Publications: HIV and HCV vaccine design

· J.M. Carlson, V.Y. Du, N. Pfeifer, A. Bansal, V.Y.F. Tan, K. Power, C.J. Brumme, A. Kreimer, C.E. DeZiel, N. Fusi, M. Schaefer, M.A. Brockman, J. Gilmour, M.A. Price, W. Kilembe, R. Haubrich, M. John, S. Mallal, R. Shapiro, J. Frater, P.R. Harrigan, T. Ndung'u, S. Allen, D. Heckerman, T.M. Allen, P.J.R. Goulder, Z.L. Brumme, E. Hunter & P.A. Goepfert. Impact of pre-adapted HIV transmission. Nature Medicine 22, 606¡V613 (2016) (doi:10.1038/nm.4100).

· K. Pfafferott, P. Deshpande, E. McKinnon, S. Merani, A. Lucas, S. Mallal, D. Heckerman, M. John, S. Gaudieri, M. Lucas. Anti-Hepatitis C virus T-cell immunity in the context of multiple exposures to the virus. PLoS One, June 2015 (doi:10.1371/journal.pone.0130420).

· C. Berger, A. Llano, J. Carlson, Z. Brumme, Mark Brockman, S. Cedeño, P.R. Harrigan, D. Kaufmann, D. Heckerman, A. Meyerhans, and C. Brander. Immune screening identifies novel T cell targets encoded by antisense reading frames of HIV-1. J. Virol 89, 4015-4019, April 2015 (doi:10.1128/JVI.03435-14).

· C. Berger, A. Llano, J. Carlson, Z. Brumme, M. Brockman, S. Cedeño, P. Harrigan, D. Kaufmann, D. Heckerman, A. Meyerhans, C. Brander.  Immune screening identifies novel T cell targets encoded by anti-sense reading frames of HIV-1.  J Virol, Jan 2015.

· F. Pereyra, D. Heckerman, J. Carlson, C. Kadie, D. Soghoian, D. Karel, A. Goldenthal, O. Davis, C. DeZiel, T. Lin, J. Peng, A. Piechocka, M. Carrington, and B. Walker. HIV Control Is Mediated in Part by CD8+ T-Cell Targeting of Specific Epitopes. J. Virol 88 12937-12948, Aug 2014.

· J. Carlson, M. Schaefer, D. Monaco, R. Batorsky, D. Claiborne, J. Prince, M. Deymier, Z. Ende, N. Klatt, C. DeZiel, Tien-Ho Lin, J. Peng, A. Seese, R. Shapiro, J. Frater, T. Ndung’u, J. Tang, P. Goepfert, J. Gilmour, M. Price, W. Kilembe, D. Heckerman, P. Goulder, T. Allen, S. Allen, and E. Hunter. Selection bias at the heterosexual HIV-1 transmission bottleneck. Science, 345(6193): 1254031, July 2014 (doi:10.1126/science.1254031).

· R. Rubsamen, C. Herst, P. Lloyd, D. Heckerman. Eliciting cytotoxic T-lymphocyte responses from synthetic vectors containing one or two epitopes in a C57BL/6 mouse model using peptide-containing biodegradable microspheres and adjuvants. Vaccine 32, 4111-4116, June 2014.

· J. Sunshine, M. Kim, J. Carlson, D. Heckerman, J. Czartoski, S. Migueles, J. Maenza, M. McElrath, J. Mullins, and N. Frahm. Increased sequence coverage through combined targeting of variant and conserved epitopes correlates with control of HIV replication.  Journal of Virology 88(2):1354-65, Jan 2014 (doi: 10.1128/JVI.02361-13).

· I. Bartha, J.Carlson, C. Brumme, P. McLaren, Z. Brumme, M. John, D. Haas, J. Martinez-Picado, J. Dalmau, C. López-Galíndez, C. Casado, A. Rauch, H. Günthard, E. Bernasconi, P. Vernazza, T. Klimkait, S. Yerly, S. O’Brien, J. Listgarten, N. Pfeifer, C. Lippert, N. Fusi, Z. Kutalik, T. Allen, V. Müller, P. Harrigan, D. Heckerman, A. Telenti, and J. Fellay.  A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control.  eLife 2013;2:e01123, October 2013 (http://dx.doi.org/10.7554/eLife.01123).

· C. Boutwell, J.M. Carlson, T. Lin, A. Seese, K. Power, J. Peng, Y. Tang, Z. Brumme, D. Heckerman, A. Schneidewind, and T. Allen.  Frequent and variable cytotoxic-T-lymphocyte escape-associated fitness costs in the human immunodeficiency virus type 1 subtype B Gag proteins.  Journal of Virology, 87(7): 3952-3965, April 2013 (10.1128/JVI.03233-12).

· C. Bronke, C.A. Almeida, E. McKinnon, S.G. Roberts, N.M.  Keane, A. Chopra, J.M. Carlson, D. Heckerman, S. Mallal, and M. John.  HIV escape mutations occur preferentially at HLA-binding sites of CD8 T-cell epitopes.  AIDS, 27(6): 899–905, March 2013 (doi: 10.1097/QAD.0b013e32835e1616).

· V. Kulkarni, M. Rosati, A. Valentin, B. Ganneru, A.K. Singh, J. Yan, M. Rolland, C. Alicea, R.K. Beach, G. Zhang, S. Le Gall, K.E. Broderick, N.Y. Sardesai, D. Heckerman, B. Mothe, C. Brander, D.B. Weiner, J.I. Mullins, G.N. Pavlakis, B.K. Felber.  HIV-1 p24-Gag derived conserved element DNA vaccine increases the breadth of immune response in mice.  PLoS ONE 8(3): e60245, March 2013 (doi:10.1371/journal.pone.0060245).

· Z.M. Ndhlovu, L.B. Chibnik, J. Proudfoot, S. Vine, A. McMullen, K. Cesa, F. Porichis, R.B. Jones, D.M. Alvino, M.G. Hart, E. Stampouloglou, A. Piechocka-Trocha, C.M. Kadie, F. Pereyra, D. Heckerman, P.L. De Jager, B.D. Walker, and D.E. Kaufmann.  High-dimensional immunomonitoring models of HIV-1–specific CD8 T-cell responses accurately identify subjects achieving spontaneous viral control.  Blood, 121(5): 801-811, Jan 2013 (doi: 10.1182/blood-2012-06-436295).

· J. Carlson, C. Brumme, E. Martin, J. Listgarten, M. Brockman, A. Le, C. Chui, L. Cotton, D. Knapp, S. Riddler, R. Haubrich, G. Nelson, N. Pfeifer, C. DeZiel, D. Heckerman, R. Apps, M. Carrington, S. Mallal, R. Harrigan, M. John, and Z. Brumme.  Correlates of protective cellular immunity revealed by analysis of population-level immune escape pathways in HIV-1.  Journal of Virology, 86(24): 13202-13216, Dec 2012 (doi: 10.1128/JVI.01998-12).

· P. C. Matthews, M. Koyanagi, H. N. Kloverpris, M. Harndahl, A. Stryhn, T. Akahoshi, H. Gatanaga  S. Oka, C. Juarez Molina, P. H. Valenzuela, R. Avila Rios, D. Cole, J. Carlson, R. P. Payne, A. Ogwu, A. Bere, T. Ndung'u, K. Gounder, F. Chen, L. Riddell, G. Luzzi, R. Shapiro, C. Brander, B. Walker, A. K. Sewell, G. Reyes Teran, D. Heckerman, E. Hunter, S. Buus, M. Takiguchi, P. J. GoulderJ.  Differential clade-specific HLA-B*3501 association with HIV-1 disease outcome is linked to immunogenicity of a single Gag epitope.  Journal of Virololgy, 86(23): 12643-54, Dec 2012 (doi: 10.1128/JVI.01381-12).

· R. Apps, Y. Qi, J. M. Carlson, H. Chen, X. Gao, R. Thomas, Y. Yuki, G. Q. Del Prete, P. Goulder, Z. L. Brumme, C. J. Brumme, M John, S. Mallal, G. Nelson, R. Bosch, D. Heckerman, J. L. Stein, K. A. Soderberg, M. A. Moody, T. N. Denny, Xue Zeng, J. Fang, A. Moffett, J. D. Lifson, J. J. Goedert, S. Buchbinder, G. D. Kirk, J. Fellay, P. McLaren, S. G. Deeks, F. Pereyra, B. Walker, N. L. Michael, A. Weintrob, S. Wolinsky, W. Liao, M. Carrington.  Influence of HLA-C Expression Level on HIV Control.  Science, 340(6128): 87-91, Nov 2012 (doi: 10.1128/JVI.02122-12).

· J.L. Prince, D.T. Claiborne, J.M. Carlson, M. Schaefer, T. Yu, S. Lahki, H.A. Prentice, L.Yue, S.A. Vishwanathan, W. Kilembe, P. Goepfert, M.A. Price, J. Gilmour, J. Mulenga, P. Farmer, C.A. Derdeyn, J. Tang, D. Heckerman, R.A. Kaslow, and S.A. Allen.  Role of transmitted Gag CTL polymorphisms in defining replicative capacity and early HIV-1 pathogenesis.  PLoS Pathogens 8(11): e1003041, Nov 2012 (doi:10.1371/journal.ppat.1003041).

· S. Nomura, N. Hosoya, Z. Brumme, M. Brockman, T. Kikuchi, M. Koga, H. Nakamura, T. Koibuchi, T. Fujii, J. Carlson, D. Heckerman, A. Tachikawa, A. Iwamoto, and T. Miura.  Significant reductions in Gag-protease mediated HIV-1 replication capacity over the course of the epidemic in Japan.  Journal of Virology, 87(3): 1465-1476, Nov 2012 (doi: 10.1128/JVI.02122-12).

· P.C. Matthews, J. Listgarten, J.M. Carlson, R. Payne, K.G. Huang, J. Frater, D. Goedhals, D. Steyn, C. van Vuuren, P. Paioni, P. Jooste, A. Ogwu, R. Shapiro, Z. Mncube, T. Ndung'u, B.D. Walker, D. Heckerman, and P.J.R. Goulder.  Co-operative additive effects between HLA alleles in control of HIV-1.  PLoS One 7(10): e47799, Oct 2012 (doi:10.1371/journal.pone.0047799).

· P.J. McLaren, S. Ripke, K. Pelak, A.C. Weintrob, N.A. Patsopoulos, X. Jia, R.L. Erlich, N.J. Lennon, C.M. Kadie, D. Heckerman, N. Gupta, D.W. Haas, S.G. Deeks, F. Pereyra, B.D. Walker, P.I.W. de Bakker, and the International HIV Controllers Study.  Fine-mapping classical HLA variation associated with durable host control of HIV-1 infection in African Americans.  Human Molecular Genetics, 21(19): 4334-4347, June 2012 (doi: 10.1093/hmg/dds226).

· M. Brockman, D. Chopera, A. Olvera, C. Brumme, J. Sela, T. Markle, E Martin, J.Carlson, A. Le, R. McGovern, P. Cheung, A. Kelleher, H. Jessen, M. Markowitz, E. Rosenberg, N. Frahm, J. Sanchez, S. Mallal, M. John, P. Harrigan, D. Heckerman, C. Brander, B. Walker, and Z. Brumme.  Uncommon pathways of immune escape attenuate HIV-1 integrase replication capacity.  Journal of Virology, April, 2012 (doi: 10.1128/JVI.07133-11).

· J. Carlson, J. Listgarten, N. Pfeifer, V. Tan, C. Kadie, B. Walker, T. Ndung'u, R. Shapiro, J. Frater, Z. Brumme, P. Goulder, and D. Heckerman.  Widespread impact of HLA restriction on immune control and escape pathways in HIV-1.B.  Journal of Virology, February, 2012 (doi: 10.1128/JVI.06728-11).

· B. Mothe, A. Llano, J. Ibarrondo, J. Zamarre, M. Schiaulini, C. Miranda, M. Ruiz-Riol, C. Berger, M. J. Herrero, E. Palou, M. Plana, M. Rolland, A. Khatri, D. Heckerman, F. Pereyra, B. Walker, D. Weiner, R. Paredes, B. Clotet, B. Felber, G. Pavlakis, J. Mullins, C. Brander.  CTL Responses of High Functional Avidity and Broad Variant Cross-Reactivity are Associated with HIV Control.  PLoS ONE 7(1):  e29717, Jan 2012 (doi:10.1371/journal.pone.0029717).

· B. Mothe, A. Llano, J. Ibarrondo, M. Daniels, C. Miranda, J. Zamarreno, V. Bach, R. Zuniga, S. Perez-Alvarez, C. Berger, M. Puertas, J. Martinez-Picado, M. Rolland, M. Farfan, J. Szinger, W. Hildebrand, O. Yang, V. Sanchez-Merino, C. Brumme, Z. Brumme, D. Heckerman, T. Allen, J. Mullins, G. Gomez, P. Goulder, B.Walker, J. Gatell, B. Clotet, B. Korber, J. Sanchez and C. Brander.  Definition of the viral targets of protective HIV-1-specific T cell responses.  Journal of Translational Medicine, 9: 208, Dec 2011 (doi:10.1186/1479-5876-9-208).

· S. Ranasinghe, M. Flanders, S. Cutler, D. Soghoian, M. Ghebremichael, I. Davis, M. Lindqvist, F. Pereyra, B. Walker, D. Heckerman, and H. Streeck.  HIV-specific CD4 T cell responses to different viral proteins have discordant associations with viral load and clinical outcome.  Journal of Virology, Oct 2011 (doi: 10.1128/JVI.05577-11).

· 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.

· C. Almeida, C. Bronke, S. Roberts, E. McKinnon, N. Keane, A. Chopra, C. Kadie, J. Carlson, D. Haas, S. Riddler, R. Haubrich, D. Heckerman, S. Mallal, and M. John.  Translation of HLA-HIV associations to the cellular level: HIV adapts to inflate CD8 T cell responses against Nef and HLA-adapted variant epitopes.  Journal of Immunology, 187(5):2502-13, Aug, 2011.

· E. Lazaro, C. Kadie, P. Stamegna, S. Zhang, P. Gourdain, N. Lai, M. Zhang, S. Martinez, D. Heckerman, and S. Le Gall.  Variable HIV peptide stability in human cytosol is critical to epitope presentation and immune escape.  J Clin Invest., 121(6): 2480-2492, June 2011.

· N. Keane, S. Roberts, C. Almeida, T. Krishnan, A. Chopra, E. Demaine, R. Laird, M. Tschochner, J. Carlson, S. Mallal, D. Heckerman, I. James, and M. John.  High-avidity, high-IFNg-producing CD8 T-cell responses following immune selection during HIV-1 infection.  Immunology and Cell Biology, doi:10.1038/icb.2011.34, May, 2011.

· P. Matthews, E. Adland, J. Listgarten, A. Leslie, N. Mkhwanazi, J. Carlson, M. Harndahl, A. Stryhn, R. Payne, A. Ogwu, K. Huang, J. Frater, P. Paioni, H. Kloverpris, P.Jooste, D. Goedhals, C. van Vuuren, D. Steyn, L. Riddell, F. Chen, G. Luzzi, T. Balachandran, T. Ndung'u, S. Buus, M. Carrington, R. Shapiro, D. Heckerman, and P. Goulder.  HLA-A*7401-mediated control of HIV viremia is independent of its linkage disequilibrium with HLA-B*5703.  Journal of Immunology, doi: 10.4049, April 2011.

· K. Huang, D. Goedhals, J. Carlson, M. Brockman, S. Mishra, Z. Brumme, S. Hickling, C. Tang, T. Miura7, C. Seebregts, D. Heckerman, T. Ndung'u, B. Walker, P. Klenerman, D. Steyn, P. Goulder, R. Phillips, Bloemfontein-Oxford Collaborative Group, C. van Vuuren, and J. Frater.  Progression to AIDS in South Africa is associated with both reverting and compensatory viral mutations.  PLoS One, 6(4):e19018, April, 2011.

· M. Rolland, N. Frahm, D. Nickle, N. Jojic, W. Deng, T. Allen, C. Brander, D. Heckerman, J. Mullins.  Increased breadth and depth of cytotoxic T lymphocytes responses against HIV-1-B Nef by inclusion of epitope variant sequences.  PLoS One, 28;6(3):e17969, March 2011.

· J. Wright, V. Novitsky, M. Brockman, Z. Brumme, C. Brumme, J. Carlson, D. Heckerman, B. Wang, E. Losina, M. Leshwedi, M. van der Stok, L. Maphumulo, N. Mkhwanazi, F. Chonco, P. Goulder, M. Essex, B. Walker, and T. Ndung'u.  Influence of Gag-Protease-mediated replication vapacity on disease progression in individuals recently infected with HIV-1 subtype C. Journal of Virology, doi:10.1128/JVI.02520-10, February, 2010.

· The International HIV Controllers Study.  The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation, Science, 330: 1551-1557, December 10 2010.

· H. Crawford, P. Matthews, M. Schaefer, J. Carlson, A. Leslie, W. Kilembe, S. Allen, T. Ndung'u, D. Heckerman, E. Hunter, and P. Goulder.  The hypervariable HIV-1 capsid protein residues comprise HLA-driven CD8+ T-cell escape mutations and covarying HLA-independent polymorphisms.  Journal of Virology, doi:10.1128/JVI.01879-10, November, 2010.

· M. Brockman, Z. Brumme, C. Brumme, T. Miura, J. Sela, P. Rosato, C. Kadie, J. Carlson, T. Markle, H. Streeck, A. Kelleher, M. Markowitz, H. Jessen, E. Rosenberg, M. Altfeld, P. Harrigan, D. Heckerman, B. Walker, and T. Allen.  Early selection in Gag by protective HLA alleles contributes to reduced HIV-1 replication capacity that may be largely compensated for in chronic infection.  Journal of Virology, 84(22): 11937-11949, November 2010.

· A. Leslie, P. Matthews, J. Listgarten, J. Carlson, C. Kadie, T. Ndung'u, C. Brander, H. Coovadia, B. Walker, D. Heckerman and P. Goulder. Additive contribution of HLA class I alleles in the immune control of HIV-1 infection. Journal of Virology, 84(19):9879-9888, October 2010.

· M. Rolland, J. Carlson, S. Manocheewa, J. Swain, E. Lanxon-Cookson, W. Deng,  C. Rousseau, D. Raugi, G. Learn, B. Maust, H. Coovadia, T. Ndung'u, P. Goulder, B. Walker, C. Brander, D. Heckerman, J. Mullins.  Amino-acid co-variation in HIV-1 Gag subtype C: HLA-mediated selection pressure and compensatory dynamics.  PLoS One, 5(9), September 1, 2010.

· M. John, D. Heckerman, I. James, L. Park, J. Carlson, A. Chopra, S. Gaudieri, D. Nolan, D. Haas, S. Riddler, R. Haubrich, and Simon Mallal.  Adaptive interactions between HLA and HIV-1: Highly divergent selection imposed by HLA class I molecules with common supertype motifs.  The Journal of Immunology, 184:4368-4377, March 2010.

· M. Koga, A. Kawana-Tachikawa, D. Heckerman, T. Odawara, H. Nakamura, T. Koibuchi, T. Fujii, T. Miura, and A. Iwamoto.  Changes in impact of HLA class I allele expression on HIV-1 plasma virus loads at a population level over time.  Microbiology and Immunology, 54(4): 196-205.  January 2010.

· 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.

· S. Avila-Rios, C. Ormsby, J. Carlson, H. Valenzuela-Ponce, J. Blanco-Heredia, D. Garrido-Rodriguez, C. Garcia-Morales, D. Heckerman, Z. Brumme, S. Mallal, M. John, E. Espinosa, and G. Reyes-Teran.  Unique features of HLA-mediated HIV evolution in a Mexican cohort: a comparative study.  Retrovirology, 6:72doi:10.1186/1742-4690-6-72, August 2009.

· Z. Brumme, M. John., J. Carlson, C. Brumme, D. Chan, M. Brockman, L. Swenson, I. Tao, S. Szeto, P. Rosato, J. Sela, C. Kadie, N. Frahm, C. Brander, D. Haas, S. Riddler, R. Haubrich, B. Walker, P. Harrigan, D. Heckerman, and S. Mallal.  HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef proteins. PLoS ONE, 4(8):e6687. doi:10.1371/journal.pone.0006687.  August 2009.

· C. Rousseau, D. Lockhart, J. Listgarten, S. Maley, C. Kadie, G. Learn, D. Nickle, D. Heckerman, W. Deng, C. Brander, T. Ndung'u, H. Coovadia, P. Goulder, B. Korber, B. Walker, J. Mullins.  Rare HLA drive additional HIV evolution compared to more frequent alleles. AIDS Res Hum Retroviruses, 25:297-303, March 2009.

· Y. Kawashima, K. Pfafferott, J. Frater, P. Matthews, R. Payne, M. Addo, H. Gatanaga, M. Fujiwara, A. Hachiya, H. Koizumi, N. Kuse, S. Oka, A. Duda, A. Prendergast, H. Crawford, A. Leslie, Z. Brumme, C. Brumme, T. Allen, C. Brander, R. Kaslow, J. Tang, E. Hunter, S. Allen, J. Mulenga, S. Branch, T. Roach, M. John, S. Mallal, A. Ogwu, R. Shapiro, J. Prado, S. Fidler, J. Weber, O. Pybus, P. Klenerman, T. Ndung'u, R. Phillips, D. Heckerman, P. Harrigan, B. Walker, M. Takiguchi, and P. Goulder.  Adaptation of HIV-1 to human leukocyte antigen class I. Nature, February 2009.

· T. Miura, M. Brockman, Z. Brumme, C. Brumme, F. Pereyra, A. Trocha, B. Block, A. Schneidewind, T. Allen, D. Heckerman, and B. Walker.  HLA-associated alterations in replication capacity of chimeric NL4-3 viruses carrying gag-protease from elite controllers of human immunodeficiency virus type 1.  Journal of Virology, 83:140-149. January 2009.

· J. Carlson, Z. Brumme, C. Rousseau, C. Brumme, P. Matthews, C. Kadie, J. Mullins, B. Walker, P. Harrigan, P. Goulder, D. Heckerman.  Phylogenetic dependency networks: Inferring patterns of CTL escape and codon covariation in HIV-1 Gag. PLoS Computational Biology, 4(11): e1000225, November 2008.

· Y. Wang, B. Li, J. Carlson, H. Streeck, A. Gladden, R. Goodman, A. Schneidewind, K. Power, I. Toth, N. Frahm, G. Alter, C. Brander, M. Carrington, B. Walker, M. Altfeld, D. Heckerman, and T. Allen.  Protective HLA class I alleles restricting acute-phase CD8+ T cell responses are associated with viral escape mutations located in highly conserved regions of HIV-1.  Journal of Virology.  November, 2008.

· D. Yerly, D. Heckerman, T. Allen, T. Suscovich, N. Jojic, C. Kadie, W. Pichler, A. Cerny, and C. Brander.  Design, expression, and processing of epitomized hepatitis C virus-encoded CTL epitopes. Journal of Immunology, 181:6361-6370, November, 2008.

· P. Matthews, A. Prendergast, A. Leslie, H. Crawford, R. Payne, C. Rousseau, I. Honeyborne, J. Carlson, C. Kadie, C. Brander, J. Mullins, H. Coovadia, T. Nding.u, B. Walker, D. Heckerman, P. Goulder. Central role of reverting mutations in HLA associations with human immunodeficiency virus set point. Journal of Virology, 82:8548-59, September, 2008.

· Z. Brumme, C. Brumme, J. Carlson, H. Streeck, M. John, Q. Eichbaum, B. Block, B. Baker, C. Kadie, M. Markowitz, H. Jessen, A. Kelleher, E. Rosenberg, J. Kaldor, Y. Yuki, M. Carrington, T. Allen, S. Mallal, M. Altfeld, D. Heckerman, and B. Walker.  Marked epitope- and allele-specific differences in rates of mutation in human immunodeficiency type 1 (HIV-1) Gag, Pol, and Nef cytotoxic T-lymphocyte epitopes in acute/early HIV-1 infection.  Journal of Virology, 82:9216-9227, September 2008.

· T. Miura, M. Brockman, C. Brumme, Z. Brumme, J. Carlson, F. Pereyra, A. Trocha, M. Addo, B. Block, A. Rothchild, B. Baker, T. Flynn, A. Schneidewind, B. Li, Y. Wang, D. Heckerman, T. Allen, and B. Walker.  Genetic characterization of human immunodeficiency virus type 1 in elite controllers: Lack of gross genetic defects or common amino acid changes. Journal of Virology, 82:8422-8430, September, 2008.

· T. Kuntzen, J. Timm, A. Berical, N. Lennon, A. Berlin, S. Young, B. Lee, D. Heckerman, J. Carlson, L. Reyor, M. Kleyman, C. McMahon, C. Birch, J. Schulze Zur Wiesch, T. Ledlie, M. Koehrsen, C. Kodira, A. Roberts, G. Lauer, H. Rosen, F. Bihl, A. Cerny, U. Spengler, Z. Liu, A. Kim, Y. Xing, A. Schneidewind, M. Madey, J. Fleckenstein, V. Park, J. Galagan, C. Nusbaum, B. Walker, G. Lake-Bakaar, E. Daar, I. Jacobson, E. Gomperts, B. Edlin, S. Donfield, R. Chung, A. Talal, T. Marion, B. Birren, M. Henn, T. Allen.  Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients. Hepatology, 48:1769-1778, July 2008.

· C. Wang, D. Blei, and D. Heckerman.  Continuous Time Dynamic Topic Models.  In Proceedings of Twenty Fourth Conference on Uncertainty in Artificial Intelligence, Helsinki, Finland, UAI Press, July 2008.  Local copy.

· Z. Brumme., I. Tao, S. Szeto, C. Brumme, J. Carlson, D. Chan, C. Kadie, N. Frahm, C. Brander, B. Walker, D. Heckerman, and P. Harrigan.  HLA-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated, AIDS, 22(11):1277-1286, July, 2008.

· P. Goepfert, W. Lumm, P. Farmer, P. Matthews, A. Prendergast, J. Carlson, C. Derdeyn, J. Tang, R. Kaslow, A. Bansal, K. Yusim, D. Heckerman, J. Mulenga, S. Allen, P. Goulder, and E. Hunter.  Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients, Journal of Experimental Medicine, 205(5):1009-1017, April, 2008.

· C. Rousseau, M. Daniels, J. Carlson C. Kadie, H. Crawford, A. Prendergast, P. Matthews, D. Raugi, B. Maust G. Learn D. Nickle N. Frahm, C. Brander, B. Walker P. Goulder, T. Bhattacharya, D. Heckerman, B. Korber, and J. Mullins.  Class-I driven evolution of human immunodeficiency virus type 1 subtype C proteome: Immune escape and viralload, Journal of Virology, doi:10.1128/JVI.02455-07, April 2008.

· J. Listgarten, Z. Brumme, C. Kadie, G. Xiaojiang, B. Walker, M. Carrington, P. Goulder, and D. Heckerman.  Statistical resolution of ambiguous HLA typing data.  PLoS Computational Biology, 4(2): e1000016, February, 2008.

· D. Yerly, D. Heckerman, T. Allen, J. Chisholm, K. Faircloth, C. Linde, N. Frahm, J. Timm, W. Pichler, A. Cerny, and C. Brander.  Increased CTL epitope variant cross-recognition and functional avidity are associated with HCV clearance. J. Virol, January 2008.

· D. Nickle, N. Jojic, D. Heckerman, V. Jojic, D. Kirovski, M. Rolland, S. Pond, J. Mullins.  Comparison of immunogen designs that optimize peptide coverage: Reply to Fischer et al., PLoS Computational Biology, 4(1):e25, January 2008.

· M. Rolland, D. Heckerman, W. Deng, C. Rousseau, H. Coovadia K. Bishop, P. Goulder, B. Walker, C. Brander, J. Mullins.  Broad and Gag-biased HIV-1 epitope repertoires are associated with lower viral loads. PLoS ONE, 3(1): e1424, January, 2008.

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· Z. Brumme, C. Brumme, D. Heckerman, B. Korber, M. Daniels, J. Carlson, C. Kadie, T. Bhattacharya, C. Chui, T. Mo, R. Hogg, J. Montaner, N. Frahm, C. Brander, B. Walker, P. Harrigan.  Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1. PLoS Pathogens, 3(7): e94, July 2007.

· J. Carlson, C. Kadie, S. Mallal, and D. Heckerman.  Leveraging hierarchical population structure in discrete association studies. PLoS ONE, 2(7): e591, July 2007.

· C. Rousseau, G. Learn, T. Bhattacharya, D. Nickle, D. Heckerman, S. Chetty, C. Brander, P. Goulder, B. Walker, P. Kiepiela, B. Korber, and J. Mullins.  Extensive intrasubtype recombination in South African Human Immunodeficiency Virus type I subtype C infections. J Virol, 81(9): 4492-4500.  May, 2007.

· D. Nickle, M. Rolland, M. Jensen, S. Pond, W. Deng, M. Seligman, D. Heckerman, J. Mullins, and N. Jojic.  Coping with viral diversity in HIV vaccine design, PLoS Computational Biology, 3(4): e75, April 2007.

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