Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation

Hunter-gatherer genomes reveal diverse demographic trajectories during the rise of farming in Eastern Africa

(2022) Shyamalika Gopalan et al.   CURRENT BIOLOGY

Ancient DNA and deep population structure in sub-Saharan African foragers

(2022) Mark Lipson et al.   NATURE

DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update)

(2022) Brad T Sherman et al.   NUCLEIC ACIDS RESEARCH

A unified genealogy of modern and ancient genomes

(2022) Anthony Wilder Wohns et al.   SCIENCE

Signatures of Convergent Evolution and Natural Selection at the Alcohol Dehydrogenase Gene Region are Correlated with Agriculture in Ethnically Diverse Africans

(2022) Michael A McQuillan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gendered movement ecology and landscape use in Hadza hunter-gatherers

(2021) Brian M. Wood et al.   Nature Human Behaviour

Heart Disease and Stroke Statistics—2021 Update: A Report From the American Heart Association

(2021) Salim S. Virani et al.   CIRCULATION

Ensembl 2022

(2021) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Analysis of anti-Plasmodium IgG profiles among Fulani nomadic pastoralists in northern Senegal to assess malaria exposure

(2020) Mame Cheikh Seck et al.   MALARIA JOURNAL

Ancient West African foragers in the context of African population history

(2020) Mark Lipson et al.   NATURE

Recovering signals of ghost archaic introgression in African populations

(2020) Arun Durvasula et al.   Science Advances

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements

(2020) M. Grace Gordon et al.   Nature Protocols

A GWAS in Latin Americans highlights the convergent evolution of lighter skin pigmentation in Eurasia

(2019) Kaustubh Adhikari et al.   Nature Communications

Genomic evidence for shared common ancestry of East African hunting-gathering populations and insights into local adaptation

(2019) Laura B. Scheinfeldt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Variant PADI3 in Central Centrifugal Cicatricial Alopecia

(2019) Liron Malki et al.   NEW ENGLAND JOURNAL OF MEDICINE

The Missing Diversity in Human Genetic Studies

(2019) Giorgio Sirugo et al.   CELL

Meta-analysis of GWA studies provides new insights on the genetic architecture of skin pigmentation in recently admixed populations

(2019) Frida Lona-Durazo et al.   BMC GENETICS

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

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

A catalog of genetic loci associated with kidney function from analyses of a million individuals

(2019) Matthias Wuttke et al.   NATURE GENETICS

Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa

(2019) Mary E. Prendergast et al.   SCIENCE

Models of archaic admixture and recent history from two-locus statistics

(2019) Aaron P. Ragsdale et al.   PLoS Genetics

The formation of human populations in South and Central Asia

(2019) Vagheesh M. Narasimhan et al.   SCIENCE

Uganda Genome Resource Enables Insights into Population History and Genomic Discovery in Africa

(2019) Deepti Gurdasani et al.   CELL

Heterogeneity in Palaeolithic Population Continuity and Neolithic Expansion in North Africa

(2019) Gerard Serra-Vidal et al.   CURRENT BIOLOGY

Accurate, scalable and integrative haplotype estimation

(2019) Olivier Delaneau et al.   Nature Communications

Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations

(2019) Jeffrey P. Spence et al.   Science Advances

Population history and genetic adaptation of the Fulani nomads: inferences from genome-wide data and the lactase persistence trait

(2019) Mário Vicente et al.   BMC GENOMICS

Mixed-model association for biobank-scale datasets

(2018) Po-Ru Loh et al.   NATURE GENETICS

Meta-analysis of genome-wide association studies for height and body mass index in ∼700000 individuals of European ancestry

(2018) Loic Yengo et al.   HUMAN MOLECULAR GENETICS

An atlas of genetic associations in UK Biobank

(2018) Oriol Canela-Xandri et al.   NATURE GENETICS

Polygenic adaptation and convergent evolution on growth and cardiac genetic pathways in African and Asian rainforest hunter-gatherers

(2018) Christina M. Bergey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The hypoxia-inducible factors HIF1α and HIF2α are dispensable for embryonic muscle development but essential for postnatal muscle regeneration

(2017) Xin Yang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Efficient Computation of the Joint Sample Frequency Spectra for Multiple Populations

(2017) John A. Kamm et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

New fossils from Jebel Irhoud, Morocco and the pan-African origin of Homo sapiens

(2017) Jean-Jacques Hublin et al.   NATURE

ClinVar: improving access to variant interpretations and supporting evidence

(2017) Melissa J Landrum et al.   NUCLEIC ACIDS RESEARCH

Loci associated with skin pigmentation identified in African populations

(2017) Nicholas G. Crawford et al.   SCIENCE

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

(2017) Carina M. Schlebusch et al.   SCIENCE

Whole-genome sequencing for an enhanced understanding of genetic variation among South Africans

(2017) Ananyo Choudhury et al.   Nature Communications

Major transcriptional changes observed in the Fulani, an ethnic group less susceptible to malaria

(2017) Jaclyn E Quin et al.   eLife

Inferences of African evolutionary history from genomic data

(2016) Marcia Holsbach Beltrame et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Transcriptional targets of TWIST1 in the cranial mesoderm regulate cell-matrix interactions and mesenchyme maintenance

(2016) Heidi Bildsoe et al.   DEVELOPMENTAL BIOLOGY

Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection

(2016) PingHsun Hsieh et al.   GENOME RESEARCH

Hyperinsulinemia and Insulin Resistance in Dopamine β-Hydroxylase Deficiency

(2016) Amy C Arnold et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

Genomics is failing on diversity

(2016) Alice B. Popejoy et al.   NATURE

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

(2016) Swapan Mallick et al.   NATURE

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

(2016) Jonathan Terhorst et al.   NATURE GENETICS

Genetic Misdiagnoses and the Potential for Health Disparities

(2016) Arjun K. Manrai et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2016) S. Fan et al.   SCIENCE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa

(2015) M. Gallego Llorente et al.   SCIENCE

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

(2015) Christopher C Chang et al.   GigaScience

SAMBLASTER: fast duplicate marking and structural variant read extraction

(2014) G. G. Faust et al.   BIOINFORMATICS

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

(2014) Heng Li   BIOINFORMATICS

selscan: An Efficient Multithreaded Program to Perform EHH-Based Scans for Positive Selection

(2014) Z. A. Szpiech et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

Defining the role of common variation in the genomic and biological architecture of adult human height

(2014) Andrew R Wood et al.   NATURE GENETICS

Requirement of MEF2A, C, and D for skeletal muscle regeneration

(2014) N. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers

(2014) G. H. Perry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history

(2014) Hie Lim Kim et al.   Nature Communications

Apparent Variation in Neanderthal Admixture among African Populations is Consistent with Gene Flow from Non-African Populations

(2013) Shuoguo Wang et al.   Genome Biology and Evolution

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Genetic inactivation or pharmacological inhibition of Pdk1 delays development and inhibits metastasis of Braf V600E ::Pten –/– melanoma

(2013) M Scortegagna et al.   ONCOGENE

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

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

(2012) Joseph Lachance et al.   CELL

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

TGF-β and BMP Signaling in Osteoblast Differentiation and Bone Formation

(2012) Guiqian Chen et al.   International Journal of Biological Sciences

Changes in the levels of cytokines, chemokines and malaria-specific antibodies in response to Plasmodium falciparum infection in children living in sympatry in Mali

(2012) Stéphanie Boström et al.   MALARIA JOURNAL

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

Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History

(2012) C. M. Schlebusch et al.   SCIENCE

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

The genetic prehistory of southern Africa

(2012) Joseph K. Pickrell et al.   Nature Communications

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

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

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

Genetic adaptation to high altitude in the Ethiopian highlands

(2012) Laura B Scheinfeldt et al.   GENOME BIOLOGY

Mutations in ANKRD11 Cause KBG Syndrome, Characterized by Intellectual Disability, Skeletal Malformations, and Macrodontia

(2011) Asli Sirmaci et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Natural genetic variation caused by small insertions and deletions in the human genome

(2011) R. E. Mills et al.   GENOME RESEARCH

Genetic Structure of Pastoral and Farmer Populations in the African Sahel

(2011) Viktor Černý et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Autosomal-Dominant Woolly Hair Resulting from Disruption of Keratin 74 (KRT74), a Potential Determinant of Human Hair Texture

(2010) Yutaka Shimomura et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Complete Khoisan and Bantu genomes from southern Africa

(2010) Stephan C. Schuster et al.   NATURE

Hundreds of variants clustered in genomic loci and biological pathways affect human height

(2010) Hana Lango Allen et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Sox proteins in melanocyte development and melanoma

(2010) Melissa L. Harris et al.   Pigment Cell & Melanoma Research

Tracking footprints of artificial selection in the dog genome

(2010) J. M. Akey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Tgfbr2 is required for development of the skull vault

(2009) Hwa-Seon Seo et al.   DEVELOPMENTAL BIOLOGY

Fast model-based estimation of ancestry in unrelated individuals

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

The Genetic Structure and History of Africans and African Americans

(2009) S. A. Tishkoff et al.   SCIENCE

A Genome-Wide Association Study of Hypertension and Blood Pressure in African Americans

(2009) Adebowale Adeyemo et al.   PLoS Genetics

Y-chromosome variation among Sudanese: Restricted gene flow, concordance with language, geography, and history

(2008) Hisham Y. Hassan et al.   AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY

Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter-gatherers and Bantu-speaking farmers

(2008) L. Quintana-Murci et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA