| review article | Q7318358 |
| scholarly article | Q13442814 |
| P356 | DOI | 10.1016/J.JTBI.2009.07.038 |
| P932 | PMC publication ID | 2760689 |
| P698 | PubMed publication ID | 19660475 |
| P5875 | ResearchGate publication ID | 26722513 |
| P894 | zbMATH Open document ID | 1403.92296 |
| P50 | author | Michael Saag | Q6834090 |
| Michael P. Busch | Q6833284 | ||
| Jesus F Salazar-Gonzalez | Q57415418 | ||
| Brandon Keele | Q68690678 | ||
| George M. Shaw | Q78514357 | ||
| Brian Gaschen | Q117221701 | ||
| Eric Delwart | Q30004089 | ||
| Bette Korber | Q30505218 | ||
| Beatrice H. Hahn | Q55293537 | ||
| Tanmoy Bhattacharya | Q55414889 | ||
| Alan S. Perelson | Q55719625 | ||
| P2093 | author name string | Ha Youn Lee | |
| Elena E Giorgi | |||
| Paul A Goepfert | |||
| J Michael Kilby | |||
| Gayathri S Athreya | |||
| Kimmy T Pham | |||
| P2860 | cites work | Relaxed phylogenetics and dating with confidence | Q21146068 |
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| Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection | Q29619510 | ||
| Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase | Q29619994 | ||
| A new cell-based assay for measuring the forward mutation rate of HIV-1. | Q30350023 | ||
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| Clinical picture of primary HIV infection presenting as a glandular-fever-like illness | Q33447605 | ||
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| Characterization of human immunodeficiency virus type 1 (HIV-1) envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B. | Q33780595 | ||
| Selection for human immunodeficiency virus type 1 envelope glycosylation variants with shorter V1-V2 loop sequences occurs during transmission of certain genetic subtypes and may impact viral RNA levels | Q33780649 | ||
| Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection | Q33825654 | ||
| Rapid production and clearance of HIV-1 and hepatitis C virus assessed by large volume plasma apheresis | Q33881912 | ||
| Dynamics of HIV viremia and antibody seroconversion in plasma donors: implications for diagnosis and staging of primary HIV infection | Q34228730 | ||
| Human immunodeficiency virus type 1 (HIV-1) diversity at time of infection is not restricted to certain risk groups or specific HIV-1 subtypes | Q34439417 | ||
| Maximum likelihood estimation of population growth rates based on the coalescent | Q34604415 | ||
| Role of maternal autologous neutralizing antibody in selective perinatal transmission of human immunodeficiency virus type 1 escape variants | Q34717113 | ||
| A novel antiviral intervention results in more accurate assessment of human immunodeficiency virus type 1 replication dynamics and T-cell decay in vivo | Q34858885 | ||
| Human immunodeficiency virus type 1 V1-V2 envelope loop sequences expand and add glycosylation sites over the course of infection, and these modifications affect antibody neutralization sensitivity | Q35101464 | ||
| Envelope variants from women recently infected with clade A human immunodeficiency virus type 1 confer distinct phenotypes that are discerned by competition and neutralization experiments. | Q35155451 | ||
| Comparing likelihood and Bayesian coalescent estimation of population parameters | Q35598550 | ||
| Viral dynamics of primary viremia and antiretroviral therapy in simian immunodeficiency virus infection | Q35895554 | ||
| Analysis of HIV-1 env gene sequences reveals evidence for a low effective number in the viral population | Q36025234 | ||
| Determination of virus burst size in vivo using a single-cycle SIV in rhesus macaques | Q36277228 | ||
| Viral dynamics of acute HIV-1 infection | Q36375339 | ||
| Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing | Q36540055 | ||
| Selection for specific sequences in the external envelope protein of human immunodeficiency virus type 1 upon primary infection | Q36647820 | ||
| Quantitating the multiplicity of infection with human immunodeficiency virus type 1 subtype C reveals a non-poisson distribution of transmitted variants | Q37145228 | ||
| Simulation and prediction of the adaptive immune response to influenza A virus infection | Q37247935 | ||
| Low-dose rectal inoculation of rhesus macaques by SIVsmE660 or SIVmac251 recapitulates human mucosal infection by HIV-1. | Q37273086 | ||
| Multiple V1/V2 env variants are frequently present during primary infection with human immunodeficiency virus type 1 | Q37568289 | ||
| Mapping trait loci by use of inferred ancestral recombination graphs | Q41078342 | ||
| Forward mutation rate of human immunodeficiency virus type 1 in a T lymphoid cell line | Q41219560 | ||
| Inheritance of defective extremities | Q43407028 | ||
| Two-sample tests for comparing intra-individual genetic sequence diversity between populations | Q43419925 | ||
| Gene genealogy in a population of variable size | Q43497317 | ||
| HIV type 1 variants transmitted to women in Kenya require the CCR5 coreceptor for entry, regardless of the genetic complexity of the infecting virus | Q45732337 | ||
| Modeling plasma virus concentration during primary HIV infection | Q45743854 | ||
| Adaptive evolution of human immunodeficiency virus-type 1 during the natural course of infection | Q45771143 | ||
| High titers of cytopathic virus in plasma of patients with symptomatic primary HIV-1 infection | Q45854355 | ||
| Selective transmission of human immunodeficiency virus type-1 variants from mothers to infants | Q45867857 | ||
| Homogeneous quasispecies in 16 out of 17 individuals during very early HIV-1 primary infection. | Q46013897 | ||
| Intermittent low-level viremia in very early primary HIV-1 infection. | Q46607265 | ||
| A robust measure of HIV-1 population turnover within chronically infected individuals. | Q47296134 | ||
| Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission | Q47878972 | ||
| A stochastic modeling of early HIV-1 population dynamics. | Q52066082 | ||
| Viral dynamics in primary HIV-1 infection. Karolinska Institutet Primary HIV Infection Study Group. | Q52070829 | ||
| A stochastic model for early HIV-1 population dynamics. | Q52230372 | ||
| Stochastic modeling of the dynamics of CD4+ T-cell infection by HIV and some Monte Carlo studies. | Q52251017 | ||
| A stochastic model for primary HIV infection: optimal timing of therapy. | Q54099933 | ||
| P2507 | corrigendum / erratum | Corrigendum to “Modeling sequence evolution in acute HIV-1 infection” [J. Theor. Biol. 261 (2009) 341–360] | Q56792871 |
| P433 | issue | 2 | |
| P407 | language of work or name | English | Q1860 |
| P921 | main subject | HIV | Q15787 |
| P6104 | maintained by WikiProject | WikiProject Mathematics | Q8487137 |
| P1104 | number of pages | 20 | |
| P304 | page(s) | 341-360 | |
| P577 | publication date | 2009-08-04 | |
| P1433 | published in | Journal of Theoretical Biology | Q2153724 |
| P1476 | title | Modeling sequence evolution in acute HIV-1 infection | |
| P478 | volume | 261 |
| Q33966648 | A limited number of simian immunodeficiency virus (SIV) env variants are transmitted to rhesus macaques vaginally inoculated with SIVmac251. |
| Q48049832 | A new pattern-based method for identifying recent HIV-1 infections from the viral env sequence |
| Q36167660 | A quantitative quasispecies theory-based model of virus escape mutation under immune selection |
| Q33653774 | A rev1-vpu polymorphism unique to HIV-1 subtype A and C strains impairs envelope glycoprotein expression from rev-vpu-env cassettes and reduces virion infectivity in pseudotyping assays |
| Q30359547 | Activities of transmitted/founder and chronic clade B HIV-1 Vpu and a C-terminal polymorphism specifically affecting virion release |
| Q34185814 | Acute HIV-1 Infection |
| Q36667979 | Adaptation to the interferon-induced antiviral state by human and simian immunodeficiency viruses |
| Q38068990 | Benchmarking of viral haplotype reconstruction programmes: an overview of the capacities and limitations of currently available programmes |
| Q38063560 | Biology as population dynamics: heuristics for transmission risk |
| Q38721805 | Characterizing HIV-1 Splicing by Using Next-Generation Sequencing |
| Q91656913 | Combining Viral Genetics and Statistical Modeling to Improve HIV-1 Time-of-infection Estimation towards Enhanced Vaccine Efficacy Assessment |
| Q41610618 | Complementary and synergistic activities of anti-V3, CD4bs and CD4i antibodies derived from a single individual can cover a wide range of HIV-1 strains |
| Q35788320 | Comprehensive Characterization of the Transmitted/Founder env Genes From a Single MSM Cohort in China |
| Q53274310 | Cross-Sectional HIV Incidence Surveillance: A Benchmarking of Approaches for Estimating the 'Mean Duration of Recent Infection'. |
| Q57874529 | Cross-Sectional HIV Incidence Surveillance: A Benchmarking of Approaches for Estimating the ‘Mean Duration of Recent Infection’ |
| Q28740329 | Cross-sectional detection of acute HIV infection: timing of transmission, inflammation and antiretroviral therapy |
| Q35140263 | Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes |
| Q37252894 | Derivation and Characterization of Pathogenic Transmitted/Founder Molecular Clones from Simian Immunodeficiency Virus SIVsmE660 and SIVmac251 following Mucosal Infection |
| Q35868993 | Designing a genome-based HIV incidence assay with high sensitivity and specificity |
| Q35140450 | Detection of minority resistance during early HIV-1 infection: natural variation and spurious detection rather than transmission and evolution of multiple viral variants. |
| Q64915534 | Development and validation of plasma miRNA biomarker signature panel for the detection of early HIV-1 infection. |
| Q28551914 | Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus |
| Q64997345 | Different pattern of stool and plasma gastrointestinal damage biomarkers during primary and chronic HIV infection. |
| Q47550759 | Dynamics of CD4 and CD8 T-Cell Subsets and Inflammatory Biomarkers during Early and Chronic HIV Infection in Mozambican Adults |
| Q36000736 | Early low-titer neutralizing antibodies impede HIV-1 replication and select for virus escape |
| Q28482493 | Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing |
| Q37312719 | Enhancement of viral escape in HIV-1 Nef by STEP vaccination |
| Q40448856 | Enhancing Virion Tethering by BST2 Sensitizes Productively and Latently HIV-infected T cells to ADCC Mediated by Broadly Neutralizing Antibodies. |
| Q92553546 | Estimating the basic reproduction number of a pathogen in a single host when only a single founder successfully infects |
| Q57484166 | Estimating the mutational fitness effects distribution during early HIV infection |
| Q35143626 | Estimating the timing of mother-to-child transmission of the human immunodeficiency virus type 1 using a viral molecular evolution model |
| Q33727328 | Estimating time since infection in early homogeneous HIV-1 samples using a poisson model |
| Q55424702 | Estimation of delay to diagnosis and incidence in HIV using indirect evidence of infection dates. |
| Q35077423 | Evolution of drug-resistant viral populations during interruption of antiretroviral therapy |
| Q42199105 | Forensic interpretation of molecular variation on networks of disease transmission and genetic inheritance. |
| Q35826158 | Generation of transmitted/founder HIV-1 infectious molecular clones and characterization of their replication capacity in CD4 T lymphocytes and monocyte-derived macrophages |
| Q34290999 | Genetic identity and biological phenotype of a transmitted/founder virus representative of nonpathogenic simian immunodeficiency virus infection in African green monkeys |
| Q50041335 | HIITE: HIV-1 Incidence and Infection Time Estimator. |
| Q36526615 | HIV transmission |
| Q35895988 | HIV-1 Vpu utilizes both cullin-RING ligase (CRL) dependent and independent mechanisms to downmodulate host proteins |
| Q33582135 | High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men. |
| Q27318508 | Human Non-neutralizing HIV-1 Envelope Monoclonal Antibodies Limit the Number of Founder Viruses during SHIV Mucosal Infection in Rhesus Macaques |
| Q35172385 | Identification, molecular cloning, and analysis of full-length hepatitis C virus transmitted/founder genotypes 1, 3, and 4 |
| Q34038460 | Identifying and characterizing recently transmitted viruses |
| Q36495198 | Impact of mutation type and amplicon characteristics on genetic diversity measures generated using a high-resolution melting diversity assay |
| Q30596338 | Independent assessment of candidate HIV incidence assays on specimens in the CEPHIA repository |
| Q35696991 | Innate immunity in acute HIV-1 infection |
| Q59357124 | Interaction Between Macrophage Migration Inhibitory Factor and CD74 in Human Immunodeficiency Virus Type I Infected Primary Monocyte-Derived Macrophages Triggers the Production of Proinflammatory Mediators and Enhances Infection of Unactivated CD4 T |
| Q35909939 | Investigating the Consequences of Interference between Multiple CD8+ T Cell Escape Mutations in Early HIV Infection |
| Q34802271 | Low Multiplicity of HIV-1 Infection and No Vaccine Enhancement in VAX003 Injection Drug Users |
| Q34120840 | Low-dose mucosal simian immunodeficiency virus infection restricts early replication kinetics and transmitted virus variants in rhesus monkeys |
| Q64968778 | Lower Broadly Neutralizing Antibody Responses in Female Versus Male HIV-1 Infected Injecting Drug Users. |
| Q33545560 | Mathematical modeling of ultradeep sequencing data reveals that acute CD8+ T-lymphocyte responses exert strong selective pressure in simian immunodeficiency virus-infected macaques but still fail to clear founder epitope sequences |
| Q36887522 | Modeling sequence evolution in HIV-1 infection with recombination |
| Q21245370 | Modeling the within-host dynamics of HIV infection |
| Q26853307 | Modelling the course of an HIV infection: insights from ecology and evolution |
| Q28601925 | Molecular clock of HIV-1 envelope genes under early immune selection |
| 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 |
| Q36532973 | Molecular identification, cloning and characterization of transmitted/founder HIV-1 subtype A, D and A/D infectious molecular clones |
| Q52567234 | Neutral theory and rapidly evolving viral pathogens. |
| Q37252676 | Neutralizing IgG at the portal of infection mediates protection against vaginal simian/human immunodeficiency virus challenge |
| Q93101105 | Parallel evolution of HIV-1 in a long-term experiment |
| Q33804531 | Pentavalent HIV-1 vaccine protects against simian-human immunodeficiency virus challenge |
| Q37415771 | Performance of the Bio-Rad Geenius HIV1/2 Supplemental Assay in Detecting "Recent" HIV Infection and Calculating Population Incidence. |
| Q58572549 | Phenotype, Polyfunctionality, and Antiviral Activity of Stimulated CD8 T-Cells From HIV Subjects Who Initiated cART at Different Time-Points After Acute Infection |
| Q37206422 | Phylogenetic inferences on HIV-1 transmission: implications for the design of prevention and treatment interventions |
| Q37272324 | Postintegration HIV-1 infection of cervical epithelial cells mediates contact-dependent productive infection of T cells |
| Q36305433 | Previously transmitted HIV-1 strains are preferentially selected during subsequent sexual transmissions |
| Q38631923 | Primary infection by a human immunodeficiency virus with atypical coreceptor tropism |
| Q34395271 | Quantifying the diversification of hepatitis C virus (HCV) during primary infection: estimates of the in vivo mutation rate |
| Q34269570 | Recombination-mediated escape from primary CD8+ T cells in acute HIV-1 infection. |
| Q34042642 | Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections |
| Q35581949 | SIVmac251 is inefficiently transmitted to rhesus macaques by penile inoculation with a single SIVenv variant found in ramp-up phase plasma |
| Q37003000 | SPMM: estimating infection duration of multivariant HIV-1 infections |
| Q35018140 | Selective transmission of R5 HIV-1 variants: where is the gatekeeper? |
| Q33390855 | Seminal plasma induces inflammation and enhances HIV-1 replication in human cervical tissue explants |
| Q30407004 | Sequential bottlenecks drive viral evolution in early acute hepatitis C virus infection |
| Q34853144 | Sexually-transmitted/founder HIV-1 cannot be directly predicted from plasma or PBMC-derived viral quasispecies in the transmitting partner |
| Q26826523 | Should we treat acute HIV infection? |
| Q35232811 | Simple mathematical models do not accurately predict early SIV dynamics |
| Q36433960 | Single-Genome Sequencing of Hepatitis C Virus in Donor-Recipient Pairs Distinguishes Modes and Models of Virus Transmission and Early Diversification |
| Q40544201 | Single-use, electricity-free amplification device for detection of HIV-1 |
| Q28483749 | Stochastic simulations suggest that HIV-1 survives close to its error threshold |
| Q33815539 | Stochastic theory of early viral infection: continuous versus burst production of virions |
| Q30238730 | Survivors Remorse: antibody-mediated protection against HIV-1. |
| Q40091554 | The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards |
| Q35926734 | The challenges of modelling antibody repertoire dynamics in HIV infection |
| Q39294118 | Time Until Emergence of HIV Test Reactivity Following Infection With HIV-1: Implications for Interpreting Test Results and Retesting After Exposure |
| Q42938571 | Timing, adherence, resistance, and ... persistence? new insight into the mechanisms of failure of HIV type 1 postexposure prophylaxis |
| Q33680395 | Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing |
| Q33849796 | Transmission of single and multiple viral variants in primary HIV-1 subtype C infection |
| Q37661224 | Understanding the effects of different HIV transmission models in individual-based microsimulation of HIV epidemic dynamics in people who inject drugs |
| Q37395749 | Use of Dried Blood Spots to Elucidate Full-Length Transmitted/Founder HIV-1 Genomes |
| Q26861425 | Using nonhuman primates to model HIV transmission |
| Q24600713 | Viral evolution and escape during acute HIV-1 infection |
| Q39400038 | Virus-Host Gene Interactions Define HIV-1 Disease Progression. |
| Q35690771 | Vpu Exploits the Cross-Talk between BST2 and the ILT7 Receptor to Suppress Anti-HIV-1 Responses by Plasmacytoid Dendritic Cells |
| Q33877419 | Wide variation in the multiplicity of HIV-1 infection among injection drug users |
| Q33619649 | Within-Epitope Interactions Can Bias CTL Escape Estimation in Early HIV Infection |
| Q56792871 | Corrigendum to “Modeling sequence evolution in acute HIV-1 infection” [J. Theor. Biol. 261 (2009) 341–360] | main subject | P921 |
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