Leveraging hierarchical population structure in discrete association studies. by Jonathan Carlson, Carl Kadie, Simon Mallal, David Heckerman

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A statistical framework for modeling HLA-dependent T cell response data. by Jennifer Listgarten, Nicole Frahm, Carl Kadie, Christian Brander, David Heckerman

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Learning transcriptional regulatory relationships using sparse graphical models. by Xiang Zhang, Wei Cheng, Jennifer Listgarten, Carl Kadie, Shunping Huang, Wei Wang, David Heckerman

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Statistical resolution of ambiguous HLA typing data. by Jennifer Listgarten, Zabrina Brumme, Carl Kadie, Gao Xiaojiang, Bruce Walker, Mary Carrington, Philip Goulder, David Heckerman

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Ranking of non-coding pathogenic variants and putative essential regions of the human genome by Alex Wells, David Heckerman, Ali Torkamani, Li Yin, Jonathan Sebat, Bing Ren, Amalio Telenti, Julia di Iulio

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Correction: Comparison of Immunogen Designs That Optimize Peptide Coverage: Reply to Fischer et al. by David C Nickle, Nebojsa Jojic, David Heckerman, Vladimir Jojic, Darko Kirovski, Morgane Rolland, Sergei Kosakovsky Pond, James I Mullins

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Comparison of immunogen designs that optimize peptide coverage: reply to Fischer et al. by David C Nickle, Nebojsa Jojic, David Heckerman, Vladimir Jojic, Darko Kirovski, Morgane Rolland, Sergei Kosakovsky Pond, James I Mullins

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Coping with viral diversity in HIV vaccine design. by David C Nickle, Morgane Rolland, Mark A Jensen, Sergei L Kosakovsky Pond, Wenjie Deng, Mark Seligman, David Heckerman, James I Mullins, Nebojsa Jojic

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Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag. by Jonathan M Carlson, Zabrina L Brumme, Christine M Rousseau, Chanson J Brumme, Philippa Matthews, Carl Kadie, James I Mullins, Bruce D Walker, P Richard Harrigan, Philip J R Goulder, David Heckerman

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Correction: Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1. by Zabrina L Brumme, Chanson J Brumme, David Heckerman, Bette T Korber, Marcus Daniels, Jonathan Carlson, Carl Kadie, Tanmoy Bhattacharya, Celia Chui, James Szinger, Theresa Mo, Robert S Hogg, Julio S. G Montaner, Nicole Frahm, Christian Brander, Bruce D Walker, P. Richard Harrigan

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Progression to AIDS in South Africa is associated with both reverting and compensatory viral mutations. by Kuan-Hsiang Gary Huang, Dominique Goedhals, Jonathan M Carlson, Mark A Brockman, Swati Mishra, Zabrina L Brumme, Stephen Hickling, Christopher S W Tang, Toshiyuki Miura, Chris Seebregts, David Heckerman, Thumbi Ndung'u, Bruce Walker, Paul Klenerman, Dewald Steyn, Philip Goulder, Rodney Phillips, Bloemfontein-Oxford Collaborative Group, Cloete van Vuuren, John Frater

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HIV-1 p24(gag) derived conserved element DNA vaccine increases the breadth of immune response in mice. by Viraj Kulkarni, Margherita Rosati, Antonio Valentin, Brunda Ganneru, Ashish K Singh, Jian Yan, Morgane Rolland, Candido Alicea, Rachel Kelly Beach, Gen-Mu Zhang, Sylvie Le Gall, Kate E Broderick, Niranjan Y Sardesai, David Heckerman, Beatriz Mothe, Christian Brander, David B Weiner, James I Mullins, George N Pavlakis, Barbara K Felber

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Role of transmitted Gag CTL polymorphisms in defining replicative capacity and early HIV-1 pathogenesis. by Jessica L Prince, Daniel T Claiborne, Jonathan M Carlson, Malinda Schaefer, Tianwei Yu, Shabir Lahki, Heather A Prentice, Ling Yue, Sundaram A Vishwanathan, William Kilembe, Paul Goepfert, Matthew A Price, Jill Gilmour, Joseph Mulenga, Paul Farmer, Cynthia A Derdeyn, Jiaming Tang, David Heckerman, Richard A Kaslow, Susan A Allen, Eric Hunter

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CTL responses of high functional avidity and broad variant cross-reactivity are associated with HIV control. by Beatriz Mothe, Anuska Llano, Javier Ibarrondo, Jennifer Zamarreño, Mattia Schiaulini, Cristina Miranda, Marta Ruiz-Riol, Christoph T Berger, M José Herrero, Eduard Palou, Montse Plana, Morgane Rolland, Ashok Khatri, David Heckerman, Florencia Pereyra, Bruce D Walker, David Weiner, Roger Paredes, Bonaventura Clotet, Barbara K Felber, George N Pavlakis, James I Mullins, Christian Brander

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HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef proteins. by Zabrina L Brumme, Mina John, Jonathan M Carlson, Chanson J Brumme, Dennison Chan, Mark A Brockman, Luke C Swenson, Iris Tao, Sharon Szeto, Pamela Rosato, Jennifer Sela, Carl M Kadie, Nicole Frahm, Christian Brander, David W Haas, Sharon A Riddler, Richard Haubrich, Bruce D Walker, P Richard Harrigan, David Heckerman, Simon Mallal

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A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control by István Bartha, Jonathan M Carlson, Chanson J Brumme, Paul J McLaren, Zabrina L Brumme, Mina John, David W Haas, Javier Martinez-Picado, Judith Dalmau, Cecilio López-Galíndez, Concepción Casado, Andri Rauch, Huldrych F Günthard, Enos Bernasconi, Pietro Vernazza, Thomas Klimkait, Sabine Yerly, Stephen J O’Brien, Jennifer Listgarten, Nico Pfeifer, Christoph Lippert, Nicolo Fusi, Zoltán Kutalik, Todd M Allen, Viktor Müller, P Richard Harrigan, David Heckerman, Amalio Telenti, Jacques Fellay, for the HIV Genome-to-Genome Study and the Swiss HIV Cohort Study

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