Published in Nature on November 28, 2002
Dynamics of HIV-1 recombination in its natural target cells. Proc Natl Acad Sci U S A (2004) 4.37
An overview of molecular epidemiology of hepatitis B virus (HBV) in India. Virol J (2008) 1.83
Adaptive value of high mutation rates of RNA viruses: separating causes from consequences. J Virol (2005) 1.46
What does virus evolution tell us about virus origins? J Virol (2011) 1.01
Reference-independent comparative metagenomics using cross-assembly: crAss. Bioinformatics (2012) 0.95
Viral mutation rates: modelling the roles of within-host viral dynamics and the trade-off between replication fidelity and speed. Proc Biol Sci (2012) 0.87
Molecular biology of the hepatitis B virus for clinicians. J Clin Exp Hepatol (2012) 0.87
Molecular evolution of the hepatitis delta virus antigen gene: recombination or positive selection? J Mol Evol (2004) 0.86
Running loose or getting lost: how HIV-1 counters and capitalizes on APOBEC3-induced mutagenesis through its Vif protein. Viruses (2012) 0.85
Explaining microbial phenotypes on a genomic scale: GWAS for microbes. Brief Funct Genomics (2013) 0.85
Models of RNA virus evolution and their roles in vaccine design. Immunome Res (2010) 0.83
A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase. Nat Genet (2011) 2.66
Emergence of drug-resistant influenza virus: population dynamical considerations. Science (2006) 2.46
Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland. J Infect Dis (2010) 2.21
Dynamic variation in cycling of hematopoietic stem cells in steady state and inflammation. J Exp Med (2011) 2.18
Emergence of minor populations of human immunodeficiency virus type 1 carrying the M184V and L90M mutations in subjects undergoing structured treatment interruptions. J Infect Dis (2003) 2.17
The effect of opinion clustering on disease outbreaks. J R Soc Interface (2008) 2.12
Population biological principles of drug-resistance evolution in infectious diseases. Lancet Infect Dis (2011) 2.11
Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV). Proc Natl Acad Sci U S A (2012) 2.07
Quantitative constraints on the scope of negative selection. Trends Immunol (2003) 2.06
Experimental tests for an evolutionary trade-off between growth rate and yield in E. coli. Am Nat (2006) 1.99
Evolution of cooperation by generalized reciprocity. Proc Biol Sci (2005) 1.96
Using an epidemiological model for phylogenetic inference reveals density dependence in HIV transmission. Mol Biol Evol (2013) 1.88
Estimating the basic reproductive number from viral sequence data. Mol Biol Evol (2011) 1.86
Stable virulence levels in the HIV epidemic of Switzerland over two decades. AIDS (2006) 1.81
Epistasis between deleterious mutations and the evolution of recombination. Trends Ecol Evol (2007) 1.79
The HIV coreceptor switch: a population dynamical perspective. Trends Microbiol (2005) 1.76
Entry and transcription as key determinants of differences in CD4 T-cell permissiveness to human immunodeficiency virus type 1 infection. J Virol (2004) 1.68
Ambiguous nucleotide calls from population-based sequencing of HIV-1 are a marker for viral diversity and the age of infection. Clin Infect Dis (2011) 1.64
Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load. PLoS Pathog (2010) 1.63
Stochastic or deterministic: what is the effective population size of HIV-1? Trends Microbiol (2006) 1.58
An evolutionary scenario for the transition to undifferentiated multicellularity. Proc Natl Acad Sci U S A (2003) 1.55
The evolution of connectivity in metabolic networks. PLoS Biol (2005) 1.54
Recombination in HIV and the evolution of drug resistance: for better or for worse? Bioessays (2004) 1.54
Long-term trends of HIV type 1 drug resistance prevalence among antiretroviral treatment-experienced patients in Switzerland. Clin Infect Dis (2009) 1.50
Inferring epidemic contact structure from phylogenetic trees. PLoS Comput Biol (2012) 1.47
Evolution of cross-feeding in microbial populations. Am Nat (2004) 1.46
Estimating the stoichiometry of human immunodeficiency virus entry. J Virol (2008) 1.36
Quantification of infectious HIV-1 plasma viral load using a boosted in vitro infection protocol. Virology (2004) 1.32
Simulating the evolution of signal transduction pathways. J Theor Biol (2006) 1.31
Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods. Philos Trans R Soc Lond B Biol Sci (2013) 1.31
The evolution of groups of cooperating bacteria and the growth rate versus yield trade-off. Microbiology (2005) 1.30
Interchromatid and interhomolog recombination in Arabidopsis thaliana. Plant Cell (2004) 1.26
The state of affairs in the kingdom of the Red Queen. Trends Ecol Evol (2008) 1.23
Stochastic interplay between mutation and recombination during the acquisition of drug resistance mutations in human immunodeficiency virus type 1. J Virol (2005) 1.18
Human immunodeficiency virus type 1 fitness is a determining factor in viral rebound and set point in chronic infection. J Virol (2003) 1.18
Rapid parasite adaptation drives selection for high recombination rates. Evolution (2007) 1.18
Exploring the complexity of the HIV-1 fitness landscape. PLoS Genet (2012) 1.17
Evolution of complexity in signaling pathways. Proc Natl Acad Sci U S A (2006) 1.14
Effect of varying epistasis on the evolution of recombination. Genetics (2006) 1.14
Humoral immunity to HIV-1: kinetics of antibody responses in chronic infection reflects capacity of immune system to improve viral set point. Blood (2004) 1.14
The effect of population structure on the emergence of drug resistance during influenza pandemics. J R Soc Interface (2007) 1.12
Rapid viral decay in simian immunodeficiency virus-infected macaques receiving quadruple antiretroviral therapy. J Virol (2006) 1.10
African descent is associated with slower CD4 cell count decline in treatment-naive patients of the Swiss HIV Cohort Study. AIDS (2009) 1.08
Assessing predicted HIV-1 replicative capacity in a clinical setting. PLoS Pathog (2011) 1.06
The effect of multifunctionality on the rate of evolution in yeast. Mol Biol Evol (2005) 1.06
Assessing the impact of adherence to anti-retroviral therapy on treatment failure and resistance evolution in HIV. J R Soc Interface (2012) 1.05
Dose-dependent infection rates of parasites produce the Allee effect in epidemiology. Proc Biol Sci (2002) 1.04
The role of migration and domestic transmission in the spread of HIV-1 non-B subtypes in Switzerland. J Infect Dis (2011) 1.03
Red Queen dynamics with non-standard fitness interactions. PLoS Comput Biol (2009) 1.03
Compensation of fitness costs and reversibility of antibiotic resistance mutations. Antimicrob Agents Chemother (2010) 1.01
Residual viral replication during antiretroviral therapy boosts human immunodeficiency virus type 1-specific CD8+ T-cell responses in subjects treated early after infection. J Virol (2002) 0.97
The evolution of network topology by selective removal. J R Soc Interface (2005) 0.96
Mutation accumulation in space and the maintenance of sexual reproduction. Ecol Lett (2006) 0.96
Evolution of stress response in the face of unreliable environmental signals. PLoS Comput Biol (2012) 0.96
Signal transduction networks: topology, response and biochemical processes. J Theor Biol (2005) 0.95
The role of epistasis on the evolution of recombination in host-parasite coevolution. Theor Popul Biol (2008) 0.94
High epitope expression levels increase competition between T cells. PLoS Comput Biol (2006) 0.93
Informed switching strongly decreases the prevalence of antibiotic resistance in hospital wards. PLoS Comput Biol (2011) 0.93
On being the right size: the impact of population size and stochastic effects on the evolution of drug resistance in hospitals and the community. PLoS Pathog (2011) 0.93
Spatial models of virus-immune dynamics. J Theor Biol (2004) 0.93
The role of recombination for the coevolutionary dynamics of HIV and the immune response. PLoS One (2011) 0.92
Viral dynamics and in vivo fitness of HIV-1 in the presence and absence of enfuvirtide. J Acquir Immune Defic Syndr (2008) 0.92
Decelerating decay of latently infected cells during prolonged therapy for human immunodeficiency virus type 1 infection. J Virol (2002) 0.92
The Red Queen and the persistence of linkage-disequilibrium oscillations in finite and infinite populations. BMC Evol Biol (2007) 0.91
Modelling cytomegalovirus replication patterns in the human host: factors important for pathogenesis. Proc Biol Sci (2006) 0.90
Recombination and drug resistance in HIV: population dynamics and stochasticity. Epidemics (2008) 0.90
On the causes of selection for recombination underlying the red queen hypothesis. Am Nat (2009) 0.90
Guanine-adenine bias: a general property of retroid viruses that is unrelated to host-induced hypermutation. Trends Genet (2005) 0.88
Bacterial growth properties at low optical densities. Antonie Van Leeuwenhoek (2009) 0.87
Contribution of peaks of virus load to simian immunodeficiency virus pathogenesis. J Virol (2002) 0.84
Pre-existence and emergence of drug resistance in a generalized model of intra-host viral dynamics. Epidemics (2012) 0.84
Social meets molecular: Combining phylogenetic and latent class analyses to understand HIV-1 transmission in Switzerland. Am J Epidemiol (2014) 0.83
Contribution of recombination to the evolutionary history of HIV. Curr Opin HIV AIDS (2015) 0.82
HIV coreceptor usage and drug treatment. J Theor Biol (2002) 0.82
HIV replication elicits little cytopathic effects in vivo: analysis of surrogate markers for virus production, cytotoxic T cell response and infected cell death. J Med Virol (2006) 0.82
Nested model reveals potential amplification of an HIV epidemic due to drug resistance. Epidemics (2012) 0.82
Plasmids and evolutionary rescue by drug resistance. Evolution (2014) 0.81
Weighting for sex acts to understand the spread of STI on networks. J Theor Biol (2012) 0.81
Estimating the fitness cost of escape from HLA presentation in HIV-1 protease and reverse transcriptase. PLoS Comput Biol (2012) 0.81
Virus-induced target cell activation reconciles set-point viral load heritability and within-host evolution. Epidemics (2013) 0.81
Principal component analysis of general patterns of HIV-1 replicative fitness in different drug environments. Epidemics (2010) 0.81
Short communication: HIV type 2 dynamics. AIDS Res Hum Retroviruses (2005) 0.80
Epitope down-modulation as a mechanism for the coexistence of competing T-cells. J Theor Biol (2004) 0.80
As it happens: current directions in experimental evolution. Biol Lett (2012) 0.79
Fixation probability of mobile genetic elements such as plasmids. Theor Popul Biol (2013) 0.79
Can high-risk fungicides be used in mixtures without selecting for fungicide resistance? Phytopathology (2014) 0.78
Predicting the evolution of sex on complex fitness landscapes. PLoS Comput Biol (2009) 0.78
On the evolution of sexual reproduction in hosts coevolving with multiple parasites. Evolution (2010) 0.77
Response to Bandeira and Faro: Closing the circle of constraints. Trends Immunol (2003) 0.75
On the role of resonance in drug failure under HIV treatment interruption. Theor Biol Med Model (2013) 0.75
Invasiveness of plant pathogens depends on the spatial scale of host distribution. Ecol Appl (2016) 0.75
Research on infectious disease dynamics. Introduction. Epidemics (2009) 0.75
Dissecting HIV Virulence: Heritability of Setpoint Viral Load, CD4+ T Cell Decline and Per-Parasite Pathogenicity. Mol Biol Evol (2017) 0.75