Published in AIDS on September 12, 2007
Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo. PLoS One (2009) 3.40
HIV-1 drug resistance mutations: an updated framework for the second decade of HAART. AIDS Rev (2008) 2.88
Deep sequencing to infer HIV-1 co-receptor usage: application to three clinical trials of maraviroc in treatment-experienced patients. J Infect Dis (2011) 2.60
Detection of low-frequency pretherapy chemokine (CXC motif) receptor 4 (CXCR4)-using HIV-1 with ultra-deep pyrosequencing. AIDS (2009) 2.55
Immune-driven recombination and loss of control after HIV superinfection. J Exp Med (2008) 2.34
Prediction of co-receptor usage of HIV-1 from genotype. PLoS Comput Biol (2010) 1.29
Comparative determination of HIV-1 co-receptor tropism by Enhanced Sensitivity Trofile, gp120 V3-loop RNA and DNA genotyping. Retrovirology (2010) 1.26
Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism. PLoS One (2012) 1.21
Detection of inferred CCR5- and CXCR4-using HIV-1 variants and evolutionary intermediates using ultra-deep pyrosequencing. PLoS Pathog (2011) 1.15
Concordance between two phenotypic assays and ultradeep pyrosequencing for determining HIV-1 tropism. Antimicrob Agents Chemother (2011) 1.07
Clinical significance of HIV-1 coreceptor usage. J Transl Med (2011) 1.07
Tissue-specific sequence alterations in the human immunodeficiency virus type 1 envelope favoring CCR5 usage contribute to persistence of dual-tropic virus in the brain. J Virol (2009) 1.06
Tropism testing in the clinical management of HIV-1 infection. Curr Opin HIV AIDS (2009) 1.03
Minor Variant Detection at Different Template Concentrations in HIV-1 Phenotypic and Genotypic Tropism Testing. Open Virol J (2008) 1.01
Bioinformatic prediction programs underestimate the frequency of CXCR4 usage by R5X4 HIV type 1 in brain and other tissues. AIDS Res Hum Retroviruses (2008) 1.00
Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis. BMC Med Inform Decis Mak (2011) 0.99
TROCAI (tropism coreceptor assay information): a new phenotypic tropism test and its correlation with Trofile enhanced sensitivity and genotypic approaches. J Clin Microbiol (2010) 0.99
Structure of HIV-1 quasi-species as early indicator for switches of co-receptor tropism. AIDS Res Ther (2010) 0.93
Virological response after short-term CCR5 antagonist exposure in HIV-infected patients: frequency of subjects with virological response and associated factors. Antimicrob Agents Chemother (2011) 0.92
High concordance between the position-specific scoring matrix and geno2pheno algorithms for genotypic interpretation of HIV-1 tropism: V3 length as the major cause of disagreement. J Clin Microbiol (2011) 0.92
Drug resistance and viral tropism in HIV-1 subtype C-infected patients in KwaZulu-Natal, South Africa: implications for future treatment options. J Acquir Immune Defic Syndr (2011) 0.91
Phylogenetic analysis consistent with a clinical history of sexual transmission of HIV-1 from a single donor reveals transmission of highly distinct variants. Retrovirology (2011) 0.89
Extreme genetic divergence is required for coreceptor switching in HIV-1 subtype C. J Acquir Immune Defic Syndr (2011) 0.88
Performance of genotypic algorithms for predicting HIV-1 tropism measured against the enhanced-sensitivity Trofile coreceptor tropism assay. J Clin Microbiol (2010) 0.87
Drug resistance and coreceptor usage in HIV type 1 subtype C-infected children initiating or failing highly active antiretroviral therapy in South Africa. AIDS Res Hum Retroviruses (2011) 0.87
Low frequency of CXCR4-using viruses in patients at the time of primary non-subtype-B HIV-1 infection. J Clin Microbiol (2010) 0.86
Characterization of a dual-tropic human immunodeficiency virus (HIV-1) strain derived from the prototypical X4 isolate HXBc2. Virology (2013) 0.86
Clustering of HIV-1 Subtypes Based on gp120 V3 Loop electrostatic properties. BMC Biophys (2012) 0.85
Correlation of the virological response to short-term maraviroc monotherapy with standard and deep-sequencing-based genotypic tropism prediction methods. Antimicrob Agents Chemother (2011) 0.85
Genotypic analysis of the V3 region of HIV from virologic nonresponders to maraviroc-containing regimens reveals distinct patterns of failure. Antimicrob Agents Chemother (2013) 0.85
Determination of the high prevalence of Dual/Mixed- or X4-tropism among HIV type 1 CRF01_AE in Hong Kong by genotyping and phenotyping methods. AIDS Res Hum Retroviruses (2013) 0.83
Bioinformatic analysis of HIV-1 entry and pathogenesis. Curr HIV Res (2014) 0.83
Pharmacotherapy of HIV-1 Infection: Focus on CCR5 Antagonist Maraviroc. Clin Med Ther (2009) 0.83
Persistence and emergence of X4 virus in HIV infection. Math Biosci Eng (2011) 0.83
Co-receptor usage and prediction of V3 genotyping algorithms in HIV-1 subtype B' from paid blood donors experienced anti-retroviral therapy in Chinese central province. Virol J (2010) 0.81
Accurate and efficient gp120 V3 loop structure based models for the determination of HIV-1 co-receptor usage. BMC Bioinformatics (2010) 0.81
The role of genetic variants of Stromal cell-Derived Factor 1 in pediatric HIV-1 infection and disease progression. PLoS One (2012) 0.80
Arginine insertion and loss of N-linked glycosylation site in HIV-1 envelope V3 region confer CXCR4-tropism. Sci Rep (2013) 0.80
Viral tropism and antiretroviral drug resistance in HIV-1 subtype C-infected patients failing highly active antiretroviral therapy in Johannesburg, South Africa. AIDS Res Hum Retroviruses (2013) 0.78
Relevance of early detection of HIV type 1 SI/CXCR4-using viruses in vertically infected children. AIDS Res Hum Retroviruses (2011) 0.78
Concordance of HIV type 1 tropism phenotype to predictions using web-based analysis of V3 sequences: composite algorithms may be needed to properly assess viral tropism. AIDS Res Hum Retroviruses (2011) 0.78
Predicted HIV-1 coreceptor usage among Kenya patients shows a high tendency for subtype d to be cxcr4 tropic. AIDS Res Ther (2012) 0.78
Position-specific automated processing of V3 env ultra-deep pyrosequencing data for predicting HIV-1 tropism. Sci Rep (2015) 0.77
A novel denaturing heteroduplex tracking assay for genotypic prediction of HIV-1 tropism. J Virol Methods (2012) 0.77
IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform. PLoS Comput Biol (2014) 0.76
Optimizing management of treatment-naïve and treatment-experienced HIV+ patients: the role of maraviroc. HIV AIDS (Auckl) (2010) 0.76
Profile of HIV type 1 coreceptor tropism among Kenyan patients from 2009 to 2010. AIDS Res Hum Retroviruses (2013) 0.76
A diagnostic HIV-1 tropism system based on sequence relatedness. J Clin Microbiol (2014) 0.75
A genotypic method for determining HIV-2 coreceptor usage enables epidemiological studies and clinical decision support. Retrovirology (2016) 0.75
Deep Sequencing of the HIV-1 env Gene Reveals Discrete X4 Lineages and Linkage Disequilibrium between X4 and R5 Viruses in the V1/V2 and V3 Variable Regions. J Virol (2016) 0.75
The Pace of Co-receptor Tropism Switch in HIV-1 Infected Individuals after Recent Infection. J Virol (2017) 0.75
Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc Natl Acad Sci U S A (2008) 16.54
Association of highly active antiretroviral therapy coverage, population viral load, and yearly new HIV diagnoses in British Columbia, Canada: a population-based study. Lancet (2010) 12.82
The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science (2010) 9.61
Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing. J Virol (2008) 7.54
The case for expanding access to highly active antiretroviral therapy to curb the growth of the HIV epidemic. Lancet (2006) 7.17
Single-strand specificity of APOBEC3G accounts for minus-strand deamination of the HIV genome. Nat Struct Mol Biol (2004) 6.26
Architecture and secondary structure of an entire HIV-1 RNA genome. Nature (2009) 6.12
Longitudinal community plasma HIV-1 RNA concentrations and incidence of HIV-1 among injecting drug users: prospective cohort study. BMJ (2009) 6.03
Changes in mitochondrial DNA as a marker of nucleoside toxicity in HIV-infected patients. N Engl J Med (2002) 4.77
Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID. Proc Natl Acad Sci U S A (2011) 4.68
Effect of medication adherence on survival of HIV-infected adults who start highly active antiretroviral therapy when the CD4+ cell count is 0.200 to 0.350 x 10(9) cells/L. Ann Intern Med (2003) 4.46
Adaptation of HIV-1 to human leukocyte antigen class I. Nature (2009) 4.24
Adherence-resistance relationships for protease and non-nucleoside reverse transcriptase inhibitors explained by virological fitness. AIDS (2006) 3.70
Expanded access to highly active antiretroviral therapy: a potentially powerful strategy to curb the growth of the HIV epidemic. J Infect Dis (2008) 3.38
Impact of HIV-1 subtype and antiretroviral therapy on protease and reverse transcriptase genotype: results of a global collaboration. PLoS Med (2005) 3.17
Improved virological outcomes in British Columbia concomitant with decreasing incidence of HIV type 1 drug resistance detection. Clin Infect Dis (2010) 3.12
Continued improvement in survival among HIV-infected individuals with newer forms of highly active antiretroviral therapy. AIDS (2007) 3.04
Multiple V1/V2 env variants are frequently present during primary infection with human immunodeficiency virus type 1. J Virol (2004) 2.91
Evidence of differential HLA class I-mediated viral evolution in functional and accessory/regulatory genes of HIV-1. PLoS Pathog (2007) 2.81
Prevalence of CXCR4 tropism among antiretroviral-treated HIV-1-infected patients with detectable viremia. J Infect Dis (2006) 2.74
Reduced susceptibility to vancomycin influences pathogenicity in Staphylococcus aureus infection. J Infect Dis (2009) 2.72
A simple, dynamic measure of antiretroviral therapy adherence predicts failure to maintain HIV-1 suppression. J Infect Dis (2006) 2.61
Deep sequencing to infer HIV-1 co-receptor usage: application to three clinical trials of maraviroc in treatment-experienced patients. J Infect Dis (2011) 2.60
Detection of low-frequency pretherapy chemokine (CXC motif) receptor 4 (CXCR4)-using HIV-1 with ultra-deep pyrosequencing. AIDS (2009) 2.55
Predicting HIV coreceptor usage on the basis of genetic and clinical covariates. Antivir Ther (2007) 2.49
When to initiate antiretroviral therapy in HIV-1-infected adults: a review for clinicians and patients. Lancet Infect Dis (2005) 2.48
Challenges in detecting HIV persistence during potentially curative interventions: a study of the Berlin patient. PLoS Pathog (2013) 2.44
Molecular and clinical epidemiology of CXCR4-using HIV-1 in a large population of antiretroviral-naive individuals. J Infect Dis (2005) 2.42
N348I in the connection domain of HIV-1 reverse transcriptase confers zidovudine and nevirapine resistance. PLoS Med (2007) 2.41
Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag. PLoS Comput Biol (2008) 2.32
Accuracy of the TRUGENE HIV-1 genotyping kit. J Clin Microbiol (2003) 2.32
Chemical dependency treatment outcomes of residents in anesthesiology: results of a survey. Anesth Analg (2005) 2.29
Variability in the human immunodeficiency virus type 1 gp120 Env protein linked to phenotype-associated changes in the V3 loop. J Virol (2002) 2.19
HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef proteins. PLoS One (2009) 2.16
Vertical T cell immunodominance and epitope entropy determine HIV-1 escape. J Clin Invest (2012) 2.05
First confirmed cases of Middle East respiratory syndrome coronavirus (MERS-CoV) infection in the United States, updated information on the epidemiology of MERS-CoV infection, and guidance for the public, clinicians, and public health authorities - May 2014. MMWR Morb Mortal Wkly Rep (2014) 2.00
Magnitude of virologic blips is associated with a higher risk for virologic rebound in HIV-infected individuals: a recurrent events analysis. J Infect Dis (2012) 2.00
Increased resilience to the development of drug resistance with modern boosted protease inhibitor-based highly active antiretroviral therapy. J Infect Dis (2008) 1.93
Impact of baseline viral load and adherence on survival of HIV-infected adults with baseline CD4 cell counts > or = 200 cells/microl. AIDS (2006) 1.92
A new perspective on V3 phenotype prediction. AIDS Res Hum Retroviruses (2003) 1.92
The direct costs of HIV/AIDS care. Lancet Infect Dis (2006) 1.87
Emergence of drug resistance is associated with an increased risk of death among patients first starting HAART. PLoS Med (2006) 1.85
Population-based V3 genotypic tropism assay: a retrospective analysis using screening samples from the A4001029 and MOTIVATE studies. AIDS (2010) 1.83
The impact of adherence on CD4 cell count responses among HIV-infected patients. J Acquir Immune Defic Syndr (2004) 1.82
Early selection in Gag by protective HLA alleles contributes to reduced HIV-1 replication capacity that may be largely compensated for in chronic infection. J Virol (2010) 1.82
Interoperability with Moby 1.0--it's better than sharing your toothbrush! Brief Bioinform (2008) 1.80
Replacement of the P1 amino acid of human immunodeficiency virus type 1 Gag processing sites can inhibit or enhance the rate of cleavage by the viral protease. J Virol (2002) 1.71
Compartmentalization and clonal amplification of HIV-1 variants in the cerebrospinal fluid during primary infection. J Virol (2009) 1.70
Is there a baseline CD4 cell count that precludes a survival response to modern antiretroviral therapy? AIDS (2003) 1.69
Characterization and selection of HIV-1 subtype C isolates for use in vaccine development. AIDS Res Hum Retroviruses (2003) 1.68
Risk of viral failure declines with duration of suppression on highly active antiretroviral therapy irrespective of adherence level. J Acquir Immune Defic Syndr (2010) 1.68
Human leukocyte antigen-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection. AIDS (2008) 1.67
HIV-1 drug resistance surveillance using dried whole blood spots. Antivir Ther (2007) 1.67
Compartmentalized human immunodeficiency virus type 1 originates from long-lived cells in some subjects with HIV-1-associated dementia. PLoS Pathog (2009) 1.66
Covariation of amino acid positions in HIV-1 protease. Virology (2003) 1.65
Increased human immunodeficiency virus type 1 (HIV-1) env compartmentalization in the presence of HIV-1-associated dementia. J Virol (2005) 1.65
Improved detection of CXCR4-using HIV by V3 genotyping: application of population-based and "deep" sequencing to plasma RNA and proviral DNA. J Acquir Immune Defic Syndr (2010) 1.65
Whole genome characterization of the mechanisms of daptomycin resistance in clinical and laboratory derived isolates of Staphylococcus aureus. PLoS One (2012) 1.59
Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections. PLoS Pathog (2011) 1.57
HLA-associated viral mutations are common in human immunodeficiency virus type 1 elite controllers. J Virol (2009) 1.54
Deep V3 sequencing for HIV type 1 tropism in treatment-naive patients: a reanalysis of the MERIT trial of maraviroc. Clin Infect Dis (2011) 1.53
Semen-specific genetic characteristics of human immunodeficiency virus type 1 env. J Virol (2005) 1.52
Clinical and immunological impact of HIV envelope V3 sequence variation after starting initial triple antiretroviral therapy. AIDS (2004) 1.51
The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time--an ultra-deep approach. PLoS Comput Biol (2010) 1.48
Processing sites in the human immunodeficiency virus type 1 (HIV-1) Gag-Pro-Pol precursor are cleaved by the viral protease at different rates. Retrovirology (2005) 1.48
Automating HIV drug resistance genotyping with RECall, a freely accessible sequence analysis tool. J Clin Microbiol (2012) 1.48
HIV-1 Populations in Semen Arise through Multiple Mechanisms. PLoS Pathog (2010) 1.47
HIV-1 replication in the central nervous system occurs in two distinct cell types. PLoS Pathog (2011) 1.45
Turnover of env variable region 1 and 2 genotypes in subjects with late-stage human immunodeficiency virus type 1 infection. J Virol (2003) 1.44
Connection domain mutations N348I and A360V in HIV-1 reverse transcriptase enhance resistance to 3'-azido-3'-deoxythymidine through both RNase H-dependent and -independent mechanisms. J Biol Chem (2008) 1.42
A simple screening approach to reduce B*5701-associated abacavir hypersensitivity on the basis of sequence variation in HIV reverse transcriptase. Clin Infect Dis (2007) 1.41
Alphavirus replicon particles as candidate HIV vaccines. IUBMB Life (2002) 1.41
Renal FcRn reclaims albumin but facilitates elimination of IgG. J Am Soc Nephrol (2009) 1.40
Cross-sectional characterization of HIV-1 env compartmentalization in cerebrospinal fluid over the full disease course. AIDS (2009) 1.40
Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usage. PLoS Comput Biol (2007) 1.39
Population-based sequencing of the V3-loop can predict the virological response to maraviroc in treatment-naive patients of the MERIT trial. J Acquir Immune Defic Syndr (2012) 1.38
Compensatory mutations at the HIV cleavage sites p7/p1 and p1/p6-gag in therapy-naive and therapy-experienced patients. Antivir Ther (2006) 1.37
Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1. Mol Biol Evol (2009) 1.37
Measuring allelic heterogeneity in Plasmodium falciparum by a heteroduplex tracking assay. Am J Trop Med Hyg (2005) 1.35
Role of low CD4 levels in the influence of human immunodeficiency virus type 1 envelope V1 and V2 regions on entry and spread in macrophages. J Virol (2005) 1.34
Determining human immunodeficiency virus coreceptor use in a clinical setting: degree of correlation between two phenotypic assays and a bioinformatic model. J Clin Microbiol (2006) 1.33
Correlation between env V1/V2 region diversification and neutralizing antibodies during primary infection by simian immunodeficiency virus sm in rhesus macaques. J Virol (2004) 1.32
Cross-sectional detection of acute HIV infection: timing of transmission, inflammation and antiretroviral therapy. PLoS One (2011) 1.32
A strongly transdominant mutation in the human immunodeficiency virus type 1 gag gene defines an Achilles heel in the virus life cycle. J Virol (2009) 1.30
Correlates of protective cellular immunity revealed by analysis of population-level immune escape pathways in HIV-1. J Virol (2012) 1.29
2004: which HIV-1 drug resistance mutations are common in clinical practice? AIDS Rev (2004) 1.29