Jonathan M. Carlson

Managing Director, Health Futures

Papiers de Collaboration

Afficher par:

- Sequential Diagnosis with Language Models
  
  Harsha Nori, M. Daswani, Christopher Kelly, Scott M. Lundberg, Marco Túlio Ribeiro, Marc Wilson, Xiaoxuan Liu, V. Sounderajah, Jonathan M. Carlson, Matthew P Lungren, Bay Gross, Peter Hames, Mustafa Suleyman, Dominic King, Eric Horvitz
  
  July 2025
  
  DOI
- 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 Projet Projet Projet
- 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 Projet Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet
- Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein.
  
  Debra Van Egeren, Alexander Novokhodko, Madison Stoddard, Uyen Tran, Bruce Zetter, Michael Rogers, Bradley L. Pentelute, Jonathan M. Carlson, Mark Hixon, Diane Joseph-McCarthy, Arijit Chakravarty
  
  PLOS ONE | April 2021, Vol 16(4): pp. e0250780
  
  DOI Publication Publication Publication Publication Publication Publication Publication Projet Projet
- 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 Projet
- 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 Projet
- HLA tapasin independence: broader peptide repertoire and HIV control.
  
  Arman A. Bashirova, Mathias Viard, Vivek Naranbhai, Alba Grifoni, Wilfredo Garcia-Beltran, Marjan Akdag, Yuko Yuki, Xiaojiang Gao, Colm O’hUigin, Malini Raghavan, Steven Wolinsky, Jay H. Bream, Priya Duggal, Jeremy Martinson, Nelson L. Michael, Gregory D. Kirk, Susan P. Buchbinder, David Haas, James J. Goedert, Steven G. Deeks, Jacques Fellay, Bruce Walker, Philip Goulder, Peter Cresswell, Tim Elliott, Alessandro Sette, Jonathan M. Carlson, Mary Carrington
  
  Proceedings of the National Academy of Sciences of the United States of America | October 2020, Vol 117(45): pp. 28232-28238
  
  DOI PDF Publication Publication Publication Publication Publication Publication Publication Projet
- 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 Projet Projet
- 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 Projet
- CD8 T cells targeting adapted epitopes in chronic HIV infection promote dendritic cell maturation and CD4 T cell trans-infection.
  
  Kai Qin, Sushma Boppana, Victor Y. Du, Jonathan M. Carlson, Ling Yue, Dario A. Dilernia, Eric Hunter, Robbie B. Mailliard, Simon A. Mallal, Anju Bansal, Paul A. Goepfert
  
  PLOS Pathogens | August 2019, Vol 15(8)
  
  DOI PDF Publication Publication Publication Publication Publication Publication Publication Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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
  
  Publication Publication Publication Github Projet
- Brief Report: Selection of HIV-1 Variants With Higher Transmission Potential by 1% Tenofovir Gel Microbicide
  
  Nobubelo K. Ngandu, Jonathan M. Carlson, Denis R. Chopera, Nonkululeko Ndabamb, Quarraisha Abdool Karim, Salim Abdool Karim, Carolyn Williamson
  
  Journal of Acquired Immune Deficiency Syndromes | September 2017, Vol 76: pp. 43-47
  
  Publication Publication Publication Github Projet
- Mother-to-Child HIV Transmission Bottleneck Selects for Consensus Virus with Lower Gag-Protease-Driven Replication Capacity
  
  Vanessa L. Naidoo, Jaclyn K. Mann, Christie Noble, Emily Adland, Jonathan M. Carlson, Jake Thomas, Chanson J. Brumme, Christina F. Thobakgale-Tshabalala, Zabrina L. Brumme, Mark A. Brockman, Philip J. R. Goulder, Thumbi Ndung'u
  
  Journal of Virology | September 2017, Vol 91: pp. e00518-17
  
  Publication Publication Github Projet
- PARV4 prevalence, phylogeny, immunology and coinfection with HIV, HBV and HCV in a multicentre African cohort
  
  Colin P. Sharp, William F. Gregory, Louise Hattingh, Amna Malik, Emily Adland, Samantha Daniels, Anriette van Zyl, Jonathan M. Carlson, Susan Wareing, Anthony Ogwu, Roger Shapiro, Lynn Riddell, Fabian Chen, Thumbi Ndung'u, Philip J.R. Goulder, Paul Klenerman, Peter Simmonds, Pieter Jooste, Philippa C. Matthews
  
  Wellcome Open Research | April 2017, Vol 2: pp. 26
  
  Publication Publication Publication Github Projet
- Paediatric non-progression following grandmother-to-child HIV transmission
  
  M.-H. Tsai, M. Muenchhof, E. Adland, A. Carlqvist, J. Roider, D. K. Cole, A. K. Sewell, Jonathan M. Carlson, T. Ndung’u, P. J. R. Goulder
  
  Retrovirology | September 2016, Vol 13: pp. 65
  
  Publication Publication Publication Github Projet
- 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 Projet
- 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
  
  Publication Publication Github Projet
- 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
  
  Publication Publication Publication Github Projet
- 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
  
  Publication Publication Github Projet
- 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 Projet
- 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 Projet
- 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 Projet
- Selection Bias at the Heterosexual HIV-1 Transmission Bottleneck
  
  Jonathan M. Carlson, Malinda Schaefer, Daniela C. Monaco, Rebecca Batorsky, Daniel T. Claiborne, Jessica Prince, Martin J. Deymier, Zachary S. Ende, Nichole R. Klatt, Charles E. DeZiel, Tien-Ho Lin, Jian Peng, Aaron M. Seese, Roger Shapiro, John Frater, Thumbi Ndung'u, Jianming Tang, Paul Goepfert, Jill Gilmour, Matt A. Price, William Kilembe, David Heckerman, Philip J. R. Goulder, Todd M. Allen, Susan Allen, Eric Hunter
  
  Science | July 2014, Vol 345(6193)
  
  Publication Publication Publication Publication Publication Projet
- 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
- 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 Projet
- 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 Projet
- 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
- 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 Projet
- 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-IFNÎ³-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
- 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 Projet
- 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
- 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
- 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 Projet
- 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 Projet
- 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 Projet
- 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
- 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 Projet
- Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naÃ¯ve 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 Projet
- 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
  
  Thèse de doctorat : Undergraduate Honors thesis, Dept. Biology, Dartmouth College | June 2003
  
  Dartmouth Kemeny Computing prize and Reed Biology Award
  
  Publication

- Sequential Diagnosis with Language Models
  
  Harsha Nori, M. Daswani, Christopher Kelly, Scott M. Lundberg, Marco Túlio Ribeiro, Marc Wilson, Xiaoxuan Liu, V. Sounderajah, Jonathan M. Carlson, Matthew P Lungren, Bay Gross, Peter Hames, Mustafa Suleyman, Dominic King, Eric Horvitz
  
  July 2025
  
  DOI
- Sequential Diagnosis with Language Models
  
  Harsha Nori, M. Daswani, Christopher Kelly, Scott M. Lundberg, Marco Túlio Ribeiro, Marc Wilson, Xiaoxuan Liu, V. Sounderajah, Jonathan M. Carlson, Matthew P Lungren, Bay Gross, Peter Hames, Mustafa Suleyman, Dominic King, Eric Horvitz
  
  July 2025
  
  DOI
- 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 Projet Projet Projet
- 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 Projet Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet
- Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein.
  
  Debra Van Egeren, Alexander Novokhodko, Madison Stoddard, Uyen Tran, Bruce Zetter, Michael Rogers, Bradley L. Pentelute, Jonathan M. Carlson, Mark Hixon, Diane Joseph-McCarthy, Arijit Chakravarty
  
  PLOS ONE | April 2021, Vol 16(4): pp. e0250780
  
  DOI Publication Publication Publication Publication Publication Publication Publication Projet Projet
- 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 Projet
- 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 Projet
- HLA tapasin independence: broader peptide repertoire and HIV control.
  
  Arman A. Bashirova, Mathias Viard, Vivek Naranbhai, Alba Grifoni, Wilfredo Garcia-Beltran, Marjan Akdag, Yuko Yuki, Xiaojiang Gao, Colm O’hUigin, Malini Raghavan, Steven Wolinsky, Jay H. Bream, Priya Duggal, Jeremy Martinson, Nelson L. Michael, Gregory D. Kirk, Susan P. Buchbinder, David Haas, James J. Goedert, Steven G. Deeks, Jacques Fellay, Bruce Walker, Philip Goulder, Peter Cresswell, Tim Elliott, Alessandro Sette, Jonathan M. Carlson, Mary Carrington
  
  Proceedings of the National Academy of Sciences of the United States of America | October 2020, Vol 117(45): pp. 28232-28238
  
  DOI PDF Publication Publication Publication Publication Publication Publication Publication Projet
- 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 Projet Projet
- 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 Projet
- CD8 T cells targeting adapted epitopes in chronic HIV infection promote dendritic cell maturation and CD4 T cell trans-infection.
  
  Kai Qin, Sushma Boppana, Victor Y. Du, Jonathan M. Carlson, Ling Yue, Dario A. Dilernia, Eric Hunter, Robbie B. Mailliard, Simon A. Mallal, Anju Bansal, Paul A. Goepfert
  
  PLOS Pathogens | August 2019, Vol 15(8)
  
  DOI PDF Publication Publication Publication Publication Publication Publication Publication Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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
  
  Publication Publication Publication Github Projet
- Mother-to-Child HIV Transmission Bottleneck Selects for Consensus Virus with Lower Gag-Protease-Driven Replication Capacity
  
  Vanessa L. Naidoo, Jaclyn K. Mann, Christie Noble, Emily Adland, Jonathan M. Carlson, Jake Thomas, Chanson J. Brumme, Christina F. Thobakgale-Tshabalala, Zabrina L. Brumme, Mark A. Brockman, Philip J. R. Goulder, Thumbi Ndung'u
  
  Journal of Virology | September 2017, Vol 91: pp. e00518-17
  
  Publication Publication Github Projet
- Brief Report: Selection of HIV-1 Variants With Higher Transmission Potential by 1% Tenofovir Gel Microbicide
  
  Nobubelo K. Ngandu, Jonathan M. Carlson, Denis R. Chopera, Nonkululeko Ndabamb, Quarraisha Abdool Karim, Salim Abdool Karim, Carolyn Williamson
  
  Journal of Acquired Immune Deficiency Syndromes | September 2017, Vol 76: pp. 43-47
  
  Publication Publication Publication Github Projet
- PARV4 prevalence, phylogeny, immunology and coinfection with HIV, HBV and HCV in a multicentre African cohort
  
  Colin P. Sharp, William F. Gregory, Louise Hattingh, Amna Malik, Emily Adland, Samantha Daniels, Anriette van Zyl, Jonathan M. Carlson, Susan Wareing, Anthony Ogwu, Roger Shapiro, Lynn Riddell, Fabian Chen, Thumbi Ndung'u, Philip J.R. Goulder, Paul Klenerman, Peter Simmonds, Pieter Jooste, Philippa C. Matthews
  
  Wellcome Open Research | April 2017, Vol 2: pp. 26
  
  Publication Publication Publication Github Projet
- Paediatric non-progression following grandmother-to-child HIV transmission
  
  M.-H. Tsai, M. Muenchhof, E. Adland, A. Carlqvist, J. Roider, D. K. Cole, A. K. Sewell, Jonathan M. Carlson, T. Ndung’u, P. J. R. Goulder
  
  Retrovirology | September 2016, Vol 13: pp. 65
  
  Publication Publication Publication Github Projet
- 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 Projet
- 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
  
  Publication Publication Github Projet
- 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
  
  Publication Publication Publication Github Projet
- 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
  
  Publication Publication Github Projet
- 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 Projet
- 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 Projet
- Selection Bias at the Heterosexual HIV-1 Transmission Bottleneck
  
  Jonathan M. Carlson, Malinda Schaefer, Daniela C. Monaco, Rebecca Batorsky, Daniel T. Claiborne, Jessica Prince, Martin J. Deymier, Zachary S. Ende, Nichole R. Klatt, Charles E. DeZiel, Tien-Ho Lin, Jian Peng, Aaron M. Seese, Roger Shapiro, John Frater, Thumbi Ndung'u, Jianming Tang, Paul Goepfert, Jill Gilmour, Matt A. Price, William Kilembe, David Heckerman, Philip J. R. Goulder, Todd M. Allen, Susan Allen, Eric Hunter
  
  Science | July 2014, Vol 345(6193)
  
  Publication Publication Publication Publication Publication Projet
- 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
- 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 Projet
- 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 Projet
- 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
- 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 Projet
- 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-IFNÎ³-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
- 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 Projet
- 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
- 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
- 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 Projet
- 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 Projet
- 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 Projet
- 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
- 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
- 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
- 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 Projet
- 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
- Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naÃ¯ve 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 Projet
- 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
  
  Thèse de doctorat : 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 Projet
- 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
- 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

- Sequential Diagnosis with Language Models
  
  Harsha Nori, M. Daswani, Christopher Kelly, Scott M. Lundberg, Marco Túlio Ribeiro, Marc Wilson, Xiaoxuan Liu, V. Sounderajah, Jonathan M. Carlson, Matthew P Lungren, Bay Gross, Peter Hames, Mustafa Suleyman, Dominic King, Eric Horvitz
  
  July 2025
  
  DOI
- 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 Projet Projet Projet
- 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 Projet Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet
- Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein.
  
  Debra Van Egeren, Alexander Novokhodko, Madison Stoddard, Uyen Tran, Bruce Zetter, Michael Rogers, Bradley L. Pentelute, Jonathan M. Carlson, Mark Hixon, Diane Joseph-McCarthy, Arijit Chakravarty
  
  PLOS ONE | April 2021, Vol 16(4): pp. e0250780
  
  DOI Publication Publication Publication Publication Publication Publication Publication Projet Projet
- 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 Projet
- 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 Projet
- HLA tapasin independence: broader peptide repertoire and HIV control.
  
  Arman A. Bashirova, Mathias Viard, Vivek Naranbhai, Alba Grifoni, Wilfredo Garcia-Beltran, Marjan Akdag, Yuko Yuki, Xiaojiang Gao, Colm O’hUigin, Malini Raghavan, Steven Wolinsky, Jay H. Bream, Priya Duggal, Jeremy Martinson, Nelson L. Michael, Gregory D. Kirk, Susan P. Buchbinder, David Haas, James J. Goedert, Steven G. Deeks, Jacques Fellay, Bruce Walker, Philip Goulder, Peter Cresswell, Tim Elliott, Alessandro Sette, Jonathan M. Carlson, Mary Carrington
  
  Proceedings of the National Academy of Sciences of the United States of America | October 2020, Vol 117(45): pp. 28232-28238
  
  DOI PDF Publication Publication Publication Publication Publication Publication Publication Projet
- 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 Projet
- CD8 T cells targeting adapted epitopes in chronic HIV infection promote dendritic cell maturation and CD4 T cell trans-infection.
  
  Kai Qin, Sushma Boppana, Victor Y. Du, Jonathan M. Carlson, Ling Yue, Dario A. Dilernia, Eric Hunter, Robbie B. Mailliard, Simon A. Mallal, Anju Bansal, Paul A. Goepfert
  
  PLOS Pathogens | August 2019, Vol 15(8)
  
  DOI PDF Publication Publication Publication Publication Publication Publication Publication Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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
  
  Publication Publication Publication Github Projet
- Mother-to-Child HIV Transmission Bottleneck Selects for Consensus Virus with Lower Gag-Protease-Driven Replication Capacity
  
  Vanessa L. Naidoo, Jaclyn K. Mann, Christie Noble, Emily Adland, Jonathan M. Carlson, Jake Thomas, Chanson J. Brumme, Christina F. Thobakgale-Tshabalala, Zabrina L. Brumme, Mark A. Brockman, Philip J. R. Goulder, Thumbi Ndung'u
  
  Journal of Virology | September 2017, Vol 91: pp. e00518-17
  
  Publication Publication Github Projet
- Brief Report: Selection of HIV-1 Variants With Higher Transmission Potential by 1% Tenofovir Gel Microbicide
  
  Nobubelo K. Ngandu, Jonathan M. Carlson, Denis R. Chopera, Nonkululeko Ndabamb, Quarraisha Abdool Karim, Salim Abdool Karim, Carolyn Williamson
  
  Journal of Acquired Immune Deficiency Syndromes | September 2017, Vol 76: pp. 43-47
  
  Publication Publication Publication Github Projet
- PARV4 prevalence, phylogeny, immunology and coinfection with HIV, HBV and HCV in a multicentre African cohort
  
  Colin P. Sharp, William F. Gregory, Louise Hattingh, Amna Malik, Emily Adland, Samantha Daniels, Anriette van Zyl, Jonathan M. Carlson, Susan Wareing, Anthony Ogwu, Roger Shapiro, Lynn Riddell, Fabian Chen, Thumbi Ndung'u, Philip J.R. Goulder, Paul Klenerman, Peter Simmonds, Pieter Jooste, Philippa C. Matthews
  
  Wellcome Open Research | April 2017, Vol 2: pp. 26
  
  Publication Publication Publication Github Projet
- Paediatric non-progression following grandmother-to-child HIV transmission
  
  M.-H. Tsai, M. Muenchhof, E. Adland, A. Carlqvist, J. Roider, D. K. Cole, A. K. Sewell, Jonathan M. Carlson, T. Ndung’u, P. J. R. Goulder
  
  Retrovirology | September 2016, Vol 13: pp. 65
  
  Publication Publication Publication Github Projet
- 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 Projet
- 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
  
  Publication Publication Github Projet
- 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
  
  Publication Publication Publication Github Projet
- 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
  
  Publication Publication Github Projet
- 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 Projet
- 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
  
  Publication Publication Publication Projet
- Selection Bias at the Heterosexual HIV-1 Transmission Bottleneck
  
  Jonathan M. Carlson, Malinda Schaefer, Daniela C. Monaco, Rebecca Batorsky, Daniel T. Claiborne, Jessica Prince, Martin J. Deymier, Zachary S. Ende, Nichole R. Klatt, Charles E. DeZiel, Tien-Ho Lin, Jian Peng, Aaron M. Seese, Roger Shapiro, John Frater, Thumbi Ndung'u, Jianming Tang, Paul Goepfert, Jill Gilmour, Matt A. Price, William Kilembe, David Heckerman, Philip J. R. Goulder, Todd M. Allen, Susan Allen, Eric Hunter
  
  Science | July 2014, Vol 345(6193)
  
  Publication Publication Publication Publication Publication Projet
- 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
- 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 Projet
- 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 Projet
- 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
- 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 Projet
- 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-IFNÎ³-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
- 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 Projet
- 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
- 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
- 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 Projet
- 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 Projet
- 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 Projet
- 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
- 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
- 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
- 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 Projet
- Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naÃ¯ve 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
- 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 Projet
- 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 Projet Projet
- Creation of a Relational Database for Identifying Potential Functional DNA Sequence Motifs in A. thaliana and Other Genomes
  
  Jonathan M. Carlson
  
  June 2003
  
  Thèse de doctorat : 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 Projet
- 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