Selection and Adaptation in the Human Genome

Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant

(2013) Yana G. Kamberov et al.   CELL

Identifying Recent Adaptations in Large-Scale Genomic Data

(2013) Sharon R. Grossman et al.   CELL

On the Immortality of Television Sets: "Function" in the Human Genome According to the Evolution-Free Gospel of ENCODE

(2013) D. Graur et al.   Genome Biology and Evolution

Is junk DNA bunk? A critique of ENCODE

(2013) W. F. Doolittle   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Divergent Whole-Genome Methylation Maps of Human and Chimpanzee Brains Reveal Epigenetic Basis of Human Regulatory Evolution

(2012) Jia Zeng et al.   AMERICAN JOURNAL OF HUMAN 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

Human Genetic Individuality

(2012) Maynard V. Olson   Annual Review of Genomics and Human Genetics

Can ENCODE tell us how much junk DNA we carry in our genome?

(2012) Deng-Ke Niu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

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

(2012) Joseph Lachance et al.   CELL

The C-value paradox, junk DNA and ENCODE

(2012) Sean R. Eddy   CURRENT BIOLOGY

Selective Sweeps in Multilocus Models of Quantitative Traits

(2012) P. Pavlidis et al.   GENETICS

Limited Evidence for Classic Selective Sweeps in African Populations

(2012) J. M. Granka et al.   GENETICS

Personal and population genomics of human regulatory variation

(2012) B. Vernot et al.   GENOME RESEARCH

Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

(2012) Wenqing Fu et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

(2012)   NATURE

Evidence of widespread selection on standing variation in Europe at height-associated SNPs

(2012) Michael C Turchin et al.   NATURE GENETICS

A Fine-Scale Chimpanzee Genetic Map from Population Sequencing

(2012) A. Auton et al.   SCIENCE

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

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

An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People

(2012) M. R. Nelson et al.   SCIENCE

Recent Explosive Human Population Growth Has Resulted in an Excess of Rare Genetic Variants

(2012) A. Keinan et al.   SCIENCE

Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions

(2012) L. D. Ward et al.   SCIENCE

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection

(2012) Yoichiro Shibata et al.   PLoS Genetics

What fraction of the human genome is functional?

(2011) C. P. Ponting et al.   GENOME RESEARCH

Comparative and demographic analysis of orang-utan genomes

(2011) Devin P. Locke et al.   NATURE

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

(2011) Kerstin Lindblad-Toh et al.   NATURE

Mapping copy number variation by population-scale genome sequencing

(2011) Ryan E. Mills et al.   NATURE

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 Golden Age of Human Population Genetics

(2011) M. Przeworski   SCIENCE

Classic Selective Sweeps Were Rare in Recent Human Evolution

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

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

(2011) L. Abi-Rached et al.   SCIENCE

A Genome-Wide Study of DNA Methylation Patterns and Gene Expression Levels in Multiple Human and Chimpanzee Tissues

(2011) Athma A. Pai et al.   PLoS Genetics

Parallel Adaptive Divergence among Geographically Diverse Human Populations

(2011) Jacob A. Tennessen et al.   PLoS Genetics

MicroRNA Expression and Regulation in Human, Chimpanzee, and Macaque Brains

(2011) Hai Yang Hu et al.   PLoS Genetics

Adaptations to Climate-Mediated Selective Pressures in Humans

(2011) Angela M. Hancock et al.   PLoS Genetics

The promise and limitations of population exomics for human evolution studies

(2011) Jacob A Tennessen et al.   GENOME BIOLOGY

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

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

Using Environmental Correlations to Identify Loci Underlying Local Adaptation

(2010) G. Coop et al.   GENETICS

Massive turnover of functional sequence in human and other mammalian genomes

(2010) S. Meader et al.   GENOME RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

A Genome-Wide Search for Signals of High-Altitude Adaptation in Tibetans

(2010) S. Xu et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Adaptation – not by sweeps alone

(2010) Jonathan K. Pritchard et al.   NATURE REVIEWS GENETICS

Genetic hitchhiking versus background selection: the controversy and its implications

(2010) W. Stephan   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Adaptations to new environments in humans: the role of subtle allele frequency shifts

(2010) A. M. Hancock et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Rate, molecular spectrum, and consequences of human mutation

(2010) M. Lynch   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequency

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

Natural selection on EPAS1 (HIF2 ) associated with low hemoglobin concentration in Tibetan highlanders

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

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski 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

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes

(2009) Laurent Duret et al.   Annual Review of Genomics and Human Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Sex-specific and lineage-specific alternative splicing in primates

(2009) R. Blekhman et al.   GENOME RESEARCH

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

(2009) J. M. Akey   GENOME RESEARCH

Detecting Ancient Admixture and Estimating Demographic Parameters in Multiple Human Populations

(2009) Jeffrey D. Wall et al.   MOLECULAR BIOLOGY AND EVOLUTION

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Origins and functional impact of copy number variation in the human genome

(2009) Donald F. Conrad et al.   NATURE

Understanding and using quantitative genetic variation

(2009) W. G. Hill   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain

(2009) Katja Nowick 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

Local DNA Topography Correlates with Functional Noncoding Regions of the Human Genome

(2009) S. C. J. Parker et al.   SCIENCE

Widespread Genomic Signatures of Natural Selection in Hominid Evolution

(2009) Graham McVicker et al.   PLoS Genetics

The Role of Geography in Human Adaptation

(2009) Graham Coop et al.   PLoS Genetics

Adaptive Evolution of UGT2B17 Copy-Number Variation

(2008) Yali Xue et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Positive Selection in the Human Genome: From Genome Scans to Biological Significance

(2008) Joanna L. Kelley et al.   Annual Review of Genomics and Human Genetics

Selective Sweep at a Quantitative Trait Locus in the Presence of Background Genetic Variation

(2008) Luis-Miguel Chevin et al.   GENETICS

Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals

(2008) I. Hellmann et al.   GENOME RESEARCH

Copy number variation and evolution in humans and chimpanzees

(2008) G. H. Perry et al.   GENOME RESEARCH

Rapidly evolving human promoter regions

(2008) Martin S Taylor et al.   NATURE GENETICS

Patterns of Positive Selection in Six Mammalian Genomes

(2008) Carolin Kosiol et al.   PLoS Genetics