Natural selection and infectious disease in human populations

Gene Editing of CCR5 in Autologous CD4 T Cells of Persons Infected with HIV

(2014) Pablo Tebas et al.   NEW ENGLAND JOURNAL OF MEDICINE

Common Risk Alleles for Inflammatory Diseases Are Targets of Recent Positive Selection

(2013) Towfique Raj et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Beyond GWASs: Illuminating the Dark Road from Association to Function

(2013) Stacey L. Edwards et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Potential Impact of Droplet Microfluidics in Biology

(2013) Thomas Schneider et al.   ANALYTICAL CHEMISTRY

Genome-Wide Association Study of Spontaneous Resolution of Hepatitis C Virus Infection: Data From Multiple Cohorts

(2013) Priya Duggal et al.   ANNALS OF INTERNAL MEDICINE

Detecting Natural Selection in Genomic Data

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

Selection and Adaptation in the Human Genome

(2013) Wenqing Fu et al.   Annual Review of Genomics and Human Genetics

The Next-Generation Sequencing Revolution and Its Impact on Genomics

(2013) Daniel C. Koboldt et al.   CELL

Identifying Recent Adaptations in Large-Scale Genomic Data

(2013) Sharon R. Grossman et al.   CELL

Crohn's Disease Loci Are Common Targets of Protozoa-Driven Selection

(2013) Rachele Cagliani et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evidence for Polygenic Adaptation to Pathogens in the Human Genome

(2013) Josephine T. Daub et al.   MOLECULAR BIOLOGY AND EVOLUTION

The big challenges of big data

(2013) Vivien Marx   NATURE

Common variants in the HLA-DRB1–HLA-DQA1 HLA class II region are associated with susceptibility to visceral leishmaniasis

(2013) Michaela Fakiola et al.   NATURE GENETICS

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Distinct Distal Gut Microbiome Diversity and Composition in Healthy Children from Bangladesh and the United States

(2013) Audrie Lin et al.   PLoS One

Multiple Instances of Ancient Balancing Selection Shared Between Humans and Chimpanzees

(2013) E. M. Leffler et al.   SCIENCE

Influence of HLA-C Expression Level on HIV Control

(2013) R. Apps et al.   SCIENCE

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Natural Selection in a Bangladeshi Population from the Cholera-Endemic Ganges River Delta

(2013) E. K. Karlsson et al.   Science Translational Medicine

Imputation-Based Meta-Analysis of Severe Malaria in Three African Populations

(2013) Gavin Band et al.   PLoS Genetics

Whole Genome Sequencing of Field Isolates Reveals a Common Duplication of the Duffy Binding Protein Gene in Malagasy Plasmodium vivax Strains

(2013) Didier Menard et al.   PLoS Neglected Tropical Diseases

The Microbiome in Infectious Disease and Inflammation

(2012) Kenya Honda et al.   Annual Review of Immunology

INRICH: interval-based enrichment analysis for genome-wide association studies

(2012) Phil H. Lee et al.   BIOINFORMATICS

A genome wide association study of pulmonary tuberculosis susceptibility in Indonesians

(2012) Eileen Png et al.   BMC Medical Genetics

What have we learned from six years of GWAS in autoimmune diseases, and what is next?

(2012) Xinli Hu et al.   CURRENT OPINION IN IMMUNOLOGY

A decade of 3C technologies: insights into nuclear organization

(2012) E. de Wit et al.   GENES & DEVELOPMENT

Limited Evidence for Classic Selective Sweeps in African Populations

(2012) J. M. Granka et al.   GENETICS

Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients

(2012) Richard B. Kennedy et al.   HUMAN GENETICS

Interrogating the major histocompatibility complex with high-throughput genomics

(2012) P. I. W. de Bakker et al.   HUMAN MOLECULAR GENETICS

Genome-wide association studies of tuberculosis in Asians identify distinct at-risk locus for young tuberculosis

(2012) Surakameth Mahasirimongkol et al.   JOURNAL OF HUMAN GENETICS

Noroviruses: The Perfect Human Pathogens?

(2012) A. J. Hall   JOURNAL OF INFECTIOUS DISEASES

Cholera

(2012) Jason B Harris et al.   LANCET

Inflammatory and immune response genes have significantly altered expression in schizophrenia

(2012) J Sainz et al.   MOLECULAR PSYCHIATRY

Genome-wide association study indicates two novel resistance loci for severe malaria

(2012) Christian Timmann et al.   NATURE

IFITM3 restricts the morbidity and mortality associated with influenza

(2012) Aaron R. Everitt et al.   NATURE

Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

(2012) Luke Jostins et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Common variants at 11p13 are associated with susceptibility to tuberculosis

(2012) Thorsten Thye et al.   NATURE GENETICS

NOD2 triggers an interleukin-32–dependent human dendritic cell program in leprosy

(2012) Mirjam Schenk et al.   NATURE MEDICINE

ENCODE Data in the UCSC Genome Browser: year 5 update

(2012) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Evolution, revolution and heresy in the genetics of infectious disease susceptibility

(2012) A. V. S. Hill   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Role of Host Genetics in Susceptibility to Influenza: A Systematic Review

(2012) Peter Horby et al.   PLoS One

Genome-Wide Association Study Confirming Association of HLA-DP with Protection against Chronic Hepatitis B and Viral Clearance in Japanese and Korean

(2012) Nao Nishida et al.   PLoS One

The ABO blood group is a trans-species polymorphism in primates

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

Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite

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

Genome-wide association study of antibody response to smallpox vaccine

(2012) Inna G. Ovsyannikova et al.   VACCINE

Glycoconjugates Play a Key Role in Campylobacter jejuni Infection: Interactions between Host and Pathogen

(2012) Christopher James Day et al.   Frontiers in Cellular and Infection Microbiology

Multi-locus genome-wide association analysis supports the role of glutamatergic synaptic transmission in the etiology of major depressive disorder

(2012) P H Lee et al.   Translational Psychiatry

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

Effects of Natural Selection and Gene Conversion on the Evolution of Human Glycophorins Coding for MNS Blood Polymorphisms in Malaria-Endemic African Populations

(2011) Wen-Ya Ko et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The role of immune dysfunction in the pathophysiology of autism

(2011) Charity Onore et al.   BRAIN BEHAVIOR AND IMMUNITY

Genome-wide association study of HPV seropositivity

(2011) D. Chen et al.   HUMAN MOLECULAR GENETICS

A genome-wide association study of chronic hepatitis B identified novel risk locus in a Japanese population

(2011) Hamdi Mbarek et al.   HUMAN MOLECULAR GENETICS

Human genetic susceptibility to intracellular pathogens

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

What did we learn from the genome-wide association study for tuberculosis susceptibility?

(2011) H.-Q. Qu et al.   JOURNAL OF MEDICAL GENETICS

Purifying Selection Can Obscure the Ancient Age of Viral Lineages

(2011) Joel O. Wertheim et al.   MOLECULAR BIOLOGY AND EVOLUTION

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Identification of two new loci at IL23R and RAB32 that influence susceptibility to leprosy

(2011) Furen Zhang et al.   NATURE GENETICS

Population genomics of parallel phenotypic evolution in stickleback across stream-lake ecological transitions

(2011) B. E. Deagle et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Classic Selective Sweeps Were Rare in Recent Human Evolution

(2011) R. D. Hernandez et al.   SCIENCE

When the World's Population Took Off: The Springboard of the Neolithic Demographic Transition

(2011) J.-P. Bocquet-Appel   SCIENCE

Genome-Wide Association Study SNPs in the Human Genome Diversity Project Populations: Does Selection Affect Unlinked SNPs with Shared Trait Associations?

(2011) Amanda M. Casto et al.   PLoS Genetics

Adaptations to Climate-Mediated Selective Pressures in Humans

(2011) Angela M. Hancock 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

Impact of Rapid Urbanization on the Rates of Infection by Vibrio cholerae O1 and Enterotoxigenic Escherichia coli in Dhaka, Bangladesh

(2011) Fahima Chowdhury et al.   PLoS Neglected Tropical Diseases

Genetic Epidemiology of Tuberculosis Susceptibility: Impact of Study Design

(2011) Catherine M. Stein   PLoS Pathogens

Common human genetic variants and HIV-1 susceptibility: a genome-wide survey in a homogeneous African population

(2010) Slavé Petrovski et al.   AIDS

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 ‘hygiene hypothesis’ for autoimmune and allergic diseases: an update

(2010) H. Okada et al.   CLINICAL AND EXPERIMENTAL IMMUNOLOGY

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

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

Replication of past candidate loci for common diseases and phenotypes in 100 genome-wide association studies

(2010) Konstantinos C M Siontis et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Knowledge gaining by human genetic studies on tuberculosis susceptibility

(2010) Hui-Qi Qu et al.   JOURNAL OF HUMAN GENETICS

Host Determinants of HIV‐1 Control in African Americans

(2010) Kimberly Pelak et al.   JOURNAL OF INFECTIOUS DISEASES

Cholera's western front

(2010) Jason B Harris et al.   LANCET

The hygiene hypothesis: an evolutionary perspective

(2010) Manuela Sironi et al.   MICROBES AND INFECTION

Ascertainment Biases in SNP Chips Affect Measures of Population Divergence

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

Integrating common and rare genetic variation in diverse human populations

(2010)   NATURE

Genome-wide association analyses identifies a susceptibility locus for tuberculosis on chromosome 18q11.2

(2010) Thorsten Thye et al.   NATURE GENETICS

Analysing biological pathways in genome-wide association studies

(2010) Kai Wang et al.   NATURE REVIEWS GENETICS

Methodological challenges of genome-wide association analysis in Africa

(2010) Yik-Ying Teo et al.   NATURE REVIEWS GENETICS

Genomewide Association Study of Leprosy

(2010)   NEW ENGLAND JOURNAL OF MEDICINE

Plasmodium vivax clinical malaria is commonly observed in Duffy-negative Malagasy people

(2010) D. Menard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Association of Trypanolytic ApoL1 Variants with Kidney Disease in African Americans

(2010) G. Genovese et al.   SCIENCE

Island Biogeography Reveals the Deep History of SIV

(2010) M. Worobey et al.   SCIENCE

The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation

(2010)   SCIENCE

Current findings, challenges and novel approaches in human genetic susceptibility to tuberculosis

(2010) Marlo Möller et al.   TUBERCULOSIS

Paleovirology—Modern Consequences of Ancient Viruses

(2010) Michael Emerman et al.   PLOS BIOLOGY

Leprosy and the Adaptation of Human Toll-Like Receptor 1

(2010) Sunny H. Wong et al.   PLoS Pathogens

The IFITM Proteins Mediate Cellular Resistance to Influenza A H1N1 Virus, West Nile Virus, and Dengue Virus

(2009) Abraham L. Brass et al.   CELL

Constructing genomic maps of positive selection in humans: Where do we go from here?

(2009) J. M. Akey   GENOME RESEARCH

Signals of recent positive selection in a worldwide sample of human populations

(2009) J. K. Pickrell et al.   GENOME RESEARCH

Parasites represent a major selective force for interleukin genes and shape the genetic predisposition to autoimmune conditions

(2009) Matteo Fumagalli et al.   JOURNAL OF EXPERIMENTAL MEDICINE

A Natural History of FUT2 Polymorphism in Humans

(2009) A. Ferrer-Admetlla et al.   MOLECULAR BIOLOGY AND EVOLUTION

Targets of Balancing Selection in the Human Genome

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

Genome-wide and fine-resolution association analysis of malaria in West Africa

(2009) Muminatou Jallow et al.   NATURE GENETICS

HLA-C cell surface expression and control of HIV/AIDS correlate with a variant upstream of HLA-C

(2009) Rasmi Thomas et al.   NATURE GENETICS

Comparative genomic and phylogeographic analysis of Mycobacterium leprae

(2009) Marc Monot et al.   NATURE GENETICS

A genome-wide association study identifies variants in the HLA-DP locus associated with chronic hepatitis B in Asians

(2009) Yoichiro Kamatani et al.   NATURE GENETICS

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

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

Genomewide Association Study of Leprosy

(2009) Fu-Ren Zhang et al.   NEW ENGLAND JOURNAL OF MEDICINE

The G428A Nonsense Mutation in FUT2 Provides Strong but Not Absolute Protection against Symptomatic GII.4 Norovirus Infection

(2009) Beatrice Carlsson et al.   PLoS One

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

The Origins of Lactase Persistence in Europe

(2009) Yuval Itan et al.   PLoS Computational Biology

Autoimmune Disease Classification by Inverse Association with SNP Alleles

(2009) Marina Sirota et al.   PLoS Genetics

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

(2009) Luis B. Barreiro et al.   PLoS Genetics

Common Genetic Variation and the Control of HIV-1 in Humans

(2009) Jacques Fellay et al.   PLoS Genetics

Designing Genome-Wide Association Studies: Sample Size, Power, Imputation, and the Choice of Genotyping Chip

(2009) Chris C. A. Spencer et al.   PLoS Genetics

The Role of Geography in Human Adaptation

(2009) Graham Coop et al.   PLoS Genetics

Endocrine dysfunction in leprosy

(2008) Â. M. O. Leal et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Leprosy as a genetic model for susceptibility to common infectious diseases

(2008) Andrea Alter et al.   HUMAN GENETICS

Genomewide Association Study of an AIDS‐Nonprogression Cohort Emphasizes the Role Played byHLAGenes (ANRS Genomewide Association Study 02)

(2008) Sophie Limou et al.   JOURNAL OF INFECTIOUS DISEASES

Gene Expression Levels Are a Target of Recent Natural Selection in the Human Genome

(2008) S. Kudaravalli et al.   MOLECULAR BIOLOGY AND EVOLUTION

A global network for investigating the genomic epidemiology of malaria

(2008) Eric Akum Achidi et al.   NATURE

Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960

(2008) Michael Worobey et al.   NATURE

Natural selection has driven population differentiation in modern humans

(2008) Luis B Barreiro et al.   NATURE GENETICS

MYH9 is associated with nondiabetic end-stage renal disease in African Americans

(2008) W H Linda Kao et al.   NATURE GENETICS

MYH9 is a major-effect risk gene for focal segmental glomerulosclerosis

(2008) Jeffrey B Kopp et al.   NATURE GENETICS

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

(2008) Mark I. McCarthy et al.   NATURE REVIEWS GENETICS

High Functional Diversity in Mycobacterium tuberculosis Driven by Genetic Drift and Human Demography

(2008) Ruth Hershberg et al.   PLOS BIOLOGY

Susceptibility to Vibrio cholerae Infection in a Cohort of Household Contacts of Patients with Cholera in Bangladesh

(2008) Jason B. Harris et al.   PLoS Neglected Tropical Diseases

Origin, Spread and Demography of the Mycobacterium tuberculosis Complex

(2008) Thierry Wirth et al.   PLoS Pathogens

Evidence for a Heritable Predisposition to Death Due to Influenza

(2007) Frederick S. Albright et al.   JOURNAL OF INFECTIOUS DISEASES