Published in Mol Biol Evol on December 22, 2011
Emerging Interaction Patterns in the Emiliania huxleyi-EhV System. Viruses (2017) 1.38
Group Selection and Contribution of Minority Variants during Virus Adaptation Determines Virus Fitness and Phenotype. PLoS Pathog (2015) 1.05
Effects of potyvirus effective population size in inoculated leaves on viral accumulation and the onset of symptoms. J Virol (2012) 1.03
The evolution and genetics of virus host shifts. PLoS Pathog (2014) 0.96
Experimental evolution of pseudogenization and gene loss in a plant RNA virus. Mol Biol Evol (2013) 0.91
Stability and fitness impact of the visually discernible Rosea1 marker in the Tobacco etch virus genome. Viruses (2013) 0.85
Evaluating the within-host fitness effects of mutations fixed during virus adaptation to different ecotypes of a new host. Philos Trans R Soc Lond B Biol Sci (2015) 0.84
Genotypic but not phenotypic historical contingency revealed by viral experimental evolution. BMC Evol Biol (2013) 0.83
Shrinkage of genome size in a plant RNA virus upon transfer of an essential viral gene into the host genome. Genome Biol Evol (2014) 0.81
Effects of introduced and indigenous viruses on native plants: exploring their disease causing potential at the agro-ecological interface. PLoS One (2014) 0.79
Viral population dynamics and virulence thresholds. Curr Opin Microbiol (2012) 0.78
Specific requirement for translation initiation factor 4E or its isoform drives plant host susceptibility to Tobacco etch virus. BMC Plant Biol (2014) 0.78
The transcriptomics of an experimentally evolved plant-virus interaction. Sci Rep (2016) 0.76
Effect of host species on the topography of fitness landscape for a plant RNA virus. J Virol (2016) 0.76
Enhanced in planta Fitness through Adaptive Mutations in EfpR, a Dual Regulator of Virulence and Metabolic Functions in the Plant Pathogen Ralstonia solanacearum. PLoS Pathog (2016) 0.76
Adaptation to fluctuating temperatures in an RNA virus is driven by the most stringent selective pressure. PLoS One (2014) 0.75
Genetic variation in fitness within a clonal population of a plant RNA virus. Virus Evol (2016) 0.75
High virulence does not necessarily impede viral adaptation to a new host: a case study using a plant RNA virus. BMC Evol Biol (2017) 0.75
The Genomic Architecture of Interactions Between Natural Genetic Polymorphisms and Environments in Yeast Growth. Genetics (2016) 0.75
Time-sampled population sequencing reveals the interplay of selection and genetic drift in experimental evolution of Potato virus Y. J Virol (2017) 0.75
The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus. Proc Natl Acad Sci U S A (2004) 4.77
Perspective: Evolution and detection of genetic robustness. Evolution (2003) 4.10
Pseudomonas syringae pv. tomato hijacks the Arabidopsis abscisic acid signalling pathway to cause disease. EMBO J (2007) 2.35
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
The evolution of sex: empirical insights into the roles of epistasis and drift. Nat Rev Genet (2007) 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
Epistasis correlates to genomic complexity. Proc Natl Acad Sci U S A (2006) 1.81
Natural selection fails to optimize mutation rates for long-term adaptation on rugged fitness landscapes. PLoS Comput Biol (2008) 1.58
The causes of epistasis. Proc Biol Sci (2011) 1.50
Extremely high mutation rate of a hammerhead viroid. Science (2009) 1.50
Molecular basis of adaptive convergence in experimental populations of RNA viruses. Genetics (2002) 1.41
The fittest versus the flattest: experimental confirmation of the quasispecies effect with subviral pathogens. PLoS Pathog (2006) 1.35
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
Effect of host species on the distribution of mutational fitness effects for an RNA virus. PLoS Genet (2011) 1.24
One is enough: in vivo effective population size is dose-dependent for a plant RNA virus. PLoS Pathog (2011) 1.23
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
The rate and spectrum of spontaneous mutations in a plant RNA virus. Genetics (2010) 1.15
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
Changes in the gene expression profile of Arabidopsis thaliana after infection with Tobacco etch virus. Virol J (2008) 1.10
The pleiotropic cost of host-specialization in Tobacco etch potyvirus. Infect Genet Evol (2008) 1.10
Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions. Genome Biol (2009) 1.06
Virus adaptation by manipulation of host's gene expression. PLoS One (2008) 1.06
In silico predicted robustness of viroid RNA secondary structures. II. Interaction between mutation pairs. Mol Biol Evol (2006) 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
The evolutionary genetics of emerging plant RNA viruses. Mol Plant Microbe Interact (2011) 1.05
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
Viroids: an Ariadne's thread into the RNA labyrinth. EMBO Rep (2006) 1.01
Replication mode and landscape topology differentially affect RNA virus mutational load and robustness. J Virol (2009) 1.01
Dynamics of a plant RNA virus intracellular accumulation: stamping machine vs. geometric replication. Genetics (2011) 0.99
Parasites and mutational load: an experimental test of a pluralistic theory for the evolution of sex. Proc Biol Sci (2005) 0.98
Application of game theory to the interaction between plant viruses during mixed infections. J Gen Virol (2009) 0.97
Measuring selection coefficients below 10(-3): method, questions, and prospects. Genetics (2011) 0.97
Upper-limit mutation rate estimation for a plant RNA virus. Biol Lett (2009) 0.95
Simple quasispecies models for the survival-of-the-flattest effect: The role of space. J Theor Biol (2007) 0.95
A meta-analysis reveals the commonalities and differences in Arabidopsis thaliana response to different viral pathogens. PLoS One (2012) 0.94
Dynamics of the establishment of systemic Potyvirus infection: independent yet cumulative action of primary infection sites. J Virol (2012) 0.94
Contribution of recombination and selection to molecular evolution of Citrus tristeza virus. J Gen Virol (2009) 0.93
Natural selection and the organ-specific differentiation of HIV-1 V3 hypervariable region. Evolution (2004) 0.92
Insights into the selective pressures restricting Pelargonium flower break virus genome variability: Evidence for host adaptation. J Virol (2006) 0.92
Dynamics of molecular evolution and phylogeography of Barley yellow dwarf virus-PAV. PLoS One (2011) 0.92
Ultradeep sequencing analysis of population dynamics of virus escape mutants in RNAi-mediated resistant plants. Mol Biol Evol (2012) 0.91
Experimental evolution of pseudogenization and gene loss in a plant RNA virus. Mol Biol Evol (2013) 0.91
Experimental evolution of an emerging plant virus in host genotypes that differ in their susceptibility to infection. Evolution (2014) 0.90
Viroids: survivors from the RNA world? Annu Rev Microbiol (2014) 0.89
Tempo and mode of plant RNA virus escape from RNA interference-mediated resistance. J Virol (2011) 0.88
Computational design of genomic transcriptional networks with adaptation to varying environments. Proc Natl Acad Sci U S A (2012) 0.88
The promiscuous evolutionary history of the family Bromoviridae. J Gen Virol (2008) 0.86
Optimal viral strategies for bypassing RNA silencing. J R Soc Interface (2010) 0.86
Estimation of the in vivo recombination rate for a plant RNA virus. J Gen Virol (2013) 0.86
Luria-delbruck estimation of turnip mosaic virus mutation rate in vivo. J Virol (2012) 0.86
Phylogeography and molecular evolution of potato virus Y. PLoS One (2012) 0.85
Error threshold in RNA quasispecies models with complementation. J Theor Biol (2010) 0.84
From hypo- to hypersuppression: effect of amino acid substitutions on the RNA-silencing suppressor activity of the Tobacco etch potyvirus HC-Pro. Genetics (2008) 0.84
Effects of the number of genome segments on primary and systemic infections with a multipartite plant RNA virus. J Virol (2013) 0.83
Genotypic but not phenotypic historical contingency revealed by viral experimental evolution. BMC Evol Biol (2013) 0.83
Quasispecies spatial models for RNA viruses with different replication modes and infection strategies. PLoS One (2011) 0.83
Transcript Profiling of Different Arabidopsis thaliana Ecotypes in Response to Tobacco etch potyvirus Infection. Front Microbiol (2012) 0.83
Structural discrimination of robustness in transcriptional feedforward loops for pattern formation. PLoS One (2011) 0.82
Population differentiation and selective constraints in Pelargonium line pattern virus. Virus Res (2010) 0.82
Model-selection-based approach for calculating cellular multiplicity of infection during virus colonization of multi-cellular hosts. PLoS One (2013) 0.82
Network design meets in silico evolutionary biology. Biochimie (2010) 0.82
The Core/E1 domain of hepatitis C virus genotype 4a in Egypt does not contain viral mutations or strains specific for hepatocellular carcinoma. J Clin Virol (2011) 0.81
r- and K-selection in experimental populations of vesicular stomatitis virus. Infect Genet Evol (2002) 0.81
Adaptive covariation between the coat and movement proteins of prunus necrotic ringspot virus. J Virol (2006) 0.81
Shrinkage of genome size in a plant RNA virus upon transfer of an essential viral gene into the host genome. Genome Biol Evol (2014) 0.81
Fate of artificial microRNA-mediated resistance to plant viruses in mixed infections. Phytopathology (2013) 0.80
Compensatory molecular evolution of HC-Pro, an RNA-silencing suppressor from a plant RNA virus. Mol Biol Evol (2009) 0.80
Fine-tuning tomato agronomic properties by computational genome redesign. PLoS Comput Biol (2012) 0.80
The causes of epistasis in genetic networks. Evolution (2011) 0.79
Robust dynamical pattern formation from a multifunctional minimal genetic circuit. BMC Syst Biol (2010) 0.79
Intra-specific variability and biological relevance of P3N-PIPO protein length in potyviruses. BMC Evol Biol (2013) 0.79
Mode of selection and experimental evolution of antiviral drugs resistance in vesicular stomatitis virus. Infect Genet Evol (2005) 0.78
Genetic diversity and potential vectors and reservoirs of Cucurbit aphid-borne yellows virus in southeastern Spain. Phytopathology (2013) 0.78
MicroRNA precursors are not structurally robust but plastic. Genome Biol Evol (2013) 0.77
Virus infection suppresses Nicotiana benthamiana adaptive phenotypic plasticity. PLoS One (2011) 0.77
Differences in accumulation and virulence determine the outcome of competition during Tobacco etch virus coinfection. PLoS One (2011) 0.77
Relocation of the NIb gene in the tobacco etch potyvirus genome. J Virol (2014) 0.77
Coinfection and superinfection in RNA virus populations: a selection-mutation model. Math Biosci (2003) 0.77
Complex dynamics of defective interfering baculoviruses during serial passage in insect cells. J Biol Phys (2013) 0.77
HC-Pro hypo- and hypersuppressor mutants: differences in viral siRNA accumulation in vivo and siRNA binding activity in vitro. Arch Virol (2009) 0.77
Genetic diversity of the movement and coat protein genes of South American isolates of Prunus necrotic ringspot virus. Arch Virol (2008) 0.77
Molecular evolution of the plant virus family Bromoviridae based on RNA3-encoded proteins. J Mol Evol (2005) 0.77
Computational design of host transcription-factors sets whose misregulation mimics the transcriptomic effect of viral infections. Sci Rep (2012) 0.76
Dynamics of alternative modes of RNA replication for positive-sense RNA viruses. J R Soc Interface (2011) 0.76
Molecular evolution and phylogeography of potato virus Y based on the CP gene. J Gen Virol (2012) 0.76
Effect of citrus hosts on the generation, maintenance and evolutionary fate of genetic variability of citrus exocortis viroid. J Gen Virol (2009) 0.76
Tridimensional model structure and patterns of molecular evolution of Pepino mosaic virus TGBp3 protein. Virol J (2011) 0.75
Emergence and phylodynamics of Citrus tristeza virus in Sicily, Italy. PLoS One (2013) 0.75
Corrigendum: Variability in mutational fitness effects prevents full lethal transitions in large quasispecies populations. Sci Rep (2015) 0.75
Molecular evolution of viral multifunctional proteins: the case of potyvirus HC-Pro. J Mol Evol (2013) 0.75
Testing the independent action hypothesis of plant pathogen mode of action: a simple and powerful new approach. Phytopathology (2015) 0.75