Patrick Charlebois

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Deep sequencing technologies have the potential to transform the study of highly variable viral pathogens by providing a rapid and cost-effective approach to sensitively characterize rapidly evolving viral quasispecies. Here, we report on a high-throughput whole HIV-1 genome deep sequencing platform that combines 454 pyrosequencing with novel assembly and(More)
Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A de novo population consensus assembly is valuable both as a single linear representation of the population and as a backbone on which intra-host variants can be accurately(More)
RNA viruses are the causative agents for AIDS, influenza, SARS, and other serious health threats. Development of rapid and broadly applicable methods for complete viral genome sequencing is highly desirable to fully understand all aspects of these infectious agents as well as for surveillance of viral pandemic threats and emerging pathogens. However,(More)
Viruses diversify over time within hosts, often undercutting the effectiveness of host defenses and therapeutic interventions. To design successful vaccines and therapeutics, it is critical to better understand viral diversification, including comprehensively characterizing the genetic variants in viral intra-host populations and modeling changes from(More)
Massively parallel sequencing offers the possibility of revolutionizing the study of viral populations by providing ultra deep sequencing (tens to hundreds of thousand fold coverage) of complete viral genomes. However, differentiation of true low frequency variants from sequencing errors remains challenging. We developed a software package, V-Phaser 2, for(More)
BACKGROUND The impact of raltegravir-resistant HIV-1 minority variants (MVs) on raltegravir treatment failure is unknown. Illumina sequencing offers greater throughput than 454, but sequence analysis tools for viral sequencing are needed. We evaluated Illumina and 454 for the detection of HIV-1 raltegravir-resistant MVs. METHODS A5262 was a single-arm(More)
The Global Operative Assessment of Laparoscopic Skill (GOALS) has been shown to meet high standards for direct observation. The purpose of this study was to investigate the reliability and validity of GOALS when applied to blinded, videotaped performances. Five novice surgeons and 5 experienced surgeons were each evaluated by 2 observers during a(More)
Viral diseases such as HIV/AIDS and Dengue have an enormous impact on human health worldwide. Despite this, application of new sequencing technologies to viral genomics has lagged. We are using genome sequence data to study how populations of single stranded RNA viruses, including HIV, Dengue, West Nile and Hepatitis C, evolve within infected individuals in(More)
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