A Hidden Markov Model Approach for Simultaneously Estimating Local Ancestry and Admixture Time Using Next Generation Sequence Data in Samples of Arbitrary Ploidy

The Genetic Cost of Neanderthal Introgression

(2016) Kelley Harris et al.   GENETICS

Genomic Evidence for Adaptive Inversion Clines inDrosophila melanogaster

(2016) Martin Kapun et al.   MOLECULAR BIOLOGY AND EVOLUTION

Parallel Evolution of Copy-Number Variation across Continents inDrosophila melanogaster

(2016) Daniel R. Schrider et al.   MOLECULAR BIOLOGY AND EVOLUTION

Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation inDrosophila melanogaster

(2016) Alan O. Bergland et al.   MOLECULAR ECOLOGY

The Genetic Cost of Neanderthal Introgression

(2016) Kelley Harris et al.   GENETICS

Uncovering the Genetic History of the Present-Day Greenlandic Population

(2015) Ida Moltke et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Drosophila Genome Nexus: A Population Genomic Resource of 623 Drosophila melanogaster Genomes, Including 197 from a Single Ancestral Range Population

(2015) Justin B. Lack et al.   GENETICS

Evidence for archaic adaptive introgression in humans

(2015) Fernando Racimo et al.   NATURE REVIEWS GENETICS

Postmating reproductive barriers contribute to the incipient sexual isolation of the United States and CaribbeanDrosophila melanogaster

(2015) Joyce Y. Kao et al.   Ecology and Evolution

The Drosophila Genome Nexus: A Population Genomic Resource of 623 Drosophila melanogaster Genomes, Including 197 from a Single Ancestral Range Population

(2015) Justin B. Lack et al.   GENETICS

ngsTools: methods for population genetics analyses from next-generation sequencing data

(2014) Matteo Fumagalli et al.   BIOINFORMATICS

The Lengths of Admixture Tracts

(2014) M. Liang et al.   GENETICS

Parallel Geographic Variation in Drosophila melanogaster

(2014) Josie A. Reinhardt et al.   GENETICS

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

(2014) W. Huang et al.   GENOME RESEARCH

The genomic landscape of Neanderthal ancestry in present-day humans

(2014) Sriram Sankararaman et al.   NATURE

A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes

(2014) Ida Moltke et al.   NATURE

A Genetic Atlas of Human Admixture History

(2014) G. Hellenthal et al.   SCIENCE

Speciation and Introgression between Mimulus nasutus and Mimulus guttatus

(2014) Yaniv Brandvain et al.   PLoS Genetics

Genomic Evidence of Rapid and Stable Adaptive Oscillations over Seasonal Time Scales in Drosophila

(2014) Alan O. Bergland et al.   PLoS Genetics

High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species

(2014) Molly Schumer et al.   eLife

RFMix: A Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference

(2013) Brian K. Maples et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Analysis of Latino populations from GALA and MEC studies reveals genomic loci with biased local ancestry estimation

(2013) Bogdan Pasaniuc et al.   BIOINFORMATICS

Inferring Admixture Histories of Human Populations Using Linkage Disequilibrium

(2013) P.-R. Loh et al.   GENETICS

Estimating Individual Admixture Proportions from Next Generation Sequencing Data

(2013) Line Skotte et al.   GENETICS

Inference of chromosomal inversion dynamics from Pool-Seq data in natural and laboratory populations ofDrosophila melanogaster

(2013) Martin Kapun et al.   MOLECULAR ECOLOGY

Genetic incompatibilities are widespread within species

(2013) Russell B. Corbett-Detig et al.   NATURE

The Genomic Signature of Crop-Wild Introgression in Maize

(2013) Matthew B. Hufford et al.   PLoS Genetics

Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies

(2012) R. Kofler et al.   BIOINFORMATICS

Fast and accurate inference of local ancestry in Latino populations

(2012) Yael Baran et al.   BIOINFORMATICS

Sequence-Based Detection and Breakpoint Assembly of Polymorphic Inversions

(2012) R. B. Corbett-Detig et al.   GENETICS

Demographic Inference Reveals African and European Admixture in the North American Drosophila melanogaster Population

(2012) P. Duchen et al.   GENETICS

Population Genetics Models of Local Ancestry

(2012) S. Gravel   GENETICS

Genomic Variation in Natural Populations of Drosophila melanogaster

(2012) C. H. Langley et al.   GENETICS

Genome-wide patterns of latitudinal differentiation among populations ofDrosophila melanogasterfrom North America

(2012) Daniel K. Fabian et al.   MOLECULAR ECOLOGY

Adaptation ofDrosophilato a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles

(2012) PABLO OROZCO-terWENGEL et al.   MOLECULAR ECOLOGY

The Drosophila melanogaster Genetic Reference Panel

(2012) Trudy F. C. Mackay et al.   NATURE

SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data

(2012) Rasmus Nielsen et al.   PLoS One

Empirical Validation of Pooled Whole Genome Population Re-Sequencing in Drosophila melanogaster

(2012) Yuan Zhu et al.   PLoS One

The Date of Interbreeding between Neandertals and Modern Humans

(2012) Sriram Sankararaman et al.   PLoS Genetics

Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster

(2012) Robert Kofler et al.   PLoS Genetics

Genomic Ancestry of North Africans Supports Back-to-Africa Migrations

(2012) Brenna M. Henn et al.   PLoS Genetics

The Many Landscapes of Recombination in Drosophila melanogaster

(2012) Josep M. Comeron et al.   PLoS Genetics

Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture

(2012) John E. Pool et al.   PLoS Genetics

The Metabochip, a Custom Genotyping Array for Genetic Studies of Metabolic, Cardiovascular, and Anthropometric Traits

(2012) Benjamin F. Voight et al.   PLoS Genetics

Circumventing Heterozygosity: Sequencing the Amplified Genome of a Single HaploidDrosophila melanogasterEmbryo

(2011) Charles H. Langley et al.   GENETICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

The History of African Gene Flow into Southern Europeans, Levantines, and Jews

(2011) Priya Moorjani et al.   PLoS Genetics

Socially-Responsive Gene Expression in Male Drosophila melanogaster Is Influenced by the Sex of the Interacting Partner

(2010) L. L. Ellis et al.   GENETICS

Genomic Differentiation Between Temperate and Tropical Australian Populations of Drosophila melanogaster

(2010) B. Kolaczkowski et al.   GENETICS

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Inference of locus-specific ancestry in closely related populations

(2009) B. Pasaniuc et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Mutations in many genes affect aggressive behavior in Drosophila melanogaster

(2009) Alexis C Edwards et al.   BMC BIOLOGY

The Genomics of Speciation in Drosophila: Diversity, Divergence, and Introgression Estimated Using Low-Coverage Genome Sequencing

(2009) Rob J. Kulathinal et al.   PLoS Genetics

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

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

Estimating Local Ancestry in Admixed Populations

(2008) Sriram Sankararaman et al.   AMERICAN JOURNAL OF HUMAN GENETICS

AFRICAN MORPHOLOGY, BEHAVIOR AND PHERMONES UNDERLIE INCIPIENT SEXUAL ISOLATION BETWEEN US AND CARIBBEANDROSOPHILA MELANOGASTER

(2008) Roman Yukilevich et al.   EVOLUTION

Evidence of Spatially Varying Selection Acting on Four Chromatin-Remodeling Loci in Drosophila melanogaster

(2008) M. T. Levine et al.   GENETICS

Inference of Historical Changes in Migration Rate From the Lengths of Migrant Tracts

(2008) J. E. Pool et al.   GENETICS

Fast and flexible simulation of DNA sequence data

(2008) G. K. Chen et al.   GENOME RESEARCH