Published in Evolution on February 14, 2017
Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94
Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet (2012) 56.72
The hitch-hiking effect of a favourable gene. Genet Res (1974) 34.74
Global trends in emerging infectious diseases. Nature (2008) 23.66
VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res (2012) 15.90
Risk factors for human disease emergence. Philos Trans R Soc Lond B Biol Sci (2001) 13.64
Chemokine receptors as HIV-1 coreceptors: roles in viral entry, tropism, and disease. Annu Rev Immunol (1999) 13.55
Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak. PLoS Med (2006) 11.14
Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat Rev Genet (2003) 10.52
A single mutation in chikungunya virus affects vector specificity and epidemic potential. PLoS Pathog (2007) 10.38
The fate of competing beneficial mutations in an asexual population. Genetica (1998) 9.60
The HIV coreceptors CXCR4 and CCR5 are differentially expressed and regulated on human T lymphocytes. Proc Natl Acad Sci U S A (1997) 8.27
Host range and emerging and reemerging pathogens. Emerg Infect Dis (2005) 5.90
Invasions by insect vectors of human disease. Annu Rev Entomol (2002) 5.09
Diseases of humans and their domestic mammals: pathogen characteristics, host range and the risk of emergence. Philos Trans R Soc Lond B Biol Sci (2001) 4.68
Quantification of CD4, CCR5, and CXCR4 levels on lymphocyte subsets, dendritic cells, and differentially conditioned monocyte-derived macrophages. Proc Natl Acad Sci U S A (1999) 4.61
Spread of Aedes albopictus and decline of Ae. aegypti (Diptera: Culicidae) in Florida. J Med Entomol (1995) 4.46
The population genetics of adaptation: the adaptation of DNA sequences. Evolution (2002) 3.97
The distribution of fitness effects among beneficial mutations. Genetics (2003) 3.97
Beneficial mutation selection balance and the effect of linkage on positive selection. Genetics (2007) 3.75
Genetic drift in an infinite population. The pseudohitchhiking model. Genetics (2000) 3.43
Chikungunya virus adapts to tiger mosquito via evolutionary convergence: a sign of things to come? Virol J (2008) 3.39
Ecology of invasive mosquitoes: effects on resident species and on human health. Ecol Lett (2005) 3.38
An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus. Nat Genet (2005) 3.15
Genome-wide mutational diversity in an evolving population of Escherichia coli. Cold Spring Harb Symp Quant Biol (2009) 3.03
Mutational and fitness landscapes of an RNA virus revealed through population sequencing. Nature (2013) 2.68
The speed of adaptation in large asexual populations. Genetics (2004) 2.59
Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature (2013) 2.53
The contribution of epistasis to the architecture of fitness in an RNA virus. Proc Natl Acad Sci U S A (2004) 2.35
Viral population analysis and minority-variant detection using short read next-generation sequencing. Philos Trans R Soc Lond B Biol Sci (2013) 2.33
Structural constraints on RNA virus evolution. J Virol (1999) 2.24
Clonal interference in large populations. Proc Natl Acad Sci U S A (2007) 2.03
Profiles of adaptation in two similar viruses. Genetics (2001) 1.99
Beneficial fitness effects are not exponential for two viruses. J Mol Evol (2008) 1.94
Recombination between Sindbis virus RNAs. J Virol (1991) 1.90
The evolutionary genetics of adaptation: a simulation study. Genet Res (1999) 1.82
Genetic variation and the fate of beneficial mutations in asexual populations. Genetics (2011) 1.77
The HIV coreceptor switch: a population dynamical perspective. Trends Microbiol (2005) 1.76
Fitness epistasis and constraints on adaptation in a human immunodeficiency virus type 1 protein region. Genetics (2010) 1.61
Clonal interference is alleviated by high mutation rates in large populations. Mol Biol Evol (2007) 1.59
Evolutionary rescue from extinction is contingent on a lower rate of environmental change. Nature (2013) 1.53
Detecting ultralow-frequency mutations by Duplex Sequencing. Nat Protoc (2014) 1.53
Sex speeds adaptation by altering the dynamics of molecular evolution. Nature (2016) 1.45
Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations. Proc Natl Acad Sci U S A (2012) 1.43
Genesis of Sindbis virus by in vivo recombination of nonreplicative RNA precursors. J Virol (1995) 1.43
Quantitative evolutionary dynamics using high-resolution lineage tracking. Nature (2015) 1.41
Clonal interference in the evolution of influenza. Genetics (2012) 1.37
Mutations of intermediate effect are responsible for adaptation in evolving Pseudomonas fluorescens populations. Biol Lett (2006) 1.36
Sex and adaptation in a changing environment. Genetics (1999) 1.36
Emergent neutrality in adaptive asexual evolution. Genetics (2011) 1.32
Naïve and memory cell turnover as drivers of CCR5-to-CXCR4 tropism switch in human immunodeficiency virus type 1: implications for therapy. J Virol (2006) 1.31
Epistasis and the adaptability of an RNA virus. Genetics (2005) 1.31
The fitness effects of synonymous mutations in DNA and RNA viruses. Mol Biol Evol (2011) 1.27
Genomewide patterns of substitution in adaptively evolving populations of the RNA bacteriophage MS2. Genetics (2009) 1.27
Epistasis between beneficial mutations and the phenotype-to-fitness Map for a ssDNA virus. PLoS Genet (2011) 1.27
Adaptation of a quantitative trait to a moving optimum. Genetics (2007) 1.18
Variable epistatic effects between mutations at host recognition sites in phiX174 bacteriophage. Evolution (2007) 1.17
Adaptive walks toward a moving optimum. Genetics (2007) 1.15
Adaptation to different rates of environmental change in Chlamydomonas. Evolution (2009) 1.12
On the experimental evolution of specialization and diversity in heterogeneous environments. Ecol Lett (2007) 1.11
Experimental evolution and genome sequencing reveal variation in levels of clonal interference in large populations of bacteriophage phiX174. BMC Evol Biol (2008) 1.10
Tempo and mode of genome evolution in a 50,000-generation experiment. Nature (2016) 1.10
The genetic basis of phenotypic adaptation II: the distribution of adaptive substitutions in the moving optimum model. Genetics (2009) 1.09
The genetic basis of phenotypic adaptation I: fixation of beneficial mutations in the moving optimum model. Genetics (2009) 1.09
Group Selection and Contribution of Minority Variants during Virus Adaptation Determines Virus Fitness and Phenotype. PLoS Pathog (2015) 1.05
Chikungunya virus 3' untranslated region: adaptation to mosquitoes and a population bottleneck as major evolutionary forces. PLoS Pathog (2013) 1.04
Near-periodic substitution and the genetic variance induced by environmental change. J Theor Biol (2005) 1.03
Population genomics of intrapatient HIV-1 evolution. Elife (2015) 0.99
Evolutionary reconstruction of a hairpin deleted from the genome of an RNA virus. Proc Natl Acad Sci U S A (1996) 0.97
Strong epistatic interactions within a single protein. Mol Biol Evol (2014) 0.95
Rescue of the RNA phage genome from RNase III cleavage. Nucleic Acids Res (1997) 0.93
Nonhomologous RNA-RNA recombination events at the 3' nontranslated region of the Sindbis virus genome: hot spots and utilization of nonviral sequences. J Virol (1996) 0.92
Cell turnover and cell tropism in HIV-1 infection. Trends Microbiol (2002) 0.90
Rapid evolution of translational control mechanisms in RNA genomes. J Mol Biol (1997) 0.90
Environment determines epistatic patterns for a ssDNA virus. Genetics (2013) 0.83
Mutations of the HIV type 1 V3 loop under selection pressure with neutralizing monoclonal antibody NM-01. AIDS Res Hum Retroviruses (1997) 0.83
Environmental heterogeneity enhances clonal interference. Evolution (2008) 0.80
Rate of novel host invasion affects adaptability of evolving RNA virus lineages. Proc Biol Sci (2015) 0.78
Dynamics of Adaptation in Experimental Yeast Populations Exposed to Gradual and Abrupt Change in Heavy Metal Concentration. Am Nat (2016) 0.75
Evolution in spatially mixed host environments increases divergence for evolved fitness and intrapopulation genetic diversity in RNA viruses. Virus Evol (2016) 0.75