On the unfounded enthusiasm for soft selective sweeps II: Examining recent evidence from humans, flies, and viruses

The Neutral Theory in Light of Natural Selection

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

The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: insights into demographic inference and model choice

(2017) Lounès Chikhi et al.   HEREDITY

Multiple Modes of Positive Selection Shaping the Patterns of Incomplete Selective Sweeps over African Populations of Drosophila melanogaster

(2017) Ha My T. Vy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome

(2017) Daniel R. Schrider et al.   MOLECULAR BIOLOGY AND EVOLUTION

Discoal: flexible coalescent simulations with selection

(2016) Andrew D. Kern et al.   BIOINFORMATICS

S/HIC: Robust Identification of Soft and Hard Sweeps Using Machine Learning

(2016) Daniel R. Schrider et al.   PLoS Genetics

More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1

(2016) Alison F Feder et al.   eLife

Soft Shoulders Ahead: Spurious Signatures of Soft and Partial Selective Sweeps Result from Linked Hard Sweeps

(2015) D. R. Schrider et al.   GENETICS

On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for ancestral population size inference?

(2015) O Mazet et al.   HEREDITY

Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps

(2015) Nandita R. Garud et al.   PLoS Genetics

The Utility of Fisher's Geometric Model in Evolutionary Genetics

(2014) O. Tenaillon   Annual Review of Ecology Evolution and Systematics

A Bayesian MCMC Approach to Assess the Complete Distribution of Fitness Effects of New Mutations: Uncovering the Potential for Adaptive Walks in Challenging Environments

(2014) C. Bank et al.   GENETICS

On the unfounded enthusiasm for soft selective sweeps

(2014) Jeffrey D Jensen   Nature Communications

Influenza Virus Drug Resistance: A Time-Sampled Population Genetics Perspective

(2014) Matthieu Foll et al.   PLoS Genetics

The impact of equilibrium assumptions on tests of selection

(2013) Jessica L. Crisci et al.   Frontiers in Genetics

Demographic Inference Reveals African and European Admixture in the North American Drosophila melanogaster Population

(2012) P. Duchen et al.   GENETICS

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

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

Classic Selective Sweeps Were Rare in Recent Human Evolution

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

MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus

(2010) Gregory Ewing et al.   BIOINFORMATICS

Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing

(2010) Will Fischer et al.   PLoS One

Recombination Rate and Selection Strength in HIV Intra-patient Evolution

(2010) Richard A. Neher et al.   PLoS Computational Biology

Drug Resistance Mutations for Surveillance of Transmitted HIV-1 Drug-Resistance: 2009 Update

(2009) Diane E. Bennett et al.   PLoS One

A General Extreme Value Theory Model for the Adaptation of DNA Sequences Under Strong Selection and Weak Mutation

(2008) Paul Joyce et al.   GENETICS

Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection

(2008) B. F. Keele et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA