Published in Artif Life on January 01, 2004
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A comparison of the effects of random and selective mass extinctions on erosion of evolutionary history in communities of digital organisms. PLoS One (2012) 0.80
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Evolution of resistance to quorum quenching in digital organisms. Artif Life (2012) 0.78
The effect of natural selection on the performance of maximum parsimony. BMC Evol Biol (2007) 0.77
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Genetically integrated traits and rugged adaptive landscapes in digital organisms. BMC Evol Biol (2015) 0.75
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Artificial evolution by viability rather than competition. PLoS One (2014) 0.75
Beware batch culture: Seasonality and niche construction predicted to favor bacterial adaptive diversification. PLoS Comput Biol (2017) 0.75
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Non-adaptive origins of evolutionary innovations increase network complexity in interacting digital organisms. Philos Trans R Soc Lond B Biol Sci (2017) 0.75
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
A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol (2005) 4.85
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
A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes. PLoS Comput Biol (2010) 2.57
The traveling-wave approach to asexual evolution: Muller's ratchet and speed of adaptation. Theor Popul Biol (2007) 2.07
Quasispecies theory in the context of population genetics. BMC Evol Biol (2005) 2.02
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
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
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
Co-infection weakens selection against epistatic mutations in RNA viruses. Genetics (2004) 1.31
The stochastic edge in adaptive evolution. Genetics (2008) 1.30
The look-ahead effect of phenotypic mutations. Biol Direct (2008) 1.28
The relationship between relative solvent accessibility and evolutionary rate in protein evolution. Genetics (2011) 1.25
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
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
Contact density affects protein evolutionary rate from bacteria to animals. J Mol Evol (2008) 1.10
Contact heterogeneity and phylodynamics: how contact networks shape parasite evolutionary trees. Interdiscip Perspect Infect Dis (2010) 1.07
Lethal mutagenesis of bacteria. Genetics (2008) 1.05
The phenotype-fitness map in experimental evolution of phages. PLoS One (2011) 1.03
Effects of population size and mutation rate on the evolution of mutational robustness. Evolution (2007) 1.03
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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
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
Breaking proteins with mutations: threads and thresholds in evolution. Mol Syst Biol (2007) 0.98
Sinonasal anatomic variants and asthma are associated with faster development of chronic rhinosinusitis in patients with allergic rhinitis. Int Forum Allergy Rhinol (2013) 0.97
Translationally optimal codons associate with aggregation-prone sites in proteins. Proteomics (2010) 0.96
Reduced mRNA secondary-structure stability near the start codon indicates functional genes in prokaryotes. Genome Biol Evol (2011) 0.95
Cross-species comparison of site-specific evolutionary-rate variation in influenza haemagglutinin. Philos Trans R Soc Lond B Biol Sci (2013) 0.95
Predicting evolutionary site variability from structure in viral proteins: buriedness, packing, flexibility, and design. J Mol Evol (2014) 0.95
Reduced stability of mRNA secondary structure near the translation-initiation site in dsDNA viruses. BMC Evol Biol (2011) 0.94
PeptideBuilder: A simple Python library to generate model peptides. PeerJ (2013) 0.93
Rapid adaptive amplification of preexisting variation in an RNA virus. J Virol (2008) 0.93
Risk factors for development of chronic rhinosinusitis in patients with allergic rhinitis. Int Forum Allergy Rhinol (2012) 0.92
Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites. Phys Biol (2015) 0.92
Short communication: dynamic constraints on the second phase compartment of HIV-infected cells. AIDS Res Hum Retroviruses (2011) 0.90
Incongruent fitness landscapes, not tradeoffs, dominate the adaptation of vesicular stomatitis virus to novel host types. J Gen Virol (2010) 0.90
Methods of modelling viral disease dynamics across the within- and between-host scales: the impact of virus dose on host population immunity. Philos Trans R Soc Lond B Biol Sci (2010) 0.86
Membrane environment imposes unique selection pressures on transmembrane domains of G protein-coupled receptors. J Mol Evol (2013) 0.85
Detecting clusters of mutations. PLoS One (2008) 0.84
Principal-oscillation-pattern analysis of gene expression. PLoS One (2012) 0.84
Eigen-genomic system dynamic-pattern analysis (ESDA): modeling mRNA degradation and self-regulation. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.83
Does mutational robustness inhibit extinction by lethal mutagenesis in viral populations? PLoS Comput Biol (2010) 0.83
Socioeconomic disparities in the presentation of acute bacterial sinusitis complications in children. Laryngoscope (2013) 0.82
Amino-acid site variability among natural and designed proteins. PeerJ (2013) 0.82
Lethal mutagenesis in a structured environment. J Theor Biol (2009) 0.82
Specific and nonspecific host adaptation during arboviral experimental evolution. J Mol Microbiol Biotechnol (2012) 0.81
Genomic evolution of vesicular stomatitis virus strains with differences in adaptability. J Virol (2010) 0.81
RNaseIII and T4 polynucleotide Kinase sequence biases and solutions during RNA-seq library construction. Biol Direct (2013) 0.80
Temporal and spatial alterations in mutant swarm size of St. Louis encephalitis virus in mosquito hosts. Infect Genet Evol (2011) 0.78
Evolution of resource competition between mutually dependent digital organisms. Artif Life (2004) 0.78
A linear relationship between fitness and the logarithm of the critical bottleneck size in vesicular stomatitis virus populations. J Virol (2008) 0.77
Kinetics of the viral cycle influence pharmacodynamics of antiretroviral therapy. Biol Direct (2011) 0.77
Congruent evolution of fitness and genetic robustness in vesicular stomatitis virus. J Virol (2013) 0.77
Tradeoff between short-term and long-term adaptation in a changing environment. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 0.77
Digital evolution in time-dependent fitness landscapes. Artif Life (2004) 0.76
Interactions between evolutionary processes at high mutation rates. Evolution (2012) 0.76
Frequency-Dependent Selection in a Periodic Environment. Physica A (2007) 0.76
Long-term control of viral replication in a Group O, human immunodeficiency virus type 1-infected individual. AIDS Res Hum Retroviruses (2014) 0.76
The role of environmental factors on the evolution of phenotypic diversity in vesicular stomatitis virus populations. J Gen Virol (2012) 0.75
Supplementary materials need the right format. Nature (2004) 0.75