| scholarly article | Q13442814 |
| P50 | author | James Mullins | Q57555076 |
| Ann C Collier | Q87874619 | ||
| Joanne D Stekler | Q88188997 | ||
| Joshua Herbeck | Q88691646 | ||
| Julie McElrath | Q22006776 | ||
| P2093 | author name string | Hong Zhao | |
| Yi Liu | |||
| Brian Birditt | |||
| Morgane Rolland | |||
| Kim Wong | |||
| Julia N Stoddard | |||
| Sherry McLaughlin | |||
| Wenjie Deng | |||
| Kurt Diem | |||
| John McNevin | |||
| Brandon S Maust | |||
| Stephanie Sorensen | |||
| Angela McKay | |||
| Dana Raugi | |||
| Indira Genowati | |||
| P2860 | cites work | Large-scale amplification, cloning and sequencing of near full-length HIV-1 subtype C genomes | Q48088168 |
| Founder Effects in the Assessment of HIV Polymorphisms and HLA Allele Associations | Q56880587 | ||
| Quantitation of HIV-1 RNA in plasma predicts outcome after seroconversion | Q72624142 | ||
| Biological and virologic characteristics of primary HIV infection | Q74429764 | ||
| Prognostic value of HIV-1 RNA, CD4 cell count, and CD4 Cell count slope for progression to AIDS and death in untreated HIV-1 infection | Q80433518 | ||
| Variable fitness impact of HIV-1 escape mutations to cytotoxic T lymphocyte (CTL) response | Q21131580 | ||
| HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC | Q21559422 | ||
| Genotypic and phenotypic characterization of HIV-1 patients with primary infection | Q22242245 | ||
| CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice | Q24286950 | ||
| A test of neutral molecular evolution based on nucleotide data | Q24532207 | ||
| Statistical method for testing the neutral mutation hypothesis by DNA polymorphism | Q24532326 | ||
| Statistical tests of neutrality of mutations | Q24532850 | ||
| Virus-specific CD8+ cytotoxic T-lymphocyte activity associated with control of viremia in primary human immunodeficiency virus type 1 infection | Q24645815 | ||
| Temporal association of cellular immune responses with the initial control of viremia in primary human immunodeficiency virus type 1 syndrome | Q24648628 | ||
| Reliable prediction of T-cell epitopes using neural networks with novel sequence representations | Q27485882 | ||
| A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood | Q27861000 | ||
| HIV-1 in semen: an isolated virus reservoir | Q28252399 | ||
| Tracking global patterns of N-linked glycosylation site variation in highly variable viral glycoproteins: HIV, SIV, and HCV envelopes and influenza hemagglutinin | Q28264707 | ||
| HyPhy: hypothesis testing using phylogenies | Q29013475 | ||
| Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations | Q29547255 | ||
| DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis | Q29615363 | ||
| Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection | Q29619510 | ||
| Prognosis in HIV-1 infection predicted by the quantity of virus in plasma | Q29619980 | ||
| Brief but efficient: acute HIV infection and the sexual transmission of HIV. | Q30341429 | ||
| HIV-1 group M conserved elements vaccine | Q33308246 | ||
| Inflammatory genital infections mitigate a severe genetic bottleneck in heterosexual transmission of subtype A and C HIV-1 | Q33402461 | ||
| Elite suppressor-derived HIV-1 envelope glycoproteins exhibit reduced entry efficiency and kinetics | Q33429049 | ||
| Molecular phylodynamics of the heterosexual HIV epidemic in the United Kingdom | Q33506612 | ||
| High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men. | Q33582135 | ||
| HIV-1 Populations in Semen Arise through Multiple Mechanisms | Q33680752 | ||
| Semen-specific genetic characteristics of human immunodeficiency virus type 1 env. | Q33717839 | ||
| Human immunodeficiency virus type 1 populations in blood and semen | Q33782102 | ||
| Evolution of envelope sequences from the genital tract and peripheral blood of women infected with clade A human immunodeficiency virus type 1. | Q33784911 | ||
| Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection | Q33825654 | ||
| Wide variation in the multiplicity of HIV-1 infection among injection drug users | Q33877419 | ||
| Selective escape from CD8+ T-cell responses represents a major driving force of human immunodeficiency virus type 1 (HIV-1) sequence diversity and reveals constraints on HIV-1 evolution | Q34092644 | ||
| Dynamics of HIV viremia and antibody seroconversion in plasma donors: implications for diagnosis and staging of primary HIV infection | Q34228730 | ||
| Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach. | Q34276766 | ||
| Early selection in Gag by protective HLA alleles contributes to reduced HIV-1 replication capacity that may be largely compensated for in chronic infection | Q34295972 | ||
| Human immunodeficiency virus type 1 env evolves toward ancestral states upon transmission to a new host. | Q34353398 | ||
| Virus population homogenization following acute human immunodeficiency virus type 1 infection | Q34360562 | ||
| In vivo evolution of HIV-1 co-receptor usage and sensitivity to chemokine-mediated suppression. | Q34445208 | ||
| Adaptation of HIV-1 to human leukocyte antigen class I | Q34604811 | ||
| Pervasive genomic recombination of HIV-1 in vivo | Q34645720 | ||
| Genetic impact of vaccination on breakthrough HIV-1 sequences from the STEP trial | Q34648825 | ||
| Selection on the human immunodeficiency virus type 1 proteome following primary infection | Q35101338 | ||
| Rapid reversion of sequence polymorphisms dominates early human immunodeficiency virus type 1 evolution | Q35634318 | ||
| HIV-1 variation before seroconversion in men who have sex with men: analysis of acute/early HIV infection in the multicenter AIDS cohort study | Q36165696 | ||
| Evolution of human immunodeficiency virus type 1 cytotoxic T-lymphocyte epitopes: fitness-balanced escape | Q36315529 | ||
| Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing | Q36540055 | ||
| Human immunodeficiency virus type 1 evolution in vivo tracked by DNA heteroduplex mobility assays. | Q36636446 | ||
| Selection for specific sequences in the external envelope protein of human immunodeficiency virus type 1 upon primary infection | Q36647820 | ||
| The relationship between AIDS and immunologic tolerance | Q36746083 | ||
| Central role of reverting mutations in HLA associations with human immunodeficiency virus set point | Q36845904 | ||
| HLA-associated clinical progression correlates with epitope reversion rates in early human immunodeficiency virus infection | Q37051649 | ||
| Human immunodeficiency virus type 1 population genetics and adaptation in newly infected individuals. | Q37110723 | ||
| Quantitating the multiplicity of infection with human immunodeficiency virus type 1 subtype C reveals a non-poisson distribution of transmitted variants | Q37145228 | ||
| Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection | Q37273158 | ||
| The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection | Q37273195 | ||
| Modeling sequence evolution in acute HIV-1 infection | Q37384535 | ||
| Multiple V1/V2 env variants are frequently present during primary infection with human immunodeficiency virus type 1 | Q37568289 | ||
| Comparison of standard PCR/cloning to single genome sequencing for analysis of HIV-1 populations | Q37630336 | ||
| HIV-1 transmission, by stage of infection | Q38875941 | ||
| Rates of HIV-1 transmission per coital act, by stage of HIV-1 infection, in Rakai, Uganda | Q38881073 | ||
| 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 | Q40344458 | ||
| Evolution of pathogenic viruses with special reference to the rates of synonymous and nonsynonymous substitutions | Q40654438 | ||
| Comprehensive, serologically equivalent DNA typing for HLA-B by PCR using sequence-specific primers (PCR-SSP). | Q41374515 | ||
| Leveraging information across HLA alleles/supertypes improves epitope prediction | Q42628685 | ||
| Male genital tract compartmentalization of human immunodeficiency virus type 1 (HIV). | Q45395687 | ||
| Natural history of human immunodeficiency virus type 1 viremia after seroconversion and proximal to AIDS in a large cohort of homosexual men. Multicenter AIDS Cohort Study | Q45743784 | ||
| Time course of viremia and antibody seroconversion following human immunodeficiency virus exposure | Q45752422 | ||
| Human immunodeficiency virus type 1 molecular evolution and the measure of selection | Q45765824 | ||
| Antigenic oscillations and shifting immunodominance in HIV-1 infections. | Q45869472 | ||
| HIV-1 genomic RNA diversification following sexual and parenteral virus transmission | Q45873185 | ||
| Homogeneous quasispecies in 16 out of 17 individuals during very early HIV-1 primary infection. | Q46013897 | ||
| HIV type 1 V3 sequence diversity in contact-traced Swedish couples at the time of sexual transmission | Q48079671 | ||
| P433 | issue | 15 | |
| P407 | language of work or name | English | Q1860 |
| P921 | main subject | demographics | Q2725376 |
| P304 | page(s) | 7523-7534 | |
| P577 | publication date | 2011-05-18 | |
| P1433 | published in | Journal of Virology | Q1251128 |
| P1476 | title | Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes | |
| P478 | volume | 85 |
| Q42270807 | Accurate quantification of within- and between-host HBV evolutionary rates requires explicit transmission chain modelling. |
| Q30781299 | An evaluation of phylogenetic methods for reconstructing transmitted HIV variants using longitudinal clonal HIV sequence data |
| Q30373040 | An integrated map of HIV genome-wide variation from a population perspective. |
| Q34057942 | Analysis of HLA A*02 association with vaccine efficacy in the RV144 HIV-1 vaccine trial |
| Q37607872 | Breast milk and in utero transmission of HIV-1 select for envelope variants with unique molecular signatures |
| Q41930784 | Capturing virus evolution by proteomic bioinformatics: Hunting for characteristic mutations in the hepatitis E virus genome |
| Q64880210 | Characterizing the multiplicity of HIV founder variants during sexual transmission among MSM. |
| Q92701175 | Clinical and evolutionary consequences of HIV adaptation to HLA: implications for vaccine and cure |
| Q39315703 | Clonal Expansion of Human Immunodeficiency Virus-Infected Cells and Human Immunodeficiency Virus Persistence During Antiretroviral Therapy. |
| Q91656913 | Combining Viral Genetics and Statistical Modeling to Improve HIV-1 Time-of-infection Estimation towards Enhanced Vaccine Efficacy Assessment |
| Q93162011 | Comparisons of Human Immunodeficiency Virus Type 1 Envelope Variants in Blood and Genital Fluids near the Time of Male-to-Female Transmission |
| Q34413887 | De novo assembly of highly diverse viral populations |
| Q28551914 | Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus |
| Q36343848 | Differential evolution of a CXCR4-using HIV-1 strain in CCR5wt/wt and CCR5∆32/∆32 hosts revealed by longitudinal deep sequencing and phylogenetic reconstruction. |
| Q34308788 | Early immune adaptation in HIV-1 revealed by population-level approaches |
| Q36253793 | Effect of the Latent Reservoir on the Evolution of HIV at the Within- and Between-Host Levels |
| Q36095984 | Evaluating Clonal Expansion of HIV-Infected Cells: Optimization of PCR Strategies to Predict Clonality |
| Q56797307 | Evolution of HIV-1 within untreated individuals and at the population scale in Uganda |
| Q36086336 | Fitness-Balanced Escape Determines Resolution of Dynamic Founder Virus Escape Processes in HIV-1 Infection. |
| Q37460075 | Genotypic and phenotypic heterogeneity in the U3R region of HIV type 1 subtype C. |
| Q92689699 | HIV Diversity and Genetic Compartmentalization in Blood and Testes during Suppressive Antiretroviral Therapy |
| Q47094945 | HIV Env conserved element DNA vaccine alters immunodominance in macaques |
| Q45323939 | HIV-1 and Hepatitis C virus selection bottleneck in Chinese people who inject drugs |
| Q37646541 | HIV-1 persistence in CD4+ T cells with stem cell-like properties |
| Q34407843 | Human immunodeficiency virus type-1 (HIV-1) continues to evolve in presence of broadly neutralizing antibodies more than ten years after infection |
| Q35798108 | Immune-mediated attenuation of HIV-1 |
| Q35142729 | 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 |
| Q37547472 | Increased sequence coverage through combined targeting of variant and conserved epitopes correlates with control of HIV replication |
| Q30658257 | Indel and Carryforward Correction (ICC): a new analysis approach for processing 454 pyrosequencing data |
| Q33900388 | Ineffectual targeting of HIV-1 Nef by cytotoxic T lymphocytes in acute infection results in no functional impairment or viremia reduction. |
| Q27339956 | Large Variations in HIV-1 Viral Load Explained by Shifting-Mosaic Metapopulation Dynamics |
| Q61806694 | Link between the numbers of particles and variants founding new HIV-1 infections depends on the timing of transmission |
| Q92523449 | Longitudinal within-host evolution of HIV Nef-mediated CD4, HLA and SERINC5 downregulation activity: a case study |
| Q58089557 | Metagenomic sequencing of HIV-1 in the blood and female genital tract reveals little quasispecies diversity during acute infection |
| Q89575126 | Molecular dating and viral load growth rates suggested that the eclipse phase lasted about a week in HIV-1 infected adults in East Africa and Thailand |
| Q56880081 | New insights into the evolutionary rate of HIV-1 at the within-host and epidemiological levels |
| Q28649472 | New insights into the evolutionary rate of hepatitis B virus at different biological scales |
| Q64106336 | Next-generation sequencing of HIV-1 single genome amplicons |
| Q42680526 | Patterns and rates of viral evolution in HIV-1 subtype B infected females and males |
| Q58762598 | Phylogenetic approach to recover integration dates of latent HIV sequences within-host |
| Q36083061 | Preparing for the availability of a partially effective HIV vaccine: some lessons from other licensed vaccines |
| Q34988757 | Quality score based identification and correction of pyrosequencing errors |
| Q37039116 | Rapid, complex adaptation of transmitted HIV-1 full-length genomes in subtype C-infected individuals with differing disease progression |
| Q38849453 | Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection |
| Q30234948 | Short-Sighted Virus Evolution and a Germline Hypothesis for Chronic Viral Infections |
| Q26851376 | Sieve analysis in HIV-1 vaccine efficacy trials |
| Q46633111 | Sieve analysis of breakthrough HIV-1 sequences in HVTN 505 identifies vaccine pressure targeting the CD4 binding site of Env-gp120. |
| Q28742542 | Specific capture and whole-genome sequencing of viruses from clinical samples |
| Q41770807 | Stable multi-infection of splenocytes during SIV infection--the basis for continuous recombination. |
| Q35099081 | Structured observations reveal slow HIV-1 CTL escape |
| Q40091554 | The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards |
| Q28541827 | The genealogical population dynamics of HIV-1 in a large transmission chain: bridging within and among host evolutionary rates |
| Q52592228 | Therapeutic conserved elements (CE) DNA vaccine induces strong T-cell responses against highly conserved viral sequences during simian-human immunodeficiency virus infection. |
| Q35914315 | Tracking the Emergence of Host-Specific Simian Immunodeficiency Virus env and nef Populations Reveals nef Early Adaptation and Convergent Evolution in Brain of Naturally Progressing Rhesus Macaques |
| Q40634933 | Transmitted/Founder HIV-1 Subtype C Viruses Show Distinctive Signature Patterns in Vif, Vpr, and Vpu That Are Under Subsequent Immune Pressure During Early Infection |
| Q34270602 | Viral diversity and diversification of major non-structural genes vif, vpr, vpu, tat exon 1 and rev exon 1 during primary HIV-1 subtype C infection |
| Q42282547 | Viral evolution in chronic hepatitis B: a branched way to HBeAg seroconversion and disease progression? |
| Q36937390 | Within-host and between-host evolutionary rates across the HIV-1 genome |
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