Published in PLoS Med on December 10, 2013
Why the proportion of transmission during early-stage HIV infection does not predict the long-term impact of treatment on HIV incidence. Proc Natl Acad Sci U S A (2014) 1.13
Phylodynamic inference for structured epidemiological models. PLoS Comput Biol (2014) 1.12
Reassessment of HIV-1 acute phase infectivity: accounting for heterogeneity and study design with simulated cohorts. PLoS Med (2015) 1.12
Timing and order of transmission events is not directly reflected in a pathogen phylogeny. Mol Biol Evol (2014) 1.08
Phylodynamic analysis of ebola virus in the 2014 sierra leone epidemic. PLoS Curr (2014) 1.03
Inferring the source of transmission with phylogenetic data. PLoS Comput Biol (2013) 0.94
Sources of HIV infection among men having sex with men and implications for prevention. Sci Transl Med (2016) 0.93
High Transmissibility During Early HIV Infection Among Men Who Have Sex With Men-San Francisco, California. J Infect Dis (2014) 0.91
Impact of sampling density on the extent of HIV clustering. AIDS Res Hum Retroviruses (2014) 0.89
Identifying Recent HIV Infections: From Serological Assays to Genomics. Viruses (2015) 0.88
How Many HIV infections may be averted by targeting primary infection in men who have sex with men? Quantification of changes in transmission-risk behavior, using an individual-based model. J Infect Dis (2014) 0.86
Ongoing HIV Transmission and the HIV Care Continuum in North Carolina. PLoS One (2015) 0.83
Mucosal Vaccination with Heterologous Viral Vectored Vaccine Targeting Subdominant SIV Accessory Antigens Strongly Inhibits Early Viral Replication. EBioMedicine (2017) 0.82
Genomic analysis of emerging pathogens: methods, application and future trends. Genome Biol (2014) 0.82
The HIV treatment cascade in acutely infected people: informing global guidelines. Curr Opin HIV AIDS (2015) 0.81
Strong influence of behavioral dynamics on the ability of testing and treating HIV to stop transmission. Sci Rep (2015) 0.81
Phylogenetically resolving epidemiologic linkage. Proc Natl Acad Sci U S A (2016) 0.81
Impact of early-stage HIV transmission on treatment as prevention. Proc Natl Acad Sci U S A (2014) 0.81
Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis. PLoS Med (2015) 0.80
Importance of Viral Sequence Length and Number of Variable and Informative Sites in Analysis of HIV Clustering. AIDS Res Hum Retroviruses (2015) 0.80
Early HIV Infections Among Men Who Have Sex with Men in Five Cities in the United States. AIDS Behav (2015) 0.79
Phylodynamic analysis of HIV sub-epidemics in Mochudi, Botswana. Epidemics (2015) 0.79
Understanding drivers of phylogenetic clustering in molecular epidemiological studies of HIV. J Infect Dis (2014) 0.78
Using HIV Sequence and Epidemiologic Data to Assess the Effect of Self-referral Testing for Acute HIV Infection on Incident Diagnoses in San Diego, California. Clin Infect Dis (2016) 0.78
Clinical and public health implications of acute and early HIV detection and treatment: a scoping review. J Int AIDS Soc (2017) 0.77
Persistence of frequently transmitted drug-resistant HIV-1 variants can be explained by high viral replication capacity. Retrovirology (2014) 0.77
Impact of Heterogeneity in Sexual Behavior on Effectiveness in Reducing HIV Transmission with Test-and-Treat Strategy. PLoS Comput Biol (2016) 0.77
Early HIV infection in the United States: a virus's eye view. PLoS Med (2013) 0.76
Spatiotemporal dynamics of HIV-1 transmission in France (1999-2014) and impact of targeted prevention strategies. Retrovirology (2017) 0.75
Phylodynamic Inference across Epidemic Scales. Mol Biol Evol (2017) 0.75
Viral Genetic Linkage Analysis in the Presence of Missing Data. PLoS One (2015) 0.75
Higher HIV RNA Viral Load in Recent Patients with Symptomatic Acute HIV Infection in Lyon University Hospitals. PLoS One (2016) 0.75
Short-Term Dynamic and Local Epidemiological Trends in the South American HIV-1B Epidemic. PLoS One (2016) 0.75
Enhanced use of phylogenetic data to inform public health approaches to HIV among men who have sex with men. Sex Health (2016) 0.75
Combining the Estimated Date of HIV Infection with a Phylogenetic Cluster Study to Better Understand HIV Spread: Application in a Paris Neighbourhood. PLoS One (2015) 0.75
Long-Range HIV Genotyping Using Viral RNA and Proviral DNA for Analysis of HIV Drug Resistance and HIV Clustering. J Clin Microbiol (2015) 0.75
Knowledge and awareness of acute human immunodeficiency virus infection among mobile app-using men who have sex with men: a missed public health opportunity. Open Forum Infect Dis (2015) 0.75
Five-year risk of HIV diagnosis subsequent to 147 hospital-based indicator diseases: a Danish nationwide population-based cohort study. Clin Epidemiol (2016) 0.75
Acute HIV infection detection and immediate treatment estimated to reduce transmission by 89% among men who have sex with men in Bangkok. J Int AIDS Soc (2017) 0.75
Phylodynamic analysis to inform prevention efforts in mixed HIV epidemics. Virus Evol (2017) 0.75
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Prevention of HIV-1 infection with early antiretroviral therapy. N Engl J Med (2011) 69.36
Relaxed phylogenetics and dating with confidence. PLoS Biol (2006) 37.68
Genotypic and phenotypic characterization of HIV-1 patients with primary infection. Science (1993) 13.87
Probability of HIV-1 transmission per coital act in monogamous, heterosexual, HIV-1-discordant couples in Rakai, Uganda. Lancet (2001) 13.32
Estimated HIV incidence in the United States, 2006-2009. PLoS One (2011) 13.03
Estimating sexual transmission of HIV from persons aware and unaware that they are infected with the virus in the USA. AIDS (2006) 11.20
Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J Virol (1999) 10.41
Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update. PLoS One (2009) 8.37
Brief but efficient: acute HIV infection and the sexual transmission of HIV. J Infect Dis (2004) 8.30
The role of acute and early HIV infection in the spread of HIV and implications for transmission prevention strategies in Lilongwe, Malawi: a modelling study. Lancet (2011) 5.87
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Role of the primary infection in epidemics of HIV infection in gay cohorts. J Acquir Immune Defic Syndr (1994) 4.81
Revised surveillance case definitions for HIV infection among adults, adolescents, and children aged <18 months and for HIV infection and AIDS among children aged 18 months to <13 years--United States, 2008. MMWR Recomm Rep (2008) 4.64
Undiagnosed HIV prevalence among adults and adolescents in the United States at the end of 2006. J Acquir Immune Defic Syndr (2010) 4.32
High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men. PLoS Pathog (2010) 3.68
An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1. PLoS Comput Biol (2009) 3.11
Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing. PLoS One (2010) 3.02
Estimating HIV incidence in the United States from HIV/AIDS surveillance data and biomarker HIV test results. Stat Med (2008) 2.90
Transmission of HIV-1 during primary infection: relationship to sexual risk and sexually transmitted infections. AIDS (2005) 2.51
Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics. PLoS Comput Biol (2007) 2.25
HIV superinfection. J Infect Dis (2005) 2.20
Phylodynamics of infectious disease epidemics. Genetics (2009) 2.15
The molecular clock of HIV-1 unveiled through analysis of a known transmission history. Proc Natl Acad Sci U S A (1999) 2.11
Transmission network parameters estimated from HIV sequences for a nationwide epidemic. J Infect Dis (2011) 1.98
Inference for nonlinear epidemiological models using genealogies and time series. PLoS Comput Biol (2011) 1.91
Estimating the basic reproductive number from viral sequence data. Mol Biol Evol (2011) 1.86
Complex population dynamics and the coalescent under neutrality. Genetics (2011) 1.81
Viral phylodynamics and the search for an 'effective number of infections'. Philos Trans R Soc Lond B Biol Sci (2010) 1.76
HIV treatment as prevention: debate and commentary--will early infection compromise treatment-as-prevention strategies? PLoS Med (2012) 1.76
National estimate of HIV prevalence in the Netherlands: comparison and applicability of different estimation tools. AIDS (2011) 1.65
The impact of transmission clusters on primary drug resistance in newly diagnosed HIV-1 infection. AIDS (2009) 1.65
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
Characterizing HIV transmission networks across the United States. Clin Infect Dis (2012) 1.54
Measuring the infectiousness of persons with HIV-1: opportunities for preventing sexual HIV-1 transmission. Curr HIV Res (2003) 1.52
Simple epidemiological dynamics explain phylogenetic clustering of HIV from patients with recent infection. PLoS Comput Biol (2012) 1.51
The rates of HIV superinfection and primary HIV incidence in a general population in Rakai, Uganda. J Infect Dis (2012) 1.49
Inferring epidemic contact structure from phylogenetic trees. PLoS Comput Biol (2012) 1.47
Flexible epidemiological model for estimates and short-term projections in generalised HIV/AIDS epidemics. Sex Transm Infect (2010) 1.44
Dynamic correlation between intrahost HIV-1 quasispecies evolution and disease progression. PLoS Comput Biol (2008) 1.39
27 years of the HIV epidemic amongst men having sex with men in the Netherlands: an in depth mathematical model-based analysis. Epidemics (2010) 1.26
Modelling tree shape and structure in viral phylodynamics. Philos Trans R Soc Lond B Biol Sci (2013) 1.12
Episodic HIV Risk Behavior Can Greatly Amplify HIV Prevalence and the Fraction of Transmissions from Acute HIV Infection. Stat Commun Infect Dis (2012) 1.00
Dates of HIV infection can be estimated for seroprevalent patients by coalescent analysis of serial next-generation sequencing data. AIDS (2011) 0.96
Treatment as prevention: toward an AIDS-free generation. Top Antivir Med (2013) 0.93
HIV-1 transmission cluster with T215D revertant mutation among newly diagnosed patients from the Basque Country, Spain. J Acquir Immune Defic Syndr (2009) 0.92
Incidence of human immunodeficiency virus type 1 dual infections in Amsterdam, The Netherlands, during 2003-2007. Clin Infect Dis (2009) 0.91
HIV-1 co-infection prevalence in two cohorts of early HIV-1 seroconverters in France. AIDS (2007) 0.83
Improving the representativeness of behavioral and clinical surveillance for persons with HIV in the United States: the rationale for developing a population-based approach. PLoS One (2007) 2.08
Simple epidemiological dynamics explain phylogenetic clustering of HIV from patients with recent infection. PLoS Comput Biol (2012) 1.51
Uropathogenic Escherichia coli are more likely than commensal E. coli to be shared between heterosexual sex partners. Am J Epidemiol (2002) 1.44
Quality of care for HIV infection provided by Ryan White Program-supported versus Non-Ryan White Program-supported facilities. PLoS One (2008) 1.15
Causal system modeling in chronic disease epidemiology: a proposal. Ann Epidemiol (2007) 1.15
HIV transmission by stage of infection and pattern of sexual partnerships. Epidemiology (2010) 1.14
Choosing an appropriate bacterial typing technique for epidemiologic studies. Epidemiol Perspect Innov (2005) 1.13
Phylodynamic inference for structured epidemiological models. PLoS Comput Biol (2014) 1.12
The effect of ongoing exposure dynamics in dose response relationships. PLoS Comput Biol (2009) 1.09
Dynamics and control of infections transmitted from person to person through the environment. Am J Epidemiol (2009) 1.06
Successes and shortcomings of polio eradication: a transmission modeling analysis. Am J Epidemiol (2013) 1.06
Episodic HIV Risk Behavior Can Greatly Amplify HIV Prevalence and the Fraction of Transmissions from Acute HIV Infection. Stat Commun Infect Dis (2012) 1.00
Informing optimal environmental influenza interventions: how the host, agent, and environment alter dominant routes of transmission. PLoS Comput Biol (2010) 0.96
Inferring the source of transmission with phylogenetic data. PLoS Comput Biol (2013) 0.94
Heterogeneity in Number and Type of Sexual Contacts in a Gay Urban Cohort. Stat Commun Infect Dis (2012) 0.94
Dynamic sex roles among men who have sex with men and transmissions from primary HIV infection. Epidemiology (2010) 0.94
Model analysis of fomite mediated influenza transmission. PLoS One (2012) 0.93
Detectable signals of episodic risk effects on acute HIV transmission: strategies for analyzing transmission systems using genetic data. Epidemics (2012) 0.86
Unlocking pathogen genotyping information for public health by mathematical modeling. Trends Microbiol (2010) 0.84
Characteristics of men who have sex with men and women and women who have sex with women and men: results from the 2003 Seattle sex survey. Sex Transm Dis (2009) 0.83
Response to Rapatski BL, Suppe F, Yorke JA. HIV epidemics driven by late disease stage transmission. J Acquir Immune Defic Syndr (2006) 0.83
A dynamic dose-response model to account for exposure patterns in risk assessment: a case study in inhalation anthrax. J R Soc Interface (2010) 0.83
HIV transmissions by stage in dynamic sexual partnerships. J Theor Biol (2012) 0.80
The dynamics of methicillin-resistant Staphylococcus aureus exposure in a hospital model and the potential for environmental intervention. BMC Infect Dis (2013) 0.78
Mathematical model comparisons of potential non-typeable Haemophilus influenzae vaccine effects. J Theor Biol (2006) 0.75
Information capacity of brain machine interfaces. Conf Proc IEEE Eng Med Biol Soc (2005) 0.75