Published in Evolution on June 01, 2004
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
Distinct viral populations differentiate and evolve independently in a single perennial host plant. J Virol (2006) 1.28
Deep molecular characterization of HIV-1 dynamics under suppressive HAART. PLoS Pathog (2011) 1.21
Arenavirus variations due to host-specific adaptation. Viruses (2013) 0.99
Evolution of hepatitis delta virus RNA genome following long-term replication in cell culture. J Virol (2005) 0.92
Single genome analysis reveals genetic characteristics of Neuroadaptation across HIV-1 envelope. Retrovirology (2014) 0.84
Quasispecies spatial models for RNA viruses with different replication modes and infection strategies. PLoS One (2011) 0.83
A machine learning approach for identifying amino acid signatures in the HIV env gene predictive of dementia. PLoS One (2012) 0.82
Genetic variation in vitro and in vivo of an attenuated Lassa vaccine candidate. J Virol (2013) 0.76
Analysis of Dominant HIV Quasispecies Suggests Independent Viral Evolution Within Spinal Granulomas Coinfected with Mycobacterium tuberculosis and HIV-1 Subtype C. AIDS Res Hum Retroviruses (2015) 0.75
Reductive genome evolution in Buchnera aphidicola. Proc Natl Acad Sci U S A (2003) 4.88
The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus. Proc Natl Acad Sci U S A (2004) 4.77
Determination of the core of a minimal bacterial gene set. Microbiol Mol Biol Rev (2004) 4.14
Perspective: Evolution and detection of genetic robustness. Evolution (2003) 4.10
A small microbial genome: the end of a long symbiotic relationship? Science (2006) 3.81
The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes. Proc Natl Acad Sci U S A (2003) 3.81
High diversity of the viral community from an Antarctic lake. Science (2009) 2.57
The contribution of epistasis to the architecture of fitness in an RNA virus. Proc Natl Acad Sci U S A (2004) 2.35
Endosymbiotic bacteria: groEL buffers against deleterious mutations. Nature (2002) 2.21
Metatranscriptomic approach to analyze the functional human gut microbiota. PLoS One (2011) 2.14
Gut microbiota disturbance during antibiotic therapy: a multi-omic approach. Gut (2012) 2.10
Legionella pneumophila pangenome reveals strain-specific virulence factors. BMC Genomics (2010) 1.98
The evolution of sex: empirical insights into the roles of epistasis and drift. Nat Rev Genet (2007) 1.93
Extreme genome reduction in Buchnera spp.: toward the minimal genome needed for symbiotic life. Proc Natl Acad Sci U S A (2002) 1.93
Distribution of fitness and virulence effects caused by single-nucleotide substitutions in Tobacco Etch virus. J Virol (2007) 1.90
Distributions of epistasis in microbes fit predictions from a fitness landscape model. Nat Genet (2007) 1.90
Genome rearrangement distances and gene order phylogeny in gamma-Proteobacteria. Mol Biol Evol (2005) 1.88
Epistasis correlates to genomic complexity. Proc Natl Acad Sci U S A (2006) 1.81
Microbiome diversity in the bronchial tracts of patients with chronic obstructive pulmonary disease. J Clin Microbiol (2012) 1.61
Natural selection fails to optimize mutation rates for long-term adaptation on rugged fitness landscapes. PLoS Comput Biol (2008) 1.58
Effect of ribavirin on the mutation rate and spectrum of hepatitis C virus in vivo. J Virol (2009) 1.58
Selection for robustness in mutagenized RNA viruses. PLoS Genet (2007) 1.58
Environmental distribution of prokaryotic taxa. BMC Microbiol (2010) 1.54
The causes of epistasis. Proc Biol Sci (2011) 1.50
Extremely high mutation rate of a hammerhead viroid. Science (2009) 1.50
Is the quasispecies concept relevant to RNA viruses? J Virol (2002) 1.48
Coexistence of Wolbachia with Buchnera aphidicola and a secondary symbiont in the aphid Cinara cedri. J Bacteriol (2004) 1.45
Molecular basis of adaptive convergence in experimental populations of RNA viruses. Genetics (2002) 1.41
Evaluating the fidelity of de novo short read metagenomic assembly using simulated data. PLoS One (2011) 1.39
Genomic analysis of the emergence and evolution of multidrug resistance during a Klebsiella pneumoniae outbreak including carbapenem and colistin resistance. J Antimicrob Chemother (2013) 1.39
Evolutionary convergence and nitrogen metabolism in Blattabacterium strain Bge, primary endosymbiont of the cockroach Blattella germanica. PLoS Genet (2009) 1.38
The striking case of tryptophan provision in the cedar aphid Cinara cedri. J Bacteriol (2008) 1.36
Why are the genomes of endosymbiotic bacteria so stable? Trends Genet (2003) 1.36
The fittest versus the flattest: experimental confirmation of the quasispecies effect with subviral pathogens. PLoS Pathog (2006) 1.35
Serratia symbiotica from the aphid Cinara cedri: a missing link from facultative to obligate insect endosymbiont. PLoS Genet (2011) 1.34
Epistasis and the adaptability of an RNA virus. Genetics (2005) 1.31
Analysis of epistatic interactions and fitness landscapes using a new geometric approach. BMC Evol Biol (2007) 1.30
The active human gut microbiota differs from the total microbiota. PLoS One (2011) 1.30
Description of Bacillus toyonensis sp. nov., a novel species of the Bacillus cereus group, and pairwise genome comparisons of the species of the group by means of ANI calculations. Syst Appl Microbiol (2013) 1.29
The cost of replication fidelity in an RNA virus. Proc Natl Acad Sci U S A (2005) 1.28
Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees. Biol Direct (2009) 1.27
The frontier between cell and organelle: genome analysis of Candidatus Carsonella ruddii. BMC Evol Biol (2007) 1.27
Evolutionary trajectories of beta-lactamase CTX-M-1 cluster enzymes: predicting antibiotic resistance. PLoS Pathog (2010) 1.26
Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life. BMC Evol Biol (2011) 1.25
Effect of host species on the distribution of mutational fitness effects for an RNA virus. PLoS Genet (2011) 1.24
Identification of the weevil immune genes and their expression in the bacteriome tissue. BMC Biol (2008) 1.24
Estimating the extent of horizontal gene transfer in metagenomic sequences. BMC Genomics (2008) 1.24
One is enough: in vivo effective population size is dose-dependent for a plant RNA virus. PLoS Pathog (2011) 1.23
Evolution of the secondary symbiont "Candidatus serratia symbiotica" in aphid species of the subfamily lachninae. Appl Environ Microbiol (2008) 1.22
Assessing gut microbial diversity from feces and rectal mucosa. Microb Ecol (2010) 1.21
Deep molecular characterization of HIV-1 dynamics under suppressive HAART. PLoS Pathog (2011) 1.21
Mobile genetic element proliferation and gene inactivation impact over the genome structure and metabolic capabilities of Sodalis glossinidius, the secondary endosymbiont of tsetse flies. BMC Genomics (2010) 1.20
A sliding window-based method to detect selective constraints in protein-coding genes and its application to RNA viruses. J Mol Evol (2002) 1.19
Genome degeneration and adaptation in a nascent stage of symbiosis. Genome Biol Evol (2014) 1.18
The evolution of the heat-shock protein GroEL from Buchnera, the primary endosymbiont of aphids, is governed by positive selection. Mol Biol Evol (2002) 1.18
GroEL and the maintenance of bacterial endosymbiosis. Trends Genet (2004) 1.18
Evidence of recombination in intrapatient populations of hepatitis C virus. PLoS One (2008) 1.16
Whole-genome sequence of Stenotrophomonas maltophilia D457, a clinical isolate and a model strain. J Bacteriol (2012) 1.16
The rate and spectrum of spontaneous mutations in a plant RNA virus. Genetics (2010) 1.15
Molecular epidemiology of a hepatitis C virus outbreak in a hemodialysis unit. J Clin Microbiol (2005) 1.14
Massive presence of insertion sequences in the genome of SOPE, the primary endosymbiont of the rice weevil Sitophilus oryzae. Int Microbiol (2008) 1.13
Mapping natural polymorphisms of hepatitis C virus NS3/4A protease and antiviral resistance to inhibitors in worldwide isolates. Antivir Ther (2008) 1.13
From phylogenetics to phylogenomics: the evolutionary relationships of insect endosymbiotic gamma-Proteobacteria as a test case. Syst Biol (2007) 1.13
In silico predicted robustness of viroids RNA secondary structures. I. The effect of single mutations. Mol Biol Evol (2006) 1.12
Fitness declines in Tobacco etch virus upon serial bottleneck transfers. J Virol (2007) 1.11
The evolutionary origin of Xanthomonadales genomes and the nature of the horizontal gene transfer process. Mol Biol Evol (2006) 1.10
The pleiotropic cost of host-specialization in Tobacco etch potyvirus. Infect Genet Evol (2008) 1.10
Changes in the gene expression profile of Arabidopsis thaliana after infection with Tobacco etch virus. Virol J (2008) 1.10
Differential effects of antibiotic therapy on the structure and function of human gut microbiota. PLoS One (2013) 1.09
Functional consequences of microbial shifts in the human gastrointestinal tract linked to antibiotic treatment and obesity. Gut Microbes (2013) 1.07
Multihost experimental evolution of a plant RNA virus reveals local adaptation and host-specific mutations. Mol Biol Evol (2011) 1.07
EnvDB, a database for describing the environmental distribution of prokaryotic taxa. Environ Microbiol Rep (2009) 1.06
Study of the viral and microbial communities associated with Crohn's disease: a metagenomic approach. Clin Transl Gastroenterol (2013) 1.06
Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions. Genome Biol (2009) 1.06
In silico predicted robustness of viroid RNA secondary structures. II. Interaction between mutation pairs. Mol Biol Evol (2006) 1.06
Virus adaptation by manipulation of host's gene expression. PLoS One (2008) 1.06
Following the very initial growth of biological RNA viral clones. J Gen Virol (2005) 1.06
Genome sequence of Lactococcus garvieae UNIUD074, isolated in Italy from a lactococcosis outbreak. J Bacteriol (2011) 1.06
Molecular evolution of a viral non-coding sequence under the selective pressure of amiRNA-mediated silencing. PLoS Pathog (2009) 1.06
Epistasis between mutations is host-dependent for an RNA virus. Biol Lett (2012) 1.05
Complete genome sequence of "Candidatus Tremblaya princeps" strain PCVAL, an intriguing translational machine below the living-cell status. J Bacteriol (2011) 1.05
Bacterial endosymbionts of insects: insights from comparative genomics. Environ Microbiol (2004) 1.04
Molecular systematics of aphids (Homoptera: Aphididae): new insights from the long-wavelength opsin gene. Mol Phylogenet Evol (2004) 1.04
Adaptation of tobacco etch potyvirus to a susceptible ecotype of Arabidopsis thaliana capacitates it for systemic infection of resistant ecotypes. Philos Trans R Soc Lond B Biol Sci (2010) 1.03
Effects of potyvirus effective population size in inoculated leaves on viral accumulation and the onset of symptoms. J Virol (2012) 1.03
New clues about the evolutionary history of metabolic losses in bacterial endosymbionts, provided by the genome of Buchnera aphidicola from the aphid Cinara tujafilina. Appl Environ Microbiol (2011) 1.02
Replication mode and landscape topology differentially affect RNA virus mutational load and robustness. J Virol (2009) 1.01
Blattabacteria, the endosymbionts of cockroaches, have small genome sizes and high genome copy numbers. Environ Microbiol (2008) 1.01
Viroids: an Ariadne's thread into the RNA labyrinth. EMBO Rep (2006) 1.01
A new subtype of hepatitis C virus genotype 1: complete genome and phylogenetic relationships of an Equatorial Guinea isolate. J Gen Virol (2006) 1.01
Structural analyses of a hypothetical minimal metabolism. Philos Trans R Soc Lond B Biol Sci (2007) 1.01
Detection of drug resistance mutations at low plasma HIV-1 RNA load in a European multicentre cohort study. J Antimicrob Chemother (2011) 1.01
Genomic determinants of protein folding thermodynamics in prokaryotic organisms. J Mol Biol (2004) 1.00