PhyloD

成立时间：March 1, 2007

论文与出版物

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- 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, 第 35 卷(8): pp. 1157-1165
  
  DOI Publication Publication Publication
- Elevated HIV infection of CD4 T cells in MRKAd5 vaccine recipients due to CD8 T cells targeting of adapted epitopes
  
  Kai Qin, Sushma Boppana, Jonathan M. Carlson, Andrew Fiore-Gartland, Jacob Files, Jie Zeng, Jeffrey Edberg, Robbie B Mailliard, Christina Ochsenbauer, Anju Bansal, Paul Goepfert
  
  Journal of Virology | June 2021, 第 95 卷(16)
  
  DOI Publication Publication Publication
- Pre-treatment integrase inhibitor resistance is uncommon in antiretroviral therapy-naive individuals with HIV-1 subtype A1 and D infections in Uganda.
  
  Suzanne M. McCluskey, Kimia Kamelian, Nicholas Musinguzi, Simone Kigozi, Yap Boum, Mwebesa B. Bwana, Conrad Muzoora, Zabrina L. Brumme, Mary Carrington, Jonathan M. Carlson, Brian Foley, Peter W. Hunt, Jeffrey N. Martin, David R. Bangsberg, P. Richard Harrigan, Mark J. Siedner, Jessica E. Haberer, Guinevere Q. Lee
  
  AIDS | May 2021, 第 35 卷(7): pp. 1083-1089
  
  DOI Publication Publication Publication
- Impact of Human Leukocyte Antigen-Associated Polymorphisms on Variability of HIV-1 Accessory and Regulatory Proteins.
  
  Doreen Kamori, Zafrul Hasan, Jonathan M. Carlson, A I Kawana-Tachikawa, Hiroyuki Gatanaga, Shinichi Oka, Takamasa Ueno
  
  AIDS Research and Human Retroviruses | April 2021, 第 37 卷(12): pp. 962-966
  
  DOI Publication Publication Publication Publication
- Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein.
  
  Debra Van Egeren, Alexander Novokhodko, Madison Stoddard, Uyen Tran, Bruce Zetter, Michael Rogers, Bradley L. Pentelute, Jonathan M. Carlson, Mark Hixon, Diane Joseph-McCarthy, Arijit Chakravarty
  
  PLOS ONE | April 2021, 第 16 卷(4): pp. e0250780
  
  DOI Publication Publication Publication Publication Publication Publication Publication 项目
- 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, 第 10 卷(1): pp. 19416-19416
  
  DOI Publication Publication
- HLA tapasin independence: broader peptide repertoire and HIV control.
  
  Arman A. Bashirova, Mathias Viard, Vivek Naranbhai, Alba Grifoni, Wilfredo Garcia-Beltran, Marjan Akdag, Yuko Yuki, Xiaojiang Gao, Colm O’hUigin, Malini Raghavan, Steven Wolinsky, Jay H. Bream, Priya Duggal, Jeremy Martinson, Nelson L. Michael, Gregory D. Kirk, Susan P. Buchbinder, David Haas, James J. Goedert, Steven G. Deeks, Jacques Fellay, Bruce Walker, Philip Goulder, Peter Cresswell, Tim Elliott, Alessandro Sette, Jonathan M. Carlson, Mary Carrington
  
  Proceedings of the National Academy of Sciences of the United States of America | October 2020, 第 117 卷(45): pp. 28232-28238
  
  DOI PDF Publication Publication Publication Publication Publication Publication Publication
- CD8 T cells targeting adapted epitopes in chronic HIV infection promote dendritic cell maturation and CD4 T cell trans-infection.
  
  Kai Qin, Sushma Boppana, Victor Y. Du, Jonathan M. Carlson, Ling Yue, Dario A. Dilernia, Eric Hunter, Robbie B. Mailliard, Simon A. Mallal, Anju Bansal, Paul A. Goepfert
  
  PLOS Pathogens | August 2019, 第 15 卷(8)
  
  DOI PDF Publication Publication Publication Publication Publication Publication Publication
- Clinical and evolutionary consequences of HIV adaptation to HLA: implications for vaccine and cure
  
  Santiago Avila-Rios, Jonathan M. Carlson, Mina John, Simon Mallal, Zabrina L Brumme
  
  Current Opinion in HIV and AIDS | May 2019, 第 14 卷(3): pp. 194-204
  
  Publication
- Genotypic and mechanistic characterization of subtype-specific hiv adaptation to host cellular immunity
  
  Natalie N Kinloch, Guinevere Q Lee, Jonathan M. Carlson, Steven W Jin, Chanson J Brumme, Helen Byakwaga, Conrad Muzoora, Mwebesa B Bwana, Kyle D Cobarrubias, Peter W Hunt, Jeff N Martin, Mary Carrington, David R Bangsberg, P Richard Harrigan, Mark A Brockman, Zabrina L Brumme
  
  Journal of Virology | January 2019, 第 93 卷(1): pp. e01502-18
  
  Publication
- Antisense-derived HIV-1 cryptic epitopes are not major drivers of viral evolution during the acute phase of infection
  
  Binghao J Peng, Jonathan M. Carlson, Michael KP Liu, Feng Gao, Nilu Goonetilleke, Andrew J McMichael, Persephone Borrow, Jill Gilmour, Sonya L Heath, Eric Hunter, Anju Bansal, Paul A Goepfert
  
  Journal of Virology | October 2018, 第 92 卷(19): pp. e00711-18
  
  Publication
- Killer cell immunoglobulin–like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1
  
  Maureen P. Martin, Vivek Naranbhai, Patrick R. Shea, Ying Qi, Veron Ramsuran, Nicolas Vince, Xiaojiang Gao, Rasmi Thomas, Zabrina L. Brumme, Jonathan M. Carlson, Steven M. Wolinsky, James J. Goedert, Bruce D. Walker, Florencia P. Segal, Steven G. Deeks, David W. Haas, Stephen A. Migueles, Mark Connors, Nelson Michael, Jacques Fellay, Emma Gostick, Sian Llewellyn-Lacey, David A. Price, Bernard A. Lafont, Phillip Pymm, Philippa M. Saunders, Jacqueline Widjaja, Shu Cheng Wong, Julian P. Vivian, Jamie Rossjohn, Andrew G. Brooks,, Mary Carrington
  
  Journal of Clinical Investigation | May 2018, 第 128 卷(5): pp. 1903-1912
  
  Publication Publication
- HLA-associated polymorphisms in the HIV-2 capsid highlight key differences between HIV-1 and HIV-2 immune adaptation
  
  Thushan I. de Silva, Aleksandra Leligdowicz, Jonathan M. Carlson, Miguel Garcia-Knight, Clayton Onyango, Nicholas Miller, Louis-Marie Yindom, Stephane Hué, Assan Jaye, Tao Dong, Matthew Cotten, Sarah L Rowland-Jones
  
  AIDS | March 2018, 第 32 卷(6): pp. 709-714
  
  Publication
- Weaker HLA footprints on HIV in the unique and highly genetically admixed host population of Mexico
  
  Maribel Soto-Nava, Santiago Avila-Ríos, Humberto Valenzuela-Ponce, Claudia García-Morales, Jonathan M. Carlson, Daniela Tapia-Trejo, Daniela Garrido-Rodriguez, Selma N. Alva-Hernández, Thalía A. García-Tellez, Akio Murakami-Ogasawara, the International HIV Adaptation Collaborative, Simon A Mallal, Mina John, Mark A. Brockman, Chanson J. Brumme, Zabrina L. Brumme, Gustavo Reyes-Teran, the HIV MexNet Group
  
  Journal of Virology | November 2017
  
  论文与出版物论文与出版物论文与出版物 Github
- Brief Report: Selection of HIV-1 Variants With Higher Transmission Potential by 1% Tenofovir Gel Microbicide
  
  Nobubelo K. Ngandu, Jonathan M. Carlson, Denis R. Chopera, Nonkululeko Ndabamb, Quarraisha Abdool Karim, Salim Abdool Karim, Carolyn Williamson
  
  Journal of Acquired Immune Deficiency Syndromes | September 2017, 第 76 卷: pp. 43-47
  
  论文与出版物论文与出版物论文与出版物 Github
- Mother-to-Child HIV Transmission Bottleneck Selects for Consensus Virus with Lower Gag-Protease-Driven Replication Capacity
  
  Vanessa L. Naidoo, Jaclyn K. Mann, Christie Noble, Emily Adland, Jonathan M. Carlson, Jake Thomas, Chanson J. Brumme, Christina F. Thobakgale-Tshabalala, Zabrina L. Brumme, Mark A. Brockman, Philip J. R. Goulder, Thumbi Ndung'u
  
  Journal of Virology | September 2017, 第 91 卷: pp. e00518-17
  
  论文与出版物论文与出版物 Github
- PARV4 prevalence, phylogeny, immunology and coinfection with HIV, HBV and HCV in a multicentre African cohort
  
  Colin P. Sharp, William F. Gregory, Louise Hattingh, Amna Malik, Emily Adland, Samantha Daniels, Anriette van Zyl, Jonathan M. Carlson, Susan Wareing, Anthony Ogwu, Roger Shapiro, Lynn Riddell, Fabian Chen, Thumbi Ndung'u, Philip J.R. Goulder, Paul Klenerman, Peter Simmonds, Pieter Jooste, Philippa C. Matthews
  
  Wellcome Open Research | April 2017, 第 2 卷: pp. 26
  
  论文与出版物论文与出版物论文与出版物 Github
- Paediatric non-progression following grandmother-to-child HIV transmission
  
  M.-H. Tsai, M. Muenchhof, E. Adland, A. Carlqvist, J. Roider, D. K. Cole, A. K. Sewell, Jonathan M. Carlson, T. Ndung’u, P. J. R. Goulder
  
  Retrovirology | September 2016, 第 13 卷: pp. 65
  
  论文与出版物论文与出版物论文与出版物 Github
- Impact of Pre-Adapted HIV Transmission
  
  Jonathan M. Carlson, Victor Y. Du, Nico Pfeifer, Anju Bansal, Vincent T. F. Tan, Karen Power, Chanson J. Brumme, Anat Kreimer, Charles E. DeZiel, Nicolo Fusi, Malinda Schaefer, Mark A. Brockman, Jill Gilmour, Matt A. Price, William Kilembe, Richard Haubrich, Mina John, Simon Mallal, Roger Shapiro, John Frater, P. Richard Harrigan, Thumbi Ndung'u, Susan Allen, David Heckerman, John Sidney, Todd M. Allen, Philip J.R. Goulder, Zabrina L. Brumme, Eric Hunter, Paul A. Goepfert
  
  Nature Medicine | May 2016, 第 22 卷: pp. 606-613
  
  Bonnie Mathieson Young Investigator Award
  
  Author's Version Publication DOI Github
- HIV-1–Specific CD8 T Cells Exhibit Limited Cross-Reactivity during Acute Infection
  
  Victor Y. Du, Anju Bansal, Jonathan M. Carlson, Jesus F. Salazar-Gonzalez, Maria G. Salazar, Kristin Ladell, Stephanie Gras, Tracy M. Josephs, Sonya L. Heath, David A. Price, Jamie Rossjohn, Eric Hunter, Paul A. Goepfert
  
  Journal of Immunology | April 2016, 第 198 卷: pp. 3276-3286
  
  论文与出版物论文与出版物 Github
- Lower Viral Loads and Slower CD4+ T-Cell Count Decline in MRKAd5 HIV-1 Vaccinees Expressing Disease-Susceptible HLA-B*58:02
  
  Ellen M. Leitman, Jacob Hurst, Masahiko Mori, James Kublin, Thumbi Ndung'u, Bruce D. Walker, Jonathan M. Carlson, Glenda E. Gray, Philippa C. Matthews, Nicole Frahm, Philip J.R. Goulder
  
  The Journal of infectious diseases | March 2016, 第 214 卷: pp. 379-389
  
  论文与出版物论文与出版物论文与出版物 Github
- CD8+ TCR bias and immunodominance in HIV-1 infection
  
  Henrik N. Kløverpris, Reuben McGregor, James E. McLaren, Kristin Ladell, Mikkel Harndahl, Anette Stryhn, Jonathan M. Carlson, Catherine Koofhethile, Bram Gerritsen, Can Kesmir, Fabian Chen, Lynn Riddell, Graz Luzzi, Alasdair Leslie, Bruce D. Walker, Thumbi Ndung'u, Søren Buus, David A. Price, Philip J.R. Goulder
  
  The Journal of Immunology | June 2015, 第 194 卷: pp. 5329-5345
  
  论文与出版物论文与出版物 Github
- HIV-1 Adaptation to HLA: A Window into Virus–Host Immune Interactions
  
  Jonathan M. Carlson, Anh Q. Le, Aniqa Shahid, Zabrina L. Brumme
  
  Trends in Microbiology | April 2015, 第 23 卷(4): pp. 212-224
  
  论文与出版物论文与出版物论文与出版物
- Impact of HLA-Driven HIV Adaptation on Virulence in Populations of High HIV Seroprevalence
  
  Rebecca Payne, Maximilian Muenchhoff, Jaclyn Mann, Hannah E. Roberts, Philippa Matthews, Emily Adland, Allison Hempenstall, Kuan-Hsiang Huang, Mark Brockman, Zabrina Brumme, Marc Sinclair, Toshiyuki Miura, John Frater, Myron Essex, Roger Shapiro, Bruce D. Walker, Thumbi Ndung'u, Angela R. McLean, Jonathan M. Carlson, Philip J. R. Goulder
  
  Proceedings of the National Academy of Sciences of the United States of America | October 2014
  
  Publication Publication
- HIV Control Is Mediated in Part by CD8+ T-Cell Targeting of Specific Epitopes
  
  Florencia Pereyra, David Heckerman, Jonathan M. Carlson, Carl Kadie, Damien Z Soghoian, Daniel Karel, Ariel Goldenthal, Oliver B Davis, Charles E DeZiel, Tienho Lin, Jian Peng, Alicja Piechocka, Mary Carrington, Bruce D Walker
  
  Journal of Virology | August 2014, 第 88 卷(22): pp. 12937-12948
  
  论文与出版物论文与出版物论文与出版物
- 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, 第 345 卷(6193)
  
  论文与出版物论文与出版物论文与出版物论文与出版物论文与出版物
- 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, 第 340 卷(6128): pp. 87-91
  
  论文与出版物论文与出版物
- 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, 第 86 卷(24): pp. 13202-13216
  
  Publication Publication
- Widespread Impact of HLA Restriction on Immune Control and Escape Pathways in HIV-1
  
  Jonathan M. Carlson, Jennifer Listgarten, Nico Pfeifer, Vincent Tan, Carl Kadie, Bruce D. Walker, Thumbi Ndung'u, Roger Shapiro, John Frater, Zabrina L. Brumme, Philip J. R. Goulder, David Heckerman
  
  Journal of Virology | May 2012, 第 86 卷(9): pp. 5230-5243
  
  论文与出版物论文与出版物论文与出版物 Github
- HIV-1 Adaptation to NK-Cell-Mediated Immune Pressure
  
  Galit Alter, David Heckerman, Arne Schneidewind, Lena Fadda, Carl Kadie, Jonathan M. Carlson, Cesar Oniangue-Ndza, Maureen Martin, Bin Li, Salim I. Khakoo, Mary Carrington, Todd M. Allen, Marcus Altfeld
  
  Nature International weekly journal of science | August 2011, 第 476 卷: pp. 96-100
  
  论文与出版物论文与出版物
- 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, 第 207 卷(1): pp. 51
  
  论文与出版物论文与出版物
- 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
  
  论文与出版物论文与出版物
- 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, 第 4 卷: pp. e1000225
  
  论文与出版物论文与出版物论文与出版物
- 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, 第 82 卷: pp. 9216-9227
  
  论文与出版物 Github
- Leveraging Hierarchical Population Structure in Discrete Association Studies
  
  Jonathan M. Carlson, Carl Kadie, Simon Mallal, David Heckerman
  
  PLoS One | July 2007, 第 2 卷: pp. e591
  
  论文与出版物

- 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, 第 35 卷(8): pp. 1157-1165
  
  DOI Publication Publication Publication
- Elevated HIV infection of CD4 T cells in MRKAd5 vaccine recipients due to CD8 T cells targeting of adapted epitopes
  
  Kai Qin, Sushma Boppana, Jonathan M. Carlson, Andrew Fiore-Gartland, Jacob Files, Jie Zeng, Jeffrey Edberg, Robbie B Mailliard, Christina Ochsenbauer, Anju Bansal, Paul Goepfert
  
  Journal of Virology | June 2021, 第 95 卷(16)
  
  DOI Publication Publication Publication
- Pre-treatment integrase inhibitor resistance is uncommon in antiretroviral therapy-naive individuals with HIV-1 subtype A1 and D infections in Uganda.
  
  Suzanne M. McCluskey, Kimia Kamelian, Nicholas Musinguzi, Simone Kigozi, Yap Boum, Mwebesa B. Bwana, Conrad Muzoora, Zabrina L. Brumme, Mary Carrington, Jonathan M. Carlson, Brian Foley, Peter W. Hunt, Jeffrey N. Martin, David R. Bangsberg, P. Richard Harrigan, Mark J. Siedner, Jessica E. Haberer, Guinevere Q. Lee
  
  AIDS | May 2021, 第 35 卷(7): pp. 1083-1089
  
  DOI Publication Publication Publication
- Impact of Human Leukocyte Antigen-Associated Polymorphisms on Variability of HIV-1 Accessory and Regulatory Proteins.
  
  Doreen Kamori, Zafrul Hasan, Jonathan M. Carlson, A I Kawana-Tachikawa, Hiroyuki Gatanaga, Shinichi Oka, Takamasa Ueno
  
  AIDS Research and Human Retroviruses | April 2021, 第 37 卷(12): pp. 962-966
  
  DOI Publication Publication Publication Publication
- Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein.
  
  Debra Van Egeren, Alexander Novokhodko, Madison Stoddard, Uyen Tran, Bruce Zetter, Michael Rogers, Bradley L. Pentelute, Jonathan M. Carlson, Mark Hixon, Diane Joseph-McCarthy, Arijit Chakravarty
  
  PLOS ONE | April 2021, 第 16 卷(4): pp. e0250780
  
  DOI Publication Publication Publication Publication Publication Publication Publication 项目
- 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, 第 10 卷(1): pp. 19416-19416
  
  DOI Publication Publication
- HLA tapasin independence: broader peptide repertoire and HIV control.
  
  Arman A. Bashirova, Mathias Viard, Vivek Naranbhai, Alba Grifoni, Wilfredo Garcia-Beltran, Marjan Akdag, Yuko Yuki, Xiaojiang Gao, Colm O’hUigin, Malini Raghavan, Steven Wolinsky, Jay H. Bream, Priya Duggal, Jeremy Martinson, Nelson L. Michael, Gregory D. Kirk, Susan P. Buchbinder, David Haas, James J. Goedert, Steven G. Deeks, Jacques Fellay, Bruce Walker, Philip Goulder, Peter Cresswell, Tim Elliott, Alessandro Sette, Jonathan M. Carlson, Mary Carrington
  
  Proceedings of the National Academy of Sciences of the United States of America | October 2020, 第 117 卷(45): pp. 28232-28238
  
  DOI PDF Publication Publication Publication Publication Publication Publication Publication
- CD8 T cells targeting adapted epitopes in chronic HIV infection promote dendritic cell maturation and CD4 T cell trans-infection.
  
  Kai Qin, Sushma Boppana, Victor Y. Du, Jonathan M. Carlson, Ling Yue, Dario A. Dilernia, Eric Hunter, Robbie B. Mailliard, Simon A. Mallal, Anju Bansal, Paul A. Goepfert
  
  PLOS Pathogens | August 2019, 第 15 卷(8)
  
  DOI PDF Publication Publication Publication Publication Publication Publication Publication
- Clinical and evolutionary consequences of HIV adaptation to HLA: implications for vaccine and cure
  
  Santiago Avila-Rios, Jonathan M. Carlson, Mina John, Simon Mallal, Zabrina L Brumme
  
  Current Opinion in HIV and AIDS | May 2019, 第 14 卷(3): pp. 194-204
  
  Publication
- Genotypic and mechanistic characterization of subtype-specific hiv adaptation to host cellular immunity
  
  Natalie N Kinloch, Guinevere Q Lee, Jonathan M. Carlson, Steven W Jin, Chanson J Brumme, Helen Byakwaga, Conrad Muzoora, Mwebesa B Bwana, Kyle D Cobarrubias, Peter W Hunt, Jeff N Martin, Mary Carrington, David R Bangsberg, P Richard Harrigan, Mark A Brockman, Zabrina L Brumme
  
  Journal of Virology | January 2019, 第 93 卷(1): pp. e01502-18
  
  Publication
- Antisense-derived HIV-1 cryptic epitopes are not major drivers of viral evolution during the acute phase of infection
  
  Binghao J Peng, Jonathan M. Carlson, Michael KP Liu, Feng Gao, Nilu Goonetilleke, Andrew J McMichael, Persephone Borrow, Jill Gilmour, Sonya L Heath, Eric Hunter, Anju Bansal, Paul A Goepfert
  
  Journal of Virology | October 2018, 第 92 卷(19): pp. e00711-18
  
  Publication
- Killer cell immunoglobulin–like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1
  
  Maureen P. Martin, Vivek Naranbhai, Patrick R. Shea, Ying Qi, Veron Ramsuran, Nicolas Vince, Xiaojiang Gao, Rasmi Thomas, Zabrina L. Brumme, Jonathan M. Carlson, Steven M. Wolinsky, James J. Goedert, Bruce D. Walker, Florencia P. Segal, Steven G. Deeks, David W. Haas, Stephen A. Migueles, Mark Connors, Nelson Michael, Jacques Fellay, Emma Gostick, Sian Llewellyn-Lacey, David A. Price, Bernard A. Lafont, Phillip Pymm, Philippa M. Saunders, Jacqueline Widjaja, Shu Cheng Wong, Julian P. Vivian, Jamie Rossjohn, Andrew G. Brooks,, Mary Carrington
  
  Journal of Clinical Investigation | May 2018, 第 128 卷(5): pp. 1903-1912
  
  Publication Publication
- HLA-associated polymorphisms in the HIV-2 capsid highlight key differences between HIV-1 and HIV-2 immune adaptation
  
  Thushan I. de Silva, Aleksandra Leligdowicz, Jonathan M. Carlson, Miguel Garcia-Knight, Clayton Onyango, Nicholas Miller, Louis-Marie Yindom, Stephane Hué, Assan Jaye, Tao Dong, Matthew Cotten, Sarah L Rowland-Jones
  
  AIDS | March 2018, 第 32 卷(6): pp. 709-714
  
  Publication
- Weaker HLA footprints on HIV in the unique and highly genetically admixed host population of Mexico
  
  Maribel Soto-Nava, Santiago Avila-Ríos, Humberto Valenzuela-Ponce, Claudia García-Morales, Jonathan M. Carlson, Daniela Tapia-Trejo, Daniela Garrido-Rodriguez, Selma N. Alva-Hernández, Thalía A. García-Tellez, Akio Murakami-Ogasawara, the International HIV Adaptation Collaborative, Simon A Mallal, Mina John, Mark A. Brockman, Chanson J. Brumme, Zabrina L. Brumme, Gustavo Reyes-Teran, the HIV MexNet Group
  
  Journal of Virology | November 2017
  
  论文与出版物论文与出版物论文与出版物 Github
- Mother-to-Child HIV Transmission Bottleneck Selects for Consensus Virus with Lower Gag-Protease-Driven Replication Capacity
  
  Vanessa L. Naidoo, Jaclyn K. Mann, Christie Noble, Emily Adland, Jonathan M. Carlson, Jake Thomas, Chanson J. Brumme, Christina F. Thobakgale-Tshabalala, Zabrina L. Brumme, Mark A. Brockman, Philip J. R. Goulder, Thumbi Ndung'u
  
  Journal of Virology | September 2017, 第 91 卷: pp. e00518-17
  
  论文与出版物论文与出版物 Github
- Brief Report: Selection of HIV-1 Variants With Higher Transmission Potential by 1% Tenofovir Gel Microbicide
  
  Nobubelo K. Ngandu, Jonathan M. Carlson, Denis R. Chopera, Nonkululeko Ndabamb, Quarraisha Abdool Karim, Salim Abdool Karim, Carolyn Williamson
  
  Journal of Acquired Immune Deficiency Syndromes | September 2017, 第 76 卷: pp. 43-47
  
  论文与出版物论文与出版物论文与出版物 Github
- PARV4 prevalence, phylogeny, immunology and coinfection with HIV, HBV and HCV in a multicentre African cohort
  
  Colin P. Sharp, William F. Gregory, Louise Hattingh, Amna Malik, Emily Adland, Samantha Daniels, Anriette van Zyl, Jonathan M. Carlson, Susan Wareing, Anthony Ogwu, Roger Shapiro, Lynn Riddell, Fabian Chen, Thumbi Ndung'u, Philip J.R. Goulder, Paul Klenerman, Peter Simmonds, Pieter Jooste, Philippa C. Matthews
  
  Wellcome Open Research | April 2017, 第 2 卷: pp. 26
  
  论文与出版物论文与出版物论文与出版物 Github
- Paediatric non-progression following grandmother-to-child HIV transmission
  
  M.-H. Tsai, M. Muenchhof, E. Adland, A. Carlqvist, J. Roider, D. K. Cole, A. K. Sewell, Jonathan M. Carlson, T. Ndung’u, P. J. R. Goulder
  
  Retrovirology | September 2016, 第 13 卷: pp. 65
  
  论文与出版物论文与出版物论文与出版物 Github
- Impact of Pre-Adapted HIV Transmission
  
  Jonathan M. Carlson, Victor Y. Du, Nico Pfeifer, Anju Bansal, Vincent T. F. Tan, Karen Power, Chanson J. Brumme, Anat Kreimer, Charles E. DeZiel, Nicolo Fusi, Malinda Schaefer, Mark A. Brockman, Jill Gilmour, Matt A. Price, William Kilembe, Richard Haubrich, Mina John, Simon Mallal, Roger Shapiro, John Frater, P. Richard Harrigan, Thumbi Ndung'u, Susan Allen, David Heckerman, John Sidney, Todd M. Allen, Philip J.R. Goulder, Zabrina L. Brumme, Eric Hunter, Paul A. Goepfert
  
  Nature Medicine | May 2016, 第 22 卷: pp. 606-613
  
  Bonnie Mathieson Young Investigator Award
  
  Author's Version Publication DOI Github
- HIV-1–Specific CD8 T Cells Exhibit Limited Cross-Reactivity during Acute Infection
  
  Victor Y. Du, Anju Bansal, Jonathan M. Carlson, Jesus F. Salazar-Gonzalez, Maria G. Salazar, Kristin Ladell, Stephanie Gras, Tracy M. Josephs, Sonya L. Heath, David A. Price, Jamie Rossjohn, Eric Hunter, Paul A. Goepfert
  
  Journal of Immunology | April 2016, 第 198 卷: pp. 3276-3286
  
  论文与出版物论文与出版物 Github
- Lower Viral Loads and Slower CD4+ T-Cell Count Decline in MRKAd5 HIV-1 Vaccinees Expressing Disease-Susceptible HLA-B*58:02
  
  Ellen M. Leitman, Jacob Hurst, Masahiko Mori, James Kublin, Thumbi Ndung'u, Bruce D. Walker, Jonathan M. Carlson, Glenda E. Gray, Philippa C. Matthews, Nicole Frahm, Philip J.R. Goulder
  
  The Journal of infectious diseases | March 2016, 第 214 卷: pp. 379-389
  
  论文与出版物论文与出版物论文与出版物 Github
- CD8+ TCR bias and immunodominance in HIV-1 infection
  
  Henrik N. Kløverpris, Reuben McGregor, James E. McLaren, Kristin Ladell, Mikkel Harndahl, Anette Stryhn, Jonathan M. Carlson, Catherine Koofhethile, Bram Gerritsen, Can Kesmir, Fabian Chen, Lynn Riddell, Graz Luzzi, Alasdair Leslie, Bruce D. Walker, Thumbi Ndung'u, Søren Buus, David A. Price, Philip J.R. Goulder
  
  The Journal of Immunology | June 2015, 第 194 卷: pp. 5329-5345
  
  论文与出版物论文与出版物 Github
- Impact of HLA-Driven HIV Adaptation on Virulence in Populations of High HIV Seroprevalence
  
  Rebecca Payne, Maximilian Muenchhoff, Jaclyn Mann, Hannah E. Roberts, Philippa Matthews, Emily Adland, Allison Hempenstall, Kuan-Hsiang Huang, Mark Brockman, Zabrina Brumme, Marc Sinclair, Toshiyuki Miura, John Frater, Myron Essex, Roger Shapiro, Bruce D. Walker, Thumbi Ndung'u, Angela R. McLean, Jonathan M. Carlson, Philip J. R. Goulder
  
  Proceedings of the National Academy of Sciences of the United States of America | October 2014
  
  Publication Publication
- HIV Control Is Mediated in Part by CD8+ T-Cell Targeting of Specific Epitopes
  
  Florencia Pereyra, David Heckerman, Jonathan M. Carlson, Carl Kadie, Damien Z Soghoian, Daniel Karel, Ariel Goldenthal, Oliver B Davis, Charles E DeZiel, Tienho Lin, Jian Peng, Alicja Piechocka, Mary Carrington, Bruce D Walker
  
  Journal of Virology | August 2014, 第 88 卷(22): pp. 12937-12948
  
  论文与出版物论文与出版物论文与出版物
- 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, 第 345 卷(6193)
  
  论文与出版物论文与出版物论文与出版物论文与出版物论文与出版物
- 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, 第 340 卷(6128): pp. 87-91
  
  论文与出版物论文与出版物
- 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, 第 86 卷(24): pp. 13202-13216
  
  Publication Publication
- Widespread Impact of HLA Restriction on Immune Control and Escape Pathways in HIV-1
  
  Jonathan M. Carlson, Jennifer Listgarten, Nico Pfeifer, Vincent Tan, Carl Kadie, Bruce D. Walker, Thumbi Ndung'u, Roger Shapiro, John Frater, Zabrina L. Brumme, Philip J. R. Goulder, David Heckerman
  
  Journal of Virology | May 2012, 第 86 卷(9): pp. 5230-5243
  
  论文与出版物论文与出版物论文与出版物 Github
- HIV-1 Adaptation to NK-Cell-Mediated Immune Pressure
  
  Galit Alter, David Heckerman, Arne Schneidewind, Lena Fadda, Carl Kadie, Jonathan M. Carlson, Cesar Oniangue-Ndza, Maureen Martin, Bin Li, Salim I. Khakoo, Mary Carrington, Todd M. Allen, Marcus Altfeld
  
  Nature International weekly journal of science | August 2011, 第 476 卷: pp. 96-100
  
  论文与出版物论文与出版物
- 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, 第 207 卷(1): pp. 51
  
  论文与出版物论文与出版物
- 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
  
  论文与出版物论文与出版物
- 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, 第 4 卷: pp. e1000225
  
  论文与出版物论文与出版物论文与出版物
- 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, 第 82 卷: pp. 9216-9227
  
  论文与出版物 Github
- Leveraging Hierarchical Population Structure in Discrete Association Studies
  
  Jonathan M. Carlson, Carl Kadie, Simon Mallal, David Heckerman
  
  PLoS One | July 2007, 第 2 卷: pp. e591
  
  论文与出版物
- 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, 第 23 卷(4): pp. 212-224
  
  论文与出版物论文与出版物论文与出版物

- 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, 第 35 卷(8): pp. 1157-1165
  
  DOI Publication Publication Publication
- Elevated HIV infection of CD4 T cells in MRKAd5 vaccine recipients due to CD8 T cells targeting of adapted epitopes
  
  Kai Qin, Sushma Boppana, Jonathan M. Carlson, Andrew Fiore-Gartland, Jacob Files, Jie Zeng, Jeffrey Edberg, Robbie B Mailliard, Christina Ochsenbauer, Anju Bansal, Paul Goepfert
  
  Journal of Virology | June 2021, 第 95 卷(16)
  
  DOI Publication Publication Publication
- Pre-treatment integrase inhibitor resistance is uncommon in antiretroviral therapy-naive individuals with HIV-1 subtype A1 and D infections in Uganda.
  
  Suzanne M. McCluskey, Kimia Kamelian, Nicholas Musinguzi, Simone Kigozi, Yap Boum, Mwebesa B. Bwana, Conrad Muzoora, Zabrina L. Brumme, Mary Carrington, Jonathan M. Carlson, Brian Foley, Peter W. Hunt, Jeffrey N. Martin, David R. Bangsberg, P. Richard Harrigan, Mark J. Siedner, Jessica E. Haberer, Guinevere Q. Lee
  
  AIDS | May 2021, 第 35 卷(7): pp. 1083-1089
  
  DOI Publication Publication Publication
- Impact of Human Leukocyte Antigen-Associated Polymorphisms on Variability of HIV-1 Accessory and Regulatory Proteins.
  
  Doreen Kamori, Zafrul Hasan, Jonathan M. Carlson, A I Kawana-Tachikawa, Hiroyuki Gatanaga, Shinichi Oka, Takamasa Ueno
  
  AIDS Research and Human Retroviruses | April 2021, 第 37 卷(12): pp. 962-966
  
  DOI Publication Publication Publication Publication
- Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein.
  
  Debra Van Egeren, Alexander Novokhodko, Madison Stoddard, Uyen Tran, Bruce Zetter, Michael Rogers, Bradley L. Pentelute, Jonathan M. Carlson, Mark Hixon, Diane Joseph-McCarthy, Arijit Chakravarty
  
  PLOS ONE | April 2021, 第 16 卷(4): pp. e0250780
  
  DOI Publication Publication Publication Publication Publication Publication Publication 项目
- 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, 第 10 卷(1): pp. 19416-19416
  
  DOI Publication Publication
- HLA tapasin independence: broader peptide repertoire and HIV control.
  
  Arman A. Bashirova, Mathias Viard, Vivek Naranbhai, Alba Grifoni, Wilfredo Garcia-Beltran, Marjan Akdag, Yuko Yuki, Xiaojiang Gao, Colm O’hUigin, Malini Raghavan, Steven Wolinsky, Jay H. Bream, Priya Duggal, Jeremy Martinson, Nelson L. Michael, Gregory D. Kirk, Susan P. Buchbinder, David Haas, James J. Goedert, Steven G. Deeks, Jacques Fellay, Bruce Walker, Philip Goulder, Peter Cresswell, Tim Elliott, Alessandro Sette, Jonathan M. Carlson, Mary Carrington
  
  Proceedings of the National Academy of Sciences of the United States of America | October 2020, 第 117 卷(45): pp. 28232-28238
  
  DOI PDF Publication Publication Publication Publication Publication Publication Publication
- CD8 T cells targeting adapted epitopes in chronic HIV infection promote dendritic cell maturation and CD4 T cell trans-infection.
  
  Kai Qin, Sushma Boppana, Victor Y. Du, Jonathan M. Carlson, Ling Yue, Dario A. Dilernia, Eric Hunter, Robbie B. Mailliard, Simon A. Mallal, Anju Bansal, Paul A. Goepfert
  
  PLOS Pathogens | August 2019, 第 15 卷(8)
  
  DOI PDF Publication Publication Publication Publication Publication Publication Publication
- Clinical and evolutionary consequences of HIV adaptation to HLA: implications for vaccine and cure
  
  Santiago Avila-Rios, Jonathan M. Carlson, Mina John, Simon Mallal, Zabrina L Brumme
  
  Current Opinion in HIV and AIDS | May 2019, 第 14 卷(3): pp. 194-204
  
  Publication
- Genotypic and mechanistic characterization of subtype-specific hiv adaptation to host cellular immunity
  
  Natalie N Kinloch, Guinevere Q Lee, Jonathan M. Carlson, Steven W Jin, Chanson J Brumme, Helen Byakwaga, Conrad Muzoora, Mwebesa B Bwana, Kyle D Cobarrubias, Peter W Hunt, Jeff N Martin, Mary Carrington, David R Bangsberg, P Richard Harrigan, Mark A Brockman, Zabrina L Brumme
  
  Journal of Virology | January 2019, 第 93 卷(1): pp. e01502-18
  
  Publication
- Antisense-derived HIV-1 cryptic epitopes are not major drivers of viral evolution during the acute phase of infection
  
  Binghao J Peng, Jonathan M. Carlson, Michael KP Liu, Feng Gao, Nilu Goonetilleke, Andrew J McMichael, Persephone Borrow, Jill Gilmour, Sonya L Heath, Eric Hunter, Anju Bansal, Paul A Goepfert
  
  Journal of Virology | October 2018, 第 92 卷(19): pp. e00711-18
  
  Publication
- Killer cell immunoglobulin–like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1
  
  Maureen P. Martin, Vivek Naranbhai, Patrick R. Shea, Ying Qi, Veron Ramsuran, Nicolas Vince, Xiaojiang Gao, Rasmi Thomas, Zabrina L. Brumme, Jonathan M. Carlson, Steven M. Wolinsky, James J. Goedert, Bruce D. Walker, Florencia P. Segal, Steven G. Deeks, David W. Haas, Stephen A. Migueles, Mark Connors, Nelson Michael, Jacques Fellay, Emma Gostick, Sian Llewellyn-Lacey, David A. Price, Bernard A. Lafont, Phillip Pymm, Philippa M. Saunders, Jacqueline Widjaja, Shu Cheng Wong, Julian P. Vivian, Jamie Rossjohn, Andrew G. Brooks,, Mary Carrington
  
  Journal of Clinical Investigation | May 2018, 第 128 卷(5): pp. 1903-1912
  
  Publication Publication
- HLA-associated polymorphisms in the HIV-2 capsid highlight key differences between HIV-1 and HIV-2 immune adaptation
  
  Thushan I. de Silva, Aleksandra Leligdowicz, Jonathan M. Carlson, Miguel Garcia-Knight, Clayton Onyango, Nicholas Miller, Louis-Marie Yindom, Stephane Hué, Assan Jaye, Tao Dong, Matthew Cotten, Sarah L Rowland-Jones
  
  AIDS | March 2018, 第 32 卷(6): pp. 709-714
  
  Publication
- Weaker HLA footprints on HIV in the unique and highly genetically admixed host population of Mexico
  
  Maribel Soto-Nava, Santiago Avila-Ríos, Humberto Valenzuela-Ponce, Claudia García-Morales, Jonathan M. Carlson, Daniela Tapia-Trejo, Daniela Garrido-Rodriguez, Selma N. Alva-Hernández, Thalía A. García-Tellez, Akio Murakami-Ogasawara, the International HIV Adaptation Collaborative, Simon A Mallal, Mina John, Mark A. Brockman, Chanson J. Brumme, Zabrina L. Brumme, Gustavo Reyes-Teran, the HIV MexNet Group
  
  Journal of Virology | November 2017
  
  论文与出版物论文与出版物论文与出版物 Github
- Mother-to-Child HIV Transmission Bottleneck Selects for Consensus Virus with Lower Gag-Protease-Driven Replication Capacity
  
  Vanessa L. Naidoo, Jaclyn K. Mann, Christie Noble, Emily Adland, Jonathan M. Carlson, Jake Thomas, Chanson J. Brumme, Christina F. Thobakgale-Tshabalala, Zabrina L. Brumme, Mark A. Brockman, Philip J. R. Goulder, Thumbi Ndung'u
  
  Journal of Virology | September 2017, 第 91 卷: pp. e00518-17
  
  论文与出版物论文与出版物 Github
- Brief Report: Selection of HIV-1 Variants With Higher Transmission Potential by 1% Tenofovir Gel Microbicide
  
  Nobubelo K. Ngandu, Jonathan M. Carlson, Denis R. Chopera, Nonkululeko Ndabamb, Quarraisha Abdool Karim, Salim Abdool Karim, Carolyn Williamson
  
  Journal of Acquired Immune Deficiency Syndromes | September 2017, 第 76 卷: pp. 43-47
  
  论文与出版物论文与出版物论文与出版物 Github
- PARV4 prevalence, phylogeny, immunology and coinfection with HIV, HBV and HCV in a multicentre African cohort
  
  Colin P. Sharp, William F. Gregory, Louise Hattingh, Amna Malik, Emily Adland, Samantha Daniels, Anriette van Zyl, Jonathan M. Carlson, Susan Wareing, Anthony Ogwu, Roger Shapiro, Lynn Riddell, Fabian Chen, Thumbi Ndung'u, Philip J.R. Goulder, Paul Klenerman, Peter Simmonds, Pieter Jooste, Philippa C. Matthews
  
  Wellcome Open Research | April 2017, 第 2 卷: pp. 26
  
  论文与出版物论文与出版物论文与出版物 Github
- Paediatric non-progression following grandmother-to-child HIV transmission
  
  M.-H. Tsai, M. Muenchhof, E. Adland, A. Carlqvist, J. Roider, D. K. Cole, A. K. Sewell, Jonathan M. Carlson, T. Ndung’u, P. J. R. Goulder
  
  Retrovirology | September 2016, 第 13 卷: pp. 65
  
  论文与出版物论文与出版物论文与出版物 Github
- Impact of Pre-Adapted HIV Transmission
  
  Jonathan M. Carlson, Victor Y. Du, Nico Pfeifer, Anju Bansal, Vincent T. F. Tan, Karen Power, Chanson J. Brumme, Anat Kreimer, Charles E. DeZiel, Nicolo Fusi, Malinda Schaefer, Mark A. Brockman, Jill Gilmour, Matt A. Price, William Kilembe, Richard Haubrich, Mina John, Simon Mallal, Roger Shapiro, John Frater, P. Richard Harrigan, Thumbi Ndung'u, Susan Allen, David Heckerman, John Sidney, Todd M. Allen, Philip J.R. Goulder, Zabrina L. Brumme, Eric Hunter, Paul A. Goepfert
  
  Nature Medicine | May 2016, 第 22 卷: pp. 606-613
  
  Bonnie Mathieson Young Investigator Award
  
  Author's Version Publication DOI Github
- HIV-1–Specific CD8 T Cells Exhibit Limited Cross-Reactivity during Acute Infection
  
  Victor Y. Du, Anju Bansal, Jonathan M. Carlson, Jesus F. Salazar-Gonzalez, Maria G. Salazar, Kristin Ladell, Stephanie Gras, Tracy M. Josephs, Sonya L. Heath, David A. Price, Jamie Rossjohn, Eric Hunter, Paul A. Goepfert
  
  Journal of Immunology | April 2016, 第 198 卷: pp. 3276-3286
  
  论文与出版物论文与出版物 Github
- Lower Viral Loads and Slower CD4+ T-Cell Count Decline in MRKAd5 HIV-1 Vaccinees Expressing Disease-Susceptible HLA-B*58:02
  
  Ellen M. Leitman, Jacob Hurst, Masahiko Mori, James Kublin, Thumbi Ndung'u, Bruce D. Walker, Jonathan M. Carlson, Glenda E. Gray, Philippa C. Matthews, Nicole Frahm, Philip J.R. Goulder
  
  The Journal of infectious diseases | March 2016, 第 214 卷: pp. 379-389
  
  论文与出版物论文与出版物论文与出版物 Github
- CD8+ TCR bias and immunodominance in HIV-1 infection
  
  Henrik N. Kløverpris, Reuben McGregor, James E. McLaren, Kristin Ladell, Mikkel Harndahl, Anette Stryhn, Jonathan M. Carlson, Catherine Koofhethile, Bram Gerritsen, Can Kesmir, Fabian Chen, Lynn Riddell, Graz Luzzi, Alasdair Leslie, Bruce D. Walker, Thumbi Ndung'u, Søren Buus, David A. Price, Philip J.R. Goulder
  
  The Journal of Immunology | June 2015, 第 194 卷: pp. 5329-5345
  
  论文与出版物论文与出版物 Github
- HIV-1 Adaptation to HLA: A Window into Virus–Host Immune Interactions
  
  Jonathan M. Carlson, Anh Q. Le, Aniqa Shahid, Zabrina L. Brumme
  
  Trends in Microbiology | April 2015, 第 23 卷(4): pp. 212-224
  
  论文与出版物论文与出版物论文与出版物
- 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, 第 88 卷(22): pp. 12937-12948
  
  论文与出版物论文与出版物论文与出版物
- 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, 第 345 卷(6193)
  
  论文与出版物论文与出版物论文与出版物论文与出版物论文与出版物
- 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, 第 340 卷(6128): pp. 87-91
  
  论文与出版物论文与出版物
- 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, 第 86 卷(24): pp. 13202-13216
  
  Publication Publication
- Widespread Impact of HLA Restriction on Immune Control and Escape Pathways in HIV-1
  
  Jonathan M. Carlson, Jennifer Listgarten, Nico Pfeifer, Vincent Tan, Carl Kadie, Bruce D. Walker, Thumbi Ndung'u, Roger Shapiro, John Frater, Zabrina L. Brumme, Philip J. R. Goulder, David Heckerman
  
  Journal of Virology | May 2012, 第 86 卷(9): pp. 5230-5243
  
  论文与出版物论文与出版物论文与出版物 Github
- HIV-1 Adaptation to NK-Cell-Mediated Immune Pressure
  
  Galit Alter, David Heckerman, Arne Schneidewind, Lena Fadda, Carl Kadie, Jonathan M. Carlson, Cesar Oniangue-Ndza, Maureen Martin, Bin Li, Salim I. Khakoo, Mary Carrington, Todd M. Allen, Marcus Altfeld
  
  Nature International weekly journal of science | August 2011, 第 476 卷: pp. 96-100
  
  论文与出版物论文与出版物
- 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
  
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