Now showing items 1-8 of 8

    • Amino-Acid Co-Variation in HIV-1 Gag Subtype C: HLA-Mediated Selection Pressure and Compensatory Dynamics 

      Rolland, Morgane; Manocheewa, Siriphan; Lanxon-Cookson, Erinn; Deng, Wenjie; Rousseau, Christine M.; Raugi, Dana N.; Learn, Gerald H.; Maust, Brandon S.; Coovadia, Hoosen; Ndung'u, Thumbi; Heckerman, David E.; Mullins, James I.; Carlson, Jonathan Courtland; Swain, Jabaris; Goulder, Philip J.; Walker, Bruce David; Brander, Christian (Public Library of Science, 2010)
      Background: Despite high potential for HIV-1 genetic variation, the emergence of some mutations is constrained by fitness costs, and may be associated with compensatory amino acid (AA) co-variation. To characterize the ...
    • Broad and Gag-Biased HIV-1 Epitope Repertoires are Associated with Lower Viral Loads 

      Rolland, Morgane; Heckerman, David; Deng, Wenjie; Rousseau, Christine M.; Coovadia, Hoosen; Bishop, Karen; Goulder, Philip J.; Walker, Bruce David; Brander, Christian; Mullins, James I. (Public Library of Science, 2008)
      Background: HLA class-I alleles differ in their ability to control HIV replication through cell-mediated immune responses. No consistent associations have been found between the breadth of Cytotoxic T Lymphocytes (CTL) ...
    • CD8 T Cell Response and Evolutionary Pressure to HIV-1 Cryptic Epitopes Derived from Antisense Transcription 

      Bansal, Anju; Yan, Jiyu; Akinsiku, Olusimidele T.; Schaefer, Malinda; Sabbaj, Steffanie; Bet, Anne; Levy, David N.; Heath, Sonya; Tang, Jianming; Kaslow, Richard A.; Ndung’u, Thumbi; Heckerman, David; Hunter, Eric; Goepfert, Paul A.; Carlson, Jonathan Courtland; Walker, Bruce David; Goulder, Philip J. (The Rockefeller University Press, 2010)
      Retroviruses pack multiple genes into relatively small genomes by encoding several genes in the same genomic region with overlapping reading frames. Both sense and antisense HIV-1 transcripts contain open reading frames ...
    • Immunodominance and Viral Ditness in Gag May Contribute to Differential Viral Control in HLA-B*7 Supertype Individuals Acutely Infected with HIV-1C 

      Gounder, K; Leshwedi, M; van der Stok, M; Chonco, F; Padayachee, N; Ndimande, B; Mokgoro, M; Jaggernath, M; Wright, J; Walker, Bruce David; Goulder, Philip J. (BioMed Central, 2012)
    • Immunodominant HIV-1 Cd4+ T Cell Epitopes in Chronic Untreated Clade C HIV-1 Infection 

      Ramduth, Danni; Day, Cheryl L.; Thobakgale, Christina F.; Mkhwanazi, Nompumelelo P.; de Pierres, Chantal; Reddy, Sharon; van der Stok, Mary; Mncube, Zenele; Nair, Kriebashne; Moodley, Eshia S.; Coovadia, Hoosen M.; Kiepiela, Photini; Kaufmann, Daniel; Streeck, Hendrik; Goulder, Philip J.; Walker, Bruce David (Public Library of Science, 2009)
      Background: A dominance of Gag-specific CD8+ T cell responses is significantly associated with a lower viral load in individuals with chronic, untreated clade C human immunodeficiency virus type 1 (HIV-1) infection. This ...
    • Immunodominant HIV-1-specific HLA-B- and HLA-C-restricted CD8+ T cells do not differ in polyfunctionality 

      Mkhwanazi, Nompumelelo; Thobakgale, Christina F.; van der Stok, Mary; Reddy, Shabashini; Mncube, Zenele; Chonco, Fundisiwe; Walker, Bruce David; Altfeld, Marcus; Goulder, Philip J.; Ndung'u, Thumbi (Academic Press, 2010)
      HIV-1 specific HLA-B-restricted CD8+ T cell responses differ from HLA-C-restricted responses in antiviral effectiveness. To investigate possible reasons for these differences, we characterized the frequency and polyfunctionality ...
    • Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag 

      Brumme, Zabrina L.; Rousseau, Christine M.; Brumme, Chanson J.; Matthews, Philippa; Kadie, Carl; Mullins, James I.; Harrigan, P. Richard; Heckerman, David; Carlson, Jonathan M.; Walker, Bruce David; Goulder, Philip J. (Public Library of Science, 2008)
      HIV avoids elimination by cytotoxic T-lymphocytes (CTLs) through the evolution of escape mutations. Although there is mounting evidence that these escape pathways are broadly consistent among individuals with similar human ...
    • Statistical Resolution of Ambiguous HLA Typing Data 

      Listgarten, Jennifer; Brumme, Zabrina; Kadie, Carl; Xiaojiang, Gao; Walker, Bruce David; Carrington, Mary; Goulder, Philip J.; Heckerman, David (Public Library of Science, 2008)
      High-resolution HLA typing plays a central role in many areas of immunology, such as in identifying immunogenetic risk factors for disease, in studying how the genomes of pathogens evolve in response to immune selection ...