Published in Evolution on March 01, 2007
Adaptive laboratory evolution -- principles and applications for biotechnology. Microb Cell Fact (2013) 1.29
Evolution of mutational robustness in the yeast genome: a link to essential genes and meiotic recombination hotspots. PLoS Genet (2009) 1.11
Competition between high- and higher-mutating strains of Escherichia coli. Biol Lett (2011) 1.04
Experiments on the role of deleterious mutations as stepping stones in adaptive evolution. Proc Natl Acad Sci U S A (2013) 1.03
A population-based experimental model for protein evolution: effects of mutation rate and selection stringency on evolutionary outcomes. Biochemistry (2013) 0.97
The effect of genetic robustness on evolvability in digital organisms. BMC Evol Biol (2008) 0.94
Thermal adaptation of viruses and bacteria. Biophys J (2010) 0.94
Loss of genetic redundancy in reductive genome evolution. PLoS Comput Biol (2011) 0.94
HIV-2 genetic evolution in patients with advanced disease is faster than that in matched HIV-1 patients. J Virol (2010) 0.93
Costs and benefits of mutational robustness in RNA viruses. Cell Rep (2014) 0.86
Impacts of mutation effects and population size on mutation rate in asexual populations: a simulation study. BMC Evol Biol (2010) 0.85
Inferring positive selection in humans from genomic data. Investig Genet (2015) 0.83
Different Evolutionary Paths to Complexity for Small and Large Populations of Digital Organisms. PLoS Comput Biol (2016) 0.83
Evolution of functional diversification within quasispecies. Genome Biol Evol (2014) 0.79
Quasi-species evolution in subdivided populations favours maximally deleterious mutations. Proc Biol Sci (2007) 0.77
Environmental noise, genetic diversity and the evolution of evolvability and robustness in model gene networks. PLoS One (2012) 0.77
The effects of low-impact mutations in digital organisms. Theor Biol Med Model (2011) 0.75
Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature (2009) 11.36
Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat Rev Genet (2003) 10.52
Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell (2008) 6.91
Why highly expressed proteins evolve slowly. Proc Natl Acad Sci U S A (2005) 6.19
Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc Natl Acad Sci U S A (2008) 5.29
A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol (2005) 4.85
The evolutionary origin of complex features. Nature (2003) 4.81
Parallel changes in gene expression after 20,000 generations of evolution in Escherichiacoli. Proc Natl Acad Sci U S A (2003) 4.63
Negative epistasis between beneficial mutations in an evolving bacterial population. Science (2011) 4.47
Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature (2012) 4.35
Perspective: Evolution and detection of genetic robustness. Evolution (2003) 4.10
Tests of parallel molecular evolution in a long-term experiment with Escherichia coli. Proc Natl Acad Sci U S A (2006) 3.39
Thermodynamic prediction of protein neutrality. Proc Natl Acad Sci U S A (2005) 3.30
The evolutionary consequences of erroneous protein synthesis. Nat Rev Genet (2009) 3.11
Genome sequences of Escherichia coli B strains REL606 and BL21(DE3). J Mol Biol (2009) 3.10
Second-order selection for evolvability in a large Escherichia coli population. Science (2011) 3.02
Experimental evolution. Trends Ecol Evol (2012) 3.02
Repeatability and contingency in the evolution of a key innovation in phage lambda. Science (2012) 2.95
Does evolutionary theory need a rethink? Nature (2014) 2.82
The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss. MBio (2012) 2.58
A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes. PLoS Comput Biol (2010) 2.57
Cryptic population dynamics: rapid evolution masks trophic interactions. PLoS Biol (2007) 2.44
Long-term experimental evolution in Escherichia coli. XII. DNA topology as a key target of selection. Genetics (2004) 2.10
Long-term dynamics of adaptation in asexual populations. Science (2013) 2.09
The traveling-wave approach to asexual evolution: Muller's ratchet and speed of adaptation. Theor Popul Biol (2007) 2.07
Genome dynamics during experimental evolution. Nat Rev Genet (2013) 2.07
Evolution of global regulatory networks during a long-term experiment with Escherichia coli. Bioessays (2007) 2.03
Quasispecies theory in the context of population genetics. BMC Evol Biol (2005) 2.02
Parallel changes in global protein profiles during long-term experimental evolution in Escherichia coli. Genetics (2006) 2.00
Experimental tests for an evolutionary trade-off between growth rate and yield in E. coli. Am Nat (2006) 1.99
Translationally optimal codons associate with structurally sensitive sites in proteins. Mol Biol Evol (2009) 1.96
T cell dynamics and the response to HAART in a cohort of HIV-1-infected elite suppressors. Clin Infect Dis (2009) 1.94
Analysis of human immunodeficiency virus type 1 viremia and provirus in resting CD4+ T cells reveals a novel source of residual viremia in patients on antiretroviral therapy. J Virol (2009) 1.89
Adaptive radiation from resource competition in digital organisms. Science (2004) 1.86
Thermodynamics of neutral protein evolution. Genetics (2006) 1.83
Dynamics of insertion sequence elements during experimental evolution of bacteria. Res Microbiol (2004) 1.83
Limits on replenishment of the resting CD4+ T cell reservoir for HIV in patients on HAART. PLoS Pathog (2007) 1.81
Structural determinants of the rate of protein evolution in yeast. Mol Biol Evol (2006) 1.75
Decay dynamics of HIV-1 depend on the inhibited stages of the viral life cycle. Proc Natl Acad Sci U S A (2008) 1.72
Long-term experimental evolution in Escherichia coli. XI. Rejection of non-transitive interactions as cause of declining rate of adaptation. BMC Evol Biol (2002) 1.71
Balancing robustness and evolvability. PLoS Biol (2006) 1.64
An experimental test of evolutionary trade-offs during temperature adaptation. Proc Natl Acad Sci U S A (2007) 1.62
Avida: a software platform for research in computational evolutionary biology. Artif Life (2004) 1.62
Natural selection fails to optimize mutation rates for long-term adaptation on rugged fitness landscapes. PLoS Comput Biol (2008) 1.58
Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load. Proc Natl Acad Sci U S A (2012) 1.56
Sexual reproduction reshapes the genetic architecture of digital organisms. Proc Biol Sci (2006) 1.55
Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli. G3 (Bethesda) (2011) 1.53
Pervasive joint influence of epistasis and plasticity on mutational effects in Escherichia coli. Nat Genet (2004) 1.49
Death and cannibalism in a seasonal environment facilitate bacterial coexistence. Ecol Lett (2008) 1.46
Understanding the differences between genome sequences of Escherichia coli B strains REL606 and BL21(DE3) and comparison of the E. coli B and K-12 genomes. J Mol Biol (2009) 1.46
Escherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects. Mol Biol Evol (2010) 1.41
On the conservative nature of intragenic recombination. Proc Natl Acad Sci U S A (2005) 1.37
Density-dependent selection in vesicular stomatitis virus. J Virol (2004) 1.37
Long-term experimental evolution in Escherichia coli. XIII. Phylogenetic history of a balanced polymorphism. J Mol Evol (2005) 1.37
Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding. BMC Evol Biol (2003) 1.34
Co-infection weakens selection against epistatic mutations in RNA viruses. Genetics (2004) 1.31
Analysis of epistatic interactions and fitness landscapes using a new geometric approach. BMC Evol Biol (2007) 1.30
The stochastic edge in adaptive evolution. Genetics (2008) 1.30
Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populations. BMC Evol Biol (2010) 1.30
The look-ahead effect of phenotypic mutations. Biol Direct (2008) 1.28
Pleiotropic effects of beneficial mutations in Escherichia coli. Evolution (2005) 1.28
Tracing ancestors and relatives of Escherichia coli B, and the derivation of B strains REL606 and BL21(DE3). J Mol Biol (2009) 1.26
The relationship between relative solvent accessibility and evolutionary rate in protein evolution. Genetics (2011) 1.25
Expression profiles reveal parallel evolution of epistatic interactions involving the CRP regulon in Escherichia coli. PLoS Genet (2008) 1.23
Evolutionary changes in heat-inducible gene expression in lines of Escherichia coli adapted to high temperature. Physiol Genomics (2003) 1.23
Stability and the evolvability of function in a model protein. Biophys J (2004) 1.21
Maximum allowed solvent accessibilites of residues in proteins. PLoS One (2013) 1.18
New experimental and theoretical approaches towards the understanding of the emergence of viral infections. Introduction. Philos Trans R Soc Lond B Biol Sci (2010) 1.18
Low-level HIV-1 replication and the dynamics of the resting CD4+ T cell reservoir for HIV-1 in the setting of HAART. BMC Infect Dis (2008) 1.15
Integrating sequence variation and protein structure to identify sites under selection. Mol Biol Evol (2012) 1.15
Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli. MBio (2014) 1.14
The genetic basis of parallel and divergent phenotypic responses in evolving populations of Escherichia coli. Proc Biol Sci (2008) 1.12
Contact density affects protein evolutionary rate from bacteria to animals. J Mol Evol (2008) 1.10
Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli. Science (2014) 1.10
Tempo and mode of genome evolution in a 50,000-generation experiment. Nature (2016) 1.10
Identification and dynamics of a beneficial mutation in a long-term evolution experiment with Escherichia coli. BMC Evol Biol (2009) 1.08
Contact heterogeneity and phylodynamics: how contact networks shape parasite evolutionary trees. Interdiscip Perspect Infect Dis (2010) 1.07
Ecological and evolutionary dynamics of coexisting lineages during a long-term experiment with Escherichia coli. Proc Natl Acad Sci U S A (2012) 1.07
Task-switching costs promote the evolution of division of labor and shifts in individuality. Proc Natl Acad Sci U S A (2012) 1.07
Lethal mutagenesis of bacteria. Genetics (2008) 1.05
Ecological specialization and adaptive decay in digital organisms. Am Nat (2006) 1.04
The phenotype-fitness map in experimental evolution of phages. PLoS One (2011) 1.03
Experiments on the role of deleterious mutations as stepping stones in adaptive evolution. Proc Natl Acad Sci U S A (2013) 1.03
Modeling coding-sequence evolution within the context of residue solvent accessibility. BMC Evol Biol (2012) 1.02
Constraints on the dominant mechanism for HIV viral dynamics in patients on raltegravir. Antivir Ther (2009) 1.02
Selective pressures for accurate altruism targeting: evidence from digital evolution for difficult-to-test aspects of inclusive fitness theory. Proc Biol Sci (2010) 1.00
Detecting positive and purifying selection at synonymous sites in yeast and worm. Mol Biol Evol (2010) 1.00
Selection for mutational robustness in finite populations. J Theor Biol (2006) 0.99
Parasites and mutational load: an experimental test of a pluralistic theory for the evolution of sex. Proc Biol Sci (2005) 0.98
Rescue of social motility lost during evolution of Myxococcus xanthus in an asocial environment. J Bacteriol (2002) 0.98
Breaking proteins with mutations: threads and thresholds in evolution. Mol Syst Biol (2007) 0.98
Parallel genetic and phenotypic evolution of DNA superhelicity in experimental populations of Escherichia coli. Mol Biol Evol (2010) 0.98