James I. Mullins

Curiously modern DNA for a "250 million-year-old" bacterium.

Evidence for human immunodeficiency virus type 1 replication in vivo in CD14(+) monocytes and its potential role as a source of virus in patients on highly active antiretroviral therapy.

Site-directed mutagenesis facilitated by DpnI selection on hemimethylated DNA.

Equal plasma viral loads predict a similar rate of CD4+ T cell decline in human immunodeficiency virus (HIV) type 1- and HIV-2-infected individuals from Senegal, West Africa.

Molecular cloning and characterization of Antheraea mylitta cytoplasmic polyhedrosis virus genome segment 9.

Human immunodeficiency virus type 1 bound to B cells: relationship to virus replicating in CD4+ T cells and circulating in plasma.

Selection for human immunodeficiency virus type 1 recombinants in a patient with rapid progression to AIDS.

Virus population homogenization following acute human immunodeficiency virus type 1 infection.

Cellular gene expression upon human immunodeficiency virus type 1 infection of CD4(+)-T-cell lines.

Genetic characterization of rebounding human immunodeficiency virus type 1 in plasma during multiple interruptions of highly active antiretroviral therapy.

Consensus and ancestral state HIV vaccines.

Evolutionary indicators of human immunodeficiency virus type 1 reservoirs and compartments.

Multiple viral genetic analyses detect low-level human immunodeficiency virus type 1 replication during effective highly active antiretroviral therapy.

Persistence of extraordinarily low levels of genetically homogeneous human immunodeficiency virus type 1 in exposed seronegative individuals.

Predicting demographic group structures based on DNA sequence data.

Enhanced detection of human immunodeficiency virus type 1-specific T-cell responses to highly variable regions by using peptides based on autologous virus sequences.

Potential impact of recombination on sitewise approaches for detecting positive natural selection.

Molecular epidemiology of dual HIV-1/HIV-2 seropositive adults from Senegal, West Africa.

Importance and detection of virus reservoirs and compartments of HIV infection.

Improved coreceptor usage prediction and genotypic monitoring of R5-to-X4 transition by motif analysis of human immunodeficiency virus type 1 env V3 loop sequences.

Dual HIV-1 infection associated with rapid disease progression.

Influence of random genetic drift on human immunodeficiency virus type 1 env evolution during chronic infection.

Clinical and immunological impact of HIV envelope V3 sequence variation after starting initial triple antiretroviral therapy.

Differences in the expressed HLA class I alleles effect the differential clustering of HIV type 1-specific T cell responses in infected Chinese and caucasians.

Persistence of low levels of simian immunodeficiency virus in macaques that were transiently viremic by conventional testing.

Compartmentalization of human immunodeficiency virus type 1 between blood monocytes and CD4+ T cells during infection.

Immunogen sequence: the fourth tier of AIDS vaccine design.

Pervasive genomic recombination of HIV-1 in vivo.

Molecular clock-like evolution of human immunodeficiency virus type 1.

Longitudinal and cross-sectional studies of HIV-1 RNA and DNA loads in blood and the female genital tract.

No evidence for recombination between HIV type 1 and HIV type 2 within the envelope region in dually seropositive individuals from Senegal.

Preferential detection of HIV subtype C' over subtype A in cervical cells from a dually infected woman.

Changes in human immunodeficiency virus type 1 fitness and genetic diversity during disease progression.

Evidence that low-level viremias during effective highly active antiretroviral therapy result from two processes: expression of archival virus and replication of virus.

Nef induces multiple genes involved in cholesterol synthesis and uptake in human immunodeficiency virus type 1-infected T cells.

HIV-infected individuals receiving effective antiviral therapy for extended periods of time continually replenish their viral reservoir.

Control of human immunodeficiency virus replication by cytotoxic T lymphocytes targeting subdominant epitopes.

Sampling designs for HIV molecular epidemiology with application to Honduras.

Waiting times for the appearance of cytotoxic T-lymphocyte escape mutants in chronic HIV-1 infection.

Conflicting selective forces affect T cell receptor contacts in an immunodominant human immunodeficiency virus epitope.

Human immunodeficiency virus type 1 env evolves toward ancestral states upon transmission to a new host.

Fitness cost of escape mutations in p24 Gag in association with control of human immunodeficiency virus type 1.

Density-dependent decay in HIV-1 dynamics.

A reliable phenotype predictor for human immunodeficiency virus type 1 subtype C based on envelope V3 sequences.

Large-scale amplification, cloning and sequencing of near full-length HIV-1 subtype C genomes.

Evolution of intrahost HIV-1 genetic diversity during chronic infection.

Selection on the human immunodeficiency virus type 1 proteome following primary infection.

Differential selection pressure exerted on HIV by CTL targeting identical epitopes but restricted by distinct HLA alleles from the same HLA supertype.

Comprehensive epitope analysis of cross-clade Gag-specific T-cell responses in individuals with early HIV-1 infection in the US epidemic.

CD8+ T-cell responses to different HIV proteins have discordant associations with viral load.

Control of human immunodeficiency virus type 1 is associated with HLA-B*13 and targeting of multiple gag-specific CD8+ T-cell epitopes.

Extensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections.

Presenting plasma HIV RNA level and rate of CD4 T-cell decline.

Enhanced detection of human immunodeficiency virus type 1 (HIV-1) Nef-specific T cells recognizing multiple variants in early HIV-1 infection.

Founder effects in the assessment of HIV polymorphisms and HLA allele associations.

Coping with viral diversity in HIV vaccine design.

Decay of the HIV reservoir in patients receiving antiretroviral therapy for extended periods: implications for eradication of virus.

Compensatory mutation partially restores fitness and delays reversion of escape mutation within the immunodominant HLA-B*5703-restricted Gag epitope in chronic human immunodeficiency virus type 1 infection.

Prevalence and genetic diversity of HIV type 1 subtypes A and D in women attending antenatal clinics in Uganda.

Reconstruction and function of ancestral center-of-tree human immunodeficiency virus type 1 proteins.

HIV-specific probabilistic models of protein evolution.

ViroBLAST: a stand-alone BLAST web server for flexible queries of multiple databases and user's datasets.

Methods used to examine compartmentalization of viral populations between the genital tract and peripheral blood.

HIV type 1 superinfection with a dual-tropic virus and rapid progression to AIDS: a case report.

HIV-1 over time: fitness loss or robustness gain?

Evolution of human immunodeficiency virus type 1 cytotoxic T-lymphocyte epitopes: fitness-balanced escape.

Recognition of HIV-1 peptides by host CTL is related to HIV-1 similarity to human proteins.

Novel cytotoxic T-lymphocyte escape mutation by a three-amino-acid insertion in the human immunodeficiency virus type 1 p6Pol and p6Gag late domain associated with drug resistance.

HIV-1 group M conserved elements vaccine.

Blood monocytes harbor HIV type 1 strains with diversified phenotypes including macrophage-specific CCR5 virus.

Broad and Gag-biased HIV-1 epitope repertoires are associated with lower viral loads.

Lack of evidence for changing virulence of HIV-1 in North America.

Persistence of HIV in gut-associated lymphoid tissue despite long-term antiretroviral therapy.

Increased detection of HIV-specific T cell responses by combination of central sequences with comparable immunogenicity.

Env length and N-linked glycosylation following transmission of human immunodeficiency virus Type 1 subtype B viruses.

HIV-1 variation before seroconversion in men who have sex with men: analysis of acute/early HIV infection in the multicenter AIDS cohort study.

Male genital tract compartmentalization of human immunodeficiency virus type 1 (HIV).

HLA class I-driven evolution of human immunodeficiency virus type 1 subtype c proteome: immune escape and viral load.

Comparison of immunogen designs that optimize peptide coverage: reply to Fischer et al.

Central role of reverting mutations in HLA associations with human immunodeficiency virus set point.

Evolution of CCR5 use before and during coreceptor switching.

Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag.

Emergence of multiclass drug-resistance in HIV-2 in antiretroviral-treated individuals in Senegal: implications for HIV-2 treatment in resouce-limited West Africa.

Rare HLA drive additional HIV evolution compared to more frequent alleles.

Monotypic human immunodeficiency virus type 1 genotypes across the uterine cervix and in blood suggest proliferation of cells with provirus.

Variable fitness impact of HIV-1 escape mutations to cytotoxic T lymphocyte (CTL) response.

Increased mutations in Env and Pol suggest greater HIV-1 replication in sputum-derived viruses compared with blood-derived viruses.

Viral evolution and escape during primary human immunodeficiency virus-1 infection: implications for vaccine design.

Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes.

HIV-1 superinfection in the antiretroviral therapy era: are seroconcordant sexual partners at risk?

Preinfection human immunodeficiency virus (HIV)-specific cytotoxic T lymphocytes failed to prevent HIV type 1 infection from strains genetically unrelated to viruses in long-term exposed partners.

Fidelity of SNP array genotyping using Epstein Barr virus-transformed B-lymphocyte cell lines: implications for genome-wide association studies.

Evidence for limited genetic compartmentalization of HIV-1 between lung and blood.

Conserved HIV-1 epitopes continuously elicit subdominant cytotoxic T-lymphocyte responses.

Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1.

Multistage genomewide association study identifies a locus at 1q41 associated with rate of HIV-1 disease progression to clinical AIDS.

Virus-specific CD8+ T-cell responses better define HIV disease progression than HLA genotype.

Restriction of HIV-1 genotypes in breast milk does not account for the population transmission genetic bottleneck that occurs following transmission.

DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites.

Genetic analyses of HIV-1 env sequences demonstrate limited compartmentalization in breast milk and suggest viral replication within the breast that increases with mastitis.

Multiple-cohort genetic association study reveals CXCR6 as a new chemokine receptor involved in long-term nonprogression to AIDS.

Amino-acid co-variation in HIV-1 Gag subtype C: HLA-mediated selection pressure and compensatory dynamics.

Viral evolution and escape during acute HIV-1 infection.

Estimating the impact of plasma HIV-1 RNA reductions on heterosexual HIV-1 transmission risk.

Comment on "The origins of sexually transmitted HIV among men who have sex with men".

Dendritic cells reveal a broad range of MHC class I epitopes for HIV-1 in persons with suppressed viral load on antiretroviral therapy.

Screening low-frequency SNPS from genome-wide association study reveals a new risk allele for progression to AIDS.

HIV-1 envelope subregion length variation during disease progression.

Preclinical evaluation of HIV-1 therapeutic ex vivo dendritic cell vaccines expressing consensus Gag antigens and conserved Gag epitopes.

Mutation of HIV-1 genomes in a clinical population treated with the mutagenic nucleoside KP1461.

Dynamics of viral evolution and CTL responses in HIV-1 infection.

Genetic impact of vaccination on breakthrough HIV-1 sequences from the STEP trial.

Viral linkage in HIV-1 seroconverters and their partners in an HIV-1 prevention clinical trial.

Increased breadth and depth of cytotoxic T lymphocytes responses against HIV-1-B Nef by inclusion of epitope variant sequences.

Genital HIV-1 RNA predicts risk of heterosexual HIV-1 transmission.

Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes.

Preparing for the availability of a partially effective HIV vaccine: some lessons from other licensed vaccines.

CD39/adenosine pathway is involved in AIDS progression.

HIV-2 integrase variation in integrase inhibitor-naïve adults in Senegal, West Africa.

Phenotypic susceptibility of HIV-2 to raltegravir: integrase mutations Q148R and N155H confer raltegravir resistance.

Is the virulence of HIV changing? A meta-analysis of trends in prognostic markers of HIV disease progression and transmission.

Definition of the viral targets of protective HIV-1-specific T cell responses.

Genomewide association study for determinants of HIV-1 acquisition and viral set point in HIV-1 serodiscordant couples with quantified virus exposure.

CTL responses of high functional avidity and broad variant cross-reactivity are associated with HIV control.

Towards an HIV cure: a global scientific strategy.

MRKAd5 HIV-1 Gag/Pol/Nef Vaccine-Induced T-Cell Responses Inadequately Predict Distance of Breakthrough HIV-1 Sequences to the Vaccine or Viral Load.

Increased HIV-1 vaccine efficacy against viruses with genetic signatures in Env V2.

Three main mutational pathways in HIV-2 lead to high-level raltegravir and elvitegravir resistance: implications for emerging HIV-2 treatment regimens.

Partner characteristics predicting HIV-1 set point in sexually acquired HIV-1 among African seroconverters.

An increasing proportion of monotypic HIV-1 DNA sequences during antiretroviral treatment suggests proliferation of HIV-infected cells.

A sensitive real-time PCR based assay to estimate the impact of amino acid substitutions on the competitive replication fitness of human immunodeficiency virus type 1 in cell culture.

Coverage of primary mother-to-child HIV transmission isolates by second-generation broadly neutralizing antibodies.

Plasma viral loads during early HIV-1 infection are similar in subtype C- and non-subtype C-infected African seroconverters.

Human immunodeficiency viruses appear compartmentalized to the female genital tract in cross-sectional analyses but genital lineages do not persist over time.

HIV-1 conserved-element vaccines: relationship between sequence conservation and replicative capacity.

HIV-1 p24(gag) derived conserved element DNA vaccine increases the breadth of immune response in mice.

Complex patterns of protease inhibitor resistance among antiretroviral treatment-experienced HIV-2 patients from Senegal: implications for second-line therapy.

Superior Control of HIV-1 Replication by CD8+ T Cells Targeting Conserved Epitopes: Implications for HIV Vaccine Design.

Fitness costs of mutations at the HIV-1 capsid hexamerization interface.

Indel and Carryforward Correction (ICC): a new analysis approach for processing 454 pyrosequencing data.

Selective induction of CTL helper rather than killer activity by natural epitope variants promotes dendritic cell-mediated HIV-1 dissemination.

Factors affecting relative fitness measurements in pairwise competition assays of human immunodeficiency viruses.

Association Study of Common Genetic Variants and HIV-1 Acquisition in 6,300 Infected Cases and 7,200 Controls.

Inferring viral population structures using heteroduplex mobility and DNA sequence analyses.

Quality score based identification and correction of pyrosequencing errors.

Improved detection of rare HIV-1 variants using 454 pyrosequencing.

Adhesion and fusion efficiencies of human immunodeficiency virus type 1 (HIV-1) surface proteins.

Increased sequence coverage through combined targeting of variant and conserved epitopes correlates with control of HIV replication.

Toll-like receptor polymorphism associations with HIV-1 outcomes among sub-Saharan Africans.

HIV-1 subtype C is not associated with higher risk of heterosexual HIV-1 transmission: a multinational study among HIV-1 serodiscordant couples.

Variants in host viral replication cycle genes are associated with heterosexual HIV-1 acquisition in Africans.

Altered response hierarchy and increased T-cell breadth upon HIV-1 conserved element DNA vaccination in macaques.

The impact of viral evolution and frequency of variant epitopes on primary and memory human immunodeficiency virus type 1-specific CD8⁺ T cell responses.

Impact of mutations in highly conserved amino acids of the HIV-1 Gag-p24 and Env-gp120 proteins on viral replication in different genetic backgrounds.

Validation of an oligonucleotide ligation assay for quantification of human immunodeficiency virus type 1 drug-resistant mutants by use of massively parallel sequencing.

Analysis of HLA A*02 association with vaccine efficacy in the RV144 HIV-1 vaccine trial.

Lack of resistance to integrase inhibitors among antiretroviral-naive subjects with primary HIV-1 infection, 2007-2013.

HIV-1 superinfection with a triple-class drug-resistant strain in a patient successfully controlled with antiretroviral treatment.

Dendritic cells restore CD8+ T cell reactivity to autologous HIV-1.

An HIV epidemic model based on viral load dynamics: value in assessing empirical trends in HIV virulence and community viral load.

HIV latency. Proliferation of cells with HIV integrated into cancer genes contributes to persistent infection.

HIV-1 conserved elements p24CE DNA vaccine induces humoral immune responses with broad epitope recognition in macaques.

CD8 and CD4 epitope predictions in RV144: no strong evidence of a T-cell driven sieve effect in HIV-1 breakthrough sequences from trial participants.

Host genetic and viral determinants of HIV-1 RNA set point among HIV-1 seroconverters from sub-saharan Africa.

Spontaneous control of HIV-1 viremia in a subject with protective HLA-B plus HLA-C alleles and HLA-C associated single nucleotide polymorphisms.

Vaccine-induced Human Antibodies Specific for the Third Variable Region of HIV-1 gp120 Impose Immune Pressure on Infecting Viruses.

Performance of commonly used genotypic assays and comparison with phenotypic assays of HIV-1 coreceptor tropism in acutely HIV-1-infected patients.

Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial.

p21(WAF1/CIP1) RNA expression in highly HIV-1 exposed, uninfected individuals.

In vitro activity of dolutegravir against wild-type and integrase inhibitor-resistant HIV-2.

A human immune data-informed vaccine concept elicits strong and broad T-cell specificities associated with HIV-1 control in mice and macaques.

How often does treatment of primary HIV lead to post-treatment control?