Published in AIDS on July 13, 2006
An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1. PLoS Comput Biol (2009) 3.11
A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences. Nucleic Acids Res (2009) 2.06
Genomic diversity and evolution of the lyssaviruses. PLoS One (2008) 1.98
Consensus drug resistance mutations for epidemiological surveillance: basic principles and potential controversies. Antivir Ther (2008) 1.58
Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1. J Virol (2007) 1.57
The HIV-1 subtype C epidemic in South America is linked to the United Kingdom. PLoS One (2010) 1.19
COMET: adaptive context-based modeling for ultrafast HIV-1 subtype identification. Nucleic Acids Res (2014) 1.15
The Impact of HIV Genetic Polymorphisms and Subtype Differences on the Occurrence of Resistance to Antiretroviral Drugs. Mol Biol Int (2012) 1.03
Role of HIV Subtype Diversity in the Development of Resistance to Antiviral Drugs. Viruses (2010) 1.00
The increasing genetic diversity of HIV-1 in the UK, 2002-2010. AIDS (2014) 0.89
HIV diversity and drug resistance from plasma and non-plasma analytes in a large treatment programme in western Kenya. J Int AIDS Soc (2014) 0.87
Phylogenetic and geospatial evaluation of HIV-1 subtype diversity at the largest HIV center in Rhode Island. Infect Genet Evol (2014) 0.83
A classification approach for genotyping viral sequences based on multidimensional scaling and linear discriminant analysis. BMC Bioinformatics (2010) 0.76
BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol (2007) 74.13
Relaxed phylogenetics and dating with confidence. PLoS Biol (2006) 37.68
Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol (2012) 32.00
Pandemic potential of a strain of influenza A (H1N1): early findings. Science (2009) 26.24
Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature (2009) 17.96
Estimating the rate of intersubtype recombination in early HIV-1 group M strains. J Virol (2012) 12.78
Hospital outbreak of Middle East respiratory syndrome coronavirus. N Engl J Med (2013) 11.85
Bayesian phylogeography finds its roots. PLoS Comput Biol (2009) 10.99
Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol Biol Evol (2005) 8.42
Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update. PLoS One (2009) 8.37
Rise and fall of the Beringian steppe bison. Science (2004) 7.91
Many-core algorithms for statistical phylogenetics. Bioinformatics (2009) 6.70
An automated genotyping system for analysis of HIV-1 and other microbial sequences. Bioinformatics (2005) 5.60
BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics. Syst Biol (2011) 5.40
Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. J Mol Evol (2002) 5.24
Antiretroviral drug resistance testing in adult HIV-1 infection: 2008 recommendations of an International AIDS Society-USA panel. Clin Infect Dis (2008) 5.20
Clinical features and virological analysis of a case of Middle East respiratory syndrome coronavirus infection. Lancet Infect Dis (2013) 4.87
Phylogeography takes a relaxed random walk in continuous space and time. Mol Biol Evol (2010) 4.82
Episodic sexual transmission of HIV revealed by molecular phylodynamics. PLoS Med (2008) 4.76
IFITM3 restricts the morbidity and mortality associated with influenza. Nature (2012) 4.66
Evolutionary analysis of the dynamics of viral infectious disease. Nat Rev Genet (2009) 4.56
The molecular population genetics of HIV-1 group O. Genetics (2004) 4.53
SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics. Bioinformatics (2011) 4.41
Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Mol Biol Evol (2012) 4.16
Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty. Infect Genet Evol (2007) 4.11
LEDGF/p75 functions downstream from preintegration complex formation to effect gene-specific HIV-1 integration. Genes Dev (2007) 3.96
HIV-1 protease and reverse transcriptase mutations for drug resistance surveillance. AIDS (2007) 3.94
Once-daily atomoxetine treatment for children and adolescents with attention deficit hyperactivity disorder: a randomized, placebo-controlled study. Am J Psychiatry (2002) 3.89
Human T-lymphotropic virus 1: recent knowledge about an ancient infection. Lancet Infect Dis (2007) 3.80
Impact of late diagnosis and treatment on life expectancy in people with HIV-1: UK Collaborative HIV Cohort (UK CHIC) Study. BMJ (2011) 3.72
British HIV Association Guidelines for the treatment of HIV-1-infected adults with antiretroviral therapy 2008. HIV Med (2008) 3.67
Update of the drug resistance mutations in HIV-1: Spring 2008. Top HIV Med (2008) 3.66
2011 update of the drug resistance mutations in HIV-1. Top Antivir Med (2011) 3.66
The genesis and source of the H7N9 influenza viruses causing human infections in China. Nature (2013) 3.60
Effect of transmitted drug resistance on virological and immunological response to initial combination antiretroviral therapy for HIV (EuroCoord-CHAIN joint project): a European multicohort study. Lancet Infect Dis (2011) 3.59
Update of the drug resistance mutations in HIV-1: March 2013. Top Antivir Med (2013) 3.58
Update of the drug resistance mutations in HIV-1: December 2009. Top HIV Med (2009) 3.52
Prevalence of drug-resistant HIV-1 variants in untreated individuals in Europe: implications for clinical management. J Infect Dis (2005) 3.52
Virological monitoring and resistance to first-line highly active antiretroviral therapy in adults infected with HIV-1 treated under WHO guidelines: a systematic review and meta-analysis. Lancet Infect Dis (2009) 3.37
Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus. Emerg Infect Dis (2013) 3.35
Human infection with MERS coronavirus after exposure to infected camels, Saudi Arabia, 2013. Emerg Infect Dis (2014) 3.25
Impact of HIV-1 subtype and antiretroviral therapy on protease and reverse transcriptase genotype: results of a global collaboration. PLoS Med (2005) 3.17
Emergence of drug resistance in HIV type 1-infected patients after receipt of first-line highly active antiretroviral therapy: a systematic review of clinical trials. Clin Infect Dis (2008) 3.15
Recent human-to-poultry host jump, adaptation, and pandemic spread of Staphylococcus aureus. Proc Natl Acad Sci U S A (2009) 3.10
Accommodating the effect of ancient DNA damage on inferences of demographic histories. Mol Biol Evol (2008) 3.07
Update of the drug resistance mutations in HIV-1: Fall 2006. Top HIV Med (2006) 3.06
Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups. Proc Natl Acad Sci U S A (2005) 3.04
Inferring confidence sets of possibly misspecified gene trees. Proc Biol Sci (2002) 2.98
Mutation of a single residue renders human tetherin resistant to HIV-1 Vpu-mediated depletion. PLoS Pathog (2009) 2.92
Update of the Drug Resistance Mutations in HIV-1. Top HIV Med (2008) 2.91
Update of the drug resistance mutations in HIV-1: December 2010. Top HIV Med (2010) 2.91
Disease-associated XMRV sequences are consistent with laboratory contamination. Retrovirology (2010) 2.90
The emergence of HIV/AIDS in the Americas and beyond. Proc Natl Acad Sci U S A (2007) 2.89
Update of the drug resistance mutations in HIV-1: 2007. Top HIV Med (2007) 2.79
Gene3D: comprehensive structural and functional annotation of genomes. Nucleic Acids Res (2007) 2.75
A Bayesian phylogenetic method to estimate unknown sequence ages. Mol Biol Evol (2010) 2.73
U.S. Human immunodeficiency virus type 1 epidemic: date of origin, population history, and characterization of early strains. J Virol (2003) 2.64
Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak. Nature (2006) 2.61
Transmission of drug-resistant HIV-1 is stabilizing in Europe. J Infect Dis (2009) 2.60
Transmission of HIV-1 during primary infection: relationship to sexual risk and sexually transmitted infections. AIDS (2005) 2.51
Time trends in primary resistance to HIV drugs in the United Kingdom: multicentre observational study. BMJ (2005) 2.51
Spread, circulation, and evolution of the Middle East respiratory syndrome coronavirus. MBio (2014) 2.50
Rate of AIDS diseases or death in HIV-infected antiretroviral therapy-naive individuals with high CD4 cell count. AIDS (2007) 2.47
Long term probability of detection of HIV-1 drug resistance after starting antiretroviral therapy in routine clinical practice. AIDS (2005) 2.45
Poxvirus genomes: a phylogenetic analysis. J Gen Virol (2004) 2.40
HIV-1 pol gene variation is sufficient for reconstruction of transmissions in the era of antiretroviral therapy. AIDS (2004) 2.35
Complete genomic sequence of human coronavirus OC43: molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission event. J Virol (2005) 2.35
Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolution. Mol Biol Evol (2007) 2.34
Viral population analysis and minority-variant detection using short read next-generation sequencing. Philos Trans R Soc Lond B Biol Sci (2013) 2.33
Ancient hybridization and an Irish origin for the modern polar bear matriline. Curr Biol (2011) 2.33
HIV evolutionary dynamics within and among hosts. AIDS Rev (2006) 2.32
Tracing the origin and history of the HIV-2 epidemic. Proc Natl Acad Sci U S A (2003) 2.31
Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics. PLoS Comput Biol (2007) 2.25
Inference of viral evolutionary rates from molecular sequences. Adv Parasitol (2003) 2.23
Simian immunodeficiency virus envelope glycoprotein counteracts tetherin/BST-2/CD317 by intracellular sequestration. Proc Natl Acad Sci U S A (2009) 2.21
Clinically validated genotype analysis: guiding principles and statistical concerns. Antivir Ther (2004) 2.14
Inferring the rate and time-scale of dengue virus evolution. Mol Biol Evol (2003) 2.11
Molecular phylodynamics of the heterosexual HIV epidemic in the United Kingdom. PLoS Pathog (2009) 2.10
Dynamics of total, linear nonintegrated, and integrated HIV-1 DNA in vivo and in vitro. J Infect Dis (2008) 2.08
HIV-associated central nervous system diseases in the recent combination antiretroviral therapy era. Eur J Neurol (2010) 2.06