Loci associated with skin pigmentation identified in African populations

Inference on the Genetic Basis of Eye and Skin Color in an Admixed Population via Bayesian Linear Mixed Models

(2017) Luke R. Lloyd-Jones et al.   GENETICS

The age of the hominin fossils from Jebel Irhoud, Morocco, and the origins of the Middle Stone Age

(2017) Daniel Richter et al.   NATURE

The colours of humanity: the evolution of pigmentation in the human lineage

(2017) Nina G. Jablonski et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

TFAP2 paralogs regulate melanocyte differentiation in parallel with MITF

(2017) Hannah E. Seberg et al.   PLoS Genetics

Inference on the Genetic Basis of Eye and Skin Color in an Admixed Population via Bayesian Linear Mixed Models

(2017) Luke R. Lloyd-Jones et al.   GENETICS

Colocalization of GWAS and eQTL Signals Detects Target Genes

(2016) Farhad Hormozdiari et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Inferences of African evolutionary history from genomic data

(2016) Marcia Holsbach Beltrame 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

Next-generation genotype imputation service and methods

(2016) Sayantan Das et al.   NATURE GENETICS

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

(2016) Jonathan Terhorst et al.   NATURE GENETICS

A high-throughput functional genomics workflow based on CRISPR/Cas9-mediated targeted mutagenesis in zebrafish

(2016) Gaurav K Varshney et al.   Nature Protocols

Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals

(2016) B. Vernot et al.   SCIENCE

Tracing the Route of Modern Humans out of Africa by Using 225 Human Genome Sequences from Ethiopians and Egyptians

(2015) Luca Pagani et al.   AMERICAN JOURNAL OF HUMAN GENETICS

4DGenome: a comprehensive database of chromatin interactions

(2015) Li Teng et al.   BIOINFORMATICS

High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9

(2015) Gaurav K. Varshney et al.   GENOME RESEARCH

Genetics of skin color variation in Europeans: genome-wide association studies with functional follow-up

(2015) Fan Liu et al.   HUMAN GENETICS

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

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

A method to predict the impact of regulatory variants from DNA sequence

(2015) Dongwon Lee et al.   NATURE GENETICS

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

CRISPR-STAT: an easy and reliable PCR-based method to evaluate target-specific sgRNA activity

(2015) Blake Carrington et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

ENCODE data at the ENCODE portal

(2015) Cricket A. Sloan et al.   NUCLEIC ACIDS RESEARCH

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

(2015) et al.   SCIENCE

A hidden Markov model for investigating recent positive selection through haplotype structure

(2015) Hua Chen et al.   THEORETICAL POPULATION BIOLOGY

High level of inbreeding in final phase of 1000 Genomes Project

(2015) Steven Gazal et al.   Scientific Reports

Transcription factor MITF and remodeller BRG1 define chromatin organisation at regulatory elements in melanoma cells

(2015) Patrick Laurette et al.   eLife

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

(2015) Christopher C Chang et al.   GigaScience

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

(2014) Heng Li   BIOINFORMATICS

Novel genomic signals of recent selection in an Ethiopian population

(2014) Fasil Tekola-Ayele et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Identifying Causal Variants at Loci with Multiple Signals of Association

(2014) F. Hormozdiari et al.   GENETICS

Genome-wide transcriptome analysis of human epidermal melanocytes

(2014) Kirk D. Haltaufderhyde et al.   GENOMICS

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

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

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

(2014) Andrew R Wood et al.   NATURE GENETICS

A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness

(2014) Jared O'Connell et al.   PLoS Genetics

Admixture in Latin America: Geographic Structure, Phenotypic Diversity and Self-Perception of Ancestry Based on 7,342 Individuals

(2014) Andrés Ruiz-Linares et al.   PLoS Genetics

An intracellular anion channel critical for pigmentation

(2014) Nicholas W Bellono et al.   eLife

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

The zebrafish reference genome sequence and its relationship to the human genome

(2013) Kerstin Howe et al.   NATURE

Evolutionary mix-and-match with MFS transporters

(2013) M. G. Madej et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CRL4 Complex Regulates Mammalian Oocyte Survival and Reprogramming by Activation of TET Proteins

(2013) C. Yu et al.   SCIENCE

The Light Skin Allele of SLC24A5 in South Asians and Europeans Shares Identity by Descent

(2013) Chandana Basu Mallick et al.   PLoS Genetics

Genetic Architecture of Skin and Eye Color in an African-European Admixed Population

(2013) Sandra Beleza et al.   PLoS Genetics

Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool

(2012) Luca Pagani et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2012) T. Rausch et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter

(2012) M. Visser et al.   GENOME RESEARCH

The Timing of Pigmentation Lightening in Europeans

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

The genetic differentiation at quantitative trait loci under local adaptation

(2012) VALÉRIE LE CORRE et al.   MOLECULAR ECOLOGY

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Transcriptome Analysis Reveals Markers of Aberrantly Activated Innate Immunity in Vitiligo Lesional and Non-Lesional Skin

(2012) Richard Yu et al.   PLoS One

Evolutionarily Assembled cis-Regulatory Module at a Human Ciliopathy Locus

(2012) J. H. Lee et al.   SCIENCE

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

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

The NIH Roadmap Epigenomics Program data resource

(2012) Lisa Helbling Chadwick   Epigenomics

The genetic prehistory of southern Africa

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

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Epidermal Keratinocytes from Light vs. Dark Skin Exhibit Differential Degradation of Melanosomes

(2011) Jody P. Ebanks et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

A linear complexity phasing method for thousands of genomes

(2011) Olivier Delaneau et al.   NATURE METHODS

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

(2011) Daniel L. Ayres et al.   SYSTEMATIC BIOLOGY

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Melanocortin 1 receptor genotype: an important determinant of the damage response of melanocytes to ultraviolet radiation

(2010) Ana Luisa Kadekaro et al.   FASEB JOURNAL

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

(2010) A. McKenna et al.   GENOME RESEARCH

Fine-scale recombination rate differences between sexes, populations and individuals

(2010) Augustine Kong et al.   NATURE

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

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Common SNPs explain a large proportion of the heritability for human height

(2010) Jian Yang et al.   NATURE GENETICS

Variance component model to account for sample structure in genome-wide association studies

(2010) Hyun Min Kang et al.   NATURE GENETICS

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

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

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

(2010) Oliver Stegle et al.   PLoS Computational Biology

Web-Based, Participant-Driven Studies Yield Novel Genetic Associations for Common Traits

(2010) Nicholas Eriksson et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast model-based estimation of ancestry in unrelated individuals

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

AP-1 and KIF13A coordinate endosomal sorting and positioning during melanosome biogenesis

(2009) Cédric Delevoye et al.   JOURNAL OF CELL BIOLOGY

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

The Genetic Structure and History of Africans and African Americans

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

Evolution of the human pygmy phenotype

(2009) George H. Perry et al.   TRENDS IN ECOLOGY & EVOLUTION

Three Genome-wide Association Studies and a Linkage Analysis Identify HERC2 as a Human Iris Color Gene

(2008) Manfred Kayser et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Fast and flexible simulation of DNA sequence data

(2008) G. K. Chen et al.   GENOME RESEARCH

Blue eye color in humans may be caused by a perfectly associated founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression

(2008) Hans Eiberg et al.   HUMAN GENETICS

Natural selection has driven population differentiation in modern humans

(2008) Luis B Barreiro et al.   NATURE GENETICS

Arabidopsis DDB1-CUL4 ASSOCIATED FACTOR1 Forms a Nuclear E3 Ubiquitin Ligase with DDB1 and CUL4 That Is Involved in Multiple Plant Developmental Processes

(2008) Y. Zhang et al.   PLANT CELL

A Genome-Wide Association Study Identifies Novel Alleles Associated with Hair Color and Skin Pigmentation

(2008) Jiali Han et al.   PLoS Genetics