Portrait of Jonathan M. Carlson

Jonathan M. Carlson

Senior Researcher


I am a Senior Researcher in the Nature + Computing group at Microsoft Research in Redmond. Previously, I was with Microsoft Research in Los Angeles, where I joined after completing my Ph.D. in the department of Computer Science and Engineering and the University of Washington.

My area of expertise is machine learning and applied statistics for computation biology, with a specific emphasis on viruses and other microbes. Much of my research has been focused on HIV evolution, though I'm also interested in microbial metagenomics as well.

If you're interested in the tools I've developed for HIV, please see our PhyloD web app.

For information on project PREMONITION, see the project page

Research Highlights

Impact of pre-adapted HIV transmission May 2016
HIV adapts to our immune response. So what? That's been a surprisingly difficult question to answer, beyond very focused questions about very special epitopes. So we teamed up with Paul Goepfert of UAB, Eric Hunter of Emory, and a several other labs to answer the question. First, we built a model of HIV adaptation and trained it on 4000 people. Armed with this model, we looked at a number of data sets to see how adaptation predicts disease progression, then Paul's designed a series of functional studies to validate the results. Not only does HIV adaptation within a patient predict rapid disease progression, but infection by a pre-adapted virus–a virus that already carries mutations specific to the new host–results in dysfunctional immune responses and rapid progression. Thus suggests HIV is finding universal holes in our immune response, and bolsters claims that we should be pursuing vaccines that target regions of the virus that are relatively conserved. Moreover, these results highlight the interactions between host and virus genetics, explaining many of the "protective" effects commonly attributed to HLA alleles, and confounding estimates such as the "heritability" of viral load that ignore such interactions. Read more… or Watch the video…


Project Premonition

Established: March 2, 2015

Interested in evaluating Project Premonition technologies and data? Sign up here Project Premonition aims to detect pathogens before they cause outbreaks Emerging infectious diseases such as Zika, Ebola, Chikungunya and MERS are dangerous and unpredictable. Public health organizations need data as early as possible to predict disease spread and plan responses. Yet early data is very difficult to obtain, because it must be proactively collected from potential disease sources in the environment. Researchers estimate between…


Established: March 1, 2007

HIV, like most retroviruses, is characterized by a tremendous rate of mutation, which leads to a high level of genetic diversity within and among patients. This genetic variation is the substrate for rapid within-host evolution. As our immune system learns to target the virus, the virus adapts, leading to an endless game of cat-and-mouse. From a scientific perspective, this provides a useful opportunity: if HIV is constantly adapting to our individual immune responses, then studying…



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, May 16, 2016, View abstract, View external link
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, in PLoS Pathogens, May 1, 2016, View abstract, View external link


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, in Journal of Virology, November 15, 2015, View abstract, View external link
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, in Plos Medicine, November 1, 2015, View abstract, View external link
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, in PLOS Computational Biology, February 3, 2015, View abstract, View external link


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, in Virology, Elsevier, November 1, 2014, View abstract, View external link
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, in Proceedings of the National Academy of Sciences of the United States of America, October 31, 2014, View abstract, View external link
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, in PLoS One, October 28, 2014, View abstract, View external link
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, in Science, Science, July 12, 2014, View abstract, Download PDF, View external link
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, in PLoS Genet, April 24, 2014, View abstract, View external link


A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control
Istvan Bartha, Jonathan M. Carlson, Chanson J Brumme, Paul J McLaren, Zabrina L Brumme, Mina John, David W Haas, Javier Martinez-Picado, Judith Dalmau, Cecilio López-Galíndez, Concepción Casado, Andri Rauch, Huldrych F Günthard, Enos Bernasconi, Pietro Vernazza, Thomas Klimkait, Sabine Yerly, Stephen J O’Brien, Jennifer Listgarten, Nico Pfeifer, Christoph Lippert, Nicolo Fusi, Zoltán Kutalik, Todd M Allen, Viktor Müller, P Richard Harrigan, David Heckerman, Amalio Telenti, Jacques Fellay, in eLife, October 29, 2013, View abstract, Download PDF
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, in Science, April 5, 2013, View abstract, View external link
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, in Journal of Virology, February 1, 2013, View abstract, View external link


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, in Journal of Virololgy, December 5, 2012, View abstract, View external link
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, December 4, 2012, View abstract, View external link
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, November 5, 2012, View abstract, View external link
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, in Journal of Virology, September 26, 2012, View abstract, View external link
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, April 11, 2012, View abstract, View external link


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 22, 2011, View abstract, View external link
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, April 15, 2011, View abstract, View external link
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 2, 2011, View abstract, View external link


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, in Journal of Virology, November 1, 2010, View abstract, View external link


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, January 1, 2009, View abstract, View external link


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, January 1, 2008, View abstract, Download PDF, View external link
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, in Journal of Virology, January 1, 2008, View abstract, View external link
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, in Journal of Virology, January 1, 2008, View abstract, View external link
Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients
Thomas Kuntzen, Joerg Timm, Andrew Berical, Niall Lennon, Aaron M. Berlin, Sarah K. Young, Bongshin Lee, David Heckerman, Jonathan M. Carlson, Laura L. Reyor, Marianna Kleyman, Cory M. McMahon, Christopher Birch, Julian Schulze zur Wiesch, Timothy Ledlie, Michael Koehrsen, Chinnappa Kodira, Andrew D. Roberts, Georg M. Lauer, Hugo R. Rosen, Florian Bihl, Andreas Cerny, Ulrich Spengler, Zhimin Liu, Arthur Y. Kim, Yanming Xing, Arne Schneidewind, Margaret A. Madey, Jaquelyn F. Fleckenstein, Vicki M. Park, James E. Galagan, Chad Nusbaum, Bruce D. Walker, Gerond V. Lake-Bakaar, Eric S. Daar, Ira M. Jacobson, Edward D. Gomperts, Brian R. Edlin, Sharyne M. Donfield, Raymond T. Chung, Andrew H. Talal, Tony Marion, Bruce W. Birren, Matthew R. Henn, Todd M. Allen, in Hepatology, January 1, 2008, View abstract, View external link


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, in Science, American Association for the Advancement of Science, January 1, 2007, View abstract, View external link




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The Coming Genomics Software Revolution


July 24, 2014


Lee Hood, Eliezer Van Allen, Jonathan Carlson, and Ravi Pandya


Institute for Systems Biology, Harvard University, Microsoft Research, Microsoft



March 2016

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My models of viral escape have achieved broad recognition in the HIV community, where they have led to the discovery of novel viral-host interactions, insights into mechanisms of natural immune control, and the identification of vaccine candidates that are moving toward clinical trials. I have co-authored over 60 papers in the field with dozens of labs, including publications in Science and Nature, and have served on advisory panels and committees for the Institutes of Medicine, the Gates Foundation and the Center for HIV/AIDS Vaccine Immunology.