Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing

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

(2010) T. M. T. Love et al.   JOURNAL OF VIROLOGY

Hepatitis C Virus Transmission Bottlenecks Analyzed by Deep Sequencing

(2010) G. P. Wang et al.   JOURNAL OF VIROLOGY

Wide Variation in the Multiplicity of HIV-1 Infection among Injection Drug Users

(2010) K. J. Bar et al.   JOURNAL OF VIROLOGY

Mosaic HIV-1 vaccines expand the breadth and depth of cellular immune responses in rhesus monkeys

(2010) Dan H Barouch et al.   NATURE MEDICINE

Mosaic vaccines elicit CD8+ T lymphocyte responses that confer enhanced immune coverage of diverse HIV strains in monkeys

(2010) Sampa Santra et al.   NATURE MEDICINE

High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men

(2010) Hui Li et al.   PLoS Pathogens

Rare HLA Drive Additional HIV Evolution Compared to More Frequent Alleles

(2009) Christine M. Rousseau et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

Systematic artifacts in metagenomes from complex microbial communities

(2009) Vicente Gomez-Alvarez et al.   ISME Journal

Evolution of HLA-B*5703 HIV-1 escape mutations in HLA-B*5703–positive individuals and their transmission recipients

(2009) Hayley Crawford et al.   JOURNAL OF EXPERIMENTAL MEDICINE

The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection

(2009) Nilu Goonetilleke et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection

(2009) Jesus F. Salazar-Gonzalez et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Modeling sequence evolution in acute HIV-1 infection

(2009) Ha Youn Lee et al.   JOURNAL OF THEORETICAL BIOLOGY

Ultradeep Pyrosequencing Detects Complex Patterns of CD8+ T-Lymphocyte Escape in Simian Immunodeficiency Virus-Infected Macaques

(2009) B. N. Bimber et al.   JOURNAL OF VIROLOGY

Quantitating the Multiplicity of Infection with Human Immunodeficiency Virus Type 1 Subtype C Reveals a Non-Poisson Distribution of Transmitted Variants

(2009) M.-R. Abrahams et al.   JOURNAL OF VIROLOGY

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

Quantitative Deep Sequencing Reveals Dynamic HIV-1 Escape and Large Population Shifts during CCR5 Antagonist Therapy In Vivo

(2009) Athe M. N. Tsibris et al.   PLoS One

HIV Evolution in Early Infection: Selection Pressures, Patterns of Insertion and Deletion, and the Impact of APOBEC

(2009) Natasha Wood et al.   PLoS Pathogens

Transmission and Long-Term Stability of Compensated CD8 Escape Mutations

(2008) A. Schneidewind et al.   JOURNAL OF VIROLOGY

Induction of Plasma (TRAIL), TNFR-2, Fas Ligand, and Plasma Microparticles after Human Immunodeficiency Virus Type 1 (HIV-1) Transmission: Implications for HIV-1 Vaccine Design

(2008) N. Gasper-Smith et al.   JOURNAL OF VIROLOGY

Marked Epitope- and Allele-Specific Differences in Rates of Mutation in Human Immunodeficiency Type 1 (HIV-1) Gag, Pol, and Nef Cytotoxic T-Lymphocyte Epitopes in Acute/Early HIV-1 Infection

(2008) Z. L. Brumme et al.   JOURNAL OF VIROLOGY

Immune control of an SIV challenge by a T-cell-based vaccine in rhesus monkeys

(2008) Jinyan Liu et al.   NATURE

Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection

(2008) B. F. Keele et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA