Jonathan M. Carlson

T-cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibody titers and disease severity

Rebecca Elyanow, Thomas M. Snyder, Sudeb C. Dalai, Rachel M. Gittelman, Boonyaratanakornkit J, Wald A, Selke S, Wener Mh, Morishima C, Greninger Al, Michael Gale, Tien-Ying Hsiang, Lichen Jing, Holbrook Mr, Ian M. Kaplan, Damon H May, H. Jabran Zahid, Jonathan M. Carlson, Lance Baldo, Thomas Manley, Harlan S Robins, David M Koelle

JCI Insight | April 2022, Vol 7(10)

DOI Preprint Publication Project Project Project

Longitudinal analysis of T cell receptor repertoires reveals shared patterns of antigen-specific response to SARS-CoV-2 infection

Rachel M Gittelman, Enrico Lavezzo, Thomas M Snyder, H. Jabran Zahid, Cara L Carty, Rebecca Elyanow, Sudeb Dalai, Ilan Kirsch, Lance Baldo, Laura Manuto, Elisa Franchin, Claudia Del Vecchio, Monia Pacenti, Caterina Boldrin, Margherita Cattai, Francesca Saluzzo, Andrea Padoan, Mario Plebani, Fabio Simeoni, Jessica Bordini, Nicola I Lorè, Dejan Lazarević, Daniela M Cirillo, Paolo Ghia, Stefano Toppo, Jonathan M. Carlson, Harlan S Robins, Andrea Crisanti, Giovanni Tonon

JCI Insight | April 2022, Vol 7(10)

DOI Publication Project Project

Immunosequencing of the T-cell receptor repertoire reveals signatures specific for diagnosis and characterization of early Lyme disease

Julia Greissl, Mitch Pesesky, Sudeb C. Dalai, Alison W. Rebman, Mark J. Soloski, Elizabeth J. Horn, Jennifer N. Dines, Rachel M. Gittelman, Thomas M. Snyder, Ryan O. Emerson, Ted Meeds, Thomas Manley, Ian M. Kaplan, Lance Baldo, Jonathan M. Carlson, Harlan S. Robins, John N. Aucott

medRxiv | August 2021

DOI PDF Publication Project

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 Project

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 Project

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 Project

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 Project

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

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Diagnosis and Tracking of Past SARS-CoV-2 Infection in a Large Study of Vo’, Italy Through T-Cell Receptor Sequencing

Rachel M Gittelman, Enrico Lavezzo, Thomas M Snyder, H Jabran Zahid, Rebecca Elyanow, Sudeb Dalai, Ilan Kirsch, Lance Baldo, Laura Manuto, Elisa Franchin, Claudia Del Vecchio, Fabio Simeoni, Jessica Bordini, Nicola I LorÃ, Dejan Lazarevic, Daniela M Cirillo, Paolo Ghia, Stefano Toppo, Jonathan M. Carlson, Harlan S Robins, Giovanni Tonon, Andrea Crisanti

medRxiv | November 2020

Updated February 11, 2021

DOI 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 Project

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

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A large-scale database of T-cell receptor beta (TCRβ) sequences and binding associations from natural and synthetic exposure to SARS-CoV-2

Sean Nolan, Marissa Vignali, Mark Klinger, Jennifer N Dines, Ian M Kaplan, Emily Svejnoha, Tracy Craft, Katie Boland, Mitch Pesesky, Rachel M Gittelman, Thomas M Snyder, Christopher J Gooley, Simona Semprini, Claudio Cerchione, Massimiliano Mazza, Ottavia M Delmonte, Kerry Dobbs, Gonzalo Carreño-Tarragona, Santiago Barrio, Vittorio Sambri, Giovanni Martinelli, Jason D Goldman, James R Heath, Luigi D Notarangelo, Jonathan M. Carlson, Joaquin Martinez-Lopez, Harlan S Robins

August 2020

DOI Publication Publication Publication Publication Project Project

Magnitude and Dynamics of the T-Cell Response to SARS-CoV-2 Infection at Both Individual and Population Levels

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 N 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, Julia Greissl, Lance Baldo, Simona Semprini, Claudio Cerchione, Massimiliano Mazza, Ottavia M Delmonte, Kerry Dobbs, 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, James R Heath, Helen C Su, Luigi D Notarangelo, Joaquin Martinez-Lopez, Jonathan M. Carlson, Harlan S Robins

medRxiv | August 2020

Updated September 17, 2020

DOI Publication Publication Publication Publication Project

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)

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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 Project

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 Project

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 Project

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 Project

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 Project

Elevated HLA-A expression impairs HIV control through inhibition of NKG2A-expressing cells.

Veron Ramsuran, Vivek Naranbhai, Amir Horowitz, Ying Qi, Maureen P. Martin, Yuko Yuki, Xiaojiang Gao, Victoria Walker-Sperling, Gregory Q. Del Prete, Douglas K. Schneider, Jeffrey D. Lifson, Jacques Fellay, Steven G. Deeks, Jeffrey N. Martin, James J. Goedert, Steven M. Wolinsky, Nelson L. Michael, Gregory D. Kirk, Susan Buchbinder, David Haas, Thumbi Ndung’u, Philip Goulder, Peter Parham, Bruce D. Walker, Jonathan M. Carlson, Mary Carrington

Science | January 2018, Vol 359: pp. 86-90

Publication 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

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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

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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

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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

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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

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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 Project

Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus

Damien C. Tully, Colin B. Ogilvie, Rebecca E. Batorsky, David J. Bean, Karen A. Power, Musie Ghebremichael, Hunter E. Bedard, Adrianne D. Gladden, Aaron M. Seese, Molly A. Amero, Kimberly Lane, Graham McGrath, Suzane B. Bazner, Jake Tinsley, Niall J. Lennon, Matthew R. Henn, Zabrina L. Brumme, Philip J. Norris, Eric S. Rosenberg, Kenneth H. Mayer, Heiko Jessen, Sergei L. Kosakovsky Pond, Bruce D. Walker, Marcus Altfeld, Todd M. Allen, Jonathan M. Carlson

PLoS Pathogens | May 2016

Publication Publication

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

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A strong association of human leukocyte antigen-associated Pol and Gag mutations with clinical parameters in HIV-1 subtype A/E infection.

Giang Van Tran, Takayuki Chikata, Jonathan M. Carlson, Hayato Murakoshi, Dung Hoai Nguyen, Yoshiko Tamura, Tomohiro Akahoshi, Nozomi Kuse, Keiko Sakai, Sachiko Sakai, Kyle Cobarrubias, Shinichi Oka, Zabrina L Brumme, Kinh Van Nguyen, Masafumi Takiguchi

AIDS | March 2016, Vol 30: pp. 681-689

Publication Publication

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

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Population-Level Immune-Mediated Adaptation in HIV-1 Polymerase during the North American Epidemic

Natalie N Kinloch, Daniel R MacMillan, Anh Q Le, Laura A Cotton, David R Bangsberg, Susan Buchbinder, Mary Carrington, Jonathan Fuchs, P Richard Harrigan, Beryl Koblin, Margot Kushel, Martin Markowitz, Kenneth Mayer, MJ Milloy, Martin T Schechter, Theresa Wagner, Bruce D Walker, Jonathan M. Carlson, Art FY Poon, Zabrina L Brumme

Journal of Virology | November 2015, Vol 90: pp. 1244-1258

Publication Publication

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 Africa

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

Plos Medicine | November 2015

Publication Publication

Enhanced Recognition of HIV-1 Cryptic Epitopes Restricted by HLA Class I Alleles Associated With a Favorable Clinical Outcome.

Anju Bansa, Tiffanie Mann, Sarah Sterrett, Binghao J Peng, Anne Bet, Jonathan M. Carlson, Paul A Goepfert

Journal of Acquired Immune Deficiency Syndromes | September 2015

Publication Publication

HLA Class-II Associated HIV Polymorphisms Predict Escape from CD4+ T Cell Responses

Nathan Erdmann, Victor Y. Du, Jonathan M. Carlson, Malinda Schaefer, Alexander Jureka, Sarah Sterrett, Ling Yue, Dario Dilernia, Shabir Lakhi, Jianming Tang, John Sidney, Jill Gilmour, Susan Allen, Eric Hunter, Sonya Heath, Anju Bansal, Paul A. Goepfert

PLoS Pathog | August 2015

Publication Publication

Prevalence and Characteristics of Hepatitis B Virus (HBV) Coinfection among HIV-Positive Women in South Africa and Botswana

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

July 2015

Publication Publication

HLA-A is a Predictor of Hepatitis B e Antigen Status in HIV-Positive African Adults

Philippa C Matthews, Jonathan M. Carlson, Apostolos Beloukas, Amna Malik, Pieter Jooste, Anthony Ogwu, Roger Shapiro, Lynn Riddell, Fabian Chen, Graz Luzzi, Gerald Jesuthasan, Katie Jeffery, Nebojsa Jojic, Thumbi Ndung'u, Mary Carrington, Philip JR Goulder, Anna Maria Geretti, Paul Klenerman

The Journal of Infectious Diseases | July 2015, Vol 213: pp. 1248-1252

Publication Publication

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

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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 Project

Immune screening identifies novel T cell targets encoded by anti-sense reading frames of HIV-1

Christopher T. Berger, Anuska Llano, Jonathan M. Carlson, Zabrina L. Brumme, Mark A. Brockman, Samandhy Cedeno, P. Richard Harrigan, Daniel E. Kaufmann, David Heckerman, Andreas Meyerhans, Christian Brander

Journal of virology | April 2015, Vol 89: pp. 4015-4019

Publication Publication

Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial

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, Meera Bose, 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, SL Pond, Jonathan M. Carlson, Nelson L Michael, William R Schief, James I Mullins, Jerome H Kim , Peter B Gilbert

PLOS Computational Biology | February 2015

Publication Publication

A molecular switch in immunodominant HIV-1-specific CD8 T-cell epitopes shapes differential HLA-restricted escape

Henrik N Kløverpris, David K Cole, Anna Fuller, Jonathan M. Carlson, Konrad Beck, Andrea J Schauenburg, Pierre J Rizkallah, Søren Buus, Andrew K Sewel, Philip Goulder

Retrovirology | February 2015

Publication Publication

Nef-mediated down-regulation of CD4 and HLA class I in HIV-1 subtype C infection: Association with disease progression and influence of immune pressure

Jaclyn K Mann, Denis Chopera, Saleha Omarjee, Xiaomei T Kuang, Anh Q Le, Gursev Anmole, Ryan Danroth, Philip Mwimanzi, Tarylee Reddy, Jonathan M. Carlson, Mopo Radebe, Philip JR Goulder, Bruce D Walker, Salim Abdool Karim, Vladimir Novitsky, Carolyn Williamson, Mark A Brockman, Zabrina L Brumme, Thumbi Ndung'u

Virology | November 2014, pp. 214-225

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 Project

CD8 and CD4 Epitope Predictions in RV144: No Strong Evidence of a T-Cell Driven Sieve Effect in HIV-1 Breakthrough Sequences from Trial Participants

Kalpana Dommaraju, Gustavo Kijak, Jonathan M. Carlson, Brendan B Larsen, Sodsai Tovanabutra, Dan E Geraghty, Wenjie Deng, Brandon S Maust, Paul T Edlefsen, Eric Sanders-Buell, Silvia Ratto-Kim, Supachai Rerks-Ngarm, Sorachai Nitayaphan, Punnee Pitisuttihum, Jaranit Kaewkungwal, Robert J O'Connell, Merlin L Robb, Nelson L Michael, James I Mullins, Jerome H Kim, Morgane Rolland

PLoS One | October 2014

Publication Publication

Early immune adaptation in HIV-1 revealed by population-level approaches

Eric Martin, Jonathan M. Carlson, Anh Q Le, Denis R Chopera, Rachel McGovern, Manal A Rahman, Carmond Ng, Heiko Jessen, Anthony D Kelleher, Martin Markowitz, Todd M Allen, MJ Milloy, Mary Carrington, Mark A Wainberg, Zabrina L Brumme

Retrovirology | August 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 Project

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)

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Differential Escape Patterns within the Dominant HLA-B*57:03-Restricted HIV Gag Epitope Reflect Distinct Clade-Specific Functional Constraints

Payne RP, Branch S, Kloverpris H, Matthews PC, Koofhethile K, Strong T, Adland E, Frater J, Ndung'u T, Hunter E, Haubrich R, Harrigan PR, Brumme ZL, Mallal S, John M, Jooste P, Shapiro R, Walker BD, Jonathan M. Carlson, Landis C, Prado JG, Goulder PJ

Journal of Virology | May 2014

Publication Publication

Genotypic and Functional Impact of HIV-1 Adaptation to Its Host Population during the North American Epidemic

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 FY Poon , Zabrina L Brumme

PLoS Genet | April 2014

Publication Publication

Host-Specific Adaptation of HIV-1 Subtype B in the Japanese Population

Takayuki Chikata, Jonathan M. Carlson, Yoshiko Tamura, Mohamed Ali Borghan, Takuya Naruto, Masao Hashimoto, Hayato Murakoshi, Anh Q. Le, Simon Mallal, Mina John, Hiroyuki Gatanaga, Shinichi Oka, Zabrina L. Brumme , Masafumi Takiguchi

Journal of Virology | March 2014, Vol 88(9): pp. 4764-4775

Publication Publication

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

Jennifer Listgarten, Christoph Lippert, Nicolo Fusi, David Heckerman, Jonathan M. Carlson

eLife | October 2013

Publication

Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection

Akihisa Shimizu, Ai Kawana-Tachikawa, Atsushi Yamagata, Chung Yong Han, Dayong Zhu, Yusuke Sato, Hitomi Nakamura, Tomohiko Koibuchi, Jonathan M. Carlson, Eric Martin, Chanson Brumme, Yi Shi, George Gao, Zabrina L Brumme, Shuya Fukai, Aikichi Iwamoto

Scientific Reports | October 2013

Publication Publication

Nef-Specific CD8+ T Cell Responses Contribute to HIV-1 Immune Control

Emily Adland, Jonathan M. Carlson, Paolo Paioni, Henrik Kloverpris, Roger Shapiro, Anthony Ogwu, Lynn Riddell, Graz Luzzi, Fabian Chen, Thambiah Balachandran, David Heckerman, Anette Stryhn, Anne Edwards, Thumbi Ndung'u, Bruce D Walker, Soren Buus, Philip Goulder , Philippa C Matthews

PloS One | September 2013

Publication Publication

Increased Sequence Coverage through Combined Targeting of Variant and Conserved Epitopes Correlates with Control of HIV Replication

Justine Sunshine, Moon Kim, Jonathan M. Carlson, David Heckerman, Julie Czartoski, Stephen A. Migueles, Janine Maenza, M. Juliana McElrath, James I. Mullins, Nicole Frahm

Journal of Virology | August 2013, Vol 88(2): pp. 1354-1365

Publication Publication

HLA-A*68: 02-restricted Gag-specific cytotoxic T lymphocyte responses can drive selection pressure on HIV but are subdominant and ineffective

Henrik N. Klverpris, Anette Stryhn, Mikkel Harndahl, Jonathan M. Carlson, Alasdair J. Leslie, Fabian Chen, Lynn Riddell, Joseph Mulenga, Bruce D. Walker, Thumbi N'dung'u, Soren Buus , Philip Goulder

AIDS Official Journal of the International Aids Society | July 2013

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 Project

HIV escape mutations occur preferentially at HLA-binding sites of CD8 T-cell epitopes

Corine Bronke, Coral-Ann M. Almeida, Elizabeth McKinnon, Steven G. Roberts, Niamh M. Keane, Abha Chopra, Jonathan M. Carlson, David Heckerman, Simon Mallal, Mina John

AIDS, Basic Science | March 2013, Vol 27(6): pp. 899-905

Publication Publication

Distinct HIV-1 Escape Patterns Selected by Cytotoxic T Cells with Identical Epitope Specificity

Yuichi Yagitaa, Nozomi Kusea, Kimiko Kurokib, Hiroyuki Gatanagaa, Jonathan M. Carlson, Takayuki Chikataa, Zabrina L. Brummee, Hayato Murakoshia, Tomohiro Akahoshia, Nico Pfeiferd, Simon Mallalg, Mina Johng, Toyoyuki Oseb, Haruki Matsubarab, Ryo Kandab, Yuko Fukunagab, Kazutaka Hondaa, Yuka Kawashimaa, Yasuo Ariumia, Shinichi Okaa, Katsumi Maenakab, Masafumi Takiguchia

Journal of Virology | February 2013

Publication Publication

Frequent and Variable Cytotoxic-T-Lymphocyte Escape-Associated Fitness Costs in the Human Immunodeficiency Virus Type 1 Subtype B Gag Proteins

Christian L Boutwell, Jonathan M. Carlson, Tien-Ho Lin, Aaron Seese, Karen A Power, Jian Peng, Yanhua Tang, Zabrina L Brumme, David Heckerman, Arne Schneidewind, Todd M Allen

January 2013

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 Project

Differential Clade-Specific HLA-B*3501 Association with HIV-1 Disease Outcome Is Linked to Immunogenicity of a Single Gag Epitope

Philippa C. Matthews, Madoka Koyanagi, Henrik N. Kloverpris, Mikkel Harndahl, Anette Stryhn, Tomohiro Akahoshi, Hiroyuki Gatanaga, Shinichi Oka, Claudia Juarez Molina, Humberto Valenzuela Ponce, Santiago Avila Rios, David Cole, Jonathan M. Carlson, Rebecca P. Payne, Anthony Ogwu, Alfred Bere, Thumbi Ndung'u, Kamini Gounder, Fabian Chen, Lynn Riddell, Graz Luzzi, Roger Shaprio, Christian Brander, Bruce Walker, Andrew K. sewell, Gustavo Reyes Teran, David Heckerman, Eric Hunter, Soren Buus, Masafumi Takiguchi, Philip J.R. Goulder

Journal of Virololgy | December 2012, Vol 86(23): pp. 12643-12654

Publication Publication

Significant Reductions in Gag-Protease-Mediated HIV-1 Replication Capacity during the Course of the Epidemic in Japan

Shigeru Nomura, Noriaki Hosoya, Zabrina L. Brumme, Mark A. Brockman, Tadashi Kikuchi, Michiko Koga, Hitomi Nakamura, Tomohiko Koibuchi, Takeshi Fujii, Jonathan M. Carlson, David Heckerman, Ai Kawana-Tachikawa, Aikichi Iwamoto, Toshiyuki Miura

Journal of Virology | November 2012, Vol 87(3): pp. 1465-1476

Publication Publication

Role of Transmitted Gag CTL Polymorphisms in Defining Replicative Capacity and Early HIV-1 Pathogenesis

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 Geopfert, Matthew A. Price, Jill Gilmour, Joseph Mulenga, Paul Farmer, Cynthia A. Derdeyn, Jiaming Tang, David Heckerman, Richard A. Kaslow, Susan A. Allen, Eric Hunter

PLoS Pathogens | November 2012, pp. e1003041

Publication Publication

Co-operative additive effects between HLA alleles in control of HIV-1

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

PLoS ONE | October 2012, pp. e47799

Publication Publication

Intersubtype differences in the effect of a rare p24 Gag mutation on HIV-1 replicative fitness

Denis R. Chopera, Laura A. Cotton, Alexander Zawaira, Jaclyn K. Mann, Nobubelo K. Ngandu, Roman Ntale, Jonathan M. Carlson, Koleka Mlisana, Zenda Woodman, Debra de Assis Rosa, Eric Martin, Toshiyuki Miura, Florencia Pereyra, Bruce D. Walker, Clive M. Gray, Darren P. Martin, Thumbi Ndung'u, Mark A. Brockman, Salim Abdool Karim, Zabrina L. Brumme, Carolyn Williamson

Journal of Virology | September 2012

Publication Publication

HIV Control through a Single Nucleotide on the HLA-B Locus

Henrik N. Kloverpris, Mikkel Harndahl, Alasdair J. Leslie, Jonathan M. Carlson, Nasreen Ismail, Mary van der Stok, Kuan-Hsiang Gary Huang, Fabian Chen, Lynn Riddell, Dewald Steyn, Dominique Goedhals, Cloete van Vuuren, John Frater, Bruce D. Walker, Mary Carrington, Thumbi Ndung'u, Soren Buus, Philip Goulder

Journal of Virology | August 2012

Publication Publication

Aminopeptidase Substrate Preference Affects HIV Epitope Presentation and Predicts Immune Escape Patterns in HIV-Infected Individuals

Shao Chong Zhang, Eric Martin, Mariko Shimada, Sasha Blue Godfrey, Jennifer Fricke, Shirley Locastro, Nicole Y Lai, Paul Liebesny, Jonathan M. Carlson, Chanson J Brumme, Oluwatobi Awele Ogbechie, Huabiao Chen, Bruce D Walker, Zabrina L Brumme, Daniel G Kavanagh, Sylvie Le Gall

The Journal of Immunology | June 2012

Publication Publication

Minor contribution of HLA class I-associated selective pressure to the variability of HIV-1 accessory protein Vpu

Zafrul Hasan, Jonathan M. Carlson, Hiroyuki Gatanaga, Anh Le, Chanson J Brumme, Shinichi Oka, Zabrina L Brumme , Takamasa Ueno

May 2012

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 Project

Uncommon Pathways of Immune Escape Attenuate HIV-1 Integrase Replication Capacity

Mark A. Brockman, Denis R. Chopera, Alex Olvera, Chanson J. Brumme, Jennifer Sela, Tristan J. Markle, Eric Martin, Jonathan M. Carlson, Anh Q. Le, Rachel McGovern, Peter K. Cheung, Anthony D. Kelleher, Heiko Jessen, Martin Markowitz, Eric Rosenberg, Nicole Frahm, Jorge Sanchez, Simon Mallal, Mina John, P. Richard Harrigan, David Heckerman, Christian Brander, Bruce D. Walker, Zabrina L. Brumme

Journal of Virology | April 2012

Publication Publication

Learning Transcriptional Regulatory Relationships Using Sparse Graphical Models

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

February 2012

Publication Publication Publication

High-avidity, high-IFNγ-producing CD8 T-cell responses following immune selection during HIV-1 infection

Niamh M. Keane, Stevens G. Roberts, Coral-Ann M. Almedia, Tanya Krishnan, Abha Chopra, Emma Demaine, Rebecca Laird, Monika Tschochner, Jonathan M. Carlson, Simon Mallal, David Heckerman, Ian James, Mina John

Immunology and Cell Biology | February 2012, Vol 90(2): pp. 224-234

Publication Publication

Lack of Association between HLA Class II Alleles and In Vitro Replication Capacities of Recombinant Viruses Encoding HIV-1 Subtype C Gag-Protease from Chronically Infected Individuals

Jaclyn K. Wright, Zabrina L. Brumme, Boris Julg, Mary van der Stok, Zenele Mncube, Xiaojiang Gao, Jonathan M. Carlson, Philip J. R. Goulder, Bruce D. Walker, Mark A. Brockman, Thumbi Ndung'u

Journal of Virology | November 2011

Publication Publication

Translation of HLA-HIV Associations to the Cellular Level: HIV Adapts To Inflate CD8 T Cell Responses against Nef and HLA-Adapted Variant Epitopes

Coral-Ann M. Almeida, Corine Bronke, Steven G. Roberts, Elizabeth McKinnon, Niamh M. Keane, Abha Chopra, Carl Kadie, Jonathan M. Carlson, David W. Haas, Sharon A. Riddler, Richard Haubrich, David Heckerman, Simon Mallal , Mina John

The Journal of Immunology | September 2011

Publication Publication

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 Project

Progression to AIDS in South Africa Is Associated with both Reverting and Compensatory Viral Mutations

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, Bloemfotnein-Oxford Collaborative Group, Cloete van Vuuren, John Frater

April 2011

Publication Publication

HLA-A*7401-Mediated Control of HIV Viremia Is Independent of Its Linkage Disequilibrium with HLA-B*5703

Philippa C. Matthews, Emily Adland, Jennifer Listgarten, Alasdair Leslie, Nompumelelo Mkhwanazi, Jonathan M. Carlson, Mikkel Harndahl, Anette Stryhn, Rebecca P. Payne, Anthony Ogwu, Kuan-Hsiang Gary Huang, John Frater, Paolo Paioni, Henrik Kolverpris, Pieter Jooste, Dominique Goedhals, Cloete van Vuuren, Dewald Steyn, Lynn Riddell, Fabian Chen, Graz Luzzi, Thambiah Balachandran, Thumbi Ndung'u, Soren Buus, Mary Carrington, Roger Shapiro, David Heckerman, Philip J. R. Goulder

The Journal of Immunology | April 2011

Publication Publication

Influence of Gag-Protease-Mediated Replication Capacity on Disease Progression in Individuals Recently Infected with HIV-1 Subtype C

Jaclyn K. Wright, Vladimir Novitsky, Mark A. Brockman, Zabrina L. Brumme, Chanson J. Brumme, Jonathan M. Carlson, David Heckerman, Bingxia Wang, Elena Losina, Mopo Leshwedi, Mary van der Stok, Lungile Maphumulo, Nompumelelo Mkhwanazi, Fundisiwe Chonco, Philip J. R. Goulder, Max Essex, Bruce D. Walker, Thumbi Ndung'u

February 2011

Publication Publication

The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation

Jonathan M. Carlson, The International HIV Controllers Study

Science | December 2010

Publication Publication

The hypervariable HIV-1 capsid protein residues comprise HLA-driven CD8+ T-cell escape mutations and covarying HLA-independent polymorphisms

Hayley Crawford, Philippa C. Matthews, Malinda Schaefer, Jonathan M. Carlson, Alasdair Leslie, William Kilembe, Susan Allen, Thumbi Ndung'u, David Heckerman, Eric Hunter, Philip J. R. Goulder

Journal of Virology | November 2010

Publication Publication

Early Selection in Gag by Protective HLA Alleles Contributes to Reduced HIV-1 Replication Capacity That May Be Largely Compensated for in Chronic Infection

Mark A Brockman, Zabrina L Brumme, Chanson J Brumme, Toshiyuki Miura, Jennifer Sela, Pamela C Rosato, Carl Kadie, Jonathan M. Carlson, Tristan J Markle, Hendrik Streeck, Anthony D Kelleher, Martin Markowitz, Heiko Jessen, Eric Rosenberg, Marcus Altfeld, P Richard Harrigan, David Heckerman, Bruce D Walker, Todd M Allen

Journal of Virology | November 2010, Vol 84(22): pp. 11937-11949

Publication Publication

Gag-Protease-Mediated Replication Capacity in HIV-1 1 Subtype C Chronic Infection: Associations with HLA Type and Clinical Parameters

Jaclyn K. Wright, Zabrina L. Brumme, Jonathan M. Carlson, David Heckerman, Carl Kadie, Chanson J. Brumme, Bingxia Wang, Elena Losina, Toshiyuki Miura, Fundisiwe Chonco, Mary van der Stok, Zenele Mncube, Karen Bishop, Philip J.R. Goulder , Bruce D. Walker, Mark A. Brockman, Thumbi Ndung'u

Journal of Virology | October 2010

Publication Publication Publication

Amino-Acid Co-Variation in HIV-1 Gag Subtype C: HLA-Mediated Selection Pressure and Compensatory Dynamics

Morgane Rolland, Jonathan M. Carlson, Siriphan Manocheewa, J. Victor Swain, Erinn Lanxon-Cookson, Wenjie Deng, Christine M. Rousseau, Dana N. Raugi, Gerald H. Learn, Brandon S. Maust, Hoosen Coovadia, Thumbi Ndung'u, Philip J. R. Goulder, Bruce D. Walker, Christian Brander, David Heckerman, James I. Mullins

PLoS ONE | September 2010, pp. e12463

Publication Publication

Adaptive Interactions between HLA and HIV-1: Highly Divergent Selection Imposed by HLA Class I Molecules with Common Supertype Motifs

Mina John, David Heckerman, Ian James, Lawrence P. Park, Jonathan M. Carlson, Abha Chopra, Silvana Gaudieri, David Nolan, David W. Haas, Sharon A. Riddler, Richard Haubrich, Simon Mallal

The Journal of Immunology | March 2010, Vol 184(8): pp. 4368-4377

Publication Publication

Additive Contribution of HLA Class I Alleles in the Immune Control of HIV-1 Infection

Alasdair Leslie, Philippa C. Matthews, Jennifer Listgarten, Jonathan M. Carlson, Carl Kadie, Thumbi Ndung'u, Christian Brander, Hoosen Coovadia, Bruce D. Walker, David Heckerman, Philip J. R. Goulder

Journal of Virology | February 2010, Vol 84(19): pp. 9879-9888

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 Project

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 Project

Identifying HLA-Associated Polymorphisms in HIV-1

Zabrina L. Brumme, Art F. Y. Poon, Jonathan M. Carlson, Bruce D. Walker

HIV Molecular Immunology 2010 | January 2010

Publication

PhyloDet: A Scalable Visualization Tool for Mapping Multiple Traits to Large Evolutionary Trees

Bongshin Lee, Lev Nachmanson, George Robertson, Jonathan M. Carlson, David Heckerman

Bioinformatics | October 2009, Vol 25(19): pp. 2611-2612

Publication Publication

HLA-Associated Immune Escape Pathways in HIV-1 Subtype B Gag, Pol and Nef Proteins

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 Kadie, Nicole Frahm, Christian Brander, David W. Haas, Sharon Riddler, Richard Haubrich, Bruce D. Walker, P. Richard Harrigan, David Heckerman, Simon Mallal

August 2009

Publication

Unique Features of HLA-mediated HIV Evolution in a Mexican Cohort: A Comparative Study

Santiago Avila-Rios, Christopher E. Ormsby, Jonathan M. Carlson, Humberto Valenzuela-Ponce, Juan Blanco-Heredia, Daniela Garrido-Rodriguez, Claudia Garcia-Morales, David Heckerman, Zabrina L. Brumme, Simon Mallal, Mina John, Enrique Espinosa, Gustavo Reyes-Teran

Retrovirology | August 2009

Publication Publication

HLA-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection

Zabrina L. Brumme, Iris Tao, Sharon Szeto, Chanson J. Brumme, Jonathan M. Carlson, Dennison Chan, Carl Kadie, Nicole Frahm, Christian Brander, Bruce Walker, David Heckerman, P. Richard Harrigan

July 2009

Publication

Estimating false discovery rates for contingency tables

Jonathan M. Carlson, David Heckerman, Guy Shani

MSR-TR-2009-53 | May 2009

Publication

HLA footprints on HIV-1 are associated with inter-clade polymorphisms and intra-clade phylogenetic clustering

Philippa C Matthews, Alasdair J Leslie, Aris Katzourakis, Hayley Crawford, Rebecca Payne, Andrew Prendergast, Karen Power, Anthony D Kelleher, Paul Klenerman, Jonathan M. Carlson, David Heckerman, Thumbi Ndung'u, Bruce D Walker, Todd M Allen, Oliver G Pybus, Philip J R Goulder

Journal of Virology | January 2009, pp. JVI.02017-08

Publication

Protective HLA class I Alleles That Restrict Acute-Phase CD8+ T-Cell Responses Are Associated with Viral Escape Mutations Located in Highly Conserved Regions of Human Immunodeficiency Virus Type 1

Yaoyu E. Wang, Bin Li, Jonathan M. Carlson, Hendrik Streeck, Adrianne D. Gladden, Robert Goodman, Arne Schneidewind, Karen A. Power, Ildiko Toth, Nicole Frahm, Galit Alter, Christian Brander, Mary Carrington, Bruce D. Walker, Marcus Altfeld, David Heckerman, Todd M. Allen

Journal of Virology | January 2009, Vol 83(4): pp. 1845-1855

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 Project

Central Role of Reverting Mutations in HLA Associations with Human Immunodeficiency Virus Set Point

Philippa C. Matthews, Andrew Prendergast, Alasdair Leslie, Hayley Crawford, Rebecca Payne, Christine Rousseau, Isobella Honeyborne, Jonathan M. Carlson, Carl Kadie, Christian Brander, Karen Bishop, Nonkululeko Mlotshwa, James I. Mullins, Hoosen Coovadia, Thumbi Ndung'u, Bruce D. Walker, David Heckerman, Philip J. Goulder

Journal of Virology | September 2008, Vol 82(17): pp. 8548-8559

Publication Publication

Det. (Distance Encoded Tree): A Scalable Visualization Tool for Mapping Multiple Traits to Large Evolutionary Trees

Bongshin Lee, Lev Nachmanson, George Robertson, Jonathan M. Carlson, David Heckerman

MSR-TR-2008-97 | July 2008

Publication

HIV evolution in response to HLA-restricted CTL selection pressures: a population-based perspective

Jonathan M. Carlson, Zabrina L. Brumme

Microbes and Infection | April 2008, Vol 10: pp. 455-461

Publication Publication

Genetic Characterization of Human Immunodeficiency Virus type 1 in Elite Controllers: Lack of gross genetic defects or common amino acid changes

Toshiyuki Miura, Mark A. Brockman, Chanson J. Brumme, Zabrina L. Brumme, Jonathan M. Carlson, Florencia Pereyra, Alicja Trocha, Marylyn M. Addo, Brian L. Block, Alissa C. Rothchild, Brett M. Baker, Theresa Flynn, Arne Schneidewind, Bin Li, Yaoyu E. Wang, David Heckerman, Todd M. Allen, Bruce D. Walker

Journal of Virology | January 2008, pp. JVI.00535-8

Publication Publication Publication

HLA Class I-Driven Evolution of Human Immunodeficiency Virus Type 1 Subtype C Proteome: immune Escape and Viral Load

Christine M. Rousseau, Marcus G. Daniels, Jonathan M. Carlson, Carl Kadie, Hayley Crawford, Andrew Prendergast, Philippa Matthews, Rebecca Payne, Morgane Rolland, Dana N. Raugi, Brandon S. Maust, Gerald H. Learn, David C. Nickle, Hoosen Coovadia, Thumbi Ndung'u, Nicole Frahm, Christian Brander, Bruce D. Walker, Philip J. R. Goulder, Tanmoy Bhattacharya, David Heckerman, Bette T. Korber, James I. Mullins

Journal of Virology | January 2008, Vol 82: pp. 6434-6446

Publication

Human leukocyte antigen-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection

Zabrina L Brumme, Iris Tao, Sharon Szeto, Chanson J Brumme, Jonathan M. Carlson, Dennison Chan, Carl Kadie, Nicole Frahm, Christian Brander, Bruce Walker, David Heckerman, P. Richard Harrigan

AIDS | January 2008

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 Project

Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients

Thomas Kuntzen, Joerg Timm, Andrew Berical, Niall Lennon, Aaron M. Berlin, Sarah K. Young, Bongshin Lee, David Heckerman, Jonathan M. Carlson, Laura L. Reyor, Marianna Kleyman, Cory M. McMahon, Christopher Birch, Julian Schulze zur Wiesch, Timothy Ledlie, Michael Koehrsen, Chinnappa Kodira, Andrew D. Roberts, Georg M. Lauer, Hugo R. Rosen, Florian Bihl, Andreas Cerny, Ulrich Spengler, Zhimin Liu, Arthur Y. Kim, Yanming Xing, Arne Schneidewind, Margaret A. Madey, Jaquelyn F. Fleckenstein, Vicki M. Park, James E. Galagan, Chad Nusbaum, Bruce D. Walker, Gerond V. Lake-Bakaar, Eric S. Daar, Ira M. Jacobson, Edward D. Gomperts, Brian R. Edlin, Sharyne M. Donfield, Raymond T. Chung, Andrew H. Talal, Tony Marion, Bruce W. Birren, Matthew R. Henn, Todd M. Allen

Hepatology | January 2008, Vol 48: pp. 1769-1778

Publication

Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients

Paul A. Goepfert, Wendy Lumm, Paul Farmer, Philippa Matthews, Andrew Prendergast, Jonathan M. Carlson, Cynthia A. Derdeyn, Jianming Tang, Richard A. Kaslow, Anju Bansal, Karina Yusim, David Heckerman, Joseph Mulenga, Susan Allen, Philip J. R. Goulder, Eric Hunter

Journal of Experimental Medicine | January 2008, Vol 205: pp. 1009-1017

Publication Publication

Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1

Zabrina L Brumme, Chanson J Brumme, David Heckerman, Bette T Korber, Marcus Daniels, 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, Jonathan M. Carlson

PLoS Pathogens | July 2007

Publication

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 Project

SCOPE: a web server for practical de novo motif discovery

Jonathan M. Carlson, Arijit Chakravarty, Rhadika S. Khetani, Charles E. DeZiel, Robert H. Gross

Nucleic Acids Research | July 2007, Vol 35: pp. W259-264

Publication

A novel ensemble learning method for de novo computational identification of DNA binding sites

Arijit Chakravarty, Radhika Khetani, Robert Gross, Jonathan M. Carlson

BMC Bioinformatics | January 2007, pp. 249

Publication

Founder Effects in the Assessment of HIV Polymorphisms and HLA Allele Associations

Tanmoy Bhattacharya, Marcus Daniels, David Heckerman, Brian Foley, Nicole Frahm, Carl Kadie, Jonathan M. Carlson, Karina Yusim, Ben McMahon, Brian Gaschen, Simon Mallal, James I. Mullins, David C. Nickle, Joshua Herbeck, Christine Rousseau, Gerald H. Learn, Toshiyuki Miura, Christian Brander, Bruce Walker, Bette Korber

Science | January 2007, Vol 315: pp. 1583-1586

Publication

SPACER: identification of cis-regulatory elements with non-contiguous critical residues

Arijit Chakravarty, Jonathan M. Carlson, Radhika S. Khetani, Charles E. DeZiel, Robert H. Gross

Bioinformatics | January 2007, Vol 23(8): pp. 1029-1031

Publication

Identifying the effects of human immune pressure on the evolution of HIV.

Jonathan M. Carlson, Carl Kadie, David Heckerman

December 2006

Publication

BEAM: A Beam Search Algorithm for the Identification of Cis-Regulatory Elements in Groups of Genes

Arijit Chakravarty*, Robert H. Gross, Jonathan M. Carlson

Journal of Computational Biology | January 2006, Vol 13: pp. 686-701

PMID: 16706719

Publication

Bounded search for de novo identification of degenerate cis-regulatory elements

Arijit Chakravarty*, Radhika Khetani, Robert Gross, Jonathan M. Carlson

BMC Bioinformatics | January 2006, Vol 7: pp. 254

Publication

Creation of a Relational Database for Identifying Potential Functional DNA Sequence Motifs in A. thaliana and Other Genomes

Jonathan M. Carlson

June 2003

PhD Thesis: Undergraduate Honors thesis, Dept. Biology, Dartmouth College | June 2003

Dartmouth Kemeny Computing prize and Reed Biology Award

Publication

T-cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibody titers and disease severity

Rebecca Elyanow, Thomas M. Snyder, Sudeb C. Dalai, Rachel M. Gittelman, Boonyaratanakornkit J, Wald A, Selke S, Wener Mh, Morishima C, Greninger Al, Michael Gale, Tien-Ying Hsiang, Lichen Jing, Holbrook Mr, Ian M. Kaplan, Damon H May, H. Jabran Zahid, Jonathan M. Carlson, Lance Baldo, Thomas Manley, Harlan S Robins, David M Koelle

JCI Insight | April 2022, Vol 7(10)

DOI Preprint Publication Project Project Project

Longitudinal analysis of T cell receptor repertoires reveals shared patterns of antigen-specific response to SARS-CoV-2 infection

Rachel M Gittelman, Enrico Lavezzo, Thomas M Snyder, H. Jabran Zahid, Cara L Carty, Rebecca Elyanow, Sudeb Dalai, Ilan Kirsch, Lance Baldo, Laura Manuto, Elisa Franchin, Claudia Del Vecchio, Monia Pacenti, Caterina Boldrin, Margherita Cattai, Francesca Saluzzo, Andrea Padoan, Mario Plebani, Fabio Simeoni, Jessica Bordini, Nicola I Lorè, Dejan Lazarević, Daniela M Cirillo, Paolo Ghia, Stefano Toppo, Jonathan M. Carlson, Harlan S Robins, Andrea Crisanti, Giovanni Tonon

JCI Insight | April 2022, Vol 7(10)

DOI Publication Project Project

Immunosequencing of the T-cell receptor repertoire reveals signatures specific for diagnosis and characterization of early Lyme disease

Julia Greissl, Mitch Pesesky, Sudeb C. Dalai, Alison W. Rebman, Mark J. Soloski, Elizabeth J. Horn, Jennifer N. Dines, Rachel M. Gittelman, Thomas M. Snyder, Ryan O. Emerson, Ted Meeds, Thomas Manley, Ian M. Kaplan, Lance Baldo, Jonathan M. Carlson, Harlan S. Robins, John N. Aucott

medRxiv | August 2021

DOI PDF Publication Project

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

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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)

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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

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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

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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

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Diagnosis and Tracking of Past SARS-CoV-2 Infection in a Large Study of Vo’, Italy Through T-Cell Receptor Sequencing

Rachel M Gittelman, Enrico Lavezzo, Thomas M Snyder, H Jabran Zahid, Rebecca Elyanow, Sudeb Dalai, Ilan Kirsch, Lance Baldo, Laura Manuto, Elisa Franchin, Claudia Del Vecchio, Fabio Simeoni, Jessica Bordini, Nicola I LorÃ, Dejan Lazarevic, Daniela M Cirillo, Paolo Ghia, Stefano Toppo, Jonathan M. Carlson, Harlan S Robins, Giovanni Tonon, Andrea Crisanti

medRxiv | November 2020

Updated February 11, 2021

DOI 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

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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

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A large-scale database of T-cell receptor beta (TCRβ) sequences and binding associations from natural and synthetic exposure to SARS-CoV-2

Sean Nolan, Marissa Vignali, Mark Klinger, Jennifer N Dines, Ian M Kaplan, Emily Svejnoha, Tracy Craft, Katie Boland, Mitch Pesesky, Rachel M Gittelman, Thomas M Snyder, Christopher J Gooley, Simona Semprini, Claudio Cerchione, Massimiliano Mazza, Ottavia M Delmonte, Kerry Dobbs, Gonzalo Carreño-Tarragona, Santiago Barrio, Vittorio Sambri, Giovanni Martinelli, Jason D Goldman, James R Heath, Luigi D Notarangelo, Jonathan M. Carlson, Joaquin Martinez-Lopez, Harlan S Robins

August 2020

DOI Publication Publication Publication Publication Project Project

Magnitude and Dynamics of the T-Cell Response to SARS-CoV-2 Infection at Both Individual and Population Levels

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 N 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, Julia Greissl, Lance Baldo, Simona Semprini, Claudio Cerchione, Massimiliano Mazza, Ottavia M Delmonte, Kerry Dobbs, 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, James R Heath, Helen C Su, Luigi D Notarangelo, Joaquin Martinez-Lopez, Jonathan M. Carlson, Harlan S Robins

medRxiv | August 2020

Updated September 17, 2020

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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)

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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

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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 Project

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

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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

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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

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Elevated HLA-A expression impairs HIV control through inhibition of NKG2A-expressing cells.

Veron Ramsuran, Vivek Naranbhai, Amir Horowitz, Ying Qi, Maureen P. Martin, Yuko Yuki, Xiaojiang Gao, Victoria Walker-Sperling, Gregory Q. Del Prete, Douglas K. Schneider, Jeffrey D. Lifson, Jacques Fellay, Steven G. Deeks, Jeffrey N. Martin, James J. Goedert, Steven M. Wolinsky, Nelson L. Michael, Gregory D. Kirk, Susan Buchbinder, David Haas, Thumbi Ndung’u, Philip Goulder, Peter Parham, Bruce D. Walker, Jonathan M. Carlson, Mary Carrington

Science | January 2018, Vol 359: pp. 86-90

Publication 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

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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

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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

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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

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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

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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 Project

Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus

Damien C. Tully, Colin B. Ogilvie, Rebecca E. Batorsky, David J. Bean, Karen A. Power, Musie Ghebremichael, Hunter E. Bedard, Adrianne D. Gladden, Aaron M. Seese, Molly A. Amero, Kimberly Lane, Graham McGrath, Suzane B. Bazner, Jake Tinsley, Niall J. Lennon, Matthew R. Henn, Zabrina L. Brumme, Philip J. Norris, Eric S. Rosenberg, Kenneth H. Mayer, Heiko Jessen, Sergei L. Kosakovsky Pond, Bruce D. Walker, Marcus Altfeld, Todd M. Allen, Jonathan M. Carlson

PLoS Pathogens | May 2016

Publication Publication

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

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A strong association of human leukocyte antigen-associated Pol and Gag mutations with clinical parameters in HIV-1 subtype A/E infection.

Giang Van Tran, Takayuki Chikata, Jonathan M. Carlson, Hayato Murakoshi, Dung Hoai Nguyen, Yoshiko Tamura, Tomohiro Akahoshi, Nozomi Kuse, Keiko Sakai, Sachiko Sakai, Kyle Cobarrubias, Shinichi Oka, Zabrina L Brumme, Kinh Van Nguyen, Masafumi Takiguchi

AIDS | March 2016, Vol 30: pp. 681-689

Publication Publication

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

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Population-Level Immune-Mediated Adaptation in HIV-1 Polymerase during the North American Epidemic

Natalie N Kinloch, Daniel R MacMillan, Anh Q Le, Laura A Cotton, David R Bangsberg, Susan Buchbinder, Mary Carrington, Jonathan Fuchs, P Richard Harrigan, Beryl Koblin, Margot Kushel, Martin Markowitz, Kenneth Mayer, MJ Milloy, Martin T Schechter, Theresa Wagner, Bruce D Walker, Jonathan M. Carlson, Art FY Poon, Zabrina L Brumme

Journal of Virology | November 2015, Vol 90: pp. 1244-1258

Publication Publication

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 Africa

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

Plos Medicine | November 2015

Publication Publication

Enhanced Recognition of HIV-1 Cryptic Epitopes Restricted by HLA Class I Alleles Associated With a Favorable Clinical Outcome.

Anju Bansa, Tiffanie Mann, Sarah Sterrett, Binghao J Peng, Anne Bet, Jonathan M. Carlson, Paul A Goepfert

Journal of Acquired Immune Deficiency Syndromes | September 2015

Publication Publication

HLA Class-II Associated HIV Polymorphisms Predict Escape from CD4+ T Cell Responses

Nathan Erdmann, Victor Y. Du, Jonathan M. Carlson, Malinda Schaefer, Alexander Jureka, Sarah Sterrett, Ling Yue, Dario Dilernia, Shabir Lakhi, Jianming Tang, John Sidney, Jill Gilmour, Susan Allen, Eric Hunter, Sonya Heath, Anju Bansal, Paul A. Goepfert

PLoS Pathog | August 2015

Publication Publication

Prevalence and Characteristics of Hepatitis B Virus (HBV) Coinfection among HIV-Positive Women in South Africa and Botswana

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

July 2015

Publication Publication

HLA-A is a Predictor of Hepatitis B e Antigen Status in HIV-Positive African Adults

Philippa C Matthews, Jonathan M. Carlson, Apostolos Beloukas, Amna Malik, Pieter Jooste, Anthony Ogwu, Roger Shapiro, Lynn Riddell, Fabian Chen, Graz Luzzi, Gerald Jesuthasan, Katie Jeffery, Nebojsa Jojic, Thumbi Ndung'u, Mary Carrington, Philip JR Goulder, Anna Maria Geretti, Paul Klenerman

The Journal of Infectious Diseases | July 2015, Vol 213: pp. 1248-1252

Publication Publication

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

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Immune screening identifies novel T cell targets encoded by anti-sense reading frames of HIV-1

Christopher T. Berger, Anuska Llano, Jonathan M. Carlson, Zabrina L. Brumme, Mark A. Brockman, Samandhy Cedeno, P. Richard Harrigan, Daniel E. Kaufmann, David Heckerman, Andreas Meyerhans, Christian Brander

Journal of virology | April 2015, Vol 89: pp. 4015-4019

Publication Publication

Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial

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, Meera Bose, 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, SL Pond, Jonathan M. Carlson, Nelson L Michael, William R Schief, James I Mullins, Jerome H Kim , Peter B Gilbert

PLOS Computational Biology | February 2015

Publication Publication

A molecular switch in immunodominant HIV-1-specific CD8 T-cell epitopes shapes differential HLA-restricted escape

Henrik N Kløverpris, David K Cole, Anna Fuller, Jonathan M. Carlson, Konrad Beck, Andrea J Schauenburg, Pierre J Rizkallah, Søren Buus, Andrew K Sewel, Philip Goulder

Retrovirology | February 2015

Publication Publication

Nef-mediated down-regulation of CD4 and HLA class I in HIV-1 subtype C infection: Association with disease progression and influence of immune pressure

Jaclyn K Mann, Denis Chopera, Saleha Omarjee, Xiaomei T Kuang, Anh Q Le, Gursev Anmole, Ryan Danroth, Philip Mwimanzi, Tarylee Reddy, Jonathan M. Carlson, Mopo Radebe, Philip JR Goulder, Bruce D Walker, Salim Abdool Karim, Vladimir Novitsky, Carolyn Williamson, Mark A Brockman, Zabrina L Brumme, Thumbi Ndung'u

Virology | November 2014, pp. 214-225

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

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CD8 and CD4 Epitope Predictions in RV144: No Strong Evidence of a T-Cell Driven Sieve Effect in HIV-1 Breakthrough Sequences from Trial Participants

Kalpana Dommaraju, Gustavo Kijak, Jonathan M. Carlson, Brendan B Larsen, Sodsai Tovanabutra, Dan E Geraghty, Wenjie Deng, Brandon S Maust, Paul T Edlefsen, Eric Sanders-Buell, Silvia Ratto-Kim, Supachai Rerks-Ngarm, Sorachai Nitayaphan, Punnee Pitisuttihum, Jaranit Kaewkungwal, Robert J O'Connell, Merlin L Robb, Nelson L Michael, James I Mullins, Jerome H Kim, Morgane Rolland

PLoS One | October 2014

Publication Publication

Early immune adaptation in HIV-1 revealed by population-level approaches

Eric Martin, Jonathan M. Carlson, Anh Q Le, Denis R Chopera, Rachel McGovern, Manal A Rahman, Carmond Ng, Heiko Jessen, Anthony D Kelleher, Martin Markowitz, Todd M Allen, MJ Milloy, Mary Carrington, Mark A Wainberg, Zabrina L Brumme

Retrovirology | August 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

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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)

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Differential Escape Patterns within the Dominant HLA-B*57:03-Restricted HIV Gag Epitope Reflect Distinct Clade-Specific Functional Constraints

Payne RP, Branch S, Kloverpris H, Matthews PC, Koofhethile K, Strong T, Adland E, Frater J, Ndung'u T, Hunter E, Haubrich R, Harrigan PR, Brumme ZL, Mallal S, John M, Jooste P, Shapiro R, Walker BD, Jonathan M. Carlson, Landis C, Prado JG, Goulder PJ

Journal of Virology | May 2014

Publication Publication

Genotypic and Functional Impact of HIV-1 Adaptation to Its Host Population during the North American Epidemic

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 FY Poon , Zabrina L Brumme

PLoS Genet | April 2014

Publication Publication

Host-Specific Adaptation of HIV-1 Subtype B in the Japanese Population

Takayuki Chikata, Jonathan M. Carlson, Yoshiko Tamura, Mohamed Ali Borghan, Takuya Naruto, Masao Hashimoto, Hayato Murakoshi, Anh Q. Le, Simon Mallal, Mina John, Hiroyuki Gatanaga, Shinichi Oka, Zabrina L. Brumme , Masafumi Takiguchi

Journal of Virology | March 2014, Vol 88(9): pp. 4764-4775

Publication Publication

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

Jennifer Listgarten, Christoph Lippert, Nicolo Fusi, David Heckerman, Jonathan M. Carlson

eLife | October 2013

Publication

Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection

Akihisa Shimizu, Ai Kawana-Tachikawa, Atsushi Yamagata, Chung Yong Han, Dayong Zhu, Yusuke Sato, Hitomi Nakamura, Tomohiko Koibuchi, Jonathan M. Carlson, Eric Martin, Chanson Brumme, Yi Shi, George Gao, Zabrina L Brumme, Shuya Fukai, Aikichi Iwamoto

Scientific Reports | October 2013

Publication Publication

Nef-Specific CD8+ T Cell Responses Contribute to HIV-1 Immune Control

Emily Adland, Jonathan M. Carlson, Paolo Paioni, Henrik Kloverpris, Roger Shapiro, Anthony Ogwu, Lynn Riddell, Graz Luzzi, Fabian Chen, Thambiah Balachandran, David Heckerman, Anette Stryhn, Anne Edwards, Thumbi Ndung'u, Bruce D Walker, Soren Buus, Philip Goulder , Philippa C Matthews

PloS One | September 2013

Publication Publication

Increased Sequence Coverage through Combined Targeting of Variant and Conserved Epitopes Correlates with Control of HIV Replication

Justine Sunshine, Moon Kim, Jonathan M. Carlson, David Heckerman, Julie Czartoski, Stephen A. Migueles, Janine Maenza, M. Juliana McElrath, James I. Mullins, Nicole Frahm

Journal of Virology | August 2013, Vol 88(2): pp. 1354-1365

Publication Publication

HLA-A*68: 02-restricted Gag-specific cytotoxic T lymphocyte responses can drive selection pressure on HIV but are subdominant and ineffective

Henrik N. Klverpris, Anette Stryhn, Mikkel Harndahl, Jonathan M. Carlson, Alasdair J. Leslie, Fabian Chen, Lynn Riddell, Joseph Mulenga, Bruce D. Walker, Thumbi N'dung'u, Soren Buus , Philip Goulder

AIDS Official Journal of the International Aids Society | July 2013

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 Project

HIV escape mutations occur preferentially at HLA-binding sites of CD8 T-cell epitopes

Corine Bronke, Coral-Ann M. Almeida, Elizabeth McKinnon, Steven G. Roberts, Niamh M. Keane, Abha Chopra, Jonathan M. Carlson, David Heckerman, Simon Mallal, Mina John

AIDS, Basic Science | March 2013, Vol 27(6): pp. 899-905

Publication Publication

Distinct HIV-1 Escape Patterns Selected by Cytotoxic T Cells with Identical Epitope Specificity

Yuichi Yagitaa, Nozomi Kusea, Kimiko Kurokib, Hiroyuki Gatanagaa, Jonathan M. Carlson, Takayuki Chikataa, Zabrina L. Brummee, Hayato Murakoshia, Tomohiro Akahoshia, Nico Pfeiferd, Simon Mallalg, Mina Johng, Toyoyuki Oseb, Haruki Matsubarab, Ryo Kandab, Yuko Fukunagab, Kazutaka Hondaa, Yuka Kawashimaa, Yasuo Ariumia, Shinichi Okaa, Katsumi Maenakab, Masafumi Takiguchia

Journal of Virology | February 2013

Publication Publication

Frequent and Variable Cytotoxic-T-Lymphocyte Escape-Associated Fitness Costs in the Human Immunodeficiency Virus Type 1 Subtype B Gag Proteins

Christian L Boutwell, Jonathan M. Carlson, Tien-Ho Lin, Aaron Seese, Karen A Power, Jian Peng, Yanhua Tang, Zabrina L Brumme, David Heckerman, Arne Schneidewind, Todd M Allen

January 2013

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 Project

Differential Clade-Specific HLA-B*3501 Association with HIV-1 Disease Outcome Is Linked to Immunogenicity of a Single Gag Epitope

Philippa C. Matthews, Madoka Koyanagi, Henrik N. Kloverpris, Mikkel Harndahl, Anette Stryhn, Tomohiro Akahoshi, Hiroyuki Gatanaga, Shinichi Oka, Claudia Juarez Molina, Humberto Valenzuela Ponce, Santiago Avila Rios, David Cole, Jonathan M. Carlson, Rebecca P. Payne, Anthony Ogwu, Alfred Bere, Thumbi Ndung'u, Kamini Gounder, Fabian Chen, Lynn Riddell, Graz Luzzi, Roger Shaprio, Christian Brander, Bruce Walker, Andrew K. sewell, Gustavo Reyes Teran, David Heckerman, Eric Hunter, Soren Buus, Masafumi Takiguchi, Philip J.R. Goulder

Journal of Virololgy | December 2012, Vol 86(23): pp. 12643-12654

Publication Publication

Significant Reductions in Gag-Protease-Mediated HIV-1 Replication Capacity during the Course of the Epidemic in Japan

Shigeru Nomura, Noriaki Hosoya, Zabrina L. Brumme, Mark A. Brockman, Tadashi Kikuchi, Michiko Koga, Hitomi Nakamura, Tomohiko Koibuchi, Takeshi Fujii, Jonathan M. Carlson, David Heckerman, Ai Kawana-Tachikawa, Aikichi Iwamoto, Toshiyuki Miura

Journal of Virology | November 2012, Vol 87(3): pp. 1465-1476

Publication Publication

Role of Transmitted Gag CTL Polymorphisms in Defining Replicative Capacity and Early HIV-1 Pathogenesis

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 Geopfert, Matthew A. Price, Jill Gilmour, Joseph Mulenga, Paul Farmer, Cynthia A. Derdeyn, Jiaming Tang, David Heckerman, Richard A. Kaslow, Susan A. Allen, Eric Hunter

PLoS Pathogens | November 2012, pp. e1003041

Publication Publication

Co-operative additive effects between HLA alleles in control of HIV-1

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

PLoS ONE | October 2012, pp. e47799

Publication Publication

Intersubtype differences in the effect of a rare p24 Gag mutation on HIV-1 replicative fitness

Denis R. Chopera, Laura A. Cotton, Alexander Zawaira, Jaclyn K. Mann, Nobubelo K. Ngandu, Roman Ntale, Jonathan M. Carlson, Koleka Mlisana, Zenda Woodman, Debra de Assis Rosa, Eric Martin, Toshiyuki Miura, Florencia Pereyra, Bruce D. Walker, Clive M. Gray, Darren P. Martin, Thumbi Ndung'u, Mark A. Brockman, Salim Abdool Karim, Zabrina L. Brumme, Carolyn Williamson

Journal of Virology | September 2012

Publication Publication

HIV Control through a Single Nucleotide on the HLA-B Locus

Henrik N. Kloverpris, Mikkel Harndahl, Alasdair J. Leslie, Jonathan M. Carlson, Nasreen Ismail, Mary van der Stok, Kuan-Hsiang Gary Huang, Fabian Chen, Lynn Riddell, Dewald Steyn, Dominique Goedhals, Cloete van Vuuren, John Frater, Bruce D. Walker, Mary Carrington, Thumbi Ndung'u, Soren Buus, Philip Goulder

Journal of Virology | August 2012

Publication Publication

Aminopeptidase Substrate Preference Affects HIV Epitope Presentation and Predicts Immune Escape Patterns in HIV-Infected Individuals

Shao Chong Zhang, Eric Martin, Mariko Shimada, Sasha Blue Godfrey, Jennifer Fricke, Shirley Locastro, Nicole Y Lai, Paul Liebesny, Jonathan M. Carlson, Chanson J Brumme, Oluwatobi Awele Ogbechie, Huabiao Chen, Bruce D Walker, Zabrina L Brumme, Daniel G Kavanagh, Sylvie Le Gall

The Journal of Immunology | June 2012

Publication Publication

Minor contribution of HLA class I-associated selective pressure to the variability of HIV-1 accessory protein Vpu

Zafrul Hasan, Jonathan M. Carlson, Hiroyuki Gatanaga, Anh Le, Chanson J Brumme, Shinichi Oka, Zabrina L Brumme , Takamasa Ueno

May 2012

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 Project

Uncommon Pathways of Immune Escape Attenuate HIV-1 Integrase Replication Capacity

Mark A. Brockman, Denis R. Chopera, Alex Olvera, Chanson J. Brumme, Jennifer Sela, Tristan J. Markle, Eric Martin, Jonathan M. Carlson, Anh Q. Le, Rachel McGovern, Peter K. Cheung, Anthony D. Kelleher, Heiko Jessen, Martin Markowitz, Eric Rosenberg, Nicole Frahm, Jorge Sanchez, Simon Mallal, Mina John, P. Richard Harrigan, David Heckerman, Christian Brander, Bruce D. Walker, Zabrina L. Brumme

Journal of Virology | April 2012

Publication Publication

Learning Transcriptional Regulatory Relationships Using Sparse Graphical Models

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

February 2012

Publication Publication Publication

High-avidity, high-IFNγ-producing CD8 T-cell responses following immune selection during HIV-1 infection

Niamh M. Keane, Stevens G. Roberts, Coral-Ann M. Almedia, Tanya Krishnan, Abha Chopra, Emma Demaine, Rebecca Laird, Monika Tschochner, Jonathan M. Carlson, Simon Mallal, David Heckerman, Ian James, Mina John

Immunology and Cell Biology | February 2012, Vol 90(2): pp. 224-234

Publication Publication

Lack of Association between HLA Class II Alleles and In Vitro Replication Capacities of Recombinant Viruses Encoding HIV-1 Subtype C Gag-Protease from Chronically Infected Individuals

Jaclyn K. Wright, Zabrina L. Brumme, Boris Julg, Mary van der Stok, Zenele Mncube, Xiaojiang Gao, Jonathan M. Carlson, Philip J. R. Goulder, Bruce D. Walker, Mark A. Brockman, Thumbi Ndung'u

Journal of Virology | November 2011

Publication Publication

Translation of HLA-HIV Associations to the Cellular Level: HIV Adapts To Inflate CD8 T Cell Responses against Nef and HLA-Adapted Variant Epitopes

Coral-Ann M. Almeida, Corine Bronke, Steven G. Roberts, Elizabeth McKinnon, Niamh M. Keane, Abha Chopra, Carl Kadie, Jonathan M. Carlson, David W. Haas, Sharon A. Riddler, Richard Haubrich, David Heckerman, Simon Mallal , Mina John

The Journal of Immunology | September 2011

Publication Publication

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 Project

Progression to AIDS in South Africa Is Associated with both Reverting and Compensatory Viral Mutations

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, Bloemfotnein-Oxford Collaborative Group, Cloete van Vuuren, John Frater

April 2011

Publication Publication

HLA-A*7401-Mediated Control of HIV Viremia Is Independent of Its Linkage Disequilibrium with HLA-B*5703

Philippa C. Matthews, Emily Adland, Jennifer Listgarten, Alasdair Leslie, Nompumelelo Mkhwanazi, Jonathan M. Carlson, Mikkel Harndahl, Anette Stryhn, Rebecca P. Payne, Anthony Ogwu, Kuan-Hsiang Gary Huang, John Frater, Paolo Paioni, Henrik Kolverpris, Pieter Jooste, Dominique Goedhals, Cloete van Vuuren, Dewald Steyn, Lynn Riddell, Fabian Chen, Graz Luzzi, Thambiah Balachandran, Thumbi Ndung'u, Soren Buus, Mary Carrington, Roger Shapiro, David Heckerman, Philip J. R. Goulder

The Journal of Immunology | April 2011

Publication Publication

Influence of Gag-Protease-Mediated Replication Capacity on Disease Progression in Individuals Recently Infected with HIV-1 Subtype C

Jaclyn K. Wright, Vladimir Novitsky, Mark A. Brockman, Zabrina L. Brumme, Chanson J. Brumme, Jonathan M. Carlson, David Heckerman, Bingxia Wang, Elena Losina, Mopo Leshwedi, Mary van der Stok, Lungile Maphumulo, Nompumelelo Mkhwanazi, Fundisiwe Chonco, Philip J. R. Goulder, Max Essex, Bruce D. Walker, Thumbi Ndung'u

February 2011

Publication Publication

The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation

Jonathan M. Carlson, The International HIV Controllers Study

Science | December 2010

Publication Publication

The hypervariable HIV-1 capsid protein residues comprise HLA-driven CD8+ T-cell escape mutations and covarying HLA-independent polymorphisms

Hayley Crawford, Philippa C. Matthews, Malinda Schaefer, Jonathan M. Carlson, Alasdair Leslie, William Kilembe, Susan Allen, Thumbi Ndung'u, David Heckerman, Eric Hunter, Philip J. R. Goulder

Journal of Virology | November 2010

Publication Publication

Early Selection in Gag by Protective HLA Alleles Contributes to Reduced HIV-1 Replication Capacity That May Be Largely Compensated for in Chronic Infection

Mark A Brockman, Zabrina L Brumme, Chanson J Brumme, Toshiyuki Miura, Jennifer Sela, Pamela C Rosato, Carl Kadie, Jonathan M. Carlson, Tristan J Markle, Hendrik Streeck, Anthony D Kelleher, Martin Markowitz, Heiko Jessen, Eric Rosenberg, Marcus Altfeld, P Richard Harrigan, David Heckerman, Bruce D Walker, Todd M Allen

Journal of Virology | November 2010, Vol 84(22): pp. 11937-11949

Publication Publication

Gag-Protease-Mediated Replication Capacity in HIV-1 1 Subtype C Chronic Infection: Associations with HLA Type and Clinical Parameters

Jaclyn K. Wright, Zabrina L. Brumme, Jonathan M. Carlson, David Heckerman, Carl Kadie, Chanson J. Brumme, Bingxia Wang, Elena Losina, Toshiyuki Miura, Fundisiwe Chonco, Mary van der Stok, Zenele Mncube, Karen Bishop, Philip J.R. Goulder , Bruce D. Walker, Mark A. Brockman, Thumbi Ndung'u

Journal of Virology | October 2010

Publication Publication Publication

Amino-Acid Co-Variation in HIV-1 Gag Subtype C: HLA-Mediated Selection Pressure and Compensatory Dynamics

Morgane Rolland, Jonathan M. Carlson, Siriphan Manocheewa, J. Victor Swain, Erinn Lanxon-Cookson, Wenjie Deng, Christine M. Rousseau, Dana N. Raugi, Gerald H. Learn, Brandon S. Maust, Hoosen Coovadia, Thumbi Ndung'u, Philip J. R. Goulder, Bruce D. Walker, Christian Brander, David Heckerman, James I. Mullins

PLoS ONE | September 2010, pp. e12463

Publication Publication

Adaptive Interactions between HLA and HIV-1: Highly Divergent Selection Imposed by HLA Class I Molecules with Common Supertype Motifs

Mina John, David Heckerman, Ian James, Lawrence P. Park, Jonathan M. Carlson, Abha Chopra, Silvana Gaudieri, David Nolan, David W. Haas, Sharon A. Riddler, Richard Haubrich, Simon Mallal

The Journal of Immunology | March 2010, Vol 184(8): pp. 4368-4377

Publication Publication

Additive Contribution of HLA Class I Alleles in the Immune Control of HIV-1 Infection

Alasdair Leslie, Philippa C. Matthews, Jennifer Listgarten, Jonathan M. Carlson, Carl Kadie, Thumbi Ndung'u, Christian Brander, Hoosen Coovadia, Bruce D. Walker, David Heckerman, Philip J. R. Goulder

Journal of Virology | February 2010, Vol 84(19): pp. 9879-9888

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 Project

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 Project

PhyloDet: A Scalable Visualization Tool for Mapping Multiple Traits to Large Evolutionary Trees

Bongshin Lee, Lev Nachmanson, George Robertson, Jonathan M. Carlson, David Heckerman

Bioinformatics | October 2009, Vol 25(19): pp. 2611-2612

Publication Publication

HLA-Associated Immune Escape Pathways in HIV-1 Subtype B Gag, Pol and Nef Proteins

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 Kadie, Nicole Frahm, Christian Brander, David W. Haas, Sharon Riddler, Richard Haubrich, Bruce D. Walker, P. Richard Harrigan, David Heckerman, Simon Mallal

August 2009

Publication

Unique Features of HLA-mediated HIV Evolution in a Mexican Cohort: A Comparative Study

Santiago Avila-Rios, Christopher E. Ormsby, Jonathan M. Carlson, Humberto Valenzuela-Ponce, Juan Blanco-Heredia, Daniela Garrido-Rodriguez, Claudia Garcia-Morales, David Heckerman, Zabrina L. Brumme, Simon Mallal, Mina John, Enrique Espinosa, Gustavo Reyes-Teran

Retrovirology | August 2009

Publication Publication

HLA-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection

Zabrina L. Brumme, Iris Tao, Sharon Szeto, Chanson J. Brumme, Jonathan M. Carlson, Dennison Chan, Carl Kadie, Nicole Frahm, Christian Brander, Bruce Walker, David Heckerman, P. Richard Harrigan

July 2009

Publication

HLA footprints on HIV-1 are associated with inter-clade polymorphisms and intra-clade phylogenetic clustering

Philippa C Matthews, Alasdair J Leslie, Aris Katzourakis, Hayley Crawford, Rebecca Payne, Andrew Prendergast, Karen Power, Anthony D Kelleher, Paul Klenerman, Jonathan M. Carlson, David Heckerman, Thumbi Ndung'u, Bruce D Walker, Todd M Allen, Oliver G Pybus, Philip J R Goulder

Journal of Virology | January 2009, pp. JVI.02017-08

Publication

Protective HLA class I Alleles That Restrict Acute-Phase CD8+ T-Cell Responses Are Associated with Viral Escape Mutations Located in Highly Conserved Regions of Human Immunodeficiency Virus Type 1

Yaoyu E. Wang, Bin Li, Jonathan M. Carlson, Hendrik Streeck, Adrianne D. Gladden, Robert Goodman, Arne Schneidewind, Karen A. Power, Ildiko Toth, Nicole Frahm, Galit Alter, Christian Brander, Mary Carrington, Bruce D. Walker, Marcus Altfeld, David Heckerman, Todd M. Allen

Journal of Virology | January 2009, Vol 83(4): pp. 1845-1855

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 Project

Central Role of Reverting Mutations in HLA Associations with Human Immunodeficiency Virus Set Point

Philippa C. Matthews, Andrew Prendergast, Alasdair Leslie, Hayley Crawford, Rebecca Payne, Christine Rousseau, Isobella Honeyborne, Jonathan M. Carlson, Carl Kadie, Christian Brander, Karen Bishop, Nonkululeko Mlotshwa, James I. Mullins, Hoosen Coovadia, Thumbi Ndung'u, Bruce D. Walker, David Heckerman, Philip J. Goulder

Journal of Virology | September 2008, Vol 82(17): pp. 8548-8559

Publication Publication

HIV evolution in response to HLA-restricted CTL selection pressures: a population-based perspective

Jonathan M. Carlson, Zabrina L. Brumme

Microbes and Infection | April 2008, Vol 10: pp. 455-461

Publication Publication

Human leukocyte antigen-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection

Zabrina L Brumme, Iris Tao, Sharon Szeto, Chanson J Brumme, Jonathan M. Carlson, Dennison Chan, Carl Kadie, Nicole Frahm, Christian Brander, Bruce Walker, David Heckerman, P. Richard Harrigan

AIDS | January 2008

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 Project

HLA Class I-Driven Evolution of Human Immunodeficiency Virus Type 1 Subtype C Proteome: immune Escape and Viral Load

Christine M. Rousseau, Marcus G. Daniels, Jonathan M. Carlson, Carl Kadie, Hayley Crawford, Andrew Prendergast, Philippa Matthews, Rebecca Payne, Morgane Rolland, Dana N. Raugi, Brandon S. Maust, Gerald H. Learn, David C. Nickle, Hoosen Coovadia, Thumbi Ndung'u, Nicole Frahm, Christian Brander, Bruce D. Walker, Philip J. R. Goulder, Tanmoy Bhattacharya, David Heckerman, Bette T. Korber, James I. Mullins

Journal of Virology | January 2008, Vol 82: pp. 6434-6446

Publication

Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients

Paul A. Goepfert, Wendy Lumm, Paul Farmer, Philippa Matthews, Andrew Prendergast, Jonathan M. Carlson, Cynthia A. Derdeyn, Jianming Tang, Richard A. Kaslow, Anju Bansal, Karina Yusim, David Heckerman, Joseph Mulenga, Susan Allen, Philip J. R. Goulder, Eric Hunter

Journal of Experimental Medicine | January 2008, Vol 205: pp. 1009-1017

Publication Publication

Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients

Thomas Kuntzen, Joerg Timm, Andrew Berical, Niall Lennon, Aaron M. Berlin, Sarah K. Young, Bongshin Lee, David Heckerman, Jonathan M. Carlson, Laura L. Reyor, Marianna Kleyman, Cory M. McMahon, Christopher Birch, Julian Schulze zur Wiesch, Timothy Ledlie, Michael Koehrsen, Chinnappa Kodira, Andrew D. Roberts, Georg M. Lauer, Hugo R. Rosen, Florian Bihl, Andreas Cerny, Ulrich Spengler, Zhimin Liu, Arthur Y. Kim, Yanming Xing, Arne Schneidewind, Margaret A. Madey, Jaquelyn F. Fleckenstein, Vicki M. Park, James E. Galagan, Chad Nusbaum, Bruce D. Walker, Gerond V. Lake-Bakaar, Eric S. Daar, Ira M. Jacobson, Edward D. Gomperts, Brian R. Edlin, Sharyne M. Donfield, Raymond T. Chung, Andrew H. Talal, Tony Marion, Bruce W. Birren, Matthew R. Henn, Todd M. Allen

Hepatology | January 2008, Vol 48: pp. 1769-1778

Publication

Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1

Zabrina L Brumme, Chanson J Brumme, David Heckerman, Bette T Korber, Marcus Daniels, 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, Jonathan M. Carlson

PLoS Pathogens | July 2007

Publication

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 Project

SCOPE: a web server for practical de novo motif discovery

Jonathan M. Carlson, Arijit Chakravarty, Rhadika S. Khetani, Charles E. DeZiel, Robert H. Gross

Nucleic Acids Research | July 2007, Vol 35: pp. W259-264

Publication

Founder Effects in the Assessment of HIV Polymorphisms and HLA Allele Associations

Tanmoy Bhattacharya, Marcus Daniels, David Heckerman, Brian Foley, Nicole Frahm, Carl Kadie, Jonathan M. Carlson, Karina Yusim, Ben McMahon, Brian Gaschen, Simon Mallal, James I. Mullins, David C. Nickle, Joshua Herbeck, Christine Rousseau, Gerald H. Learn, Toshiyuki Miura, Christian Brander, Bruce Walker, Bette Korber

Science | January 2007, Vol 315: pp. 1583-1586

Publication

A novel ensemble learning method for de novo computational identification of DNA binding sites

Arijit Chakravarty, Radhika Khetani, Robert Gross, Jonathan M. Carlson

BMC Bioinformatics | January 2007, pp. 249

Publication

SPACER: identification of cis-regulatory elements with non-contiguous critical residues

Arijit Chakravarty, Jonathan M. Carlson, Radhika S. Khetani, Charles E. DeZiel, Robert H. Gross

Bioinformatics | January 2007, Vol 23(8): pp. 1029-1031

Publication

Identifying the effects of human immune pressure on the evolution of HIV.

Jonathan M. Carlson, Carl Kadie, David Heckerman

December 2006

Publication

Creation of a Relational Database for Identifying Potential Functional DNA Sequence Motifs in A. thaliana and Other Genomes

Jonathan M. Carlson

June 2003

PhD Thesis: Undergraduate Honors thesis, Dept. Biology, Dartmouth College | June 2003

Dartmouth Kemeny Computing prize and Reed Biology Award

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 Project

Identifying HLA-Associated Polymorphisms in HIV-1

Zabrina L. Brumme, Art F. Y. Poon, Jonathan M. Carlson, Bruce D. Walker

HIV Molecular Immunology 2010 | January 2010

Publication

Central Role of Reverting Mutations in HLA Associations with Human Immunodeficiency Virus Set Point

Philippa C. Matthews, Andrew Prendergast, Alasdair Leslie, Hayley Crawford, Rebecca Payne, Christine Rousseau, Isobella Honeyborne, Jonathan M. Carlson, Carl Kadie, Christian Brander, Karen Bishop, Nonkululeko Mlotshwa, James I. Mullins, Hoosen Coovadia, Thumbi Ndung'u, Bruce D. Walker, David Heckerman, Philip J. Goulder

Journal of Virology | September 2008, Vol 82(17): pp. 8548-8559

Publication Publication

Estimating false discovery rates for contingency tables

Jonathan M. Carlson, David Heckerman, Guy Shani

MSR-TR-2009-53 | May 2009

Publication

Det. (Distance Encoded Tree): A Scalable Visualization Tool for Mapping Multiple Traits to Large Evolutionary Trees

Bongshin Lee, Lev Nachmanson, George Robertson, Jonathan M. Carlson, David Heckerman

MSR-TR-2008-97 | July 2008

Publication

Genetic Characterization of Human Immunodeficiency Virus type 1 in Elite Controllers: Lack of gross genetic defects or common amino acid changes

Toshiyuki Miura, Mark A. Brockman, Chanson J. Brumme, Zabrina L. Brumme, Jonathan M. Carlson, Florencia Pereyra, Alicja Trocha, Marylyn M. Addo, Brian L. Block, Alissa C. Rothchild, Brett M. Baker, Theresa Flynn, Arne Schneidewind, Bin Li, Yaoyu E. Wang, David Heckerman, Todd M. Allen, Bruce D. Walker

Journal of Virology | January 2008, pp. JVI.00535-8

Publication Publication Publication

Bounded search for de novo identification of degenerate cis-regulatory elements

Arijit Chakravarty*, Radhika Khetani, Robert Gross, Jonathan M. Carlson

BMC Bioinformatics | January 2006, Vol 7: pp. 254

Publication

BEAM: A Beam Search Algorithm for the Identification of Cis-Regulatory Elements in Groups of Genes

Arijit Chakravarty*, Robert H. Gross, Jonathan M. Carlson

Journal of Computational Biology | January 2006, Vol 13: pp. 686-701

PMID: 16706719

Publication

T-cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibody titers and disease severity

Rebecca Elyanow, Thomas M. Snyder, Sudeb C. Dalai, Rachel M. Gittelman, Boonyaratanakornkit J, Wald A, Selke S, Wener Mh, Morishima C, Greninger Al, Michael Gale, Tien-Ying Hsiang, Lichen Jing, Holbrook Mr, Ian M. Kaplan, Damon H May, H. Jabran Zahid, Jonathan M. Carlson, Lance Baldo, Thomas Manley, Harlan S Robins, David M Koelle

JCI Insight | April 2022, Vol 7(10)

DOI Preprint Publication Project Project Project

Longitudinal analysis of T cell receptor repertoires reveals shared patterns of antigen-specific response to SARS-CoV-2 infection

Rachel M Gittelman, Enrico Lavezzo, Thomas M Snyder, H. Jabran Zahid, Cara L Carty, Rebecca Elyanow, Sudeb Dalai, Ilan Kirsch, Lance Baldo, Laura Manuto, Elisa Franchin, Claudia Del Vecchio, Monia Pacenti, Caterina Boldrin, Margherita Cattai, Francesca Saluzzo, Andrea Padoan, Mario Plebani, Fabio Simeoni, Jessica Bordini, Nicola I Lorè, Dejan Lazarević, Daniela M Cirillo, Paolo Ghia, Stefano Toppo, Jonathan M. Carlson, Harlan S Robins, Andrea Crisanti, Giovanni Tonon

JCI Insight | April 2022, Vol 7(10)

DOI Publication Project Project

Immunosequencing of the T-cell receptor repertoire reveals signatures specific for diagnosis and characterization of early Lyme disease

Julia Greissl, Mitch Pesesky, Sudeb C. Dalai, Alison W. Rebman, Mark J. Soloski, Elizabeth J. Horn, Jennifer N. Dines, Rachel M. Gittelman, Thomas M. Snyder, Ryan O. Emerson, Ted Meeds, Thomas Manley, Ian M. Kaplan, Lance Baldo, Jonathan M. Carlson, Harlan S. Robins, John N. Aucott

medRxiv | August 2021

DOI PDF Publication Project

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

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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)

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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

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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

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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

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Diagnosis and Tracking of Past SARS-CoV-2 Infection in a Large Study of Vo’, Italy Through T-Cell Receptor Sequencing

Rachel M Gittelman, Enrico Lavezzo, Thomas M Snyder, H Jabran Zahid, Rebecca Elyanow, Sudeb Dalai, Ilan Kirsch, Lance Baldo, Laura Manuto, Elisa Franchin, Claudia Del Vecchio, Fabio Simeoni, Jessica Bordini, Nicola I LorÃ, Dejan Lazarevic, Daniela M Cirillo, Paolo Ghia, Stefano Toppo, Jonathan M. Carlson, Harlan S Robins, Giovanni Tonon, Andrea Crisanti

medRxiv | November 2020

Updated February 11, 2021

DOI 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

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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

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Magnitude and Dynamics of the T-Cell Response to SARS-CoV-2 Infection at Both Individual and Population Levels

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 N 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, Julia Greissl, Lance Baldo, Simona Semprini, Claudio Cerchione, Massimiliano Mazza, Ottavia M Delmonte, Kerry Dobbs, 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, James R Heath, Helen C Su, Luigi D Notarangelo, Joaquin Martinez-Lopez, Jonathan M. Carlson, Harlan S Robins

medRxiv | August 2020

Updated September 17, 2020

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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)

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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

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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 Project

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

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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

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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

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Elevated HLA-A expression impairs HIV control through inhibition of NKG2A-expressing cells.

Veron Ramsuran, Vivek Naranbhai, Amir Horowitz, Ying Qi, Maureen P. Martin, Yuko Yuki, Xiaojiang Gao, Victoria Walker-Sperling, Gregory Q. Del Prete, Douglas K. Schneider, Jeffrey D. Lifson, Jacques Fellay, Steven G. Deeks, Jeffrey N. Martin, James J. Goedert, Steven M. Wolinsky, Nelson L. Michael, Gregory D. Kirk, Susan Buchbinder, David Haas, Thumbi Ndung’u, Philip Goulder, Peter Parham, Bruce D. Walker, Jonathan M. Carlson, Mary Carrington

Science | January 2018, Vol 359: pp. 86-90

Publication 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

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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

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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

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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

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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

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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 Project

Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus

Damien C. Tully, Colin B. Ogilvie, Rebecca E. Batorsky, David J. Bean, Karen A. Power, Musie Ghebremichael, Hunter E. Bedard, Adrianne D. Gladden, Aaron M. Seese, Molly A. Amero, Kimberly Lane, Graham McGrath, Suzane B. Bazner, Jake Tinsley, Niall J. Lennon, Matthew R. Henn, Zabrina L. Brumme, Philip J. Norris, Eric S. Rosenberg, Kenneth H. Mayer, Heiko Jessen, Sergei L. Kosakovsky Pond, Bruce D. Walker, Marcus Altfeld, Todd M. Allen, Jonathan M. Carlson

PLoS Pathogens | May 2016

Publication Publication

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

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A strong association of human leukocyte antigen-associated Pol and Gag mutations with clinical parameters in HIV-1 subtype A/E infection.

Giang Van Tran, Takayuki Chikata, Jonathan M. Carlson, Hayato Murakoshi, Dung Hoai Nguyen, Yoshiko Tamura, Tomohiro Akahoshi, Nozomi Kuse, Keiko Sakai, Sachiko Sakai, Kyle Cobarrubias, Shinichi Oka, Zabrina L Brumme, Kinh Van Nguyen, Masafumi Takiguchi

AIDS | March 2016, Vol 30: pp. 681-689

Publication Publication

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

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Population-Level Immune-Mediated Adaptation in HIV-1 Polymerase during the North American Epidemic

Natalie N Kinloch, Daniel R MacMillan, Anh Q Le, Laura A Cotton, David R Bangsberg, Susan Buchbinder, Mary Carrington, Jonathan Fuchs, P Richard Harrigan, Beryl Koblin, Margot Kushel, Martin Markowitz, Kenneth Mayer, MJ Milloy, Martin T Schechter, Theresa Wagner, Bruce D Walker, Jonathan M. Carlson, Art FY Poon, Zabrina L Brumme

Journal of Virology | November 2015, Vol 90: pp. 1244-1258

Publication Publication

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 Africa

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

Plos Medicine | November 2015

Publication Publication

Enhanced Recognition of HIV-1 Cryptic Epitopes Restricted by HLA Class I Alleles Associated With a Favorable Clinical Outcome.

Anju Bansa, Tiffanie Mann, Sarah Sterrett, Binghao J Peng, Anne Bet, Jonathan M. Carlson, Paul A Goepfert

Journal of Acquired Immune Deficiency Syndromes | September 2015

Publication Publication

HLA Class-II Associated HIV Polymorphisms Predict Escape from CD4+ T Cell Responses

Nathan Erdmann, Victor Y. Du, Jonathan M. Carlson, Malinda Schaefer, Alexander Jureka, Sarah Sterrett, Ling Yue, Dario Dilernia, Shabir Lakhi, Jianming Tang, John Sidney, Jill Gilmour, Susan Allen, Eric Hunter, Sonya Heath, Anju Bansal, Paul A. Goepfert

PLoS Pathog | August 2015

Publication Publication

Prevalence and Characteristics of Hepatitis B Virus (HBV) Coinfection among HIV-Positive Women in South Africa and Botswana

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

July 2015

Publication Publication

HLA-A is a Predictor of Hepatitis B e Antigen Status in HIV-Positive African Adults

Philippa C Matthews, Jonathan M. Carlson, Apostolos Beloukas, Amna Malik, Pieter Jooste, Anthony Ogwu, Roger Shapiro, Lynn Riddell, Fabian Chen, Graz Luzzi, Gerald Jesuthasan, Katie Jeffery, Nebojsa Jojic, Thumbi Ndung'u, Mary Carrington, Philip JR Goulder, Anna Maria Geretti, Paul Klenerman

The Journal of Infectious Diseases | July 2015, Vol 213: pp. 1248-1252

Publication Publication

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

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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

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Immune screening identifies novel T cell targets encoded by anti-sense reading frames of HIV-1

Christopher T. Berger, Anuska Llano, Jonathan M. Carlson, Zabrina L. Brumme, Mark A. Brockman, Samandhy Cedeno, P. Richard Harrigan, Daniel E. Kaufmann, David Heckerman, Andreas Meyerhans, Christian Brander

Journal of virology | April 2015, Vol 89: pp. 4015-4019

Publication Publication

Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial

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, Meera Bose, 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, SL Pond, Jonathan M. Carlson, Nelson L Michael, William R Schief, James I Mullins, Jerome H Kim , Peter B Gilbert

PLOS Computational Biology | February 2015

Publication Publication

A molecular switch in immunodominant HIV-1-specific CD8 T-cell epitopes shapes differential HLA-restricted escape

Henrik N Kløverpris, David K Cole, Anna Fuller, Jonathan M. Carlson, Konrad Beck, Andrea J Schauenburg, Pierre J Rizkallah, Søren Buus, Andrew K Sewel, Philip Goulder

Retrovirology | February 2015

Publication Publication

Nef-mediated down-regulation of CD4 and HLA class I in HIV-1 subtype C infection: Association with disease progression and influence of immune pressure

Jaclyn K Mann, Denis Chopera, Saleha Omarjee, Xiaomei T Kuang, Anh Q Le, Gursev Anmole, Ryan Danroth, Philip Mwimanzi, Tarylee Reddy, Jonathan M. Carlson, Mopo Radebe, Philip JR Goulder, Bruce D Walker, Salim Abdool Karim, Vladimir Novitsky, Carolyn Williamson, Mark A Brockman, Zabrina L Brumme, Thumbi Ndung'u

Virology | November 2014, pp. 214-225

Publication Publication

CD8 and CD4 Epitope Predictions in RV144: No Strong Evidence of a T-Cell Driven Sieve Effect in HIV-1 Breakthrough Sequences from Trial Participants

Kalpana Dommaraju, Gustavo Kijak, Jonathan M. Carlson, Brendan B Larsen, Sodsai Tovanabutra, Dan E Geraghty, Wenjie Deng, Brandon S Maust, Paul T Edlefsen, Eric Sanders-Buell, Silvia Ratto-Kim, Supachai Rerks-Ngarm, Sorachai Nitayaphan, Punnee Pitisuttihum, Jaranit Kaewkungwal, Robert J O'Connell, Merlin L Robb, Nelson L Michael, James I Mullins, Jerome H Kim, Morgane Rolland

PLoS One | October 2014

Publication Publication

Early immune adaptation in HIV-1 revealed by population-level approaches

Eric Martin, Jonathan M. Carlson, Anh Q Le, Denis R Chopera, Rachel McGovern, Manal A Rahman, Carmond Ng, Heiko Jessen, Anthony D Kelleher, Martin Markowitz, Todd M Allen, MJ Milloy, Mary Carrington, Mark A Wainberg, Zabrina L Brumme

Retrovirology | August 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

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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)

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Differential Escape Patterns within the Dominant HLA-B*57:03-Restricted HIV Gag Epitope Reflect Distinct Clade-Specific Functional Constraints

Payne RP, Branch S, Kloverpris H, Matthews PC, Koofhethile K, Strong T, Adland E, Frater J, Ndung'u T, Hunter E, Haubrich R, Harrigan PR, Brumme ZL, Mallal S, John M, Jooste P, Shapiro R, Walker BD, Jonathan M. Carlson, Landis C, Prado JG, Goulder PJ

Journal of Virology | May 2014

Publication Publication

Genotypic and Functional Impact of HIV-1 Adaptation to Its Host Population during the North American Epidemic

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 FY Poon , Zabrina L Brumme

PLoS Genet | April 2014

Publication Publication

Host-Specific Adaptation of HIV-1 Subtype B in the Japanese Population

Takayuki Chikata, Jonathan M. Carlson, Yoshiko Tamura, Mohamed Ali Borghan, Takuya Naruto, Masao Hashimoto, Hayato Murakoshi, Anh Q. Le, Simon Mallal, Mina John, Hiroyuki Gatanaga, Shinichi Oka, Zabrina L. Brumme , Masafumi Takiguchi

Journal of Virology | March 2014, Vol 88(9): pp. 4764-4775

Publication Publication

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

Jennifer Listgarten, Christoph Lippert, Nicolo Fusi, David Heckerman, Jonathan M. Carlson

eLife | October 2013

Publication

Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection

Akihisa Shimizu, Ai Kawana-Tachikawa, Atsushi Yamagata, Chung Yong Han, Dayong Zhu, Yusuke Sato, Hitomi Nakamura, Tomohiko Koibuchi, Jonathan M. Carlson, Eric Martin, Chanson Brumme, Yi Shi, George Gao, Zabrina L Brumme, Shuya Fukai, Aikichi Iwamoto

Scientific Reports | October 2013

Publication Publication

Nef-Specific CD8+ T Cell Responses Contribute to HIV-1 Immune Control

Emily Adland, Jonathan M. Carlson, Paolo Paioni, Henrik Kloverpris, Roger Shapiro, Anthony Ogwu, Lynn Riddell, Graz Luzzi, Fabian Chen, Thambiah Balachandran, David Heckerman, Anette Stryhn, Anne Edwards, Thumbi Ndung'u, Bruce D Walker, Soren Buus, Philip Goulder , Philippa C Matthews

PloS One | September 2013

Publication Publication

Increased Sequence Coverage through Combined Targeting of Variant and Conserved Epitopes Correlates with Control of HIV Replication

Justine Sunshine, Moon Kim, Jonathan M. Carlson, David Heckerman, Julie Czartoski, Stephen A. Migueles, Janine Maenza, M. Juliana McElrath, James I. Mullins, Nicole Frahm

Journal of Virology | August 2013, Vol 88(2): pp. 1354-1365

Publication Publication

HLA-A*68: 02-restricted Gag-specific cytotoxic T lymphocyte responses can drive selection pressure on HIV but are subdominant and ineffective

Henrik N. Klverpris, Anette Stryhn, Mikkel Harndahl, Jonathan M. Carlson, Alasdair J. Leslie, Fabian Chen, Lynn Riddell, Joseph Mulenga, Bruce D. Walker, Thumbi N'dung'u, Soren Buus , Philip Goulder

AIDS Official Journal of the International Aids Society | July 2013

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

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HIV escape mutations occur preferentially at HLA-binding sites of CD8 T-cell epitopes

Corine Bronke, Coral-Ann M. Almeida, Elizabeth McKinnon, Steven G. Roberts, Niamh M. Keane, Abha Chopra, Jonathan M. Carlson, David Heckerman, Simon Mallal, Mina John

AIDS, Basic Science | March 2013, Vol 27(6): pp. 899-905

Publication Publication

Distinct HIV-1 Escape Patterns Selected by Cytotoxic T Cells with Identical Epitope Specificity

Yuichi Yagitaa, Nozomi Kusea, Kimiko Kurokib, Hiroyuki Gatanagaa, Jonathan M. Carlson, Takayuki Chikataa, Zabrina L. Brummee, Hayato Murakoshia, Tomohiro Akahoshia, Nico Pfeiferd, Simon Mallalg, Mina Johng, Toyoyuki Oseb, Haruki Matsubarab, Ryo Kandab, Yuko Fukunagab, Kazutaka Hondaa, Yuka Kawashimaa, Yasuo Ariumia, Shinichi Okaa, Katsumi Maenakab, Masafumi Takiguchia

Journal of Virology | February 2013

Publication Publication

Frequent and Variable Cytotoxic-T-Lymphocyte Escape-Associated Fitness Costs in the Human Immunodeficiency Virus Type 1 Subtype B Gag Proteins

Christian L Boutwell, Jonathan M. Carlson, Tien-Ho Lin, Aaron Seese, Karen A Power, Jian Peng, Yanhua Tang, Zabrina L Brumme, David Heckerman, Arne Schneidewind, Todd M Allen

January 2013

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 Project

Differential Clade-Specific HLA-B*3501 Association with HIV-1 Disease Outcome Is Linked to Immunogenicity of a Single Gag Epitope

Philippa C. Matthews, Madoka Koyanagi, Henrik N. Kloverpris, Mikkel Harndahl, Anette Stryhn, Tomohiro Akahoshi, Hiroyuki Gatanaga, Shinichi Oka, Claudia Juarez Molina, Humberto Valenzuela Ponce, Santiago Avila Rios, David Cole, Jonathan M. Carlson, Rebecca P. Payne, Anthony Ogwu, Alfred Bere, Thumbi Ndung'u, Kamini Gounder, Fabian Chen, Lynn Riddell, Graz Luzzi, Roger Shaprio, Christian Brander, Bruce Walker, Andrew K. sewell, Gustavo Reyes Teran, David Heckerman, Eric Hunter, Soren Buus, Masafumi Takiguchi, Philip J.R. Goulder

Journal of Virololgy | December 2012, Vol 86(23): pp. 12643-12654

Publication Publication

Significant Reductions in Gag-Protease-Mediated HIV-1 Replication Capacity during the Course of the Epidemic in Japan

Shigeru Nomura, Noriaki Hosoya, Zabrina L. Brumme, Mark A. Brockman, Tadashi Kikuchi, Michiko Koga, Hitomi Nakamura, Tomohiko Koibuchi, Takeshi Fujii, Jonathan M. Carlson, David Heckerman, Ai Kawana-Tachikawa, Aikichi Iwamoto, Toshiyuki Miura

Journal of Virology | November 2012, Vol 87(3): pp. 1465-1476

Publication Publication

Role of Transmitted Gag CTL Polymorphisms in Defining Replicative Capacity and Early HIV-1 Pathogenesis

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 Geopfert, Matthew A. Price, Jill Gilmour, Joseph Mulenga, Paul Farmer, Cynthia A. Derdeyn, Jiaming Tang, David Heckerman, Richard A. Kaslow, Susan A. Allen, Eric Hunter

PLoS Pathogens | November 2012, pp. e1003041

Publication Publication

Co-operative additive effects between HLA alleles in control of HIV-1

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

PLoS ONE | October 2012, pp. e47799

Publication Publication

Intersubtype differences in the effect of a rare p24 Gag mutation on HIV-1 replicative fitness

Denis R. Chopera, Laura A. Cotton, Alexander Zawaira, Jaclyn K. Mann, Nobubelo K. Ngandu, Roman Ntale, Jonathan M. Carlson, Koleka Mlisana, Zenda Woodman, Debra de Assis Rosa, Eric Martin, Toshiyuki Miura, Florencia Pereyra, Bruce D. Walker, Clive M. Gray, Darren P. Martin, Thumbi Ndung'u, Mark A. Brockman, Salim Abdool Karim, Zabrina L. Brumme, Carolyn Williamson

Journal of Virology | September 2012

Publication Publication

HIV Control through a Single Nucleotide on the HLA-B Locus

Henrik N. Kloverpris, Mikkel Harndahl, Alasdair J. Leslie, Jonathan M. Carlson, Nasreen Ismail, Mary van der Stok, Kuan-Hsiang Gary Huang, Fabian Chen, Lynn Riddell, Dewald Steyn, Dominique Goedhals, Cloete van Vuuren, John Frater, Bruce D. Walker, Mary Carrington, Thumbi Ndung'u, Soren Buus, Philip Goulder

Journal of Virology | August 2012

Publication Publication

Aminopeptidase Substrate Preference Affects HIV Epitope Presentation and Predicts Immune Escape Patterns in HIV-Infected Individuals

Shao Chong Zhang, Eric Martin, Mariko Shimada, Sasha Blue Godfrey, Jennifer Fricke, Shirley Locastro, Nicole Y Lai, Paul Liebesny, Jonathan M. Carlson, Chanson J Brumme, Oluwatobi Awele Ogbechie, Huabiao Chen, Bruce D Walker, Zabrina L Brumme, Daniel G Kavanagh, Sylvie Le Gall

The Journal of Immunology | June 2012

Publication Publication

Minor contribution of HLA class I-associated selective pressure to the variability of HIV-1 accessory protein Vpu

Zafrul Hasan, Jonathan M. Carlson, Hiroyuki Gatanaga, Anh Le, Chanson J Brumme, Shinichi Oka, Zabrina L Brumme , Takamasa Ueno

May 2012

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 Project

Uncommon Pathways of Immune Escape Attenuate HIV-1 Integrase Replication Capacity

Mark A. Brockman, Denis R. Chopera, Alex Olvera, Chanson J. Brumme, Jennifer Sela, Tristan J. Markle, Eric Martin, Jonathan M. Carlson, Anh Q. Le, Rachel McGovern, Peter K. Cheung, Anthony D. Kelleher, Heiko Jessen, Martin Markowitz, Eric Rosenberg, Nicole Frahm, Jorge Sanchez, Simon Mallal, Mina John, P. Richard Harrigan, David Heckerman, Christian Brander, Bruce D. Walker, Zabrina L. Brumme

Journal of Virology | April 2012

Publication Publication

Learning Transcriptional Regulatory Relationships Using Sparse Graphical Models

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

February 2012

Publication Publication Publication

High-avidity, high-IFNγ-producing CD8 T-cell responses following immune selection during HIV-1 infection

Niamh M. Keane, Stevens G. Roberts, Coral-Ann M. Almedia, Tanya Krishnan, Abha Chopra, Emma Demaine, Rebecca Laird, Monika Tschochner, Jonathan M. Carlson, Simon Mallal, David Heckerman, Ian James, Mina John

Immunology and Cell Biology | February 2012, Vol 90(2): pp. 224-234

Publication Publication

Lack of Association between HLA Class II Alleles and In Vitro Replication Capacities of Recombinant Viruses Encoding HIV-1 Subtype C Gag-Protease from Chronically Infected Individuals

Jaclyn K. Wright, Zabrina L. Brumme, Boris Julg, Mary van der Stok, Zenele Mncube, Xiaojiang Gao, Jonathan M. Carlson, Philip J. R. Goulder, Bruce D. Walker, Mark A. Brockman, Thumbi Ndung'u

Journal of Virology | November 2011

Publication Publication

Translation of HLA-HIV Associations to the Cellular Level: HIV Adapts To Inflate CD8 T Cell Responses against Nef and HLA-Adapted Variant Epitopes

Coral-Ann M. Almeida, Corine Bronke, Steven G. Roberts, Elizabeth McKinnon, Niamh M. Keane, Abha Chopra, Carl Kadie, Jonathan M. Carlson, David W. Haas, Sharon A. Riddler, Richard Haubrich, David Heckerman, Simon Mallal , Mina John

The Journal of Immunology | September 2011

Publication Publication

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 Project

Progression to AIDS in South Africa Is Associated with both Reverting and Compensatory Viral Mutations

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, Bloemfotnein-Oxford Collaborative Group, Cloete van Vuuren, John Frater

April 2011

Publication Publication

HLA-A*7401-Mediated Control of HIV Viremia Is Independent of Its Linkage Disequilibrium with HLA-B*5703

Philippa C. Matthews, Emily Adland, Jennifer Listgarten, Alasdair Leslie, Nompumelelo Mkhwanazi, Jonathan M. Carlson, Mikkel Harndahl, Anette Stryhn, Rebecca P. Payne, Anthony Ogwu, Kuan-Hsiang Gary Huang, John Frater, Paolo Paioni, Henrik Kolverpris, Pieter Jooste, Dominique Goedhals, Cloete van Vuuren, Dewald Steyn, Lynn Riddell, Fabian Chen, Graz Luzzi, Thambiah Balachandran, Thumbi Ndung'u, Soren Buus, Mary Carrington, Roger Shapiro, David Heckerman, Philip J. R. Goulder

The Journal of Immunology | April 2011

Publication Publication

Influence of Gag-Protease-Mediated Replication Capacity on Disease Progression in Individuals Recently Infected with HIV-1 Subtype C

Jaclyn K. Wright, Vladimir Novitsky, Mark A. Brockman, Zabrina L. Brumme, Chanson J. Brumme, Jonathan M. Carlson, David Heckerman, Bingxia Wang, Elena Losina, Mopo Leshwedi, Mary van der Stok, Lungile Maphumulo, Nompumelelo Mkhwanazi, Fundisiwe Chonco, Philip J. R. Goulder, Max Essex, Bruce D. Walker, Thumbi Ndung'u

February 2011

Publication Publication

The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation

Jonathan M. Carlson, The International HIV Controllers Study

Science | December 2010

Publication Publication

The hypervariable HIV-1 capsid protein residues comprise HLA-driven CD8+ T-cell escape mutations and covarying HLA-independent polymorphisms

Hayley Crawford, Philippa C. Matthews, Malinda Schaefer, Jonathan M. Carlson, Alasdair Leslie, William Kilembe, Susan Allen, Thumbi Ndung'u, David Heckerman, Eric Hunter, Philip J. R. Goulder

Journal of Virology | November 2010

Publication Publication

Early Selection in Gag by Protective HLA Alleles Contributes to Reduced HIV-1 Replication Capacity That May Be Largely Compensated for in Chronic Infection

Mark A Brockman, Zabrina L Brumme, Chanson J Brumme, Toshiyuki Miura, Jennifer Sela, Pamela C Rosato, Carl Kadie, Jonathan M. Carlson, Tristan J Markle, Hendrik Streeck, Anthony D Kelleher, Martin Markowitz, Heiko Jessen, Eric Rosenberg, Marcus Altfeld, P Richard Harrigan, David Heckerman, Bruce D Walker, Todd M Allen

Journal of Virology | November 2010, Vol 84(22): pp. 11937-11949

Publication Publication

Gag-Protease-Mediated Replication Capacity in HIV-1 1 Subtype C Chronic Infection: Associations with HLA Type and Clinical Parameters

Jaclyn K. Wright, Zabrina L. Brumme, Jonathan M. Carlson, David Heckerman, Carl Kadie, Chanson J. Brumme, Bingxia Wang, Elena Losina, Toshiyuki Miura, Fundisiwe Chonco, Mary van der Stok, Zenele Mncube, Karen Bishop, Philip J.R. Goulder , Bruce D. Walker, Mark A. Brockman, Thumbi Ndung'u

Journal of Virology | October 2010

Publication Publication Publication

Amino-Acid Co-Variation in HIV-1 Gag Subtype C: HLA-Mediated Selection Pressure and Compensatory Dynamics

Morgane Rolland, Jonathan M. Carlson, Siriphan Manocheewa, J. Victor Swain, Erinn Lanxon-Cookson, Wenjie Deng, Christine M. Rousseau, Dana N. Raugi, Gerald H. Learn, Brandon S. Maust, Hoosen Coovadia, Thumbi Ndung'u, Philip J. R. Goulder, Bruce D. Walker, Christian Brander, David Heckerman, James I. Mullins

PLoS ONE | September 2010, pp. e12463

Publication Publication

Adaptive Interactions between HLA and HIV-1: Highly Divergent Selection Imposed by HLA Class I Molecules with Common Supertype Motifs

Mina John, David Heckerman, Ian James, Lawrence P. Park, Jonathan M. Carlson, Abha Chopra, Silvana Gaudieri, David Nolan, David W. Haas, Sharon A. Riddler, Richard Haubrich, Simon Mallal

The Journal of Immunology | March 2010, Vol 184(8): pp. 4368-4377

Publication Publication

Additive Contribution of HLA Class I Alleles in the Immune Control of HIV-1 Infection

Alasdair Leslie, Philippa C. Matthews, Jennifer Listgarten, Jonathan M. Carlson, Carl Kadie, Thumbi Ndung'u, Christian Brander, Hoosen Coovadia, Bruce D. Walker, David Heckerman, Philip J. R. Goulder

Journal of Virology | February 2010, Vol 84(19): pp. 9879-9888

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 Project

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 Project

Identifying HLA-Associated Polymorphisms in HIV-1

Zabrina L. Brumme, Art F. Y. Poon, Jonathan M. Carlson, Bruce D. Walker

HIV Molecular Immunology 2010 | January 2010

Publication

PhyloDet: A Scalable Visualization Tool for Mapping Multiple Traits to Large Evolutionary Trees

Bongshin Lee, Lev Nachmanson, George Robertson, Jonathan M. Carlson, David Heckerman

Bioinformatics | October 2009, Vol 25(19): pp. 2611-2612

Publication Publication

HLA-Associated Immune Escape Pathways in HIV-1 Subtype B Gag, Pol and Nef Proteins

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 Kadie, Nicole Frahm, Christian Brander, David W. Haas, Sharon Riddler, Richard Haubrich, Bruce D. Walker, P. Richard Harrigan, David Heckerman, Simon Mallal

August 2009

Publication

Unique Features of HLA-mediated HIV Evolution in a Mexican Cohort: A Comparative Study

Santiago Avila-Rios, Christopher E. Ormsby, Jonathan M. Carlson, Humberto Valenzuela-Ponce, Juan Blanco-Heredia, Daniela Garrido-Rodriguez, Claudia Garcia-Morales, David Heckerman, Zabrina L. Brumme, Simon Mallal, Mina John, Enrique Espinosa, Gustavo Reyes-Teran

Retrovirology | August 2009

Publication Publication

HLA-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection

Zabrina L. Brumme, Iris Tao, Sharon Szeto, Chanson J. Brumme, Jonathan M. Carlson, Dennison Chan, Carl Kadie, Nicole Frahm, Christian Brander, Bruce Walker, David Heckerman, P. Richard Harrigan

July 2009

Publication

HLA footprints on HIV-1 are associated with inter-clade polymorphisms and intra-clade phylogenetic clustering

Philippa C Matthews, Alasdair J Leslie, Aris Katzourakis, Hayley Crawford, Rebecca Payne, Andrew Prendergast, Karen Power, Anthony D Kelleher, Paul Klenerman, Jonathan M. Carlson, David Heckerman, Thumbi Ndung'u, Bruce D Walker, Todd M Allen, Oliver G Pybus, Philip J R Goulder

Journal of Virology | January 2009, pp. JVI.02017-08

Publication

Protective HLA class I Alleles That Restrict Acute-Phase CD8+ T-Cell Responses Are Associated with Viral Escape Mutations Located in Highly Conserved Regions of Human Immunodeficiency Virus Type 1

Yaoyu E. Wang, Bin Li, Jonathan M. Carlson, Hendrik Streeck, Adrianne D. Gladden, Robert Goodman, Arne Schneidewind, Karen A. Power, Ildiko Toth, Nicole Frahm, Galit Alter, Christian Brander, Mary Carrington, Bruce D. Walker, Marcus Altfeld, David Heckerman, Todd M. Allen

Journal of Virology | January 2009, Vol 83(4): pp. 1845-1855

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 Project

Central Role of Reverting Mutations in HLA Associations with Human Immunodeficiency Virus Set Point

Philippa C. Matthews, Andrew Prendergast, Alasdair Leslie, Hayley Crawford, Rebecca Payne, Christine Rousseau, Isobella Honeyborne, Jonathan M. Carlson, Carl Kadie, Christian Brander, Karen Bishop, Nonkululeko Mlotshwa, James I. Mullins, Hoosen Coovadia, Thumbi Ndung'u, Bruce D. Walker, David Heckerman, Philip J. Goulder

Journal of Virology | September 2008, Vol 82(17): pp. 8548-8559

Publication Publication

HIV evolution in response to HLA-restricted CTL selection pressures: a population-based perspective

Jonathan M. Carlson, Zabrina L. Brumme

Microbes and Infection | April 2008, Vol 10: pp. 455-461

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 Project

HLA Class I-Driven Evolution of Human Immunodeficiency Virus Type 1 Subtype C Proteome: immune Escape and Viral Load

Christine M. Rousseau, Marcus G. Daniels, Jonathan M. Carlson, Carl Kadie, Hayley Crawford, Andrew Prendergast, Philippa Matthews, Rebecca Payne, Morgane Rolland, Dana N. Raugi, Brandon S. Maust, Gerald H. Learn, David C. Nickle, Hoosen Coovadia, Thumbi Ndung'u, Nicole Frahm, Christian Brander, Bruce D. Walker, Philip J. R. Goulder, Tanmoy Bhattacharya, David Heckerman, Bette T. Korber, James I. Mullins

Journal of Virology | January 2008, Vol 82: pp. 6434-6446

Publication

Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients

Paul A. Goepfert, Wendy Lumm, Paul Farmer, Philippa Matthews, Andrew Prendergast, Jonathan M. Carlson, Cynthia A. Derdeyn, Jianming Tang, Richard A. Kaslow, Anju Bansal, Karina Yusim, David Heckerman, Joseph Mulenga, Susan Allen, Philip J. R. Goulder, Eric Hunter

Journal of Experimental Medicine | January 2008, Vol 205: pp. 1009-1017

Publication Publication

Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients

Thomas Kuntzen, Joerg Timm, Andrew Berical, Niall Lennon, Aaron M. Berlin, Sarah K. Young, Bongshin Lee, David Heckerman, Jonathan M. Carlson, Laura L. Reyor, Marianna Kleyman, Cory M. McMahon, Christopher Birch, Julian Schulze zur Wiesch, Timothy Ledlie, Michael Koehrsen, Chinnappa Kodira, Andrew D. Roberts, Georg M. Lauer, Hugo R. Rosen, Florian Bihl, Andreas Cerny, Ulrich Spengler, Zhimin Liu, Arthur Y. Kim, Yanming Xing, Arne Schneidewind, Margaret A. Madey, Jaquelyn F. Fleckenstein, Vicki M. Park, James E. Galagan, Chad Nusbaum, Bruce D. Walker, Gerond V. Lake-Bakaar, Eric S. Daar, Ira M. Jacobson, Edward D. Gomperts, Brian R. Edlin, Sharyne M. Donfield, Raymond T. Chung, Andrew H. Talal, Tony Marion, Bruce W. Birren, Matthew R. Henn, Todd M. Allen

Hepatology | January 2008, Vol 48: pp. 1769-1778

Publication

Genetic Characterization of Human Immunodeficiency Virus type 1 in Elite Controllers: Lack of gross genetic defects or common amino acid changes

Toshiyuki Miura, Mark A. Brockman, Chanson J. Brumme, Zabrina L. Brumme, Jonathan M. Carlson, Florencia Pereyra, Alicja Trocha, Marylyn M. Addo, Brian L. Block, Alissa C. Rothchild, Brett M. Baker, Theresa Flynn, Arne Schneidewind, Bin Li, Yaoyu E. Wang, David Heckerman, Todd M. Allen, Bruce D. Walker

Journal of Virology | January 2008, pp. JVI.00535-8

Publication Publication Publication

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 Project

SCOPE: a web server for practical de novo motif discovery

Jonathan M. Carlson, Arijit Chakravarty, Rhadika S. Khetani, Charles E. DeZiel, Robert H. Gross

Nucleic Acids Research | July 2007, Vol 35: pp. W259-264

Publication

Founder Effects in the Assessment of HIV Polymorphisms and HLA Allele Associations

Tanmoy Bhattacharya, Marcus Daniels, David Heckerman, Brian Foley, Nicole Frahm, Carl Kadie, Jonathan M. Carlson, Karina Yusim, Ben McMahon, Brian Gaschen, Simon Mallal, James I. Mullins, David C. Nickle, Joshua Herbeck, Christine Rousseau, Gerald H. Learn, Toshiyuki Miura, Christian Brander, Bruce Walker, Bette Korber

Science | January 2007, Vol 315: pp. 1583-1586

Publication

A novel ensemble learning method for de novo computational identification of DNA binding sites

Arijit Chakravarty, Radhika Khetani, Robert Gross, Jonathan M. Carlson

BMC Bioinformatics | January 2007, pp. 249

Publication

SPACER: identification of cis-regulatory elements with non-contiguous critical residues

Arijit Chakravarty, Jonathan M. Carlson, Radhika S. Khetani, Charles E. DeZiel, Robert H. Gross

Bioinformatics | January 2007, Vol 23(8): pp. 1029-1031

Publication

Bounded search for de novo identification of degenerate cis-regulatory elements

Arijit Chakravarty*, Radhika Khetani, Robert Gross, Jonathan M. Carlson

BMC Bioinformatics | January 2006, Vol 7: pp. 254

Publication

BEAM: A Beam Search Algorithm for the Identification of Cis-Regulatory Elements in Groups of Genes

Arijit Chakravarty*, Robert H. Gross, Jonathan M. Carlson

Journal of Computational Biology | January 2006, Vol 13: pp. 686-701

PMID: 16706719

Publication

A large-scale database of T-cell receptor beta (TCRβ) sequences and binding associations from natural and synthetic exposure to SARS-CoV-2

Sean Nolan, Marissa Vignali, Mark Klinger, Jennifer N Dines, Ian M Kaplan, Emily Svejnoha, Tracy Craft, Katie Boland, Mitch Pesesky, Rachel M Gittelman, Thomas M Snyder, Christopher J Gooley, Simona Semprini, Claudio Cerchione, Massimiliano Mazza, Ottavia M Delmonte, Kerry Dobbs, Gonzalo Carreño-Tarragona, Santiago Barrio, Vittorio Sambri, Giovanni Martinelli, Jason D Goldman, James R Heath, Luigi D Notarangelo, Jonathan M. Carlson, Joaquin Martinez-Lopez, Harlan S Robins

August 2020

DOI Publication Publication Publication Publication Project Project

Creation of a Relational Database for Identifying Potential Functional DNA Sequence Motifs in A. thaliana and Other Genomes

Jonathan M. Carlson

June 2003

PhD Thesis: Undergraduate Honors thesis, Dept. Biology, Dartmouth College | June 2003

Dartmouth Kemeny Computing prize and Reed Biology Award

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 Project

Human leukocyte antigen-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection

Zabrina L Brumme, Iris Tao, Sharon Szeto, Chanson J Brumme, Jonathan M. Carlson, Dennison Chan, Carl Kadie, Nicole Frahm, Christian Brander, Bruce Walker, David Heckerman, P. Richard Harrigan

AIDS | January 2008

Publication Publication

Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1

Zabrina L Brumme, Chanson J Brumme, David Heckerman, Bette T Korber, Marcus Daniels, 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, Jonathan M. Carlson

PLoS Pathogens | July 2007

Publication

Identifying the effects of human immune pressure on the evolution of HIV.

Jonathan M. Carlson, Carl Kadie, David Heckerman

December 2006

Publication

Estimating false discovery rates for contingency tables

Jonathan M. Carlson, David Heckerman, Guy Shani

MSR-TR-2009-53 | May 2009

Publication

Det. (Distance Encoded Tree): A Scalable Visualization Tool for Mapping Multiple Traits to Large Evolutionary Trees

Bongshin Lee, Lev Nachmanson, George Robertson, Jonathan M. Carlson, David Heckerman

MSR-TR-2008-97 | July 2008

Publication