Insights into human genetic variation and population history from 929 diverse genomes

Multiple Deeply Divergent Denisovan Ancestries in Papuans

(2019) Guy S. Jacobs et al.   CELL

Efficiently Inferring the Demographic History of Many Populations With Allele Count Data

(2019) Jack Kamm et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

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

(2018) Sharon R. Browning et al.   CELL

Variation graph toolkit improves read mapping by representing genetic variation in the reference

(2018) Erik Garrison et al.   NATURE BIOTECHNOLOGY

Y Chromosome Sequences Reveal a Short Beringian Standstill, Rapid Expansion, and early Population structure of Native American Founders

(2018) Thomaz Pinotti et al.   CURRENT BIOLOGY

Tracing the peopling of the world through genomics

(2017) Rasmus Nielsen et al.   NATURE

A Neolithic expansion, but strong genetic structure, in the independent history of New Guinea

(2017) Anders Bergström et al.   SCIENCE

A high-coverage Neandertal genome from Vindija Cave in Croatia

(2017) Kay Prüfer et al.   SCIENCE

Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals

(2017) Cosimo Posth et al.   Nature Communications

Genotype Imputation with Millions of Reference Samples

(2016) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The mutation rate in human evolution and demographic inference

(2016) Aylwyn Scally   CURRENT OPINION IN GENETICS & DEVELOPMENT

Modeling Human Population Separation History Using Physically Phased Genomes

(2016) Shiya Song et al.   GENETICS

A genomic history of Aboriginal Australia

(2016) Anna-Sapfo Malaspinas et al.   NATURE

Genomic insights into the origin of farming in the ancient Near East

(2016) Iosif Lazaridis et al.   NATURE

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

(2016) Swapan Mallick et al.   NATURE

Genomic analyses inform on migration events during the peopling of Eurasia

(2016) Luca Pagani et al.   NATURE

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

(2016) Grace X Y Zheng et al.   NATURE BIOTECHNOLOGY

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences

(2016) G David Poznik et al.   NATURE GENETICS

Robust and scalable inference of population history from hundreds of unphased whole genomes

(2016) Jonathan Terhorst et al.   NATURE GENETICS

Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals

(2016) B. Vernot et al.   SCIENCE

Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes

(2016) Jerome Kelleher et al.   PLoS Computational Biology

Modeling Human Population Separation History Using Physically Phased Genomes

(2016) Shiya Song et al.   GENETICS

Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas

(2016) B. Llamas et al.   Science Advances

Accurate Non-parametric Estimation of Recent Effective Population Size from Segments of Identity by Descent

(2015) Sharon R. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

scrm: efficiently simulating long sequences using the approximated coalescent with recombination

(2015) Paul R. Staab et al.   BIOINFORMATICS

Denisovan Ancestry in East Eurasian and Native American Populations

(2015) Pengfei Qin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic evidence for two founding populations of the Americas

(2015) Pontus Skoglund 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

Large multiallelic copy number variations in humans

(2015) Robert E Handsaker et al.   NATURE GENETICS

Genomic evidence for the Pleistocene and recent population history of Native Americans

(2015) M. Raghavan et al.   SCIENCE

Toward better understanding of artifacts in variant calling from high-coverage samples

(2014) Heng Li   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

(2014) Iosif Lazaridis et al.   NATURE

The genomic landscape of Neanderthal ancestry in present-day humans

(2014) Sriram Sankararaman et al.   NATURE

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

(2014) Qiaomei Fu et al.   NATURE

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

Ancient west Eurasian ancestry in southern and eastern Africa

(2014) J. K. Pickrell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resurrecting Surviving Neandertal Lineages from Modern Human Genomes

(2014) B. Vernot et al.   SCIENCE

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

(2014) Olivier Delaneau et al.   Nature Communications

CrossMap: a versatile tool for coordinate conversion between genome assemblies

(2013) Hao Zhao et al.   BIOINFORMATICS

Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females

(2013) G. D. Poznik et al.   SCIENCE

Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data

(2012) Goo Jun et al.   AMERICAN JOURNAL OF HUMAN GENETICS

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

The Relationship Between FST and the Frequency of the Most Frequent Allele

(2012) M. Jakobsson et al.   GENETICS

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

Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania

(2011) David Reich et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

pegas: an R package for population genetics with an integrated-modular approach

(2010) E. Paradis   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genetic history of an archaic hominin group from Denisova Cave in Siberia

(2010) David Reich et al.   NATURE

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

A Worldwide Survey of Human Male Demographic History Based on Y-SNP and Y-STR Data from the HGDP-CEPH Populations

(2009) W. Shi et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2008) Mattias Jakobsson et al.   NATURE

Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation

(2008) J. Z. Li et al.   SCIENCE