Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences

The Neutral Theory in Light of Natural Selection

(2018) Andrew D Kern et al.   MOLECULAR BIOLOGY AND EVOLUTION

Population genomic analysis of elongated skulls reveals extensive female-biased immigration in Early Medieval Bavaria

(2018) Krishna R. Veeramah et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inference of Distribution of Fitness Effects and Proportion of Adaptive Substitutions from Polymorphism Data

(2017) Paula Tataru et al.   GENETICS

Inference of the Distribution of Selection Coefficients for New Nonsynonymous Mutations Using Large Samples

(2017) Bernard Y. Kim et al.   GENETICS

Accuracy of Demographic Inferences from the Site Frequency Spectrum: The Case of the Yoruba Population

(2017) Marguerite Lapierre et al.   GENETICS

An Upper Limit on the Functional Fraction of the Human Genome

(2017) Dan Graur   Genome Biology and Evolution

Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow

(2017) M. Ravinet et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Deleterious variants in Asian rice and the potential cost of domestication

(2017) Qingpo Liu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Characterization of noncoding regulatory DNA in the human genome

(2017) Ran Elkon et al.   NATURE BIOTECHNOLOGY

Inference of Distribution of Fitness Effects and Proportion of Adaptive Substitutions from Polymorphism Data

(2017) Paula Tataru et al.   GENETICS

Inference of the Distribution of Selection Coefficients for New Nonsynonymous Mutations Using Large Samples

(2017) Bernard Y. Kim et al.   GENETICS

Accuracy of Demographic Inferences from the Site Frequency Spectrum: The Case of the Yoruba Population

(2017) Marguerite Lapierre et al.   GENETICS

A survey of methods and tools to detect recent and strong positive selection

(2017) Pavlos Pavlidis et al.   Journal of Biological Research-Thessaloniki

Empirical Bayes Estimation of Coalescence Times from Nucleotide Sequence Data

(2016) Leandra King et al.   GENETICS

SLiM 2: Flexible, Interactive Forward Genetic Simulations

(2016) Benjamin C. Haller et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2016) Swapan Mallick et al.   NATURE

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

A Genomic Map of the Effects of Linked Selection in Drosophila

(2016) Eyal Elyashiv et al.   PLoS Genetics

Empirical Bayes Estimation of Coalescence Times from Nucleotide Sequence Data

(2016) Leandra King et al.   GENETICS

Quantification of GC-biased gene conversion in the human genome

(2015) Sylvain Glémin et al.   GENOME RESEARCH

Inference of Gorilla Demographic and Selective History from Whole-Genome Sequence Data

(2015) Kimberly F. McManus et al.   MOLECULAR BIOLOGY AND EVOLUTION

The consequences of not accounting for background selection in demographic inference

(2015) Gregory B. Ewing et al.   MOLECULAR ECOLOGY

Detecting recent selective sweeps while controlling for mutation rate and background selection

(2015) Christian D. Huber et al.   MOLECULAR ECOLOGY

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Genome-wide patterns and properties of de novo mutations in humans

(2015) Laurent C Francioli et al.   NATURE GENETICS

The UCSC Genome Browser database: 2016 update

(2015) Matthew L. Speir et al.   NUCLEIC ACIDS RESEARCH

Crossovers are associated with mutation and biased gene conversion at recombination hotspots

(2015) Barbara Arbeithuber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global diversity, population stratification, and selection of human copy-number variation

(2015) Peter H. Sudmant et al.   SCIENCE

Natural Selection Constrains Neutral Diversity across A Wide Range of Species

(2015) Russell B. Corbett-Detig et al.   PLOS BIOLOGY

Biased Gene Conversion Skews Allele Frequencies in Human Populations, Increasing the Disease Burden of Recessive Alleles

(2014) Joseph Lachance et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

Defining functional DNA elements in the human genome

(2014) M. Kellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Background Selection as Baseline for Nucleotide Variation across the Drosophila Genome

(2014) Josep M. Comeron   PLoS Genetics

8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage

(2014) Chris M. Rands et al.   PLoS Genetics

Estimating Variable Effective Population Sizes from Multiple Genomes: A Sequentially Markov Conditional Sampling Distribution Approach

(2013) S. Sheehan et al.   GENETICS

Distortions in Genealogies due to Purifying Selection and Recombination

(2013) L. E. Nicolaisen et al.   GENETICS

The influence of genomic context on mutation patterns in the human genome inferred from rare variants

(2013) V. M. Schaibley et al.   GENOME RESEARCH

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

Visualizing genomic information across chromosomes with PhenoGram

(2013) Daniel Wolfe et al.   BioData Mining

Differential Relationship of DNA Replication Timing to Different Forms of Human Mutation and Variation

(2012) Amnon Koren et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genomic evidence for elevated mutation rates in highly expressed genes

(2012) Chungoo Park et al.   EMBO REPORTS

The Effects of Deleterious Mutations on Evolution at Linked Sites

(2012) Brian Charlesworth   GENETICS

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

The Joint Effects of Background Selection and Genetic Recombination on Local Gene Genealogies

(2011) Kai Zeng et al.   GENETICS

Ongoing GC-Biased Evolution Is Widespread in the Human Genome and Enriched Near Recombination Hot Spots

(2011) Sol Katzman et al.   Genome Biology and Evolution

Bayesian inference of ancient human demography from individual genome sequences

(2011) Ilan Gronau et al.   NATURE GENETICS

Recombination rates in admixed individuals identified by ancestry-based inference

(2011) Daniel Wegmann et al.   NATURE GENETICS

Classic Selective Sweeps Were Rare in Recent Human Evolution

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

Natural Selection Affects Multiple Aspects of Genetic Variation at Putatively Neutral Sites across the Human Genome

(2011) Kirk E. Lohmueller et al.   PLoS Genetics

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

(2010) Augustine Kong et al.   NATURE

Genetic hitchhiking versus background selection: the controversy and its implications

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

What can we learn about the distribution of fitness effects of new mutations from DNA sequence data?

(2010) P. D. Keightley et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Detecting positive selection within genomes: the problem of biased gene conversion

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

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Human mutation rate associated with DNA replication timing

(2009) John A Stamatoyannopoulos et al.   NATURE GENETICS

Widespread Genomic Signatures of Natural Selection in Hominid Evolution

(2009) Graham McVicker et al.   PLoS Genetics

Pervasive Hitchhiking at Coding and Regulatory Sites in Humans

(2009) James J. Cai et al.   PLoS Genetics