SIV Genome-Wide Pyrosequencing Provides a Comprehensive and Unbiased View of Variation within and outside CD8 T Lymphocyte Epitopes

Experimental Analysis of Sources of Error in Evolutionary Studies Based on Roche/454 Pyrosequencing of Viral Genomes

(2012) E. A. Becker et al.   Genome Biology and Evolution

LabKey Server: An open source platform for scientific data integration, analysis and collaboration

(2011) Elizabeth K Nelson et al.   BMC BIOINFORMATICS

Epitope-Specific CD8+ T Lymphocytes Cross-Recognize Mutant Simian Immunodeficiency Virus (SIV) Sequences but Fail To Contain Very Early Evolution and Eventual Fixation of Epitope Escape Mutations during SIV Infection

(2011) E. M. Cale et al.   JOURNAL OF VIROLOGY

Transcriptionally Abundant Major Histocompatibility Complex Class I Alleles Are Fundamental to Nonhuman Primate Simian Immunodeficiency Virus-Specific CD8+ T Cell Responses

(2011) M. L. Budde et al.   JOURNAL OF VIROLOGY

Conditional CD8+ T Cell Escape during Acute Simian Immunodeficiency Virus Infection

(2011) S. L. O'Connor et al.   JOURNAL OF VIROLOGY

Novel, Divergent Simian Hemorrhagic Fever Viruses in a Wild Ugandan Red Colobus Monkey Discovered Using Direct Pyrosequencing

(2011) Michael Lauck et al.   PLoS One

A Comparison of Parallel Pyrosequencing and Sanger Clone-Based Sequencing and Its Impact on the Characterization of the Genetic Diversity of HIV-1

(2011) Binhua Liang et al.   PLoS One

Viral CTL Escape Mutants Are Generated in Lymph Nodes and Subsequently Become Fixed in Plasma and Rectal Mucosa during Acute SIV Infection of Macaques

(2011) Thomas H. Vanderford et al.   PLoS Pathogens

Whole-Genome Characterization of Human and Simian Immunodeficiency Virus Intrahost Diversity by Ultradeep Pyrosequencing

(2010) B. N. Bimber et al.   JOURNAL OF VIROLOGY

Macaque Long-Term Nonprogressors Resist Superinfection with Multiple CD8+ T Cell Escape Variants of Simian Immunodeficiency Virus

(2010) J. T. Weinfurter et al.   JOURNAL OF VIROLOGY

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

(2010) Will Fischer et al.   PLoS One

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Low-Abundance Drug-Resistant Viral Variants in Chronically HIV-Infected, Antiretroviral Treatment–Naive Patients Significantly Impact Treatment Outcomes

(2009) Birgitte B. Simen et al.   JOURNAL OF INFECTIOUS DISEASES

Mauritian Cynomolgus Macaques Share Two Exceptionally Common Major Histocompatibility Complex Class I Alleles That Restrict Simian Immunodeficiency Virus-Specific CD8+ T Cells

(2009) B. J. Burwitz et al.   JOURNAL OF VIROLOGY

HLA-Associated Viral Mutations Are Common in Human Immunodeficiency Virus Type 1 Elite Controllers

(2009) T. Miura et al.   JOURNAL OF VIROLOGY

T-Cell Vaccine Strategies for Human Immunodeficiency Virus, the Virus with a Thousand Faces

(2009) B. T. Korber et al.   JOURNAL OF VIROLOGY

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

Small effective population sizes and rare nonsynonymous variants in potyviruses

(2009) Austin L. Hughes   VIROLOGY

Genetic and antigenic features of the transmitted virus

(2009) Brandon F Keele et al.   Current Opinion in HIV and AIDS

Comprehensive Immunological Evaluation Reveals Surprisingly Few Differences between Elite Controller and Progressor Mamu-B*17-Positive Simian Immunodeficiency Virus-Infected Rhesus Macaques

(2008) N. J. Maness et al.   JOURNAL OF VIROLOGY

Genetic Characterization of Human Immunodeficiency Virus Type 1 in Elite Controllers: Lack of Gross Genetic Defects or Common Amino Acid Changes

(2008) T. Miura et al.   JOURNAL OF VIROLOGY

HLA Class I-Driven Evolution of Human Immunodeficiency Virus Type 1 Subtype C Proteome: Immune Escape and Viral Load

(2008) C. M. Rousseau et al.   JOURNAL OF VIROLOGY

HLA-B57/B*5801 Human Immunodeficiency Virus Type 1 Elite Controllers Select for Rare Gag Variants Associated with Reduced Viral Replication Capacity and Strong Cytotoxic T-Lymphotye Recognition

(2008) T. Miura et al.   JOURNAL OF VIROLOGY

Protective HLA Class I Alleles That Restrict Acute-Phase CD8+ T-Cell Responses Are Associated with Viral Escape Mutations Located in Highly Conserved Regions of Human Immunodeficiency Virus Type 1

(2008) Y. E. Wang et al.   JOURNAL OF VIROLOGY