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

Optimization of pyrosequencing reads by superior successive incorporation efficiency of improved 2′-deoxyadenosine-5′-triphosphate analogs

(2011) Tomoharu Kajiyama et al.   ANALYTICAL BIOCHEMISTRY

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

(2011) Elizabeth K Nelson et al.   BMC BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

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

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

High-throughput DNA sequencing - concepts and limitations

(2010) Martin Kircher et al.   BIOESSAYS

Dynamics of haplotype frequency change in a CD8+TL epitope of simian immunodeficiency virus

(2010) Austin L. Hughes et al.   INFECTION GENETICS AND EVOLUTION

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

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

Hepatitis C Virus Transmission Bottlenecks Analyzed by Deep Sequencing

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

Dynamics of HIV-1 Quasispecies during Antiviral Treatment Dissected Using Ultra-Deep Pyrosequencing

(2010) Charlotte Hedskog 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

Massively parallel pyrosequencing in HIV research

(2009) Frederic D Bushman et al.   AIDS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Estimation of Allele Frequencies From High-Coverage Genome-Sequencing Projects

(2009) M. Lynch   GENETICS

Infection with "Escaped" Virus Variants Impairs Control of Simian Immunodeficiency Virus SIVmac239 Replication in Mamu-B*08-Positive Macaques

(2009) L. E. Valentine 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

Phylogenetic Analysis of Population-Based and Deep Sequencing Data to Identify Coevolving Sites in the nef Gene of HIV-1

(2009) A. F.Y. Poon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Major histocompatibility complex genotyping with massively parallel pyrosequencing

(2009) Roger W Wiseman et al.   NATURE MEDICINE

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

Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations

(2009) Gabriella Rozera et al.   Retrovirology