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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Prevalence and Characteristics of Hepatitis B Virus (HBV) Coinfection among HIV-Positive Women in South Africa and Botswana. by Philippa C Matthews, Apostolos Beloukas, Amna Malik, Jonathan M Carlson, Pieter Jooste, Anthony Ogwu, Roger Shapiro, Lynn Riddell, Fabian Chen, Graz Luzzi, Manjeetha Jaggernath, Gerald Jesuthasan, Katie Jeffery, Thumbi Ndung'u, Philip J R Goulder, Anna Maria Geretti, Paul Klenerman

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Nef-specific CD8+ T cell responses contribute to HIV-1 immune control. by Emily Adland, Jonathan M Carlson, Paolo Paioni, Henrik Kløverpris, Roger Shapiro, Anthony Ogwu, Lynn Riddell, Graz Luzzi, Fabian Chen, Thambiah Balachandran, David Heckerman, Anette Stryhn, Anne Edwards, Thumbi Ndung'u, Bruce D Walker, Søren Buus, Philip Goulder, Philippa C Matthews

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Co-operative additive effects between HLA alleles in control of HIV-1. by Philippa C Matthews, Jennifer Listgarten, Jonathan M Carlson, Rebecca Payne, Kuan-Hsiang Gary Huang, John Frater, Dominique Goedhals, Dewald Steyn, Cloete van Vuuren, Paolo Paioni, Pieter Jooste, Anthony Ogwu, Roger Shapiro, Zenele Mncube, Thumbi Ndung'u, Bruce D Walker, David Heckerman, Philip J R Goulder

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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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Selection of an HLA-C*03:04-Restricted HIV-1 p24 Gag Sequence Variant Is Associated with Viral Escape from KIR2DL3+ Natural Killer Cells: Data from an Observational Cohort in South... by Angelique Hölzemer, Christina F Thobakgale, Camilo A Jimenez Cruz, Wilfredo F Garcia-Beltran, Jonathan M Carlson, Nienke H van Teijlingen, Jaclyn K Mann, Manjeetha Jaggernath, Seung-gu Kang, Christian Körner, Amy W Chung, Jamie L Schafer, David T Evans, Galit Alter, Bruce D Walker, Philip J Goulder, Mary Carrington, Pia Hartmann, Thomas Pertel, Ruhong Zhou, Thumbi Ndung'u, Marcus Altfeld

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Genotypic and functional impact of HIV-1 adaptation to its host population during the North American epidemic. by Laura A Cotton, Xiaomei T Kuang, Anh Q Le, Jonathan M Carlson, Benjamin Chan, Denis R Chopera, Chanson J Brumme, Tristan J Markle, Eric Martin, Aniqa Shahid, Gursev Anmole, Philip Mwimanzi, Pauline Nassab, Kali A Penney, Manal A Rahman, M-J Milloy, Martin T Schechter, Martin Markowitz, Mary Carrington, Bruce D Walker, Theresa Wagner, Susan Buchbinder, Jonathan Fuchs, Beryl Koblin, Kenneth H Mayer, P Richard Harrigan, Mark A Brockman, Art F Y Poon, Zabrina L Brumme

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A large-scale database of T-cell receptor beta sequences and binding associations from natural and synthetic exposure to SARS-CoV-2 by Sean Nolan, Marissa Vignali, Mark Klinger, Jennifer N. Dines, Ian M. Kaplan, Emily Svejnoha, Tracy Craft, Katie Boland, Mitchell W. Pesesky, Rachel M. Gittelman, Thomas M. Snyder, Christopher J. Gooley, Simona Semprini, Claudio Cerchione, Fabio Nicolini, Massimiliano Mazza, Ottavia M. Delmonte, Kerry Dobbs, Gonzalo Carreño-Tarragona, Santiago Barrio, Vittorio Sambri, Giovanni Martinelli, Jason D. Goldman, Jason D. Goldman, James R. Heath, Luigi D. Notarangelo, Joaquin Martinez-Lopez, Bryan Howie, Jonathan M. Carlson, Harlan S. Robins

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Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial. by Paul T Edlefsen, Morgane Rolland, Tomer Hertz, Sodsai Tovanabutra, Andrew J Gartland, Allan C deCamp, Craig A Magaret, Hasan Ahmed, Raphael Gottardo, Michal Juraska, Connor McCoy, Brendan B Larsen, Eric Sanders-Buell, Chris Carrico, Sergey Menis, Gustavo H Kijak, Meera Bose, RV144 Sequencing Team, Miguel A Arroyo, Robert J O'Connell, Sorachai Nitayaphan, Punnee Pitisuttithum, Jaranit Kaewkungwal, Supachai Rerks-Ngarm, Merlin L Robb, Tatsiana Kirys, Ivelin S Georgiev, Peter D Kwong, Konrad Scheffler, Sergei L Kosakovsky Pond, Jonathan M Carlson, Nelson L Michael, William R Schief, James I Mullins, Jerome H Kim, Peter B Gilbert

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Magnitude and dynamics of the T-cell response to SARS-CoV-2 infection at both individual and population levels by Thomas M. Snyder, Rachel M. Gittelman, Mark Klinger, Damon H. May, Edward J. Osborne, Ruth Taniguchi, H. Jabran Zahid, Ian M. Kaplan, Jennifer N. Dines, Matthew T. Noakes, Ravi Pandya, Xiaoyu Chen, Summer Elasady, Emily Svejnoha, Peter Ebert, Mitchell W. Pesesky, Patricia De Almeida, Hope O’Donnell, Quinn DeGottardi, Gladys Keitany, Jennifer Lu, Allen Vong, Rebecca Elyanow, Paul Fields, Hussein Al-Asadi, Julia Greissl, Lance Baldo, Simona Semprini, Claudio Cerchione, Fabio Nicolini, Massimiliano Mazza, Ottavia M. Delmonte, Kerry Dobbs, Rocio Laguna-Goya, Gonzalo Carreño-Tarragona, Santiago Barrio, Luisa Imberti, Alessandra Sottini, Eugenia Quiros-Roldan, Camillo Rossi, Andrea Biondi, Laura Rachele Bettini, Mariella D’Angio, Paolo Bonfanti, Miranda F. Tompkins, Camille Alba, Clifton Dalgard, Vittorio Sambri, Giovanni Martinelli, Jason D. Goldman, Jason D. Goldman, James R. Heath, Helen C. Su, Luigi D. Notarangelo, Estela Paz-Artal, Joaquin Martinez-Lopez, Bryan Howie, Jonathan M. Carlson, Harlan S. Robins

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