Portrait of Jonathan Carlson

Jonathan Carlson

Senior Researcher


I am a Researcher in the Nature + Computing and Machine Learning groups at Microsoft Research. I am interested in the development and application of statistical and machine learning methods to biological data, working in close collaboration with biological and medical researchers. I am especially interested in applications in immunology, virology and genetics, as well as the development of more general techniques that transcend specific disciplines. My current primary focus is to develop statistical models that help us understand HIV’s adaptive response to the immune system.

I joined the Escience group at Microsoft as a researcher in 2008, and have been focusing on applied machine learning and statistics for HIV ever since. My approach is fundamentally interdisciplinary, as I seek to use computational tools to gain real biological insight and always work in close collaboration with biologists. I received my BA in 2003 from Dartmouth, where I was awarded the top senior thesis prizes in both biology and computer science, and my Ph.D in computer science in 2009 from the University of Washington, where I was awarded the university’s distinguished dissertation award and was a finalist for the US Council of Graduate School’s dissertation award.


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…



Impact of Pre-Adapted HIV Transmission
Jonathan 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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.