Published in Nature on December 14, 2006
Evolutionary analysis of the dynamics of viral infectious disease. Nat Rev Genet (2009) 4.56
Genomic epidemiology of a dengue virus epidemic in urban Singapore. J Virol (2009) 2.74
Evidence of a large, international network of HCV transmission in HIV-positive men who have sex with men. Gastroenterology (2009) 2.10
Libyan medical education; time to move forward. Libyan J Med (2008) 1.99
A public health model for the molecular surveillance of HIV transmission in San Diego, California. AIDS (2009) 1.81
Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses. Mol Biol Evol (2010) 1.80
Coalescent genealogy samplers: windows into population history. Trends Ecol Evol (2008) 1.71
Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1. J Virol (2007) 1.57
Role of individual's T-cell immunome in controlling HIV-1 progression. Immunology (2014) 1.39
Sequence diversity of hepatitis C virus: implications for immune control and therapy. World J Gastroenterol (2007) 1.21
The genealogical population dynamics of HIV-1 in a large transmission chain: bridging within and among host evolutionary rates. PLoS Comput Biol (2014) 1.18
Virus movement maintains local virus population diversity. Proc Natl Acad Sci U S A (2007) 1.16
Social networks shape the transmission dynamics of hepatitis C virus. PLoS One (2010) 1.10
Sequence editing by Apolipoprotein B RNA-editing catalytic component [corrected] and epidemiological surveillance of transmitted HIV-1 drug resistance. AIDS (2008) 1.09
HIV phylogenetics. BMJ (2007) 1.07
Libya, HIV, and open communication. Retrovirology (2006) 1.07
Developing and evaluating comprehensive HIV infection control strategies: issues and challenges. Clin Infect Dis (2010) 1.02
Extensive HLA-driven viral diversity following a narrow-source HIV-1 outbreak in rural China. Blood (2011) 1.01
Evolution and molecular epidemiology of subtype C HIV-1 in Zimbabwe. AIDS (2009) 1.00
Multiple introductions of HIV into men who have sex with men were found in Zhengzhou City, China. AIDS Res Hum Retroviruses (2012) 1.00
Population genetic analysis infers migration pathways of Phytophthora ramorum in US nurseries. PLoS Pathog (2009) 0.93
Associations between phylogenetic clustering and HLA profile among HIV-infected individuals in San Diego, California. J Infect Dis (2012) 0.90
The Libyan HIV Outbreak How do we find the truth? Libyan J Med (2007) 0.90
Rethinking the role of the local community in HIV epidemic spread in sub-Saharan Africa: a proximate-determinants approach. HIV Ther (2009) 0.89
Seroprevalence of HBV, HCV & HIV co-infection and risk factors analysis in Tripoli-Libya. PLoS One (2014) 0.87
Phylogeny and phylodinamic of Hepatitis C in Italy. BMC Infect Dis (2012) 0.84
Viral phylogeny in court: the unusual case of the Valencian anesthetist. BMC Biol (2013) 0.81
Detection of transmission clusters of HIV-1 subtype C over a 21-year period in Cape Town, South Africa. PLoS One (2014) 0.80
Potential for human immunodeficiency virus parenteral transmission in the Middle East and North Africa: an analysis using hepatitis C virus as a proxy biomarker. World J Gastroenterol (2014) 0.79
Hepatitis C virus molecular evolution: transmission, disease progression and antiviral therapy. World J Gastroenterol (2014) 0.78
Co-infections and transmission networks of HCV, HIV-1 and HPgV among people who inject drugs. Sci Rep (2015) 0.77
Investigation of hepatitis B virus and human immunodeficiency virus transmission among severely mentally ill residents at a long term care facility. PLoS One (2012) 0.77
Key role of human leukocyte antigen in modulating human immunodeficiency virus progression: An overview of the possible applications. World J Virol (2015) 0.76
Guidelines for the detection of a common source of hepatitis B virus infections. Hepat Mon (2011) 0.76
'Libyan Trial': a verdict running counter to scientific evidence. Retrovirology (2006) 0.75
Impacts and shortcomings of genetic clustering methods for infectious disease outbreaks. Virus Evol (2016) 0.75
Phylogenetic Exploration of Nosocomial Transmission Chains of 2009 Influenza A/H1N1 among Children Admitted at Red Cross War Memorial Children's Hospital, Cape Town, South Africa in 2011. PLoS One (2015) 0.75
Interrupting transmission of HIV and other sexually transmitted infections in Rhode Island. Med Health R I (2012) 0.75
Advanced molecular surveillance of hepatitis C virus. Viruses (2015) 0.75
HS1,2 Ig enhancer alleles association to AIDS progression in a pediatric cohort infected with a monophyletic HIV-strain. Biomed Res Int (2014) 0.75
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
Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts. Nature (2003) 13.24
Estimating the rate of intersubtype recombination in early HIV-1 group M strains. J Virol (2012) 12.78
Bayesian phylogeography finds its roots. PLoS Comput Biol (2009) 10.99
The genomic and epidemiological dynamics of human influenza A virus. Nature (2008) 10.26
Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol Biol Evol (2005) 8.42
Unifying the epidemiological and evolutionary dynamics of pathogens. Science (2004) 8.33
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
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
An index of substitution saturation and its application. Mol Phylogenet Evol (2003) 4.71
HIV viral load monitoring in resource-limited regions: optional or necessary? Clin Infect Dis (2006) 4.56
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
Recent epidemic of acute hepatitis C virus in HIV-positive men who have sex with men linked to high-risk sexual behaviours. AIDS (2007) 4.40
Use of a T cell-based assay for monitoring efficacy of antituberculosis therapy. Clin Infect Dis (2004) 4.26
Adaptation of HIV-1 to human leukocyte antigen class I. Nature (2009) 4.24
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
Global distribution and prevalence of hepatitis C virus genotypes. Hepatology (2014) 3.95
The genesis and source of the H7N9 influenza viruses causing human infections in China. Nature (2013) 3.60
Characteristics, determinants, and clinical relevance of CD4 T cell recovery to <500 cells/microL in HIV type 1-infected individuals receiving potent antiretroviral therapy. Clin Infect Dis (2005) 3.57
Prevalence of drug-resistant HIV-1 variants in untreated individuals in Europe: implications for clinical management. J Infect Dis (2005) 3.52
CD4 T-lymphocyte recovery in individuals with advanced HIV-1 infection receiving potent antiretroviral therapy for 4 years: the Swiss HIV Cohort Study. Arch Intern Med (2003) 3.41
Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus. Emerg Infect Dis (2013) 3.35
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
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
A patient with HIV-1 superinfection. N Engl J Med (2002) 2.93
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
An autochthonous case of Zika due to possible sexual transmission, Florence, Italy, 2014. Euro Surveill (2016) 2.79
A Bayesian phylogenetic method to estimate unknown sequence ages. Mol Biol Evol (2010) 2.73
Chronic rhinoviral infection in lung transplant recipients. Am J Respir Crit Care Med (2006) 2.73
Ancient co-speciation of simian foamy viruses and primates. Nature (2005) 2.71
U.S. Human immunodeficiency virus type 1 epidemic: date of origin, population history, and characterization of early strains. J Virol (2003) 2.64
Use of dried whole blood spots to measure CD4+ lymphocyte counts in HIV-1-infected patients. Lancet (2003) 2.64
Evolutionary genetics of human enterovirus 71: origin, population dynamics, natural selection, and seasonal periodicity of the VP1 gene. J Virol (2010) 2.50
Spread, circulation, and evolution of the Middle East respiratory syndrome coronavirus. MBio (2014) 2.50
Host switch leads to emergence of Plasmodium vivax malaria in humans. Mol Biol Evol (2005) 2.45
Invasion and maintenance of dengue virus type 2 and type 4 in the Americas. J Virol (2005) 2.44
Discovery and analysis of the first endogenous lentivirus. Proc Natl Acad Sci U S A (2007) 2.43
Long-term evolution and transmission dynamics of swine influenza A virus. Nature (2011) 2.39
Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolution. Mol Biol Evol (2007) 2.34
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
Stimulation of HIV-specific cellular immunity by structured treatment interruption fails to enhance viral control in chronic HIV infection. Proc Natl Acad Sci U S A (2002) 2.32
Tracing the origin and history of the HIV-2 epidemic. Proc Natl Acad Sci U S A (2003) 2.31
A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution. Proc Natl Acad Sci U S A (2008) 2.28
Virologic, immunologic, and clinical benefits from early combined antiretroviral therapy in infants with perinatal HIV-1 infection. AIDS (2006) 2.26
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
Increasing prevalence of HIV-1 subtype A in Greece: estimating epidemic history and origin. J Infect Dis (2007) 2.21
Mutations in HIV-1 reverse transcriptase potentially associated with hypersusceptibility to nonnucleoside reverse-transcriptase inhibitors: effect on response to efavirenz-based therapy in an urban observational cohort. J Infect Dis (2004) 2.21
PENTA 2009 guidelines for the use of antiretroviral therapy in paediatric HIV-1 infection. HIV Med (2009) 2.16
Inferring the rate and time-scale of dengue virus evolution. Mol Biol Evol (2003) 2.11
Precision and accuracy of a procedure for detecting recent human immunodeficiency virus infections by calculating the antibody avidity index by an automated immunoassay-based method. J Clin Microbiol (2002) 2.11
Persistent microbial translocation and immune activation in HIV-1-infected South Africans receiving combination antiretroviral therapy. J Infect Dis (2010) 2.10
Molecular phylodynamics of the heterosexual HIV epidemic in the United Kingdom. PLoS Pathog (2009) 2.10
Temporal and spatial dynamics of human immunodeficiency virus type 1 circulating recombinant forms 08_BC and 07_BC in Asia. J Virol (2008) 2.07
Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans. Proc Natl Acad Sci U S A (2011) 2.06
A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences. Nucleic Acids Res (2009) 2.06
The global spread of hepatitis C virus 1a and 1b: a phylodynamic and phylogeographic analysis. PLoS Med (2009) 2.06
Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. Mol Biol Evol (2012) 2.02
New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features. BMC Genomics (2007) 1.97
Quantifiable cytotoxic T lymphocyte responses and HLA-related risk of progression to AIDS. Proc Natl Acad Sci U S A (2004) 1.97
Chikungunya virus in North-Eastern Italy: a seroprevalence survey. Am J Trop Med Hyg (2010) 1.94
CD4-guided scheduled treatment interruptions compared with continuous therapy for patients infected with HIV-1: results of the Staccato randomised trial. Lancet (2006) 1.91
Spatial phylodynamics of HIV-1 epidemic emergence in east Africa. AIDS (2009) 1.91
Phylodynamic reconstruction reveals norovirus GII.4 epidemic expansions and their molecular determinants. PLoS Pathog (2010) 1.88
Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission. PLoS Pathog (2011) 1.87