Published in AIDS on January 14, 2009
The global transmission network of HIV-1. J Infect Dis (2013) 1.68
Characterizing HIV transmission networks across the United States. Clin Infect Dis (2012) 1.54
Using HIV networks to inform real time prevention interventions. PLoS One (2014) 1.29
Evaluating the impact of Mexico's drug policy reforms on people who inject drugs in Tijuana, B.C., Mexico, and San Diego, CA, United States: a binational mixed methods research agenda. Harm Reduct J (2014) 1.22
Epistemic fault lines in biomedical and social approaches to HIV prevention. J Int AIDS Soc (2011) 1.14
Using Molecular HIV Surveillance Data to Understand Transmission Between Subpopulations in the United States. J Acquir Immune Defic Syndr (2015) 1.09
HIV-1 clade B pol evolution following primary infection. PLoS One (2013) 1.07
Developing and evaluating comprehensive HIV infection control strategies: issues and challenges. Clin Infect Dis (2010) 1.02
Using HIV transmission networks to investigate community effects in HIV prevention trials. PLoS One (2011) 0.94
Antiretroviral therapy as prevention: linking the mainframe to Main Street. Clin Infect Dis (2011) 0.92
Associations between phylogenetic clustering and HLA profile among HIV-infected individuals in San Diego, California. J Infect Dis (2012) 0.90
HIV Transmission Networks in the San Diego-Tijuana Border Region. EBioMedicine (2015) 0.90
Transmission clustering among newly diagnosed HIV patients in Chicago, 2008 to 2011: using phylogenetics to expand knowledge of regional HIV transmission patterns. J Acquir Immune Defic Syndr (2015) 0.90
Evolutionary history of HIV-1 subtype B and CRF01_AE transmission clusters among men who have sex with men (MSM) in Kuala Lumpur, Malaysia. PLoS One (2013) 0.87
Near real-time monitoring of HIV transmission hotspots from routine HIV genotyping: an implementation case study. Lancet HIV (2016) 0.85
Targeting HIV Prevention Based on Molecular Epidemiology Among Deeply Sampled Subnetworks of Men Who Have Sex With Men. Clin Infect Dis (2015) 0.84
Molecular analysis allows inference into HIV transmission among young men who have sex with men in the United States. AIDS (2015) 0.83
The relatedness of HIV epidemics in the United States-Mexico border region. AIDS Res Hum Retroviruses (2010) 0.82
Linkage of viral sequences among HIV-infected village residents in Botswana: estimation of linkage rates in the presence of missing data. PLoS Comput Biol (2014) 0.82
Centralized HIV Program Oversight. Medicine (Baltimore) (2015) 0.82
Community HIV-1 drug resistance is associated with transmitted drug resistance. HIV Med (2014) 0.80
Phylodynamic profile of HIV-1 subtype B, CRF01_AE and the recently emerging CRF51_01B among men who have sex with men (MSM) in Singapore. PLoS One (2013) 0.80
Partner services in adults with acute and early HIV infection, San Diego, 1996-2014. AIDS (2016) 0.80
Impact of human immunodeficiency virus type-1 sequence diversity on antiretroviral therapy outcomes. Viruses (2014) 0.79
Prevalence of Transmitted HIV Drug Resistance Among Recently Infected Persons in San Diego, CA 1996-2013. J Acquir Immune Defic Syndr (2016) 0.78
The dynamics of the HIV epidemic among men who have sex with men (MSM) from 2005 to 2012 in Shenzhen, China. Sci Rep (2016) 0.77
Phylogenetic Investigation of a Statewide HIV-1 Epidemic Reveals Ongoing and Active Transmission Networks Among Men Who Have Sex With Men. J Acquir Immune Defic Syndr (2015) 0.77
Transmitted HIV drug resistance in treatment-naive Romanian patients. J Med Virol (2013) 0.77
Human genomics and preparedness for infectious threats. Genome Med (2009) 0.77
Can we broaden the applicability of HIV transmission cluster analyses? AIDS (2012) 0.77
Social and Genetic Networks of HIV-1 Transmission in New York City. PLoS Pathog (2017) 0.77
Local phylogenetic analysis identifies distinct trends in transmitted HIV drug resistance: implications for public health interventions. BMC Infect Dis (2013) 0.77
Molecular epidemiology identifies HIV transmission networks associated with younger age and heterosexual exposure among Korean individuals. J Med Virol (2016) 0.76
Phylogenetic Evidence of HIV-1 Transmission Between Adult and Adolescent Men Who Have Sex with Men. AIDS Res Hum Retroviruses (2016) 0.75
HIV-1 Infection and Transmission Networks of Younger People in Chicago, Illinois, 2005-2011. Public Health Rep (2016) 0.75
HIV-1 transmission patterns in antiretroviral therapy-naïve, HIV-infected North Americans based on phylogenetic analysis by population level and ultra-deep DNA sequencing. PLoS One (2014) 0.75
Concurrency and HIV transmission network characteristics among MSM with recent HIV infection. AIDS (2016) 0.75
Ensuring privacy in the study of pathogen genetics. Lancet Infect Dis (2014) 0.75
Identifying Transmission Clusters with Cluster Picker and HIV-TRACE. AIDS Res Hum Retroviruses (2016) 0.75
Spatiotemporal dynamics of HIV-1 transmission in France (1999-2014) and impact of targeted prevention strategies. Retrovirology (2017) 0.75
Interrupting transmission of HIV and other sexually transmitted infections in Rhode Island. Med Health R I (2012) 0.75
Expanding HIV-1 subtype B transmission networks among men who have sex with men in Poland. PLoS One (2017) 0.75
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89
Estimation of HIV incidence in the United States. JAMA (2008) 21.27
HyPhy: hypothesis testing using phylogenies. Bioinformatics (2004) 17.33
Review of sampling hard-to-reach and hidden populations for HIV surveillance. AIDS (2005) 13.09
Rapid evolution of the neutralizing antibody response to HIV type 1 infection. Proc Natl Acad Sci U S A (2003) 12.75
High rates of forward transmission events after acute/early HIV-1 infection. J Infect Dis (2007) 7.70
Evolution and transmission of stable CTL escape mutations in HIV infection. Nature (2001) 6.57
Recombination in HIV-1. Nature (1995) 5.72
Episodic sexual transmission of HIV revealed by molecular phylodynamics. PLoS Med (2008) 4.76
HIV-1 protease and reverse transcriptase mutations for drug resistance surveillance. AIDS (2007) 3.94
Molecular epidemiology of HIV transmission in a dental practice. Science (1992) 3.10
Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups. Proc Natl Acad Sci U S A (2005) 3.04
Real-time, universal screening for acute HIV infection in a routine HIV counseling and testing population. JAMA (2002) 2.94
A multicenter observational study of the potential benefits of initiating combination antiretroviral therapy during acute HIV infection. J Infect Dis (2006) 2.88
Routine surveillance for the detection of acute and recent HIV infections and transmission of antiretroviral resistance. AIDS (2006) 2.72
Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak. Nature (2006) 2.61
Transmission of HIV-1 during primary infection: relationship to sexual risk and sexually transmitted infections. AIDS (2005) 2.51
Selection forces and constraints on retroviral sequence variation. Science (2001) 2.17
A molecular epidemiological approach to studying the transmission of tuberculosis in Amsterdam. Clin Infect Dis (1997) 1.87
Molecular subtyping of Treponema pallidum in an Arizona County with increasing syphilis morbidity: use of specimens from ulcers and blood. J Infect Dis (2001) 1.86
Evolution of human immunodeficiency virus type 1 nucleotide sequence diversity among close contacts. Proc Natl Acad Sci U S A (1991) 1.58
Herpes simplex virus 2 serostatus and viral loads of HIV-1 in blood and semen as risk factors for HIV transmission among men who have sex with men. AIDS (2008) 1.55
Laboratory testing and rapid HIV assays: applications for HIV surveillance in hard-to-reach populations. AIDS (2001) 1.52
Clinical utility of HIV standard genotyping among antiretroviral-naive individuals with unknown duration of infection. Clin Infect Dis (2006) 1.48
HIV partner notification outcomes for HIV-infected patients by duration of infection, San Francisco, 2004 to 2006. J Acquir Immune Defic Syndr (2007) 1.27
Molecular analysis of HIV strains from a cluster of worker infections in the adult film industry, Los Angeles 2004. AIDS (2006) 1.25
A typing system for neisseria gonorrhoeae based on biotinylated oligonucleotide probes to PIB gene variable regions. J Infect Dis (2000) 1.10
Evidence for positive selection driving the evolution of HIV-1 env under potent antiviral therapy. Virology (2001) 1.06
Method used to identify previously undiagnosed infections in the HIV outbreak at Glenochil prison. Epidemiol Infect (1999) 0.96
Lessons from an HIV transmission pair. J Infect Dis (2007) 0.94
Active methamphetamine use is associated with transmitted drug resistance to non-nucleoside reverse transcriptase inhibitors in individuals with HIV infection of unknown duration. Open AIDS J (2007) 0.93
Human immunodeficiency virus transmission in household settings--United States. MMWR Morb Mortal Wkly Rep (1994) 0.82
Sex, Crimes, and HIV. Focus (2007) 0.81
HyPhy: hypothesis testing using phylogenies. Bioinformatics (2004) 17.33
Rapid evolution of the neutralizing antibody response to HIV type 1 infection. Proc Natl Acad Sci U S A (2003) 12.75
Antiretroviral treatment of adult HIV infection: 2008 recommendations of the International AIDS Society-USA panel. JAMA (2008) 11.72
Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol (2005) 10.21
Memory CD8+ T cells vary in differentiation phenotype in different persistent virus infections. Nat Med (2002) 10.03
Antiretroviral-drug resistance among patients recently infected with HIV. N Engl J Med (2002) 9.70
The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science (2010) 9.61
Antiretroviral treatment of adult HIV infection: 2010 recommendations of the International AIDS Society-USA panel. JAMA (2010) 9.26
Antiretroviral treatment of adult HIV infection: 2012 recommendations of the International Antiviral Society-USA panel. JAMA (2012) 8.94
Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics (2005) 8.62
Treatment for adult HIV infection: 2006 recommendations of the International AIDS Society-USA panel. JAMA (2006) 7.49
28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res (2007) 6.42
Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics (2010) 6.14
Automated phylogenetic detection of recombination using a genetic algorithm. Mol Biol Evol (2006) 5.94
Depletion of latent HIV-1 infection in vivo: a proof-of-concept study. Lancet (2005) 5.75
Antiretroviral treatment for adult HIV infection in 2002: updated recommendations of the International AIDS Society-USA Panel. JAMA (2002) 5.56
Antiretroviral drug resistance testing in adult HIV-1 infection: 2008 recommendations of an International AIDS Society-USA panel. Clin Infect Dis (2008) 5.20
GARD: a genetic algorithm for recombination detection. Bioinformatics (2006) 4.88
Evaluation of respondent-driven sampling. Epidemiology (2012) 4.75
Antiretroviral drug resistance testing in adults infected with human immunodeficiency virus type 1: 2003 recommendations of an International AIDS Society-USA Panel. Clin Infect Dis (2003) 4.51
Dissecting the neutralizing antibody specificities of broadly neutralizing sera from human immunodeficiency virus type 1-infected donors. J Virol (2007) 4.45
Enhanced CD4+ T-cell recovery with earlier HIV-1 antiretroviral therapy. N Engl J Med (2013) 4.26
Comparative analysis of measures of viral reservoirs in HIV-1 eradication studies. PLoS Pathog (2013) 4.05
Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection. Proc Natl Acad Sci U S A (2005) 3.94
Effect of treatment, during primary infection, on establishment and clearance of cellular reservoirs of HIV-1. J Infect Dis (2005) 3.93
Detecting individual sites subject to episodic diversifying selection. PLoS Genet (2012) 3.77
Treatment for adult HIV infection: 2004 recommendations of the International AIDS Society-USA Panel. JAMA (2004) 3.74
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
Update of the drug resistance mutations in HIV-1: March 2013. Top Antivir Med (2013) 3.58
Highly precise measurement of HIV DNA by droplet digital PCR. PLoS One (2013) 3.53
Update of the drug resistance mutations in HIV-1: December 2009. Top HIV Med (2009) 3.52
Immune activation and CD8+ T-cell differentiation towards senescence in HIV-1 infection. PLoS Biol (2004) 3.20
An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1. PLoS Comput Biol (2009) 3.11
Update of the drug resistance mutations in HIV-1: Fall 2006. Top HIV Med (2006) 3.06
Persistence of transmitted drug resistance among subjects with primary human immunodeficiency virus infection. J Virol (2008) 3.04
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
A random effects branch-site model for detecting episodic diversifying selection. Mol Biol Evol (2011) 2.88
Characterization of human immunodeficiency virus type 1 (HIV-1) envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B. J Virol (2005) 2.83
Increase in 2-long terminal repeat circles and decrease in D-dimer after raltegravir intensification in patients with treated HIV infection: a randomized, placebo-controlled trial. J Infect Dis (2013) 2.82
Update of the drug resistance mutations in HIV-1: 2007. Top HIV Med (2007) 2.79
FUBAR: a fast, unconstrained bayesian approximation for inferring selection. Mol Biol Evol (2013) 2.73
Evaluation of an HIV nucleic acid testing program with automated Internet and voicemail systems to deliver results. Ann Intern Med (2010) 2.69
A genetic algorithm approach to detecting lineage-specific variation in selection pressure. Mol Biol Evol (2004) 2.65
Transmission fitness of drug-resistant human immunodeficiency virus and the prevalence of resistance in the antiretroviral-treated population. J Infect Dis (2003) 2.54
Adaptation to different human populations by HIV-1 revealed by codon-based analyses. PLoS Comput Biol (2006) 2.48
Purifying selection can obscure the ancient age of viral lineages. Mol Biol Evol (2011) 2.43
Immune-driven recombination and loss of control after HIV superinfection. J Exp Med (2008) 2.34
Simian immunodeficiency virus engrafted with human immunodeficiency virus type 1 (HIV-1)-specific epitopes: replication, neutralization, and survey of HIV-1-positive plasma. J Virol (2006) 2.33
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
Whither or wither microbicides? Science (2008) 2.17
Phylodynamics of infectious disease epidemics. Genetics (2009) 2.15
Syringe possession arrests are associated with receptive syringe sharing in two Mexico-US border cities. Addiction (2007) 2.14
Barriers to a cure for HIV: new ways to target and eradicate HIV-1 reservoirs. Lancet (2013) 2.11
Dynamics of total, linear nonintegrated, and integrated HIV-1 DNA in vivo and in vitro. J Infect Dis (2008) 2.08
Lack of neutralizing antibody response to HIV-1 predisposes to superinfection. Virology (2006) 2.07
Multiple measures of HIV burden in blood and tissue are correlated with each other but not with clinical parameters in aviremic subjects. AIDS (2003) 2.05
Update of the drug resistance mutations in HIV-1: Fall 2005. Top HIV Med (2005) 2.04
Role of seminal shedding of herpesviruses in HIV Type 1 Transmission. J Infect Dis (2012) 1.99
A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza A virus. Mol Biol Evol (2008) 1.96
Incidence of HIV superinfection following primary infection. JAMA (2004) 1.92
Phylodynamic reconstruction reveals norovirus GII.4 epidemic expansions and their molecular determinants. PLoS Pathog (2010) 1.88
DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites. Biotechniques (2010) 1.88
A phase II randomized study of HIV-specific T-cell gene therapy in subjects with undetectable plasma viremia on combination antiretroviral therapy. Mol Ther (2002) 1.83
An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope. PLoS Comput Biol (2007) 1.82
Phylogenetic evidence for adaptive evolution of dengue viruses in nature. J Gen Virol (2002) 1.82
National prevalence of methicillin-resistant Staphylococcus aureus in inpatients at US health care facilities, 2006. Am J Infect Control (2007) 1.79
Human immunodeficiency virus type 1 clade B superinfection: evidence for differential immune containment of distinct clade B strains. J Virol (2005) 1.77
The origins of sexually transmitted HIV among men who have sex with men. Sci Transl Med (2010) 1.76
Transmission behaviors of recently HIV-infected men who have sex with men. J Acquir Immune Defic Syndr (2006) 1.73
Drug resistance mutations in HIV-1. Top HIV Med (2003) 1.72
Virologic monitoring of hepatitis B virus therapy in clinical trials and practice: recommendations for a standardized approach. Gastroenterology (2007) 1.72