Genomic insights into population history and biological adaptation in Oceania

Complex genetic admixture histories reconstructed with Approximate Bayesian Computation

(2021) Cesar A. Fortes‐Lima et al.   Molecular Ecology Resources

Multiple migrations to the Philippines during the last 50,000 years

(2021) Maximilian Larena et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ancient DNA indicates human population shifts and admixture in northern and southern China

(2020) Melinda A. Yang et al.   SCIENCE

Native American gene flow into Polynesia predating Easter Island settlement

(2020) Alexander G. Ioannidis et al.   NATURE

Three Phases of Ancient Migration Shaped the Ancestry of Human Populations in Vanuatu

(2020) Mark Lipson et al.   CURRENT BIOLOGY

Multiple Deeply Divergent Denisovan Ancestries in Papuans

(2019) Guy S. Jacobs et al.   CELL

A new species of Homo from the Late Pleistocene of the Philippines

(2019) Florent Détroit et al.   NATURE

Reduced signal for polygenic adaptation of height in UK Biobank

(2019) Jeremy J Berg et al.   eLife

The population history of northeastern Siberia since the Pleistocene

(2019) Martin Sikora et al.   NATURE

Thinking About the Evolution of Complex Traits in the Era of Genome-Wide Association Studies

(2019) Guy Sella et al.   Annual Review of Genomics and Human Genetics

Functional variants in ADH1B and ALDH2 are non-additively associated with all-cause mortality in Japanese population

(2019) Saori Sakaue et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

A method for genome-wide genealogy estimation for thousands of samples

(2019) Leo Speidel et al.   NATURE GENETICS

Polygenic Patterns of Adaptive Introgression in Modern Humans Are Mainly Shaped by Response to Pathogens

(2019) Alexandre Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

The GenomeAsia 100K Project enables genetic discoveries across Asia

(2019)   NATURE

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

(2018) Sharon R. Browning et al.   CELL

Population Turnover in Remote Oceania Shortly after Initial Settlement

(2018) Mark Lipson et al.   CURRENT BIOLOGY

The evolutionary history and human settlement of Australia and the Pacific

(2018) Anna L Gosling et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The Gateway from Near into Remote Oceania: New Insights from Genome-Wide Data

(2018) Irina Pugach et al.   MOLECULAR BIOLOGY AND EVOLUTION

Language continuity despite population replacement in Remote Oceania

(2018) Cosimo Posth et al.   Nature Ecology & Evolution

When did Homo sapiens first reach Southeast Asia and Sahul?

(2018) James F. O’Connell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence that RNA Viruses Drove Adaptive Introgression between Neanderthals and Modern Humans

(2018) David Enard et al.   CELL

Genome-wide association analyses identify 139 loci associated with macular thickness in the UK Biobank cohort

(2018) X Raymond Gao et al.   HUMAN MOLECULAR GENETICS

The UK Biobank resource with deep phenotyping and genomic data

(2018) Clare Bycroft et al.   NATURE

Trans-ethnic association study of blood pressure determinants in over 750,000 individuals

(2018) Ayush Giri et al.   NATURE GENETICS

CADD: predicting the deleteriousness of variants throughout the human genome

(2018) Philipp Rentzsch et al.   NUCLEIC ACIDS RESEARCH

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello et al.   NUCLEIC ACIDS RESEARCH

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

OSBPL10, RXRA and lipid metabolism confer African-ancestry protection against dengue haemorrhagic fever in admixed Cubans

(2017) Beatriz Sierra et al.   PLoS Pathogens

Genomic Signatures of Selective Pressures and Introgression from Archaic Hominins at Human Innate Immunity Genes

(2016) Matthieu Deschamps et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans

(2016) Sriram Sankararaman et al.   CURRENT BIOLOGY

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

(2016) Rachel M. Gittelman et al.   CURRENT BIOLOGY

A genomic history of Aboriginal Australia

(2016) Anna-Sapfo Malaspinas et al.   NATURE

Genomic insights into the peopling of the Southwest Pacific

(2016) Pontus Skoglund et al.   NATURE

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

(2016) Swapan Mallick et al.   NATURE

Chimpanzee genomic diversity reveals ancient admixture with bonobos

(2016) M. de Manuel et al.   SCIENCE

Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals

(2016) B. Vernot et al.   SCIENCE

The phenotypic legacy of admixture between modern humans and Neandertals

(2016) C. N. Simonti et al.   SCIENCE

Detection of human adaptation during the past 2000 years

(2016) Yair Field et al.   SCIENCE

Pacific Populations, Metabolic Disease and ‘Just-So Stories’: A Critique of the ‘Thrifty Genotype’ Hypothesis in Oceania

(2015) Anna L. Gosling et al.   ANNALS OF HUMAN GENETICS

Reliable ABC model choice via random forests

(2015) Pierre Pudlo et al.   BIOINFORMATICS

Denisovan Ancestry in East Eurasian and Native American Populations

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

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

WikiPathways: capturing the full diversity of pathway knowledge

(2015) Martina Kutmon et al.   NUCLEIC ACIDS RESEARCH

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

The Lengths of Admixture Tracts

(2014) M. Liang et al.   GENETICS

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

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

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

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

Population Genetics Models of Local Ancestry

(2012) S. Gravel   GENETICS

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Improved whole-chromosome phasing for disease and population genetic studies

(2012) Olivier Delaneau et al.   NATURE METHODS

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

Atg7 Modulates p53 Activity to Regulate Cell Cycle and Survival During Metabolic Stress

(2012) I. H. Lee et al.   SCIENCE

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

abc: an R package for approximate Bayesian computation (ABC)

(2012) Katalin Csilléry et al.   Methods in Ecology and Evolution

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

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

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A General Mechanistic Model for Admixture Histories of Hybrid Populations

(2011) Paul Verdu et al.   GENETICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

A linear complexity phasing method for thousands of genomes

(2011) Olivier Delaneau et al.   NATURE METHODS

Robust relationship inference in genome-wide association studies

(2010) Ani Manichaikul et al.   BIOINFORMATICS

Demographic History of Oceania Inferred from Genome-wide Data

(2010) Andreas Wollstein et al.   CURRENT BIOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

(2010) LAURENT EXCOFFIER et al.   Molecular Ecology Resources

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

OSBPL10, a novel candidate gene for high triglyceride trait in dyslipidemic Finnish subjects, regulates cellular lipid metabolism

(2009) Julia Perttilä et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

Language Phylogenies Reveal Expansion Pulses and Pauses in Pacific Settlement

(2009) R. D. Gray et al.   SCIENCE