Inferring Genome-Wide Correlations of Mutation Fitness Effects between Populations

Dissecting dynamics and differences of selective pressures in the evolution of human pigmentation

(2021) Xin Huang et al.   Biology Open

From Drift to Draft: How Much Do Beneficial Mutations Actually Contribute to Predictions of Ohta's Slightly Deleterious Model of Molecular Evolution?

(2020) Jun Chen et al.   GENETICS

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Toward an Evolutionarily Appropriate Null Model: Jointly Inferring Demography and Purifying Selection

(2020) Parul Johri et al.   GENETICS

Greater strength of selection and higher proportion of beneficial amino acid changing mutations in humans compared with mice and Drosophila melanogaster

(2020) Ying Zhen et al.   GENOME RESEARCH

polyDFEv2.0: Testing for invariance of the distribution of fitness effects within and across species

(2019) Paula Tataru et al.   BIOINFORMATICS

Demographic History of the Human Commensal Drosophila melanogaster

(2019) J Roman Arguello et al.   Genome Biology and Evolution

Comparison of the Full Distribution of Fitness Effects of New Amino Acid Mutations Across Great Apes

(2019) David Castellano et al.   GENETICS

New Methods for Inferring the Distribution of Fitness Effects for INDELs and SNPs

(2018) Henry J Barton et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene expression drives the evolution of dominance

(2018) Christian D. Huber et al.   Nature Communications

The demographic history and mutational load of African hunter-gatherers and farmers

(2018) Marie Lopez et al.   Nature Ecology & Evolution

Evidence that RNA Viruses Drove Adaptive Introgression between Neanderthals and Modern Humans

(2018) David Enard et al.   CELL

SLiM 3: Forward Genetic Simulations Beyond the Wright–Fisher Model

(2018) Benjamin C Haller et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ensembl 2019

(2018) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

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

Population Genomics in Wild Tomatoes—The Interplay of Divergence and Admixture

(2017) Ian Beddows et al.   Genome Biology and Evolution

Genetic Diversity and the Efficacy of Purifying Selection across Plant and Animal Species

(2017) Jun Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Parental influence on human germline de novo mutations in 1,548 trios from Iceland

(2017) Hákon Jónsson et al.   NATURE

Determining the factors driving selective effects of new nonsynonymous mutations

(2017) Christian D. Huber 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

Triallelic Population Genomics for Inferring Correlated Fitness Effects of Same Site Nonsynonymous Mutations

(2016) Aaron P. Ragsdale et al.   GENETICS

DNA sequence diversity and the efficiency of natural selection in animal mitochondrial DNA

(2016) J James et al.   HEREDITY

A Thousand Fly Genomes: An ExpandedDrosophilaGenome Nexus

(2016) Justin B. Lack et al.   MOLECULAR BIOLOGY AND EVOLUTION

The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)

(2016) Jacqueline MacArthur et al.   NUCLEIC ACIDS RESEARCH

Triallelic Population Genomics for Inferring Correlated Fitness Effects of Same Site Nonsynonymous Mutations

(2016) Aaron P. Ragsdale et al.   GENETICS

The fitness effect of mutations across environments: Fisher's geometrical model with multiple optima

(2015) Guillaume Martin et al.   EVOLUTION

The Drosophila Genome Nexus: A Population Genomic Resource of 623 Drosophila melanogaster Genomes, Including 197 from a Single Ancestral Range Population

(2015) Justin B. Lack et al.   GENETICS

A probabilistic method for testing and estimating selection differences between populations

(2015) Yungang He et al.   GENOME RESEARCH

Computationally Efficient Composite Likelihood Statistics for Demographic Inference

(2015) Alec J. Coffman et al.   MOLECULAR BIOLOGY AND EVOLUTION

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

SIFT missense predictions for genomes

(2015) Robert Vaser et al.   Nature Protocols

Dominance of Deleterious Alleles Controls the Response to a Population Bottleneck

(2015) Daniel J. Balick et al.   PLoS Genetics

The Drosophila Genome Nexus: A Population Genomic Resource of 623 Drosophila melanogaster Genomes, Including 197 from a Single Ancestral Range Population

(2015) Justin B. Lack et al.   GENETICS

Determinants of Mutation Rate Variation in the Human Germline

(2014) Laure Ségurel et al.   Annual Review of Genomics and Human Genetics

Uncovering adaptive evolution in the human lineage

(2014) Magdalena Gayà-Vidal et al.   BMC GENOMICS

Robust Forward Simulations of Recurrent Hitchhiking

(2014) Lawrence H. Uricchio et al.   GENETICS

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

(2014) Joanna S. Amberger et al.   NUCLEIC ACIDS RESEARCH

SENSITIVITY OF THE DISTRIBUTION OF MUTATIONAL FITNESS EFFECTS TO ENVIRONMENT, GENETIC BACKGROUND, AND ADAPTEDNESS: A CASE STUDY WITHDROSOPHILA

(2013) Alethea D. Wang et al.   EVOLUTION

Estimation of the Spontaneous Mutation Rate per Nucleotide Site in a Drosophila melanogaster Full-Sib Family

(2013) Peter D. Keightley et al.   GENETICS

A Comparison of Models to Infer the Distribution of Fitness Effects of New Mutations

(2013) A. Kousathanas et al.   GENETICS

Background Selection 20 Years on

(2013) Brian Charlesworth   JOURNAL OF HEREDITY

Population Genomic Analysis Reveals a Rich Speciation and Demographic History of Orang-utans (Pongo pygmaeus and Pongo abelii)

(2013) Xin Ma et al.   PLoS One

What limits the evolutionary emergence of pathogens?

(2012) S. Gandon et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Demographic history and rare allele sharing among human populations

(2011) S. Gravel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

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

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

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

Selection, Epistasis, and Parent‐of‐Origin Effects on Deleterious Mutations across Environments in Drosophila melanogaster

(2009) Alethea D. Wang et al.   AMERICAN NATURALIST

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

ECOLOGICAL AND EVOLUTIONARY GENOMICS IN THE WILD TOMATOES (SOLANUM SECT. LYCOPERSICON)

(2008) Leonie C. Moyle   EVOLUTION

Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome

(2008) Adam R. Boyko et al.   PLoS Genetics