We are using a key principle that we use in fighting spam to fight HIV. In the case of spam, we have spammers changing their emails to get around the spam filters. So, we go after their Achilles heel: their need to extract money. In the case of HIV, we have HIV mutating to get around our immune system. Here, we’re again looking for the Achilles heel(s) of HIV—vulnerable spots on the virus that, if they mutate, compromise the function of the virus. One step in this approach is to catalog the spots along HIV that our immune system can target. This is where PhyloD comes in. Here are some of the articles describing our search for targets using PhyloD:
• G. Alter, D. Heckerman, A. Schneidewind, L. Fadda, C. Kadie, J. Carlson, C. Oniangue-Ndza, M. Martin, B. Li, S. Khakoo, M. Carrington, T. Allen, M. and Altfeld M. HIV-1 adaptation to NK-cell-mediated immune pressure. Nature, 476 (7358): 96-100, August 2011.
• A. Bansal, J. Carlson, J. Yan, O. Akinsiku, M. Schaefer, S. Sabbaj, A. Bet, D. Levy, S. Heath, J. Tang, R. Kaslow, B. Walker, T. Ndungu, P. Goulder, D. Heckerman, E. Hunter, and P. Goepfert. CD8 T cell response and evolutionary pressure to HIV-1 cryptic epitopes derived from antisense transcription. JEM, 10.1084/jem.20092060, January 2010.
• C. Berger, J. Carlson, C. Brumme, K. Hartman, Z. Brumme, L. Henry, P. Rosato, A. Piechocka-Trocha, M. Brockman, P. Harrigan, D. Heckerman, D. Kaufmann, and Ch. Brander. Viral adaptation to immune selection pressure by HLA class I-restricted CTL responses targeting epitopes in HIV frameshift sequences. JEM, 10.1084/jem.20091808, January 2010.
We are using a key principle that we use in fighting spam to fight HIV. In the case of spam, we have spammers changing their emails to get around the spam filters. So, we go after their Achilles heel: their need to extract money. In the case of HIV, we have HIV mutating to get around our immune system. Here, we’re again looking for the Achilles heel(s) of HIV—vulnerable spots on the virus that, if they mutate, compromise the function of the virus. One step in this approach is to catalog the spots along HIV that our immune system can target. This is where PhyloD comes in. Here are some of the articles describing our search for targets using PhyloD:
• G. Alter, D. Heckerman, A. Schneidewind, L. Fadda, C. Kadie, J. Carlson, C. Oniangue-Ndza, M. Martin, B. Li, S. Khakoo, M. Carrington, T. Allen, M. and Altfeld M. HIV-1 adaptation to NK-cell-mediated immune pressure. Nature, 476 (7358): 96-100, August 2011.
• A. Bansal, J. Carlson, J. Yan, O. Akinsiku, M. Schaefer, S. Sabbaj, A. Bet, D. Levy, S. Heath, J. Tang, R. Kaslow, B. Walker, T. Ndungu, P. Goulder, D. Heckerman, E. Hunter, and P. Goepfert. CD8 T cell response and evolutionary pressure to HIV-1 cryptic epitopes derived from antisense transcription. JEM, 10.1084/jem.20092060, January 2010.
• C. Berger, J. Carlson, C. Brumme, K. Hartman, Z. Brumme, L. Henry, P. Rosato, A. Piechocka-Trocha, M. Brockman, P. Harrigan, D. Heckerman, D. Kaufmann, and Ch. Brander. Viral adaptation to immune selection pressure by HLA class I-restricted CTL responses targeting epitopes in HIV frameshift sequences. JEM, 10.1084/jem.20091808, January 2010.