts from archaic hominins

article

Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals

scientific article published on 30 January 2020

Identifying positive selection candidate loci for high-altitude adaptation in Andean populations.

scientific article

Identifying signatures of natural selection in Tibetan and Andean populations using dense genome scan data

scientific article

Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression.

scientific article published on February 2017

Implications of localized charge for human influenza A H1N1 hemagglutinin evolution: Insights from deep mutational scans

scientific article published on 25 June 2020

Inherited variation in gene expression

scientific article published on January 2009

Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast

scientific article published on 29 May 2013

Large-scale SNP analysis reveals clustered and continuous patterns of human genetic variation

scientific article

Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis

scientific article

Marker panels for genealogy-based mapping, breed demographics, and inference-of-ancestry in the dog.

scientific article

Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana.

scientific article

Methods and models for unravelling human evolutionary history

scientific article

Multiple locus linkage analysis of genomewide expression in yeast

scientific article

Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders

scientific article

On the design and analysis of gene expression studies in human populations

article

On the prospects of whole-genome association mapping in Saccharomyces cerevisiae

scientific article

Outstanding questions in the study of archaic hominin admixture.

scientific article

Parallel Selection: Evolution's Surprising Predictability ⬇️

scientific article published on May 22, 2012

Parallel adaptive divergence among geographically diverse human populations

scientific article

Patterns of deleterious variation between human populations reveal an unbalanced load.

scientific article published on 19 January 2016

Personal and population genomics of human regulatory variation

scientific article

Population genomic analysis of ALMS1 in humans reveals a surprisingly complex evolutionary history

scientific article

Population genomics and transcriptional consequences of regulatory motif variation in globally diverse Saccharomyces cerevisiae strains

scientific article published on 25 April 2013

Population genomics of intron splicing in 38 Saccharomyces cerevisiae genome sequences

scientific article

Population history and natural selection shape patterns of genetic variation in 132 genes

scientific article

Randomly distributed crossovers may generate block-like patterns of linkage disequilibrium: an act of genetic drift

scientific article published on 03 April 2003

Rare variation facilitates inferences of fine-scale population structure in humans

scientific article

Recurrent gene flow between Neanderthals and modern humans over the past 200,000 years

scientific article published on 12 July 2024

Resurrecting surviving Neandertal lineages from modern human genomes

scientific article

Robust Inference of Identity by Descent from Exome-Sequencing Data

scientific article

Selection and adaptation in the human genome

scientific article

Selection plays the hand it was dealt: evidence that human adaptation commonly targets standing genetic variation

scientific article published on August 2017

Sequence diversity, natural selection and linkage disequilibrium in the human T cell receptor alpha/delta locus

scientific article published on 20 January 2006

Signatures of natural selection on genetic variants affecting complex human traits

scientific article

Signatures of positive selection apparent in a small sample of human exomes

scientific article

Small Amounts of Archaic Admixture Provide Big Insights into Human History

scientific article

Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations

scientific article (publication date: 4 April 2012)

TRPV6 exhibits unusual patterns of polymorphism and divergence in worldwide populations

scientific article

Telomere length as a quantitative trait: genome-wide survey and genetic mapping of telomere length-control genes in yeast.

scientific article

The accessible chromatin landscape of the human genome

scientific article

The contribution of Neanderthal introgression to modern human traits

scientific article published in 2022

The effect of single nucleotide polymorphism identification strategies on estimates of linkage disequilibrium

scientific article

The evolution of gene expression QTL in Saccharomyces cerevisiae

scientific article

The genomic architecture of segmental duplications and associated copy number variants in dogs

scientific article published on 07 January 2009

The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs.

scientific article published on May 2004

The long walk to African genomics

scientific article published on 27 June 2019

The origins, determinants, and consequences of human mutations

scientific article

The phenotypic legacy of admixture between modern humans and Neandertals

scientific article

The promise and limitations of population exomics for human evolution studies

scientific article published on 14 September 2011

Tracing the peopling of the world through genomics

scientific article

Tracking footprints of artificial selection in the dog genome

scientific article

Understanding human evolutionary history: a meeting report of the Swedish Royal Academy of Sciences symposium of modern human genetic variation ⬇️

scientific article (publication date: 24 March 2012)

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