selected publications
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academic article
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137 ancient human genomes from across the Eurasian steppes.
Nature.
557.
2018
Author Correction: 137 ancient human genomes from across the Eurasian steppes.
Nature.
563.
2018
Early human dispersals within the Americas.
Science.
362.
2018
Estimating the Timing of Multiple Admixture Pulses During Local Ancestry Inference.
Genetics.
210.
2018
Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History.
Cell.
175.
2018
Human adaptation to extreme environmental conditions.
Current Opinion in Genetics & Development.
53.
2018
On the number of siblings and p-th cousins in a large population sample.
Journal of Mathematical Biology.
77.
2018
Origins and genetic legacies of the Caribbean Taino.
Proceedings of the National Academy of Sciences of the United States of America.
115.
2018
Physiological and Genetic Adaptations to Diving in Sea Nomads.
Cell.
173.
2018
Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans.
Nature.
553.
2018
The first horse herders and the impact of early Bronze Age steppe expansions into Asia.
Science.
360.
2018
A Hidden Markov Model Approach for Simultaneously Estimating Local Ancestry and Admixture Time Using Next Generation Sequence Data in Samples of Arbitrary Ploidy.
PLOS Genetics.
13.
2017
Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers.
Science.
358.
2017
Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice.
Genome Research.
27.
2017
Composite likelihood method for inferring local pedigrees.
PLOS Genetics.
13.
2017
Fast admixture analysis and population tree estimation for SNP and NGS data.
Bioinformatics.
33.
2017
Natural Selection on Genes Related to Cardiovascular Health in High-Altitude Adapted Andeans.
American Journal of Human Genetics.
101.
2017
Q&A: Where did the Neanderthals go?.
BMC Biology.
15.
2017
Selection in Europeans on Fatty Acid Desaturases Associated with Dietary Changes.
Molecular Biology and Evolution.
34.
2017
Tracing the peopling of the world through genomics.
Nature.
541.
2017
Transcriptome dynamics during proliferation and differentiation of porcine primary satellite cells.
Gene Reports.
7.
2017
A genomic history of Aboriginal Australia.
Nature.
538.
2016
Archaic Adaptive Introgression in TBX15/WARS2..
Molecular Biology and Evolution.
34.
2016
Detection of genetic variation affecting milk coagulation properties in Danish Holstein dairy cattle by analyses of pooled whole-genome sequences from phenotypically extreme samples (pool-seq).
Journal of Animal Science.
94.
2016
Estimating IBD tracts from low coverage NGS data.
Bioinformatics.
32.
2016
Genomic analyses inform on migration events during the peopling of Eurasia.
Nature.
538.
2016
Postglacial viability and colonization in North America’s ice-free corridor.
Nature.
537.
2016
The Genetic Cost of Neanderthal Introgression.
Genetics.
203.
2016
The Power of Inbreeding: NGS-Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication.
Molecular Plant.
9.
2016
A recent bottleneck of Y chromosome diversity coincides with a global change in culture.
Genome Research.
25.
2015
Convergent evolution of the genomes of marine mammals.
Nature Genetics.
47.
2015
De novo assembly of a haplotype-resolved human genome.
Nature Biotechnology.
33.
2015
Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago.
Cell.
163.
2015
Genomic Resources Notes Accepted 1 October 2014–30 November 2014.
Molecular Ecology Resources.
15.
2015
Genomic evidence for the Pleistocene and recent population history of Native Americans.
Science.
349.
2015
Greenlandic Inuit show genetic signatures of diet and climate adaptation.
Science.
349.
2015
Number of genes controlling a quantitative trait in a hybrid zone of the aposematic frog Ranitomeya imitator.
Proceedings of the Royal Society B.
282.
2015
Phylogenetic ANOVA: The Expression Variance and Evolution Model for Quantitative Trait Evolution.
Systematic Biology.
64.
2015
Population genomics of Bronze Age Eurasia.
Nature.
522.
2015
The ancestry and affiliations of Kennewick Man.
Nature.
523.
2015
The origin and evolution of maize in the Southwestern United States.
Nature Plants.
1.
2015
Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments.
Proceedings of the National Academy of Sciences of the United States of America.
112.
2015
Uncovering the Genetic History of the Present-Day Greenlandic Population.
American Journal of Human Genetics.
96.
2015
A Model-Based Approach for Identifying Signatures of Ancient Balancing Selection in Genetic Data.
PLOS Genetics.
10.
2014
A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations.
American Journal of Human Genetics.
95.
2014
A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes.
Nature.
512.
2014
ANGSD: Analysis of Next Generation Sequencing Data.
BMC Bioinformatics.
15.
2014
Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA.
Nature.
512.
2014
Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European.
Nature.
507.
2014
Error-prone polymerase activity causes multinucleotide mutations in humans.
Genome Research.
24.
2014
Genome-wide Ancestry Patterns in Rapanui Suggest Pre-European Admixture with Native Americans.
Current Biology.
24.
2014
Genomic Takeover by Transposable Elements in the Strawberry Poison Frog.
Molecular Biology and Evolution.
35.
2014
Genomic structure in Europeans dating back at least 36,200 years.
Science.
346.
2014
Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA.
Proceedings of the National Academy of Sciences of the United States of America.
111.
2014
On Detecting Incomplete Soft or Hard Selective Sweeps Using Haplotype Structure.
Molecular Biology and Evolution.
31.
2014
Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears.
Cell.
157.
2014
Speciation with gene flow in equids despite extensive chromosomal plasticity.
Proceedings of the National Academy of Sciences of the United States of America.
111.
2014
Structured RNAs and synteny regions in the pig genome.
BMC Genomics.
15.
2014
The genetic prehistory of the New World Arctic.
Science.
345.
2014
The genome of a Late Pleistocene human from a Clovis burial site in western Montana.
Nature.
506.
2014
Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil.
Current Biology.
24.
2014
Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans.
Nature.
505.
2014
Variation and association to diabetes in 2000 full mtDNA sequences mined from an exome study in a Danish population.
European Journal of Human Genetics.
22.
2014
Whole-Exome Sequencing of 2,000 Danish Individuals and the Role of Rare Coding Variants in Type 2 Diabetes.
American Journal of Human Genetics.
94.
2014
bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS).
Bioinformatics.
30.
2014
ngsTools: methods for population genetics analyses from next-generation sequencing data.
Bioinformatics.
30.
2014
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dataset
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A Hidden Markov Model Approach for Simultaneously Estimating Local Ancestry and Admixture Time Using Next Generation Sequence Data in Samples of Arbitrary Ploidy.
public-library-of-science.
2017
Accuracy for estimating the true pedigree..
public-library-of-science.
2017
Composite likelihood method for inferring local pedigrees.
public-library-of-science.
2017
Parameter estimation and LAI when a subset of loci experience natural selection in the admixed population..
public-library-of-science.
2017
Parameter estimation and LAI when admixture occurs at a constant rate, rather than in a single pulse..
public-library-of-science.
2017
AppendixS1.
dryad.
2015
Echinogammarus veneris, transcriptome shotgun assembly.
dryad.
2015
Eucyclops serrulatus, transcriptome shotgun assembly.
dryad.
2015
FASTAQ file for Echinogammarus veneris.
dryad.
2015
FASTAQ file for Eucyclops serrulatus.
dryad.
2015
Scripts.
dryad.
2015
batch_1.catalog.alleles.
dryad.
2015
batch_1.catalog.snps.
dryad.
2015
batch_1.catalog.tags.
dryad.
2015
genotypes of test population.
dryad.
2015
A Model-Based Approach for Identifying Signatures of Ancient Balancing Selection in Genetic Data.
public-library-of-science.
2014
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hide from search
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5′ tagged PCR primers.
public-library-of-science.
2013
A Scan for Positively Selected Genes in the Genomes of Humans and Chimpanzees.
public-library-of-science.
2013
Assigned sequence distribution.
public-library-of-science.
2013
Demographic parameters estimated from trio data..
public-library-of-science.
2013
Genetic Architecture of Vitamin B12 and Folate Levels Uncovered Applying Deeply Sequenced Large Datasets.
public-library-of-science.
2013
Inferring Demographic History from a Spectrum of Shared Haplotype Lengths.
public-library-of-science.
2013
Inferring the parameters of a simple admixture scenario..
public-library-of-science.
2013
Novel and previously reported genomic loci that associate with serum B12 levels at P<2.2×10−9..
public-library-of-science.
2013
Novel and previously reported genomic loci that associate with serum folate levels at P<2.2×10−9..
public-library-of-science.
2013
Novel secondary association signals at the serum B12 or serum folate loci that associate at P<5×10−8..
public-library-of-science.
2013
Observed and Expected sequence distributions sorted by 5′ tag composition.
public-library-of-science.
2013
Bacterial natural transformation by highly fragmented and damaged DNA.
Proceedings of the National Academy of Sciences of the United States of America.
2013
Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data.
BMC Bioinformatics.
2013
Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation.
Genome Research.
2013
Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes.
Diabetologia.
2013
Genetic Architecture of Vitamin B12 and Folate Levels Uncovered Applying Deeply Sequenced Large Datasets.
PLOS Genetics.
2013
Genetic Signatures Reveal High-Altitude Adaptation in a Set of Ethiopian Populations.
Molecular Biology and Evolution.
2013
Inferring Demographic History from a Spectrum of Shared Haplotype Lengths.
PLOS Genetics.
2013
Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing.
BMC Genomics.
2013
Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data.
Genetics.
2013
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.
Nature.
2013
Whole-Exome Sequencing of 2,000 Danish Individuals and the Role of Rare Coding Variants in Type 2 Diabetes.
American Journal of Human Genetics.
2013
Number of contigs and singletons obtained and successfully annotated..
public-library-of-science.
2012
Results for SNP detection variables for predicting SNP assay conversion following a backward stepwise elimination procedure..
public-library-of-science.
2012
Results for SNP detection variables for predicting SNP assay polymorphism following a backward stepwise elimination procedure..
public-library-of-science.
2012
SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data.
public-library-of-science.
2012
SNP Discovery Using Next Generation Transcriptomic Sequencing in Atlantic Herring (Clupea harengus).
public-library-of-science.
2012
Type and number of repeats of the microsatellites detected in the herring contigs using Msatcommander..
public-library-of-science.
2012
Natural Selection Affects Multiple Aspects of Genetic Variation at Putatively Neutral Sites across the Human Genome.
public-library-of-science.
2011
Novel Tools for Conservation Genomics: Comparing Two High-Throughput Approaches for SNP Discovery in the Transcriptome of the European Hake.
public-library-of-science.
2011
Predictor variables for 454 SNP data (failed/successful), backward stepwise elimination..
public-library-of-science.
2011
Predictor variables for 454 SNP data (monomorphic/polymorphic), backward stepwise elimination..
public-library-of-science.
2011
Predictor variables for GAII SNP data (failed/successful), backward stepwise elimination..
public-library-of-science.
2011
Predictor variables for GAII SNP data (monomorphic/polymorphic), backward stepwise elimination..
public-library-of-science.
2011
Summary of correlation coefficients (Spearman's ) for the three datasets divided into genic and non-genic windows..
public-library-of-science.
2011
Summary of the correlation coefficients (Spearman's ) for the three datasets..
public-library-of-science.
2011
Summary statistics for SNP validation..
public-library-of-science.
2011
Summary statistics of SNP discovery and selection..
public-library-of-science.
2011
Summary statistics of sequence assembly..
public-library-of-science.
2011
A comparison of several recent estimates of the DFE at nonsynonymous sites in humans..
public-library-of-science.
2008
Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome.
public-library-of-science.
2008
Distribution of fitness effects in African Americans by PolyPhen class..
public-library-of-science.
2008
Distribution of fitness effects under various best-fit selective models..
public-library-of-science.
2008
GO categories showing an excess of small P-values under the primate- and rodent-clade tests..
public-library-of-science.
2008
Maximum likelihood estimates of proposed distributions of deleterious fitness effects of new nonsynonymous mutations..
public-library-of-science.
2008
Numbers of ortholog sets..
public-library-of-science.
2008
Patterns of Positive Selection in Six Mammalian Genomes.
public-library-of-science.
2008
Robustness of selective and demographic inference in African American dataset..
public-library-of-science.
2008
Selected GO categories over-represented among genes predicted to be under positive selection..
public-library-of-science.
2008
Summary of individual PSGs discussed in this article..
public-library-of-science.
2008
Localizing Recent Adaptive Evolution in the Human Genome.
public-library-of-science.
2007
The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple Homolog Amplification Products by 454 Parallel Sequencing.
public-library-of-science.
2007
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preprint
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Composite Likelihood Method for Inferring Local Pedigrees.
bioRxiv.
2017
A hidden Markov model approach for simultaneously estimating local ancestry and admixture time using next generation sequence data in samples of arbitrary ploidy.
bioRxiv.
2016
Estimating the timing of multiple admixture events using 3-locus Linkage Disequilibrium.
bioRxiv.
2016
Ohana, a tool set for population genetic analyses of admixture components.
bioRxiv.
2016
Selection on the FADS region in Europeans.
bioRxiv.
2016
Archaic adaptive introgression in TBX15/WARS2.
bioRxiv.
2015
The Genetic cost of Neanderthal introgression.
bioRxiv.
2015
The origin and evolution of maize in the American Southwest.
bioRxiv.
2015
Identifying adaptive and plastic gene expression levels using a unified model for expression variance between and within species.
bioRxiv.
2014