Living in an adaptive world: Genomic dissection of the genusHomoand its immune response

Tracing the peopling of the world through genomics

(2017) Rasmus Nielsen et al.   NATURE

Introgression of Neandertal- and Denisovan-like Haplotypes Contributes to Adaptive Variation in Human Toll-like Receptors

(2016) Michael Dannemann et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

(2016) Lu Chen et al.   CELL

Host and Environmental Factors Influencing Individual Human Cytokine Responses

(2016) Rob ter Horst et al.   CELL

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity

(2016) Melanie Schirmer et al.   CELL

Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens

(2016) Yohann Nédélec et al.   CELL

Insights into the Neural and Genetic Basis of Vocal Communication

(2016) Genevieve Konopka et al.   CELL

Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations

(2016) Hélène Quach et al.   CELL

A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans

(2016) Yang Li et al.   CELL

The impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives

(2016) Yuval B Simons et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A genomic history of Aboriginal Australia

(2016) Anna-Sapfo Malaspinas 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

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals

(2016) B. Vernot et al.   SCIENCE

Social status alters immune regulation and response to infection in macaques

(2016) Noah Snyder-Mackler 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

Going global by adapting local: A review of recent human adaptation

(2016) S. Fan et al.   SCIENCE

Shaping Variation in the Human Immune System

(2016) Adrian Liston et al.   TRENDS IN IMMUNOLOGY

The Genetic Architecture of the Human Immune System: A Bioresource for Autoimmunity and Disease Pathogenesis

(2015) Mario Roederer et al.   CELL

Small Amounts of Archaic Admixture Provide Big Insights into Human History

(2015) Selina Vattathil et al.   CELL

Variation in the Human Immune System Is Largely Driven by Non-Heritable Influences

(2015) Petter Brodin et al.   CELL

Insights into hominin phenotypic and dietary evolution from ancient DNA sequence data

(2015) George H. Perry et al.   JOURNAL OF HUMAN EVOLUTION

Genome-wide patterns of selection in 230 ancient Eurasians

(2015) Iain Mathieson et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans

(2015) Ron Do et al.   NATURE GENETICS

Discovery of six new susceptibility loci and analysis of pleiotropic effects in leprosy

(2015) Hong Liu et al.   NATURE GENETICS

Estimating the mutation load in human genomes

(2015) Brenna M. Henn et al.   NATURE REVIEWS GENETICS

Evidence for archaic adaptive introgression in humans

(2015) Fernando Racimo et al.   NATURE REVIEWS GENETICS

Distance from sub-Saharan Africa predicts mutational load in diverse human genomes

(2015) Brenna M. Henn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

Unravelling the hidden ancestry of American admixed populations

(2015) Francesco Montinaro et al.   Nature Communications

Host Genetic Variation Influences Gene Expression Response to Rhinovirus Infection

(2015) Minal Çalışkan et al.   PLoS Genetics

Genetic Origins of Lactase Persistence and the Spread of Pastoralism in Africa

(2014) Alessia Ranciaro et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Characteristics of Neutral and Deleterious Protein-Coding Variation among Individuals and Populations

(2014) Wenqing Fu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Joint Analysis of Functional Genomic Data and Genome-wide Association Studies of 18 Human Traits

(2014) Joseph K. Pickrell   AMERICAN JOURNAL OF HUMAN GENETICS

Adaptations to local environments in modern human populations

(2014) Choongwon Jeong et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The distribution of deleterious genetic variation in human populations

(2014) Kirk E Lohmueller   CURRENT OPINION IN GENETICS & DEVELOPMENT

Advantageous diversity maintained by balancing selection in humans

(2014) Felix M Key et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The Red Queen's long race: human adaptation to pathogen pressure

(2014) Katherine J Siddle et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Ancient humans and the origin of modern humans

(2014) Janet Kelso et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The peopling of the African continent and the diaspora into the new world

(2014) Michael C Campbell et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Genetics of gene expression in immunity to infection

(2014) Benjamin P Fairfax et al.   CURRENT OPINION IN IMMUNOLOGY

The dissection of complex susceptibility to infectious disease: bacterial, viral and parasitic infections

(2014) Laurent Abel et al.   CURRENT OPINION IN IMMUNOLOGY

Human genome variability, natural selection and infectious diseases

(2014) Matteo Fumagalli et al.   CURRENT OPINION IN IMMUNOLOGY

The contribution of natural selection to present-day susceptibility to chronic inflammatory and autoimmune disease

(2014) Jessica F Brinkworth et al.   CURRENT OPINION IN IMMUNOLOGY

A genomic portrait of the genetic architecture and regulatory impact of microRNA expression in response to infection

(2014) K. J. Siddle et al.   GENOME RESEARCH

Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA

(2014) Emilia Huerta-Sánchez et al.   NATURE

The genomic landscape of Neanderthal ancestry in present-day humans

(2014) Sriram Sankararaman et al.   NATURE

The deleterious mutation load is insensitive to recent population history

(2014) Yuval B Simons et al.   NATURE GENETICS

The impact of whole-genome sequencing on the reconstruction of human population history

(2014) Krishna R. Veeramah et al.   NATURE REVIEWS GENETICS

Natural selection and infectious disease in human populations

(2014) Elinor K. Karlsson et al.   NATURE REVIEWS GENETICS

Impact of regulatory variation from RNA to protein

(2014) A. Battle et al.   SCIENCE

Resurrecting Surviving Neandertal Lineages from Modern Human Genomes

(2014) B. Vernot et al.   SCIENCE

Polarization of the Effects of Autoimmune and Neurodegenerative Risk Alleles in Leukocytes

(2014) T. Raj et al.   SCIENCE

Common Genetic Variants Modulate Pathogen-Sensing Responses in Human Dendritic Cells

(2014) M. N. Lee et al.   SCIENCE

Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression

(2014) B. P. Fairfax et al.   SCIENCE

The impact of agricultural emergence on the genetic history of African rainforest hunter-gatherers and agriculturalists

(2014) Etienne Patin et al.   Nature Communications

Distribution and Medical Impact of Loss-of-Function Variants in the Finnish Founder Population

(2014) Elaine T. Lim et al.   PLoS Genetics

A Model-Based Approach for Identifying Signatures of Ancient Balancing Selection in Genetic Data

(2014) Michael DeGiorgio et al.   PLoS Genetics

Selection on a Variant Associated with Improved Viral Clearance Drives Local, Adaptive Pseudogenization of Interferon Lambda 4 (IFNL4)

(2014) Felix M. Key et al.   PLoS Genetics

Systematic review: worldwide variation in the frequency of coeliac disease and changes over time

(2013) J. Y. Kang et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

Detecting Natural Selection in Genomic Data

(2013) Joseph J. Vitti et al.   Annual Review of Genetics

Identifying Recent Adaptations in Large-Scale Genomic Data

(2013) Sharon R. Grossman et al.   CELL

Genetic Variants Regulating Immune Cell Levels in Health and Disease

(2013) Valeria Orrù et al.   CELL

Gene expression drives local adaptation in humans

(2013) H. B. Fraser   GENOME RESEARCH

The adaptive variant EDARV370A is associated with straight hair in East Asians

(2013) Jingze Tan et al.   HUMAN GENETICS

Neandertal Origin of Genetic Variation at the Cluster of OAS Immunity Genes

(2013) F. L. Mendez et al.   MOLECULAR BIOLOGY AND EVOLUTION

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

(2013) Maanasa Raghavan et al.   NATURE

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

Recent human adaptation: genomic approaches, interpretation and insights

(2013) Laura B. Scheinfeldt et al.   NATURE REVIEWS GENETICS

Genetic insights into common pathways and complex relationships among immune-mediated diseases

(2013) Miles Parkes et al.   NATURE REVIEWS GENETICS

Multiple Instances of Ancient Balancing Selection Shared Between Humans and Chimpanzees

(2013) E. M. Leffler et al.   SCIENCE

Whole-Exome Sequencing Reveals a Rapid Change in the Frequency of Rare Functional Variants in a Founding Population of Humans

(2013) Ferran Casals et al.   PLoS Genetics

A Haplotype at STAT2 Introgressed from Neanderthals and Serves as a Candidate of Positive Selection in Papua New Guinea

(2012) Fernando L. Mendez et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers

(2012) Joseph Lachance et al.   CELL

Inborn errors of human STAT1: allelic heterogeneity governs the diversity of immunological and infectious phenotypes

(2012) Stephanie Boisson-Dupuis et al.   CURRENT OPINION IN IMMUNOLOGY

Linking disease associations with regulatory information in the human genome

(2012) M. A. Schaub et al.   GENOME RESEARCH

The Timing of Pigmentation Lightening in Europeans

(2012) Sandra Beleza et al.   MOLECULAR BIOLOGY AND EVOLUTION

TNF receptor 1 genetic risk mirrors outcome of anti-TNF therapy in multiple sclerosis

(2012) Adam P. Gregory et al.   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Genetics of gene expression in primary immune cells identifies cell type–specific master regulators and roles of HLA alleles

(2012) Benjamin P Fairfax et al.   NATURE GENETICS

Genome-wide scans provide evidence for positive selection of genes implicated in Lassa fever

(2012) K. G. Andersen et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Social environment is associated with gene regulatory variation in the rhesus macaque immune system

(2012) J. Tung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection

(2012) L. B. Barreiro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The great human expansion

(2012) B. M. Henn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

(2012) J. A. Tennessen et al.   SCIENCE

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

Patterns of Ancestry, Signatures of Natural Selection, and Genetic Association with Stature in Western African Pygmies

(2012) Joseph P. Jarvis et al.   PLoS Genetics

Patterns of Cis Regulatory Variation in Diverse Human Populations

(2012) Barbara E. Stranger et al.   PLoS Genetics

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

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

Genome-wide Comparison of African-Ancestry Populations from CARe and Other Cohorts Reveals Signals of Natural Selection

(2011) Gaurav Bhatia et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Perspectives on Human Population Structure at the Cusp of the Sequencing Era

(2011) John Novembre et al.   Annual Review of Genomics and Human Genetics

Genetic control of gene expression in whole blood and lymphoblastoid cell lines is largely independent

(2011) J. E. Powell et al.   GENOME RESEARCH

Human genetic susceptibility to intracellular pathogens

(2011) Fredrik O. Vannberg et al.   IMMUNOLOGICAL REVIEWS

Evolutionary genetic dissection of human interferons

(2011) Jérémy Manry et al.   JOURNAL OF EXPERIMENTAL MEDICINE

From expression QTLs to personalized transcriptomics

(2011) Stephen B. Montgomery et al.   NATURE REVIEWS GENETICS

Genetic evidence for archaic admixture in Africa

(2011) M. F. Hammer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans

(2011) L. Abi-Rached et al.   SCIENCE

Single-Tissue and Cross-Tissue Heritability of Gene Expression Via Identity-by-Descent in Related or Unrelated Individuals

(2011) Alkes L. Price et al.   PLoS Genetics

The Architecture of Gene Regulatory Variation across Multiple Human Tissues: The MuTHER Study

(2011) Alexandra C. Nica et al.   PLoS Genetics

Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution

(2011) Matteo Fumagalli et al.   PLoS Genetics

Evolutionary and Functional Analysis of Celiac Risk Loci Reveals SH2B3 as a Protective Factor against Bacterial Infection

(2010) Alexandra Zhernakova et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The role played by natural selection on Mendelian traits in humans

(2010) Lluis Quintana-Murci et al.   Annals of the New York Academy of Sciences

Life-threatening infectious diseases of childhood: single-gene inborn errors of immunity?

(2010) Alexandre Alcaïs et al.   Annals of the New York Academy of Sciences

The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation

(2010) Jonathan K. Pritchard et al.   CURRENT BIOLOGY

Human TRAF3 Adaptor Molecule Deficiency Leads to Impaired Toll-like Receptor 3 Response and Susceptibility to Herpes Simplex Encephalitis

(2010) Rebeca Pérez de Diego et al.   IMMUNITY

The hygiene hypothesis: an evolutionary perspective

(2010) Manuela Sironi et al.   MICROBES AND INFECTION

Genetic Variations in Tibetan Populations and High-Altitude Adaptation at the Himalayas

(2010) Y. Peng et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2010) David Reich et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

A map of open chromatin in human pancreatic islets

(2010) Kyle J Gaulton et al.   NATURE GENETICS

In brief

(2010)   NATURE REVIEWS NEUROSCIENCE

A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection

(2010) S. R. Grossman et al.   SCIENCE

Genetic Evidence for High-Altitude Adaptation in Tibet

(2010) T. S. Simonson et al.   SCIENCE

Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

(2010) X. Yi et al.   SCIENCE

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS

(2010) Dan L. Nicolae et al.   PLoS Genetics

Identifying Signatures of Natural Selection in Tibetan and Andean Populations Using Dense Genome Scan Data

(2010) Abigail Bigham et al.   PLoS Genetics

Positive selection of a CD36 nonsense variant in sub-Saharan Africa, but no association with severe malaria phenotypes

(2009) Andrew E. Fry et al.   HUMAN MOLECULAR GENETICS

Targets of Balancing Selection in the Human Genome

(2009) A. M. Andres et al.   MOLECULAR BIOLOGY AND EVOLUTION

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

From evolutionary genetics to human immunology: how selection shapes host defence genes

(2009) Luis B. Barreiro et al.   NATURE REVIEWS GENETICS

Genetics in geographically structured populations: defining, estimating and interpreting FST

(2009) Kent E. Holsinger et al.   NATURE REVIEWS GENETICS

Genome-wide patterns of population structure and admixture in West Africans and African Americans

(2009) K. Bryc et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Positively Selected G6PD-Mahidol Mutation Reduces Plasmodium vivax Density in Southeast Asians

(2009) C. Louicharoen et al.   SCIENCE

Common Regulatory Variation Impacts Gene Expression in a Cell Type-Dependent Manner

(2009) A. S. Dimas et al.   SCIENCE

The Origins of Lactase Persistence in Europe

(2009) Yuval Itan et al.   PLoS Computational Biology

Evolutionary Dynamics of Human Toll-Like Receptors and Their Different Contributions to Host Defense

(2009) Luis B. Barreiro 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

Proportionally more deleterious genetic variation in European than in African populations

(2008) Kirk E. Lohmueller et al.   NATURE

Genes mirror geography within Europe

(2008) John Novembre et al.   NATURE

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

(2008) Mattias Jakobsson et al.   NATURE

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

(2008) Timothy J. Ley et al.   NATURE

Natural selection has driven population differentiation in modern humans

(2008) Luis B Barreiro et al.   NATURE GENETICS

Newly identified genetic risk variants for celiac disease related to the immune response

(2008) Karen A Hunt et al.   NATURE GENETICS

Positive Selection in East Asians for an EDAR Allele that Enhances NF-κB Activation

(2008) Jarosław Bryk et al.   PLoS One