Now showing items 1-14 of 14

    • Allosteric Integrase Inhibitors Reveal a Role for Integrase During HIV-1 Maturation 

      Jurado, Kellie Ann (2015-09-20)
      Integration of the DNA copy of the HIV-1 genome is an essential step for virus replication and is mediated by a homotetrameric complex of the viral protein integrase (IN) in association with the ends of linear viral DNA ...
    • Antigen Load and Viral Sequence Diversification Determine the Functional Profile of HIV-1–Specific CD8+ T Cells 

      Brumme, Zabrina L; Anastario, Michael; Cohen, Kristin W; Jolin, Jonathan S; Brumme, Chanson J; Streeck, Hendrik; Meier, Angela; Rosenberg, Eric Scott; Alter, Galit; Allen, Todd; Walker, Bruce David; Altfeld, Marcus (Public Library of Science, 2008)
      Background: Virus-specific CD8+ T lymphocytes play a key role in the initial reduction of peak viremia during acute viral infections, but display signs of increasing dysfunction and exhaustion under conditions of chronic ...
    • Broadly directed virus-specific CD4+ T cell responses are primed during acute hepatitis C infection, but rapidly disappear from human blood with viral persistence 

      Schulze zur Wiesch, Julian; Ciuffreda, Donatella; Lewis-Ximenez, Lia; Kasprowicz, Victoria Olivia; Nolan, Brian E.; Streeck, Hendrik; Aneja, Jasneet; Reyor, Laura L.; Allen, Todd; Lohse, Ansgar W.; McGovern, Barbara; Chung, Raymond Taeyong; Kwok, William W.; Kim, Arthur Yu-Shin; Lauer, Georg (The Rockefeller University Press, 2012)
      Vigorous proliferative CD4+ T cell responses are the hallmark of spontaneous clearance of acute hepatitis C virus (HCV) infection, whereas comparable responses are absent in chronically evolving infection. Here, we ...
    • Efficient Ablation of Genes in Human Hematopoietic Stem and Effector Cells using CRISPR/Cas9 

      Mandal, Pankaj Kumar; Ferreira, Leonardo Manuel Ramos; Collins, Ryan; Meissner, Torsten B; Boutwell, C; Friesen, Max; Vrbanac, Vladimir; Garrison, Brian Scott; Stortchevoi, Alexei; Bryder, David; Musunuru, Kiran; Brand, Harrison Andrew; Tager, Andrew Martin; Allen, Todd; Talkowski, Michael Edward; Rossi, Derrick J; Cowan, Chad A. (Elsevier BV, 2014)
      Genome editing via CRISPR/Cas9 has rapidly become the tool of choice by virtue of its efficacy and ease of use. However, CRISPR/Cas9-mediated genome editing in clinically relevant human somatic cells remains untested. Here, ...
    • A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control 

      Bartha, István; Carlson, Jonathan M; Brumme, Chanson J; McLaren, Paul J; Brumme, Zabrina L; John, Mina; Haas, David W; Martinez-Picado, Javier; Dalmau, Judith; López-Galíndez, Cecilio; Casado, Concepción; Rauch, Andri; Günthard, Huldrych F; Bernasconi, Enos; Vernazza, Pietro; Klimkait, Thomas; Yerly, Sabine; O’Brien, Stephen J; Listgarten, Jennifer; Pfeifer, Nico; Lippert, Christoph; Fusi, Nicolo; Kutalik, Zoltán; Allen, Todd M; Müller, Viktor; Harrigan, P Richard; Heckerman, David; Telenti, Amalio; Fellay, Jacques (eLife Sciences Publications, Ltd, 2013)
      HIV-1 sequence diversity is affected by selection pressures arising from host genomic factors. Using paired human and viral data from 1071 individuals, we ran >3000 genome-wide scans, testing for associations between host ...
    • Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data 

      Macalalad, Alexander R.; Zody, Michael; Charlebois, Patrick; Lennon, Niall J.; Newman, Ruchi M.; Malboeuf, Christine M.; Ryan, Elizabeth Marie; Boutwell, Christian Lane; Power, Karen A.; Brackney, Doug E.; Pesko, Kendra N.; Levin, Joshua Zvi; Ebel, Gregory D.; Allen, Todd; Birren, Bruce W.; Henn, Matthew R. (Public Library of Science, 2012)
      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 ...
    • HLA Alleles Associated with Delayed Progression to AIDS Contribute Strongly to the Initial CD8+ T Cell Response against HIV-1 

      Kalife, Elizabeth T; Qi, Ying; Johnston, Mary N; Burgett, Nicole; Swartz, Martha E; Yang, Amy; Rockstroh, Juergen K; Jessen, Heiko; Carrington, Mary; Altfeld, Marcus; Streeck, Hendrik; Lichterfeld, Mathias; Alter, Galit; Yu, Xu; Meier, Angela; Allen, Todd; Rosenberg, Eric Scott; Walker, Bruce David (Public Library of Science, 2006)
      Background: Very little is known about the immunodominance patterns of HIV-1-specific T cell responses during primary HIV-1 infection and the reasons for human lymphocyte antigen (HLA) modulation of disease progression. ...
    • The Humanized BLT Mouse to Study HIV Transmission 

      Deruaz, Maud; Murooka, Thomas; Dudek, Timothy E; Vrbanac, VD; Tivet, T; Bankert, KC; Allen, Todd; Tager, Andrew Martin; Luster, Andrew David (BioMed Central, 2012)
    • Immune-Driven Recombination and Loss of Control after HIV Superinfection 

      Streeck, Hendrik; Li, Bin; Poon, Art F. Y.; Schneidewind, Anne; Gladden, Adrianne D.; Power, Karen A.; Daskalakis, Demetre; Bazner, Suzane; Zuniga, Rosario; Brander, Christian; Rosenberg, Eric Scott; Frost, Simon D. W.; Altfeld, Marcus; Allen, Todd (The Rockefeller University Press, 2008)
      After acute HIV infection, CD8^{+} T cells are able to control viral replication to a set point. This control is often lost after superinfection, although the mechanism behind this remains unclear. In this study, we ...
    • Impact of Pre-adapted HIV Transmission 

      Carlson, Jonathan M.; Du, Victor Y.; Pfeifer, Nico; Bansal, Anju; Tan, Vincent Y.F.; Power, Karen; Brumme, Chanson J.; Kreimer, Anat; DeZiel, Charles E.; Fusi, Nicolo; Schaefer, Malinda; Brockman, Mark A.; Gilmour, Jill; Price, Matt A.; Kilembe, William; Haubrich, Richard; John, Mina; Mallal, Simon; Shapiro, Roger; Frater, John; Harrigan, P. Richard; Ndung’u, Thumbi; Allen, Susan; Heckerman, David; Sidney, John; Allen, Todd M.; Goulder, Philip J.R.; Brumme, Zabrina L.; Hunter, Eric; Goepfert, Paul A. (2016)
      Human Leukocyte Antigen class I (HLA) restricted CD8+ T lymphocyte (CTL) responses are critical to HIV-1 control. Although HIV can evade these responses, the longer-term impact of viral escape mutants remains unclear, since ...
    • Impaired hepatitis C virus-specific T cell responses and recurrent hepatitis C virus in HIV coinfection 

      Kim, Arthur Yu-Shin; Schulze zur Wiesch, Julian; Kuntzen, Thomas; Timm, Joerg; Kaufmann, Daniel; Duncan, Jared E.; Jones, Andrea M.; Wurcel, Alysse G.; Davis, Benjamin Thomas; Gandhi, Rajesh Tim; Robbins, Gregory Kimball; Allen, Todd; Chung, Raymond Taeyong; Lauer, Georg; Walker, Bruce David (Public Library of Science, 2006)
      Background: Hepatitis C virus (HCV)-specific T cell responses are critical for spontaneous resolution of HCV viremia. Here we examined the effect of a lymphotropic virus, HIV-1, on the ability of coinfected patients to ...
    • Increased Breadth and Depth of Cytotoxic T Lymphocytes Responses against HIV-1-B Nef by Inclusion of Epitope Variant Sequences 

      Rolland, Morgane; Frahm, Nicole; Nickle, David C.; Jojic, Nebojsa; Deng, Wenjie; Allen, Todd; Brander, Christian; Heckerman, David E.; Mullins, James I. (Public Library of Science, 2011)
      Different vaccine approaches cope with HIV-1 diversity, ranging from centralized to variability-encompassing antigens. For all these strategies, a concern remains: how does HIV-1 diversity impact epitope recognition by the ...
    • Temporal effect of HLA-B*57 on viral control during primary HIV-1 infection 

      Vaidya, Sagar A; Streeck, Hendrik; Beckwith, Noor; Ghebremichael, Musie; Pereyra, Florencia; Kwon, Douglas S; Addo, Marylyn M; Rychert, Jenna; Routy, Jean-Pierre; Jessen, Heiko; Kelleher, Anthony D; Hecht, Frederick; Sekaly, Rafick-Pierre; Carrington, Mary; Walker, Bruce D; Allen, Todd M; Rosenberg, Eric S; Altfeld, Marcus (BioMed Central, 2013)
      Background: HLA-B alleles are associated with viral control in chronic HIV-1 infection, however, their role in primary HIV-1 disease is unclear. This study sought to determine the role of HLA-B alleles in viral control ...
    • Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection 

      Henn, Matthew R.; Charlebois, Patrick; Lennon, Niall J.; Power, Karen A.; Macalalad, Alexander R.; Berlin, Aaron M.; Malboeuf, Christine M.; Gnerre, Sante; Erlich, Rachel L.; Green, Lisa M.; Berical, Andrew; Wang, Yaoyu; Newman, Ruchi; Axten, Karen L.; Gladden, Adrianne D.; Battis, Laura; Kemper, Michael; Zeng, Qiandong; Shea, Terrance P.; Gujja, Sharvari; Zedlack, Carmen; Gasser, Olivier; Brander, Christian; Günthard, Huldrych F.; Brumme, Zabrina L.; Brumme, Chanson J.; Bazner, Suzane; Rychert, Jenna; Tinsley, Jake P.; Levin, Joshua Z.; Jessen, Heiko; Birren, Bruce W.; Boutwell, Christian Lane; Ryan, Elizabeth M.; Zody, Michael C.; Casali, Monica; Streeck, Hendrik; Bloom, Allyson Kelly; Dudek, Timothy E.; Tully, Damien C.; Hess, Christoph; Mayer, Kenneth Hugh; Rosenberg, Eric Scott; Pereyra, Florencia M.; Young, Sarah K.; Altfeld, Marcus; Walker, Bruce David; Allen, Todd (Public Library of Science, 2012)
      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. ...