The presence and impact of reference bias on population genomic studies of prehistoric human populations

Limits of long-term selection against Neandertal introgression

(2019) Martin Petr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ancient Human Genomics: The First Decade

(2018) Pontus Skoglund et al.   Annual Review of Genomics and Human Genetics

Something old, something borrowed: admixture and adaptation in human evolution

(2018) Michael Dannemann et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The evolutionary history of human populations in Europe

(2018) Iosif Lazaridis   CURRENT OPINION IN GENETICS & DEVELOPMENT

Ancient human parallel lineages within North America contributed to a coastal expansion

(2018) C. L. Scheib et al.   SCIENCE

Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations

(2018) Marieke van de Loosdrecht et al.   SCIENCE

Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation

(2018) Torsten Günther et al.   PLOS BIOLOGY

Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences

(2018) Cesare de Filippo et al.   BMC BIOLOGY

Assembly of a pan-genome from deep sequencing of 910 humans of African descent

(2018) Rachel M. Sherman et al.   NATURE GENETICS

Genome graphs and the evolution of genome inference

(2017) Benedict Paten et al.   GENOME RESEARCH

AntCaller: an accurate variant caller incorporating ancient DNA damage

(2017) Boyan Zhou et al.   MOLECULAR GENETICS AND GENOMICS

Tracing the peopling of the world through genomics

(2017) Rasmus Nielsen et al.   NATURE

Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago

(2017) Carina M. Schlebusch et al.   SCIENCE

A high-coverage Neandertal genome from Vindija Cave in Croatia

(2017) Kay Prüfer et al.   SCIENCE

The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype-based methods

(2017) Rui Martiniano et al.   PLoS Genetics

A new genus of horse from Pleistocene North America

(2017) Peter D Heintzman et al.   eLife

Genes mirror migrations and cultures in prehistoric Europe — a population genomic perspective

(2016) Torsten Günther et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Inferring Heterozygosity from Ancient and Low Coverage Genomes

(2016) Athanasios Kousathanas et al.   GENETICS

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

(2016) Swapan Mallick et al.   NATURE

Ancient DNA and human history

(2016) Montgomery Slatkin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A time transect of exomes from a Native American population before and after European contact

(2016) John Lindo et al.   Nature Communications

Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference

(2016) Aaron B. A. Shafer et al.   Methods in Ecology and Evolution

Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans

(2016) Fernando Racimo et al.   PLoS Genetics

Inferring Heterozygosity from Ancient and Low Coverage Genomes

(2016) Athanasios Kousathanas et al.   GENETICS

Genetic evidence for two founding populations of the Americas

(2015) Pontus Skoglund et al.   NATURE

Genome-wide patterns of selection in 230 ancient Eurasians

(2015) Iain Mathieson et al.   NATURE

Massive migration from the steppe was a source for Indo-European languages in Europe

(2015) Wolfgang Haak et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques

(2015) Torsten Günther et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Upper Palaeolithic genomes reveal deep roots of modern Eurasians

(2015) Eppie R. Jones et al.   Nature Communications

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

(2015) Débora Y. C. Brandt et al.   G3-Genes Genomes Genetics

Ancient human genomes suggest three ancestral populations for present-day Europeans

(2014) Iosif Lazaridis et al.   NATURE

Genome sequence of a 45,000-year-old modern human from western Siberia

(2014) Qiaomei Fu et al.   NATURE

A Paleogenomic Perspective on Evolution and Gene Function: New Insights from Ancient DNA

(2014) B. Shapiro et al.   SCIENCE

Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers

(2014) P. Skoglund et al.   SCIENCE

Genome flux and stasis in a five millennium transect of European prehistory

(2014) Cristina Gamba et al.   Nature Communications

Quantifying single nucleotide variant detection sensitivity in exome sequencing

(2013) Alison M Meynert et al.   BMC BIOINFORMATICS

Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data

(2013) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data

(2013) Y. Wang et al.   GENOME RESEARCH

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

Assessing the Effect of Sequencing Depth and Sample Size in Population Genetics Inferences

(2013) Matteo Fumagalli   PLoS One

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

Improving ancient DNA read mapping against modern reference genomes

(2012) Mikkel Schubert et al.   BMC GENOMICS

Biases and Errors on Allele Frequency Estimation and Disease Association Tests of Next-Generation Sequencing of Pooled Samples

(2012) Xiaowei Chen et al.   GENETIC EPIDEMIOLOGY

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

Assessing the Accuracy and Power of Population Genetic Inference from Low-Pass Next-Generation Sequencing Data

(2012) Jacob E. Crawford et al.   Frontiers in Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

The allele distribution in next-generation sequencing data sets is accurately described as the result of a stochastic branching process

(2011) Verena Heinrich et al.   NUCLEIC ACIDS RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Ascertainment Biases in SNP Chips Affect Measures of Population Divergence

(2010) A. Albrechtsen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Computational challenges in the analysis of ancient DNA

(2010) Kay Prüfer et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Simultaneous alignment of short reads against multiple genomes

(2009) Korbinian Schneeberger et al.   GENOME BIOLOGY

A large genome center's improvements to the Illumina sequencing system

(2008) Michael A Quail et al.   NATURE METHODS