PhyloD

HLA-associated preadaptation in HIV Vif is associated with higher set point viral load and faster CD4+ decline in Zambian transmission pairs

Sarah Connolly, Jonathan M. Carlson, Malinda Schaefer, Alfred Bere, William Kilembe, Susan Allen, Eric Hunter

AIDS | June 2021, Vol 35(8): pp. 1157-1165

DOI Publication Publication Publication

Elevated HIV infection of CD4 T cells in MRKAd5 vaccine recipients due to CD8 T cells targeting of adapted epitopes

Kai Qin, Sushma Boppana, Jonathan M. Carlson, Andrew Fiore-Gartland, Jacob Files, Jie Zeng, Jeffrey Edberg, Robbie B Mailliard, Christina Ochsenbauer, Anju Bansal, Paul Goepfert

Journal of Virology | June 2021, Vol 95(16)

DOI Publication Publication Publication

Pre-treatment integrase inhibitor resistance is uncommon in antiretroviral therapy-naive individuals with HIV-1 subtype A1 and D infections in Uganda.

Suzanne M. McCluskey, Kimia Kamelian, Nicholas Musinguzi, Simone Kigozi, Yap Boum, Mwebesa B. Bwana, Conrad Muzoora, Zabrina L. Brumme, Mary Carrington, Jonathan M. Carlson, Brian Foley, Peter W. Hunt, Jeffrey N. Martin, David R. Bangsberg, P. Richard Harrigan, Mark J. Siedner, Jessica E. Haberer, Guinevere Q. Lee

AIDS | May 2021, Vol 35(7): pp. 1083-1089

DOI Publication Publication Publication

Impact of Human Leukocyte Antigen-Associated Polymorphisms on Variability of HIV-1 Accessory and Regulatory Proteins.

Doreen Kamori, Zafrul Hasan, Jonathan M. Carlson, A I Kawana-Tachikawa, Hiroyuki Gatanaga, Shinichi Oka, Takamasa Ueno

AIDS Research and Human Retroviruses | April 2021, Vol 37(12): pp. 962-966

DOI Publication Publication Publication Publication

Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein.

Debra Van Egeren, Alexander Novokhodko, Madison Stoddard, Uyen Tran, Bruce Zetter, Michael Rogers, Bradley L. Pentelute, Jonathan M. Carlson, Mark Hixon, Diane Joseph-McCarthy, Arijit Chakravarty

PLOS ONE | April 2021, Vol 16(4): pp. e0250780

DOI Publication Publication Publication Publication Publication Publication Publication Project

Impaired ability of Nef to counteract SERINC5 is associated with reduced plasma viremia in HIV-infected individuals.

Mako Toyoda, Doreen Kamori, Toong Seng Tan, Kageaki Goebuchi, Jun Ohashi, Jonathan M. Carlson, Ai Kawana-Tachikawa, Hiroyuki Gatanaga, Shinichi Oka, Massimo Pizzato, Takamasa Ueno

Scientific Reports | November 2020, Vol 10(1): pp. 19416-19416

DOI Publication Publication

HLA tapasin independence: broader peptide repertoire and HIV control.

Arman A. Bashirova, Mathias Viard, Vivek Naranbhai, Alba Grifoni, Wilfredo Garcia-Beltran, Marjan Akdag, Yuko Yuki, Xiaojiang Gao, Colm O’hUigin, Malini Raghavan, Steven Wolinsky, Jay H. Bream, Priya Duggal, Jeremy Martinson, Nelson L. Michael, Gregory D. Kirk, Susan P. Buchbinder, David Haas, James J. Goedert, Steven G. Deeks, Jacques Fellay, Bruce Walker, Philip Goulder, Peter Cresswell, Tim Elliott, Alessandro Sette, Jonathan M. Carlson, Mary Carrington

Proceedings of the National Academy of Sciences of the United States of America | October 2020, Vol 117(45): pp. 28232-28238

DOI PDF Publication Publication Publication Publication Publication Publication Publication

CD8 T cells targeting adapted epitopes in chronic HIV infection promote dendritic cell maturation and CD4 T cell trans-infection.

Kai Qin, Sushma Boppana, Victor Y. Du, Jonathan M. Carlson, Ling Yue, Dario A. Dilernia, Eric Hunter, Robbie B. Mailliard, Simon A. Mallal, Anju Bansal, Paul A. Goepfert

PLOS Pathogens | August 2019, Vol 15(8)

DOI PDF Publication Publication Publication Publication Publication Publication Publication

Clinical and evolutionary consequences of HIV adaptation to HLA: implications for vaccine and cure

Santiago Avila-Rios, Jonathan M. Carlson, Mina John, Simon Mallal, Zabrina L Brumme

Current Opinion in HIV and AIDS | May 2019, Vol 14(3): pp. 194-204

Publication

Genotypic and mechanistic characterization of subtype-specific hiv adaptation to host cellular immunity

Natalie N Kinloch, Guinevere Q Lee, Jonathan M. Carlson, Steven W Jin, Chanson J Brumme, Helen Byakwaga, Conrad Muzoora, Mwebesa B Bwana, Kyle D Cobarrubias, Peter W Hunt, Jeff N Martin, Mary Carrington, David R Bangsberg, P Richard Harrigan, Mark A Brockman, Zabrina L Brumme

Journal of Virology | January 2019, Vol 93(1): pp. e01502-18

Publication

Antisense-derived HIV-1 cryptic epitopes are not major drivers of viral evolution during the acute phase of infection

Binghao J Peng, Jonathan M. Carlson, Michael KP Liu, Feng Gao, Nilu Goonetilleke, Andrew J McMichael, Persephone Borrow, Jill Gilmour, Sonya L Heath, Eric Hunter, Anju Bansal, Paul A Goepfert

Journal of Virology | October 2018, Vol 92(19): pp. e00711-18

Publication

Killer cell immunoglobulin–like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1

Maureen P. Martin, Vivek Naranbhai, Patrick R. Shea, Ying Qi, Veron Ramsuran, Nicolas Vince, Xiaojiang Gao, Rasmi Thomas, Zabrina L. Brumme, Jonathan M. Carlson, Steven M. Wolinsky, James J. Goedert, Bruce D. Walker, Florencia P. Segal, Steven G. Deeks, David W. Haas, Stephen A. Migueles, Mark Connors, Nelson Michael, Jacques Fellay, Emma Gostick, Sian Llewellyn-Lacey, David A. Price, Bernard A. Lafont, Phillip Pymm, Philippa M. Saunders, Jacqueline Widjaja, Shu Cheng Wong, Julian P. Vivian, Jamie Rossjohn, Andrew G. Brooks,, Mary Carrington

Journal of Clinical Investigation | May 2018, Vol 128(5): pp. 1903-1912

Publication Publication

HLA-associated polymorphisms in the HIV-2 capsid highlight key differences between HIV-1 and HIV-2 immune adaptation

Thushan I. de Silva, Aleksandra Leligdowicz, Jonathan M. Carlson, Miguel Garcia-Knight, Clayton Onyango, Nicholas Miller, Louis-Marie Yindom, Stephane Hué, Assan Jaye, Tao Dong, Matthew Cotten, Sarah L Rowland-Jones

AIDS | March 2018, Vol 32(6): pp. 709-714

Publication

Weaker HLA footprints on HIV in the unique and highly genetically admixed host population of Mexico

Maribel Soto-Nava, Santiago Avila-Ríos, Humberto Valenzuela-Ponce, Claudia García-Morales, Jonathan M. Carlson, Daniela Tapia-Trejo, Daniela Garrido-Rodriguez, Selma N. Alva-Hernández, Thalía A. García-Tellez, Akio Murakami-Ogasawara, the International HIV Adaptation Collaborative, Simon A Mallal, Mina John, Mark A. Brockman, Chanson J. Brumme, Zabrina L. Brumme, Gustavo Reyes-Teran, the HIV MexNet Group

Journal of Virology | November 2017

Publication Publication Publication Github

Brief Report: Selection of HIV-1 Variants With Higher Transmission Potential by 1% Tenofovir Gel Microbicide

Nobubelo K. Ngandu, Jonathan M. Carlson, Denis R. Chopera, Nonkululeko Ndabamb, Quarraisha Abdool Karim, Salim Abdool Karim, Carolyn Williamson

Journal of Acquired Immune Deficiency Syndromes | September 2017, Vol 76: pp. 43-47

Publication Publication Publication Github

Mother-to-Child HIV Transmission Bottleneck Selects for Consensus Virus with Lower Gag-Protease-Driven Replication Capacity

Vanessa L. Naidoo, Jaclyn K. Mann, Christie Noble, Emily Adland, Jonathan M. Carlson, Jake Thomas, Chanson J. Brumme, Christina F. Thobakgale-Tshabalala, Zabrina L. Brumme, Mark A. Brockman, Philip J. R. Goulder, Thumbi Ndung'u

Journal of Virology | September 2017, Vol 91: pp. e00518-17

Publication Publication Github

PARV4 prevalence, phylogeny, immunology and coinfection with HIV, HBV and HCV in a multicentre African cohort

Colin P. Sharp, William F. Gregory, Louise Hattingh, Amna Malik, Emily Adland, Samantha Daniels, Anriette van Zyl, Jonathan M. Carlson, Susan Wareing, Anthony Ogwu, Roger Shapiro, Lynn Riddell, Fabian Chen, Thumbi Ndung'u, Philip J.R. Goulder, Paul Klenerman, Peter Simmonds, Pieter Jooste, Philippa C. Matthews

Wellcome Open Research | April 2017, Vol 2: pp. 26

Publication Publication Publication Github

Paediatric non-progression following grandmother-to-child HIV transmission

M.-H. Tsai, M. Muenchhof, E. Adland, A. Carlqvist, J. Roider, D. K. Cole, A. K. Sewell, Jonathan M. Carlson, T. Ndung’u, P. J. R. Goulder

Retrovirology | September 2016, Vol 13: pp. 65

Publication Publication Publication Github

Impact of Pre-Adapted HIV Transmission

Jonathan M. Carlson, Victor Y. Du, Nico Pfeifer, Anju Bansal, Vincent T. F. Tan, Karen Power, Chanson J. Brumme, Anat Kreimer, Charles E. DeZiel, Nicolo Fusi, Malinda Schaefer, Mark A. Brockman, Jill Gilmour, Matt A. Price, William Kilembe, Richard Haubrich, Mina John, Simon Mallal, Roger Shapiro, John Frater, P. Richard Harrigan, Thumbi Ndung'u, Susan Allen, David Heckerman, John Sidney, Todd M. Allen, Philip J.R. Goulder, Zabrina L. Brumme, Eric Hunter, Paul A. Goepfert

Nature Medicine | May 2016, Vol 22: pp. 606-613

Bonnie Mathieson Young Investigator Award

Author's Version Publication DOI Github

HIV-1–Specific CD8 T Cells Exhibit Limited Cross-Reactivity during Acute Infection

Victor Y. Du, Anju Bansal, Jonathan M. Carlson, Jesus F. Salazar-Gonzalez, Maria G. Salazar, Kristin Ladell, Stephanie Gras, Tracy M. Josephs, Sonya L. Heath, David A. Price, Jamie Rossjohn, Eric Hunter, Paul A. Goepfert

Journal of Immunology | April 2016, Vol 198: pp. 3276-3286

Publication Publication Publication Github

Lower Viral Loads and Slower CD4+ T-Cell Count Decline in MRKAd5 HIV-1 Vaccinees Expressing Disease-Susceptible HLA-B*58:02

Ellen M. Leitman, Jacob Hurst, Masahiko Mori, James Kublin, Thumbi Ndung'u, Bruce D. Walker, Jonathan M. Carlson, Glenda E. Gray, Philippa C. Matthews, Nicole Frahm, Philip J.R. Goulder

The Journal of infectious diseases | March 2016, Vol 214: pp. 379-389

Publication Publication Publication Github

CD8+ TCR bias and immunodominance in HIV-1 infection

Henrik N. Kløverpris, Reuben McGregor, James E. McLaren, Kristin Ladell, Mikkel Harndahl, Anette Stryhn, Jonathan M. Carlson, Catherine Koofhethile, Bram Gerritsen, Can Kesmir, Fabian Chen, Lynn Riddell, Graz Luzzi, Alasdair Leslie, Bruce D. Walker, Thumbi Ndung'u, Søren Buus, David A. Price, Philip J.R. Goulder

The Journal of Immunology | June 2015, Vol 194: pp. 5329-5345

Publication Publication Publication Github

HIV-1 Adaptation to HLA: A Window into Virus–Host Immune Interactions

Jonathan M. Carlson, Anh Q. Le, Aniqa Shahid, Zabrina L. Brumme

Trends in Microbiology | April 2015, Vol 23(4): pp. 212-224

Publication Publication Publication

Impact of HLA-Driven HIV Adaptation on Virulence in Populations of High HIV Seroprevalence

Rebecca Payne, Maximilian Muenchhoff, Jaclyn Mann, Hannah E. Roberts, Philippa Matthews, Emily Adland, Allison Hempenstall, Kuan-Hsiang Huang, Mark Brockman, Zabrina Brumme, Marc Sinclair, Toshiyuki Miura, John Frater, Myron Essex, Roger Shapiro, Bruce D. Walker, Thumbi Ndung'u, Angela R. McLean, Jonathan M. Carlson, Philip J. R. Goulder

Proceedings of the National Academy of Sciences of the United States of America | October 2014

Publication Publication

HIV Control Is Mediated in Part by CD8+ T-Cell Targeting of Specific Epitopes

Florencia Pereyra, David Heckerman, Jonathan M. Carlson, Carl Kadie, Damien Z Soghoian, Daniel Karel, Ariel Goldenthal, Oliver B Davis, Charles E DeZiel, Tienho Lin, Jian Peng, Alicja Piechocka, Mary Carrington, Bruce D Walker

Journal of Virology | August 2014, Vol 88(22): pp. 12937-12948

Publication Publication Publication

Selection Bias at the Heterosexual HIV-1 Transmission Bottleneck

Jonathan M. Carlson, Malinda Schaefer, Daniela C. Monaco, Rebecca Batorsky, Daniel T. Claiborne, Jessica Prince, Martin J. Deymier, Zachary S. Ende, Nichole R. Klatt, Charles E. DeZiel, Tien-Ho Lin, Jian Peng, Aaron M. Seese, Roger Shapiro, John Frater, Thumbi Ndung'u, Jianming Tang, Paul Goepfert, Jill Gilmour, Matt A. Price, William Kilembe, David Heckerman, Philip J. R. Goulder, Todd M. Allen, Susan Allen, Eric Hunter

Science | July 2014, Vol 345(6193)

Publication Publication Publication Publication Publication

Influence of HLA-C Expression Level on HIV Control

Richard Apps, Ying Qi, Jonathan M. Carlson, Haoyan Chen, Xiaojiang Gao, Rasmi Thomas, Yuko Yuki, Greg Q. Del Prete, Philip Goulder, Zabrina L. Brumme, Chanson J. Brumme, Mina John, Simon Mallal, George Nelson, Ronald Bosch, David Heckerman, Judy L. Stein, Kelly A. Soderberg, M. Anthony Moody, Thomas N. Denny, Xue Zeng, Jingyuan Fang, Ashley Moffett, Jeffrey D. Lifson, James J. Goedert, Susan Buchbinder, Gregory D. Kirk, Jacques Fellay, Paul McLaren, Steven G. Deeks, Florencia Pereyra, Bruce Walker, Nelson L. Michael, Amy Weintrob, Steven Wolinsky, Wilson Liao, Mary Carrington

Science | April 2013, Vol 340(6128): pp. 87-91

Publication Publication

Correlates of Protective Cellular Immunity Revealed by Analysis of Population-Level Immune Escape Pathways in HIV-1

Jonathan M. Carlson, Chanson J. Brumme, Eric Martin, Jennifer Listgarten, Mark A. Brockman, Anh Q. Le, Celia K. S. Chui, Laura A. Cotton, David J. H. F. Knapp, Sharon A. Riddler, Richard Haubrich, George Nelson, Nico Pfeifer, Charles E. DeZiel, David Heckerman, Richard Apps, Mary Carrington, Simon Mallal, P. Richard Harrigan, Mina John, Zabrina L. Brumme

Journal of Virololgy | December 2012, Vol 86(24): pp. 13202-13216

Publication Publication

Widespread Impact of HLA Restriction on Immune Control and Escape Pathways in HIV-1

Jonathan M. Carlson, Jennifer Listgarten, Nico Pfeifer, Vincent Tan, Carl Kadie, Bruce D. Walker, Thumbi Ndung'u, Roger Shapiro, John Frater, Zabrina L. Brumme, Philip J. R. Goulder, David Heckerman

Journal of Virology | May 2012, Vol 86(9): pp. 5230-5243

Publication Publication Publication Github

HIV-1 Adaptation to NK-Cell-Mediated Immune Pressure

Galit Alter, David Heckerman, Arne Schneidewind, Lena Fadda, Carl Kadie, Jonathan M. Carlson, Cesar Oniangue-Ndza, Maureen Martin, Bin Li, Salim I. Khakoo, Mary Carrington, Todd M. Allen, Marcus Altfeld

Nature International weekly journal of science | August 2011, Vol 476: pp. 96-100

Publication Publication

CD8 T Cell Response and Evolutionary Pressure to HIV-1 Cryptic Epitopes Derived from Antisense Transcription

Anju Bansal, Jonathan M. Carlson, Jiyu Yan, Olusimidele T. Akinsiku, Malinda Schaefer, Steffanie Sabbaj, Anne Bet, David N. Levy, Sonya Heath, Jianming Tang, Richard A Kaslow, Bruce D. Walker, Thumbi Ndung'u, Philip J. Goulder, David Heckerman, Eric Hunter, Paul A. Goepfert

The Journal of Experimental Medicine | January 2010, Vol 207(1): pp. 51

Publication Publication

Viral adaptation to immune selection pressure by HLA class I-restricted CTL responses targeting epitopes in HIV frameshift sequences

Christopher T. Berger, Jonathan M. Carlson, Chanson J. Brumme, Kari L. Hartman, Zabrina L. Brumme, Leah M. Henry, Pamela C. Rosato, Alicja Piechocka-Trocha, Mark A. Brockman, P. Richard Harrigan, David Heckerman, Daniel E. Kaufmann, Christian Brander

JEM | January 2010

Publication Publication

Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag

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

PLoS Computational Biology | November 2008, Vol 4: pp. e1000225

Publication Publication Publication

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

Zabrina L. Brumme, Chanson J. Brumme, Jonathan M. Carlson, Hendrik Streeck, Mina John, Quentin Eichbaum, Brian L. Block, Brett Baker, Carl Kadie, Martin Markowitz, Heiko Jessen, Anthony D. Kelleher, Eric Rosenberg, John Kaldor, Yuko Yuki, Mary Carrington, Todd M. Allen, Simon Mallal, Marcus Altfeld, David Heckerman, Bruce D. Walker

Journal of Virology | January 2008, Vol 82: pp. 9216-9227

Publication Github

Leveraging Hierarchical Population Structure in Discrete Association Studies

Jonathan M. Carlson, Carl Kadie, Simon Mallal, David Heckerman

PLoS One | July 2007, Vol 2: pp. e591

Publication

HLA-associated preadaptation in HIV Vif is associated with higher set point viral load and faster CD4+ decline in Zambian transmission pairs

Sarah Connolly, Jonathan M. Carlson, Malinda Schaefer, Alfred Bere, William Kilembe, Susan Allen, Eric Hunter

AIDS | June 2021, Vol 35(8): pp. 1157-1165

DOI Publication Publication Publication

Elevated HIV infection of CD4 T cells in MRKAd5 vaccine recipients due to CD8 T cells targeting of adapted epitopes

Kai Qin, Sushma Boppana, Jonathan M. Carlson, Andrew Fiore-Gartland, Jacob Files, Jie Zeng, Jeffrey Edberg, Robbie B Mailliard, Christina Ochsenbauer, Anju Bansal, Paul Goepfert

Journal of Virology | June 2021, Vol 95(16)

DOI Publication Publication Publication

Pre-treatment integrase inhibitor resistance is uncommon in antiretroviral therapy-naive individuals with HIV-1 subtype A1 and D infections in Uganda.

Suzanne M. McCluskey, Kimia Kamelian, Nicholas Musinguzi, Simone Kigozi, Yap Boum, Mwebesa B. Bwana, Conrad Muzoora, Zabrina L. Brumme, Mary Carrington, Jonathan M. Carlson, Brian Foley, Peter W. Hunt, Jeffrey N. Martin, David R. Bangsberg, P. Richard Harrigan, Mark J. Siedner, Jessica E. Haberer, Guinevere Q. Lee

AIDS | May 2021, Vol 35(7): pp. 1083-1089

DOI Publication Publication Publication

Impact of Human Leukocyte Antigen-Associated Polymorphisms on Variability of HIV-1 Accessory and Regulatory Proteins.

Doreen Kamori, Zafrul Hasan, Jonathan M. Carlson, A I Kawana-Tachikawa, Hiroyuki Gatanaga, Shinichi Oka, Takamasa Ueno

AIDS Research and Human Retroviruses | April 2021, Vol 37(12): pp. 962-966

DOI Publication Publication Publication Publication

Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein.

Debra Van Egeren, Alexander Novokhodko, Madison Stoddard, Uyen Tran, Bruce Zetter, Michael Rogers, Bradley L. Pentelute, Jonathan M. Carlson, Mark Hixon, Diane Joseph-McCarthy, Arijit Chakravarty

PLOS ONE | April 2021, Vol 16(4): pp. e0250780

DOI Publication Publication Publication Publication Publication Publication Publication Project

Impaired ability of Nef to counteract SERINC5 is associated with reduced plasma viremia in HIV-infected individuals.

Mako Toyoda, Doreen Kamori, Toong Seng Tan, Kageaki Goebuchi, Jun Ohashi, Jonathan M. Carlson, Ai Kawana-Tachikawa, Hiroyuki Gatanaga, Shinichi Oka, Massimo Pizzato, Takamasa Ueno

Scientific Reports | November 2020, Vol 10(1): pp. 19416-19416

DOI Publication Publication

HLA tapasin independence: broader peptide repertoire and HIV control.

Arman A. Bashirova, Mathias Viard, Vivek Naranbhai, Alba Grifoni, Wilfredo Garcia-Beltran, Marjan Akdag, Yuko Yuki, Xiaojiang Gao, Colm O’hUigin, Malini Raghavan, Steven Wolinsky, Jay H. Bream, Priya Duggal, Jeremy Martinson, Nelson L. Michael, Gregory D. Kirk, Susan P. Buchbinder, David Haas, James J. Goedert, Steven G. Deeks, Jacques Fellay, Bruce Walker, Philip Goulder, Peter Cresswell, Tim Elliott, Alessandro Sette, Jonathan M. Carlson, Mary Carrington

Proceedings of the National Academy of Sciences of the United States of America | October 2020, Vol 117(45): pp. 28232-28238

DOI PDF Publication Publication Publication Publication Publication Publication Publication

CD8 T cells targeting adapted epitopes in chronic HIV infection promote dendritic cell maturation and CD4 T cell trans-infection.

Kai Qin, Sushma Boppana, Victor Y. Du, Jonathan M. Carlson, Ling Yue, Dario A. Dilernia, Eric Hunter, Robbie B. Mailliard, Simon A. Mallal, Anju Bansal, Paul A. Goepfert

PLOS Pathogens | August 2019, Vol 15(8)

DOI PDF Publication Publication Publication Publication Publication Publication Publication

Clinical and evolutionary consequences of HIV adaptation to HLA: implications for vaccine and cure

Santiago Avila-Rios, Jonathan M. Carlson, Mina John, Simon Mallal, Zabrina L Brumme

Current Opinion in HIV and AIDS | May 2019, Vol 14(3): pp. 194-204

Publication

Genotypic and mechanistic characterization of subtype-specific hiv adaptation to host cellular immunity

Natalie N Kinloch, Guinevere Q Lee, Jonathan M. Carlson, Steven W Jin, Chanson J Brumme, Helen Byakwaga, Conrad Muzoora, Mwebesa B Bwana, Kyle D Cobarrubias, Peter W Hunt, Jeff N Martin, Mary Carrington, David R Bangsberg, P Richard Harrigan, Mark A Brockman, Zabrina L Brumme

Journal of Virology | January 2019, Vol 93(1): pp. e01502-18

Publication

Antisense-derived HIV-1 cryptic epitopes are not major drivers of viral evolution during the acute phase of infection

Binghao J Peng, Jonathan M. Carlson, Michael KP Liu, Feng Gao, Nilu Goonetilleke, Andrew J McMichael, Persephone Borrow, Jill Gilmour, Sonya L Heath, Eric Hunter, Anju Bansal, Paul A Goepfert

Journal of Virology | October 2018, Vol 92(19): pp. e00711-18

Publication

Killer cell immunoglobulin–like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1

Maureen P. Martin, Vivek Naranbhai, Patrick R. Shea, Ying Qi, Veron Ramsuran, Nicolas Vince, Xiaojiang Gao, Rasmi Thomas, Zabrina L. Brumme, Jonathan M. Carlson, Steven M. Wolinsky, James J. Goedert, Bruce D. Walker, Florencia P. Segal, Steven G. Deeks, David W. Haas, Stephen A. Migueles, Mark Connors, Nelson Michael, Jacques Fellay, Emma Gostick, Sian Llewellyn-Lacey, David A. Price, Bernard A. Lafont, Phillip Pymm, Philippa M. Saunders, Jacqueline Widjaja, Shu Cheng Wong, Julian P. Vivian, Jamie Rossjohn, Andrew G. Brooks,, Mary Carrington

Journal of Clinical Investigation | May 2018, Vol 128(5): pp. 1903-1912

Publication Publication

HLA-associated polymorphisms in the HIV-2 capsid highlight key differences between HIV-1 and HIV-2 immune adaptation

Thushan I. de Silva, Aleksandra Leligdowicz, Jonathan M. Carlson, Miguel Garcia-Knight, Clayton Onyango, Nicholas Miller, Louis-Marie Yindom, Stephane Hué, Assan Jaye, Tao Dong, Matthew Cotten, Sarah L Rowland-Jones

AIDS | March 2018, Vol 32(6): pp. 709-714

Publication

Weaker HLA footprints on HIV in the unique and highly genetically admixed host population of Mexico

Maribel Soto-Nava, Santiago Avila-Ríos, Humberto Valenzuela-Ponce, Claudia García-Morales, Jonathan M. Carlson, Daniela Tapia-Trejo, Daniela Garrido-Rodriguez, Selma N. Alva-Hernández, Thalía A. García-Tellez, Akio Murakami-Ogasawara, the International HIV Adaptation Collaborative, Simon A Mallal, Mina John, Mark A. Brockman, Chanson J. Brumme, Zabrina L. Brumme, Gustavo Reyes-Teran, the HIV MexNet Group

Journal of Virology | November 2017

Publication Publication Publication Github

Mother-to-Child HIV Transmission Bottleneck Selects for Consensus Virus with Lower Gag-Protease-Driven Replication Capacity

Vanessa L. Naidoo, Jaclyn K. Mann, Christie Noble, Emily Adland, Jonathan M. Carlson, Jake Thomas, Chanson J. Brumme, Christina F. Thobakgale-Tshabalala, Zabrina L. Brumme, Mark A. Brockman, Philip J. R. Goulder, Thumbi Ndung'u

Journal of Virology | September 2017, Vol 91: pp. e00518-17

Publication Publication Github

Brief Report: Selection of HIV-1 Variants With Higher Transmission Potential by 1% Tenofovir Gel Microbicide

Nobubelo K. Ngandu, Jonathan M. Carlson, Denis R. Chopera, Nonkululeko Ndabamb, Quarraisha Abdool Karim, Salim Abdool Karim, Carolyn Williamson

Journal of Acquired Immune Deficiency Syndromes | September 2017, Vol 76: pp. 43-47

Publication Publication Publication Github

PARV4 prevalence, phylogeny, immunology and coinfection with HIV, HBV and HCV in a multicentre African cohort

Colin P. Sharp, William F. Gregory, Louise Hattingh, Amna Malik, Emily Adland, Samantha Daniels, Anriette van Zyl, Jonathan M. Carlson, Susan Wareing, Anthony Ogwu, Roger Shapiro, Lynn Riddell, Fabian Chen, Thumbi Ndung'u, Philip J.R. Goulder, Paul Klenerman, Peter Simmonds, Pieter Jooste, Philippa C. Matthews

Wellcome Open Research | April 2017, Vol 2: pp. 26

Publication Publication Publication Github

Paediatric non-progression following grandmother-to-child HIV transmission

M.-H. Tsai, M. Muenchhof, E. Adland, A. Carlqvist, J. Roider, D. K. Cole, A. K. Sewell, Jonathan M. Carlson, T. Ndung’u, P. J. R. Goulder

Retrovirology | September 2016, Vol 13: pp. 65

Publication Publication Publication Github

Impact of Pre-Adapted HIV Transmission

Jonathan M. Carlson, Victor Y. Du, Nico Pfeifer, Anju Bansal, Vincent T. F. Tan, Karen Power, Chanson J. Brumme, Anat Kreimer, Charles E. DeZiel, Nicolo Fusi, Malinda Schaefer, Mark A. Brockman, Jill Gilmour, Matt A. Price, William Kilembe, Richard Haubrich, Mina John, Simon Mallal, Roger Shapiro, John Frater, P. Richard Harrigan, Thumbi Ndung'u, Susan Allen, David Heckerman, John Sidney, Todd M. Allen, Philip J.R. Goulder, Zabrina L. Brumme, Eric Hunter, Paul A. Goepfert

Nature Medicine | May 2016, Vol 22: pp. 606-613

Bonnie Mathieson Young Investigator Award

Author's Version Publication DOI Github

HIV-1–Specific CD8 T Cells Exhibit Limited Cross-Reactivity during Acute Infection

Victor Y. Du, Anju Bansal, Jonathan M. Carlson, Jesus F. Salazar-Gonzalez, Maria G. Salazar, Kristin Ladell, Stephanie Gras, Tracy M. Josephs, Sonya L. Heath, David A. Price, Jamie Rossjohn, Eric Hunter, Paul A. Goepfert

Journal of Immunology | April 2016, Vol 198: pp. 3276-3286

Publication Publication Publication Github

Lower Viral Loads and Slower CD4+ T-Cell Count Decline in MRKAd5 HIV-1 Vaccinees Expressing Disease-Susceptible HLA-B*58:02

Ellen M. Leitman, Jacob Hurst, Masahiko Mori, James Kublin, Thumbi Ndung'u, Bruce D. Walker, Jonathan M. Carlson, Glenda E. Gray, Philippa C. Matthews, Nicole Frahm, Philip J.R. Goulder

The Journal of infectious diseases | March 2016, Vol 214: pp. 379-389

Publication Publication Publication Github

CD8+ TCR bias and immunodominance in HIV-1 infection

Henrik N. Kløverpris, Reuben McGregor, James E. McLaren, Kristin Ladell, Mikkel Harndahl, Anette Stryhn, Jonathan M. Carlson, Catherine Koofhethile, Bram Gerritsen, Can Kesmir, Fabian Chen, Lynn Riddell, Graz Luzzi, Alasdair Leslie, Bruce D. Walker, Thumbi Ndung'u, Søren Buus, David A. Price, Philip J.R. Goulder

The Journal of Immunology | June 2015, Vol 194: pp. 5329-5345

Publication Publication Publication Github

Impact of HLA-Driven HIV Adaptation on Virulence in Populations of High HIV Seroprevalence

Rebecca Payne, Maximilian Muenchhoff, Jaclyn Mann, Hannah E. Roberts, Philippa Matthews, Emily Adland, Allison Hempenstall, Kuan-Hsiang Huang, Mark Brockman, Zabrina Brumme, Marc Sinclair, Toshiyuki Miura, John Frater, Myron Essex, Roger Shapiro, Bruce D. Walker, Thumbi Ndung'u, Angela R. McLean, Jonathan M. Carlson, Philip J. R. Goulder

Proceedings of the National Academy of Sciences of the United States of America | October 2014

Publication Publication

HIV Control Is Mediated in Part by CD8+ T-Cell Targeting of Specific Epitopes

Florencia Pereyra, David Heckerman, Jonathan M. Carlson, Carl Kadie, Damien Z Soghoian, Daniel Karel, Ariel Goldenthal, Oliver B Davis, Charles E DeZiel, Tienho Lin, Jian Peng, Alicja Piechocka, Mary Carrington, Bruce D Walker

Journal of Virology | August 2014, Vol 88(22): pp. 12937-12948

Publication Publication Publication

Selection Bias at the Heterosexual HIV-1 Transmission Bottleneck

Jonathan M. Carlson, Malinda Schaefer, Daniela C. Monaco, Rebecca Batorsky, Daniel T. Claiborne, Jessica Prince, Martin J. Deymier, Zachary S. Ende, Nichole R. Klatt, Charles E. DeZiel, Tien-Ho Lin, Jian Peng, Aaron M. Seese, Roger Shapiro, John Frater, Thumbi Ndung'u, Jianming Tang, Paul Goepfert, Jill Gilmour, Matt A. Price, William Kilembe, David Heckerman, Philip J. R. Goulder, Todd M. Allen, Susan Allen, Eric Hunter

Science | July 2014, Vol 345(6193)

Publication Publication Publication Publication Publication

Influence of HLA-C Expression Level on HIV Control

Richard Apps, Ying Qi, Jonathan M. Carlson, Haoyan Chen, Xiaojiang Gao, Rasmi Thomas, Yuko Yuki, Greg Q. Del Prete, Philip Goulder, Zabrina L. Brumme, Chanson J. Brumme, Mina John, Simon Mallal, George Nelson, Ronald Bosch, David Heckerman, Judy L. Stein, Kelly A. Soderberg, M. Anthony Moody, Thomas N. Denny, Xue Zeng, Jingyuan Fang, Ashley Moffett, Jeffrey D. Lifson, James J. Goedert, Susan Buchbinder, Gregory D. Kirk, Jacques Fellay, Paul McLaren, Steven G. Deeks, Florencia Pereyra, Bruce Walker, Nelson L. Michael, Amy Weintrob, Steven Wolinsky, Wilson Liao, Mary Carrington

Science | April 2013, Vol 340(6128): pp. 87-91

Publication Publication

Correlates of Protective Cellular Immunity Revealed by Analysis of Population-Level Immune Escape Pathways in HIV-1

Jonathan M. Carlson, Chanson J. Brumme, Eric Martin, Jennifer Listgarten, Mark A. Brockman, Anh Q. Le, Celia K. S. Chui, Laura A. Cotton, David J. H. F. Knapp, Sharon A. Riddler, Richard Haubrich, George Nelson, Nico Pfeifer, Charles E. DeZiel, David Heckerman, Richard Apps, Mary Carrington, Simon Mallal, P. Richard Harrigan, Mina John, Zabrina L. Brumme

Journal of Virololgy | December 2012, Vol 86(24): pp. 13202-13216

Publication Publication

Widespread Impact of HLA Restriction on Immune Control and Escape Pathways in HIV-1

Jonathan M. Carlson, Jennifer Listgarten, Nico Pfeifer, Vincent Tan, Carl Kadie, Bruce D. Walker, Thumbi Ndung'u, Roger Shapiro, John Frater, Zabrina L. Brumme, Philip J. R. Goulder, David Heckerman

Journal of Virology | May 2012, Vol 86(9): pp. 5230-5243

Publication Publication Publication Github

HIV-1 Adaptation to NK-Cell-Mediated Immune Pressure

Galit Alter, David Heckerman, Arne Schneidewind, Lena Fadda, Carl Kadie, Jonathan M. Carlson, Cesar Oniangue-Ndza, Maureen Martin, Bin Li, Salim I. Khakoo, Mary Carrington, Todd M. Allen, Marcus Altfeld

Nature International weekly journal of science | August 2011, Vol 476: pp. 96-100

Publication Publication

CD8 T Cell Response and Evolutionary Pressure to HIV-1 Cryptic Epitopes Derived from Antisense Transcription

Anju Bansal, Jonathan M. Carlson, Jiyu Yan, Olusimidele T. Akinsiku, Malinda Schaefer, Steffanie Sabbaj, Anne Bet, David N. Levy, Sonya Heath, Jianming Tang, Richard A Kaslow, Bruce D. Walker, Thumbi Ndung'u, Philip J. Goulder, David Heckerman, Eric Hunter, Paul A. Goepfert

The Journal of Experimental Medicine | January 2010, Vol 207(1): pp. 51

Publication Publication

Viral adaptation to immune selection pressure by HLA class I-restricted CTL responses targeting epitopes in HIV frameshift sequences

Christopher T. Berger, Jonathan M. Carlson, Chanson J. Brumme, Kari L. Hartman, Zabrina L. Brumme, Leah M. Henry, Pamela C. Rosato, Alicja Piechocka-Trocha, Mark A. Brockman, P. Richard Harrigan, David Heckerman, Daniel E. Kaufmann, Christian Brander

JEM | January 2010

Publication Publication

Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag

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

PLoS Computational Biology | November 2008, Vol 4: pp. e1000225

Publication Publication Publication

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

Zabrina L. Brumme, Chanson J. Brumme, Jonathan M. Carlson, Hendrik Streeck, Mina John, Quentin Eichbaum, Brian L. Block, Brett Baker, Carl Kadie, Martin Markowitz, Heiko Jessen, Anthony D. Kelleher, Eric Rosenberg, John Kaldor, Yuko Yuki, Mary Carrington, Todd M. Allen, Simon Mallal, Marcus Altfeld, David Heckerman, Bruce D. Walker

Journal of Virology | January 2008, Vol 82: pp. 9216-9227

Publication Github

Leveraging Hierarchical Population Structure in Discrete Association Studies

Jonathan M. Carlson, Carl Kadie, Simon Mallal, David Heckerman

PLoS One | July 2007, Vol 2: pp. e591

Publication

HIV-1 Adaptation to HLA: A Window into Virus–Host Immune Interactions

Jonathan M. Carlson, Anh Q. Le, Aniqa Shahid, Zabrina L. Brumme

Trends in Microbiology | April 2015, Vol 23(4): pp. 212-224

Publication Publication Publication

HLA-associated preadaptation in HIV Vif is associated with higher set point viral load and faster CD4+ decline in Zambian transmission pairs

Sarah Connolly, Jonathan M. Carlson, Malinda Schaefer, Alfred Bere, William Kilembe, Susan Allen, Eric Hunter

AIDS | June 2021, Vol 35(8): pp. 1157-1165

DOI Publication Publication Publication

Elevated HIV infection of CD4 T cells in MRKAd5 vaccine recipients due to CD8 T cells targeting of adapted epitopes

Kai Qin, Sushma Boppana, Jonathan M. Carlson, Andrew Fiore-Gartland, Jacob Files, Jie Zeng, Jeffrey Edberg, Robbie B Mailliard, Christina Ochsenbauer, Anju Bansal, Paul Goepfert

Journal of Virology | June 2021, Vol 95(16)

DOI Publication Publication Publication

Pre-treatment integrase inhibitor resistance is uncommon in antiretroviral therapy-naive individuals with HIV-1 subtype A1 and D infections in Uganda.

Suzanne M. McCluskey, Kimia Kamelian, Nicholas Musinguzi, Simone Kigozi, Yap Boum, Mwebesa B. Bwana, Conrad Muzoora, Zabrina L. Brumme, Mary Carrington, Jonathan M. Carlson, Brian Foley, Peter W. Hunt, Jeffrey N. Martin, David R. Bangsberg, P. Richard Harrigan, Mark J. Siedner, Jessica E. Haberer, Guinevere Q. Lee

AIDS | May 2021, Vol 35(7): pp. 1083-1089

DOI Publication Publication Publication

Impact of Human Leukocyte Antigen-Associated Polymorphisms on Variability of HIV-1 Accessory and Regulatory Proteins.

Doreen Kamori, Zafrul Hasan, Jonathan M. Carlson, A I Kawana-Tachikawa, Hiroyuki Gatanaga, Shinichi Oka, Takamasa Ueno

AIDS Research and Human Retroviruses | April 2021, Vol 37(12): pp. 962-966

DOI Publication Publication Publication Publication

Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein.

Debra Van Egeren, Alexander Novokhodko, Madison Stoddard, Uyen Tran, Bruce Zetter, Michael Rogers, Bradley L. Pentelute, Jonathan M. Carlson, Mark Hixon, Diane Joseph-McCarthy, Arijit Chakravarty

PLOS ONE | April 2021, Vol 16(4): pp. e0250780

DOI Publication Publication Publication Publication Publication Publication Publication Project

Impaired ability of Nef to counteract SERINC5 is associated with reduced plasma viremia in HIV-infected individuals.

Mako Toyoda, Doreen Kamori, Toong Seng Tan, Kageaki Goebuchi, Jun Ohashi, Jonathan M. Carlson, Ai Kawana-Tachikawa, Hiroyuki Gatanaga, Shinichi Oka, Massimo Pizzato, Takamasa Ueno

Scientific Reports | November 2020, Vol 10(1): pp. 19416-19416

DOI Publication Publication

HLA tapasin independence: broader peptide repertoire and HIV control.

Arman A. Bashirova, Mathias Viard, Vivek Naranbhai, Alba Grifoni, Wilfredo Garcia-Beltran, Marjan Akdag, Yuko Yuki, Xiaojiang Gao, Colm O’hUigin, Malini Raghavan, Steven Wolinsky, Jay H. Bream, Priya Duggal, Jeremy Martinson, Nelson L. Michael, Gregory D. Kirk, Susan P. Buchbinder, David Haas, James J. Goedert, Steven G. Deeks, Jacques Fellay, Bruce Walker, Philip Goulder, Peter Cresswell, Tim Elliott, Alessandro Sette, Jonathan M. Carlson, Mary Carrington

Proceedings of the National Academy of Sciences of the United States of America | October 2020, Vol 117(45): pp. 28232-28238

DOI PDF Publication Publication Publication Publication Publication Publication Publication

CD8 T cells targeting adapted epitopes in chronic HIV infection promote dendritic cell maturation and CD4 T cell trans-infection.

Kai Qin, Sushma Boppana, Victor Y. Du, Jonathan M. Carlson, Ling Yue, Dario A. Dilernia, Eric Hunter, Robbie B. Mailliard, Simon A. Mallal, Anju Bansal, Paul A. Goepfert

PLOS Pathogens | August 2019, Vol 15(8)

DOI PDF Publication Publication Publication Publication Publication Publication Publication

Clinical and evolutionary consequences of HIV adaptation to HLA: implications for vaccine and cure

Santiago Avila-Rios, Jonathan M. Carlson, Mina John, Simon Mallal, Zabrina L Brumme

Current Opinion in HIV and AIDS | May 2019, Vol 14(3): pp. 194-204

Publication

Genotypic and mechanistic characterization of subtype-specific hiv adaptation to host cellular immunity

Natalie N Kinloch, Guinevere Q Lee, Jonathan M. Carlson, Steven W Jin, Chanson J Brumme, Helen Byakwaga, Conrad Muzoora, Mwebesa B Bwana, Kyle D Cobarrubias, Peter W Hunt, Jeff N Martin, Mary Carrington, David R Bangsberg, P Richard Harrigan, Mark A Brockman, Zabrina L Brumme

Journal of Virology | January 2019, Vol 93(1): pp. e01502-18

Publication

Antisense-derived HIV-1 cryptic epitopes are not major drivers of viral evolution during the acute phase of infection

Binghao J Peng, Jonathan M. Carlson, Michael KP Liu, Feng Gao, Nilu Goonetilleke, Andrew J McMichael, Persephone Borrow, Jill Gilmour, Sonya L Heath, Eric Hunter, Anju Bansal, Paul A Goepfert

Journal of Virology | October 2018, Vol 92(19): pp. e00711-18

Publication

Killer cell immunoglobulin–like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1

Maureen P. Martin, Vivek Naranbhai, Patrick R. Shea, Ying Qi, Veron Ramsuran, Nicolas Vince, Xiaojiang Gao, Rasmi Thomas, Zabrina L. Brumme, Jonathan M. Carlson, Steven M. Wolinsky, James J. Goedert, Bruce D. Walker, Florencia P. Segal, Steven G. Deeks, David W. Haas, Stephen A. Migueles, Mark Connors, Nelson Michael, Jacques Fellay, Emma Gostick, Sian Llewellyn-Lacey, David A. Price, Bernard A. Lafont, Phillip Pymm, Philippa M. Saunders, Jacqueline Widjaja, Shu Cheng Wong, Julian P. Vivian, Jamie Rossjohn, Andrew G. Brooks,, Mary Carrington

Journal of Clinical Investigation | May 2018, Vol 128(5): pp. 1903-1912

Publication Publication

HLA-associated polymorphisms in the HIV-2 capsid highlight key differences between HIV-1 and HIV-2 immune adaptation

Thushan I. de Silva, Aleksandra Leligdowicz, Jonathan M. Carlson, Miguel Garcia-Knight, Clayton Onyango, Nicholas Miller, Louis-Marie Yindom, Stephane Hué, Assan Jaye, Tao Dong, Matthew Cotten, Sarah L Rowland-Jones

AIDS | March 2018, Vol 32(6): pp. 709-714

Publication

Weaker HLA footprints on HIV in the unique and highly genetically admixed host population of Mexico

Maribel Soto-Nava, Santiago Avila-Ríos, Humberto Valenzuela-Ponce, Claudia García-Morales, Jonathan M. Carlson, Daniela Tapia-Trejo, Daniela Garrido-Rodriguez, Selma N. Alva-Hernández, Thalía A. García-Tellez, Akio Murakami-Ogasawara, the International HIV Adaptation Collaborative, Simon A Mallal, Mina John, Mark A. Brockman, Chanson J. Brumme, Zabrina L. Brumme, Gustavo Reyes-Teran, the HIV MexNet Group

Journal of Virology | November 2017

Publication Publication Publication Github

Mother-to-Child HIV Transmission Bottleneck Selects for Consensus Virus with Lower Gag-Protease-Driven Replication Capacity

Vanessa L. Naidoo, Jaclyn K. Mann, Christie Noble, Emily Adland, Jonathan M. Carlson, Jake Thomas, Chanson J. Brumme, Christina F. Thobakgale-Tshabalala, Zabrina L. Brumme, Mark A. Brockman, Philip J. R. Goulder, Thumbi Ndung'u

Journal of Virology | September 2017, Vol 91: pp. e00518-17

Publication Publication Github

Brief Report: Selection of HIV-1 Variants With Higher Transmission Potential by 1% Tenofovir Gel Microbicide

Nobubelo K. Ngandu, Jonathan M. Carlson, Denis R. Chopera, Nonkululeko Ndabamb, Quarraisha Abdool Karim, Salim Abdool Karim, Carolyn Williamson

Journal of Acquired Immune Deficiency Syndromes | September 2017, Vol 76: pp. 43-47

Publication Publication Publication Github

PARV4 prevalence, phylogeny, immunology and coinfection with HIV, HBV and HCV in a multicentre African cohort

Colin P. Sharp, William F. Gregory, Louise Hattingh, Amna Malik, Emily Adland, Samantha Daniels, Anriette van Zyl, Jonathan M. Carlson, Susan Wareing, Anthony Ogwu, Roger Shapiro, Lynn Riddell, Fabian Chen, Thumbi Ndung'u, Philip J.R. Goulder, Paul Klenerman, Peter Simmonds, Pieter Jooste, Philippa C. Matthews

Wellcome Open Research | April 2017, Vol 2: pp. 26

Publication Publication Publication Github

Paediatric non-progression following grandmother-to-child HIV transmission

M.-H. Tsai, M. Muenchhof, E. Adland, A. Carlqvist, J. Roider, D. K. Cole, A. K. Sewell, Jonathan M. Carlson, T. Ndung’u, P. J. R. Goulder

Retrovirology | September 2016, Vol 13: pp. 65

Publication Publication Publication Github

Impact of Pre-Adapted HIV Transmission

Jonathan M. Carlson, Victor Y. Du, Nico Pfeifer, Anju Bansal, Vincent T. F. Tan, Karen Power, Chanson J. Brumme, Anat Kreimer, Charles E. DeZiel, Nicolo Fusi, Malinda Schaefer, Mark A. Brockman, Jill Gilmour, Matt A. Price, William Kilembe, Richard Haubrich, Mina John, Simon Mallal, Roger Shapiro, John Frater, P. Richard Harrigan, Thumbi Ndung'u, Susan Allen, David Heckerman, John Sidney, Todd M. Allen, Philip J.R. Goulder, Zabrina L. Brumme, Eric Hunter, Paul A. Goepfert

Nature Medicine | May 2016, Vol 22: pp. 606-613

Bonnie Mathieson Young Investigator Award

Author's Version Publication DOI Github

HIV-1–Specific CD8 T Cells Exhibit Limited Cross-Reactivity during Acute Infection

Victor Y. Du, Anju Bansal, Jonathan M. Carlson, Jesus F. Salazar-Gonzalez, Maria G. Salazar, Kristin Ladell, Stephanie Gras, Tracy M. Josephs, Sonya L. Heath, David A. Price, Jamie Rossjohn, Eric Hunter, Paul A. Goepfert

Journal of Immunology | April 2016, Vol 198: pp. 3276-3286

Publication Publication Publication Github

Lower Viral Loads and Slower CD4+ T-Cell Count Decline in MRKAd5 HIV-1 Vaccinees Expressing Disease-Susceptible HLA-B*58:02

Ellen M. Leitman, Jacob Hurst, Masahiko Mori, James Kublin, Thumbi Ndung'u, Bruce D. Walker, Jonathan M. Carlson, Glenda E. Gray, Philippa C. Matthews, Nicole Frahm, Philip J.R. Goulder

The Journal of infectious diseases | March 2016, Vol 214: pp. 379-389

Publication Publication Publication Github

CD8+ TCR bias and immunodominance in HIV-1 infection

Henrik N. Kløverpris, Reuben McGregor, James E. McLaren, Kristin Ladell, Mikkel Harndahl, Anette Stryhn, Jonathan M. Carlson, Catherine Koofhethile, Bram Gerritsen, Can Kesmir, Fabian Chen, Lynn Riddell, Graz Luzzi, Alasdair Leslie, Bruce D. Walker, Thumbi Ndung'u, Søren Buus, David A. Price, Philip J.R. Goulder

The Journal of Immunology | June 2015, Vol 194: pp. 5329-5345

Publication Publication Publication Github

HIV-1 Adaptation to HLA: A Window into Virus–Host Immune Interactions

Jonathan M. Carlson, Anh Q. Le, Aniqa Shahid, Zabrina L. Brumme

Trends in Microbiology | April 2015, Vol 23(4): pp. 212-224

Publication Publication Publication

HIV Control Is Mediated in Part by CD8+ T-Cell Targeting of Specific Epitopes

Florencia Pereyra, David Heckerman, Jonathan M. Carlson, Carl Kadie, Damien Z Soghoian, Daniel Karel, Ariel Goldenthal, Oliver B Davis, Charles E DeZiel, Tienho Lin, Jian Peng, Alicja Piechocka, Mary Carrington, Bruce D Walker

Journal of Virology | August 2014, Vol 88(22): pp. 12937-12948

Publication Publication Publication

Selection Bias at the Heterosexual HIV-1 Transmission Bottleneck

Jonathan M. Carlson, Malinda Schaefer, Daniela C. Monaco, Rebecca Batorsky, Daniel T. Claiborne, Jessica Prince, Martin J. Deymier, Zachary S. Ende, Nichole R. Klatt, Charles E. DeZiel, Tien-Ho Lin, Jian Peng, Aaron M. Seese, Roger Shapiro, John Frater, Thumbi Ndung'u, Jianming Tang, Paul Goepfert, Jill Gilmour, Matt A. Price, William Kilembe, David Heckerman, Philip J. R. Goulder, Todd M. Allen, Susan Allen, Eric Hunter

Science | July 2014, Vol 345(6193)

Publication Publication Publication Publication Publication

Influence of HLA-C Expression Level on HIV Control

Richard Apps, Ying Qi, Jonathan M. Carlson, Haoyan Chen, Xiaojiang Gao, Rasmi Thomas, Yuko Yuki, Greg Q. Del Prete, Philip Goulder, Zabrina L. Brumme, Chanson J. Brumme, Mina John, Simon Mallal, George Nelson, Ronald Bosch, David Heckerman, Judy L. Stein, Kelly A. Soderberg, M. Anthony Moody, Thomas N. Denny, Xue Zeng, Jingyuan Fang, Ashley Moffett, Jeffrey D. Lifson, James J. Goedert, Susan Buchbinder, Gregory D. Kirk, Jacques Fellay, Paul McLaren, Steven G. Deeks, Florencia Pereyra, Bruce Walker, Nelson L. Michael, Amy Weintrob, Steven Wolinsky, Wilson Liao, Mary Carrington

Science | April 2013, Vol 340(6128): pp. 87-91

Publication Publication

Correlates of Protective Cellular Immunity Revealed by Analysis of Population-Level Immune Escape Pathways in HIV-1

Jonathan M. Carlson, Chanson J. Brumme, Eric Martin, Jennifer Listgarten, Mark A. Brockman, Anh Q. Le, Celia K. S. Chui, Laura A. Cotton, David J. H. F. Knapp, Sharon A. Riddler, Richard Haubrich, George Nelson, Nico Pfeifer, Charles E. DeZiel, David Heckerman, Richard Apps, Mary Carrington, Simon Mallal, P. Richard Harrigan, Mina John, Zabrina L. Brumme

Journal of Virololgy | December 2012, Vol 86(24): pp. 13202-13216

Publication Publication

Widespread Impact of HLA Restriction on Immune Control and Escape Pathways in HIV-1

Jonathan M. Carlson, Jennifer Listgarten, Nico Pfeifer, Vincent Tan, Carl Kadie, Bruce D. Walker, Thumbi Ndung'u, Roger Shapiro, John Frater, Zabrina L. Brumme, Philip J. R. Goulder, David Heckerman

Journal of Virology | May 2012, Vol 86(9): pp. 5230-5243

Publication Publication Publication Github

HIV-1 Adaptation to NK-Cell-Mediated Immune Pressure

Galit Alter, David Heckerman, Arne Schneidewind, Lena Fadda, Carl Kadie, Jonathan M. Carlson, Cesar Oniangue-Ndza, Maureen Martin, Bin Li, Salim I. Khakoo, Mary Carrington, Todd M. Allen, Marcus Altfeld

Nature International weekly journal of science | August 2011, Vol 476: pp. 96-100

Publication Publication

CD8 T Cell Response and Evolutionary Pressure to HIV-1 Cryptic Epitopes Derived from Antisense Transcription

Anju Bansal, Jonathan M. Carlson, Jiyu Yan, Olusimidele T. Akinsiku, Malinda Schaefer, Steffanie Sabbaj, Anne Bet, David N. Levy, Sonya Heath, Jianming Tang, Richard A Kaslow, Bruce D. Walker, Thumbi Ndung'u, Philip J. Goulder, David Heckerman, Eric Hunter, Paul A. Goepfert

The Journal of Experimental Medicine | January 2010, Vol 207(1): pp. 51

Publication Publication

Viral adaptation to immune selection pressure by HLA class I-restricted CTL responses targeting epitopes in HIV frameshift sequences

Christopher T. Berger, Jonathan M. Carlson, Chanson J. Brumme, Kari L. Hartman, Zabrina L. Brumme, Leah M. Henry, Pamela C. Rosato, Alicja Piechocka-Trocha, Mark A. Brockman, P. Richard Harrigan, David Heckerman, Daniel E. Kaufmann, Christian Brander

JEM | January 2010

Publication Publication

Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag

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

PLoS Computational Biology | November 2008, Vol 4: pp. e1000225

Publication Publication Publication

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

Zabrina L. Brumme, Chanson J. Brumme, Jonathan M. Carlson, Hendrik Streeck, Mina John, Quentin Eichbaum, Brian L. Block, Brett Baker, Carl Kadie, Martin Markowitz, Heiko Jessen, Anthony D. Kelleher, Eric Rosenberg, John Kaldor, Yuko Yuki, Mary Carrington, Todd M. Allen, Simon Mallal, Marcus Altfeld, David Heckerman, Bruce D. Walker

Journal of Virology | January 2008, Vol 82: pp. 9216-9227

Publication Github

Leveraging Hierarchical Population Structure in Discrete Association Studies

Jonathan M. Carlson, Carl Kadie, Simon Mallal, David Heckerman

PLoS One | July 2007, Vol 2: pp. e591

Publication

Impact of HLA-Driven HIV Adaptation on Virulence in Populations of High HIV Seroprevalence

Rebecca Payne, Maximilian Muenchhoff, Jaclyn Mann, Hannah E. Roberts, Philippa Matthews, Emily Adland, Allison Hempenstall, Kuan-Hsiang Huang, Mark Brockman, Zabrina Brumme, Marc Sinclair, Toshiyuki Miura, John Frater, Myron Essex, Roger Shapiro, Bruce D. Walker, Thumbi Ndung'u, Angela R. McLean, Jonathan M. Carlson, Philip J. R. Goulder

Proceedings of the National Academy of Sciences of the United States of America | October 2014

Publication Publication