Researcher, eScience Research Group Ph.D. University of Washington, 2009 carlson@microsoft.com vita

Projects

• PhyloD: Statistical modeling of HIV adaptation. We've used this approach to identify sites of HLA-mediated escape and related covariation in HIV. Code available here.
• PhyloD Viewer: Visualization tool for sequence covariation and adaptation.
• Phylo Detective: Visualization tool for viewing traits on a large phylogeny.
• False discovery rates for contingency tables: A computationally efficient means of calculating exact FDR for a set of 2x2 contingency tables or Fisher's exact test for a single table.
• Microsoft Biology Foundation: MBF is a bioinformatics library for .NET. Upcoming versions of PhyloD will be available as part of the suite of tools packaged with MBF.

Publications

Selected Publications

• 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 and David Heckerman. Journal of Virology, 86(9):5230-5243, May 2012.
• Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag. Jonathan M. Carlson, Zabrina Brumme, Christine Rousseau, Chanson Brumme, Philippa Matthews, Carl Kadie, James Mullins, Bruce D. Walker, P. Richard Harrigan, Philip J.R. Goulder, David Heckerman. PLoS Computational Biology, 4(11): e1000225, November 2008.
• Phylogenetic dependency networks: Identifying patterns of adaptation in HIV. Jonathan M. Carlson. Doctoral Dissertation, Dept. Computer Science and Engineering, University of Washington, February 2009.
  UW distinguished dissertation, Council of Graduate School's distinguished dissertation semi-finalist.
  [abstract, summary, extended summary, pdf (4MB)]

All publications (Citations)

2012

• 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 and David Heckerman. Journal of Virology, 86(9):5230-5243, May 2012.
• High-avidity, high-IFNγ-producing CD8 T-cell responses following immune selection during HIV-1 infection. Niamh M Keane, Steven G Roberts, Coral-Ann M Almeida, Tanya Krishnan, Abha Chopra, Emma Demaine, Rebecca Laird, Monika Tschochner, Jonathan M Carlson, Simon Mallal, David Heckerman, Ian James and Mina John. Immunology and Cell Biology, 90, 224-234, February 2012.
• 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 and Thumbi Ndung'u. Journal of Virology, 86(2):1273-1276, January 2012.

2011

• 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 Carlson, David W. Haas, Sharon A. Riddler, Richard Haubrich, David Heckerman, Simon Mallal and Mina John. The Journal of Immunology, 187(5):2502-2513, September, 2011.
• HIV-1 adaptation to NK-cell-mediated immune pressure. Galit Alter, David Heckerman, Arne Schneidewind, Lena Fadda, Carl M. Kadie, Jonathan M. Carlson, Cesar Oniangue-Ndza, Maureen Martin, Bin Li, Salim I. Khakoo, Mary Carrington, Todd M. Allen and Marcus Altfeld. Nature, 476(7358):96-100, August 2011.
• 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 Kloverpris, Pieter Jooste, Dominique Goedhals, Cloete van Vuuren, Dewald Steyn, Lynn Riddell, Fabian Chen, Graz Luzzi, Thambiah Balachandran, Thumbi Ndung’u, Søren Buus, Mary Carrington, Roger Shapiro, David Heckerman and Philip J. R. Goulder. Journal of Immunology, 186(10):5675-5686, May 2011.
• 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, Bloemfontein-Oxford Collaborative Group, Cloete van Vuuren, John Frater. PLoS One, 6(4):e19018, April 2011.
• 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, and Thumbi Ndung'u. Journal of Virology, 85(8):3996-4006, April 2011.

2010

• The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. The International HIV Controllers Study. Science, 330(6010):1551-1557, December 2010.
• 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, and Philip J.R. Goulder. Journal of Virology, doi: 10.1128/JVI.01879-10, November 2010.
• Early selection in Gag by protective HLA alleles contributes to reduced HIV-1 replication capacity that may be largely compensated in chronic infection. Mark A Brockman, Zabrina L Brumme, Chanson J Brumme, Toshiyuki Miura, Jennifer Sela, Pamela C Rosato, Carl M 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, and Todd M Allen. Journal of Virology, 84(22):11937-11949, November 2010.
• 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 M. 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. Jorunal of Virology, 84(20):10820-10831, October 2010.
• 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 and Philip JR Goulder. Jorunal of Virology, 84(19):9879-9888, October 2010.
• Amino-acid co-variation in HIV-1 Gag subtype C: HLA-mediated selection pressure and compensatory dynamics. Morgan 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. Groulder, Bruce D. Walker, Christian Brander, David Heckerman and James I. Mullins. PLoS One, 5(9):e12463, September 2010.
• 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 and Simon Mallal. The Journal of Immunology, 184(8):4368-4377, March 2010.
• CD8 T cell response and evolutionary pressure to HIV-1 cryptic epitopes derived from antisense transcription. Anju Bansal, Jonathan 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, and Paul A. Goepfert. Journal of Experimental Medicine, 207(1):51-59, January 2010. [Blog post]
• Viral adaptation to immune selection pressure by HLA class I-restricted CTL responses targeting epitopes in HIV frameshift sequences. Christoph 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, and Christian Brander. Journal of Experimental Medicine, 207(1):61-75, January 2010. [ScienceDaily]

2009

• 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, and Gustavo Reyes-Teran. Retrovirology, 6(1):72, August 2009.
• 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 M. Kadie, Nicole Frahm, Christian Brander, David W. Haas, Sharon A. Riddler, Richard Haubrich, Bruce D. Walker, P. Richard Harrigan, David Heckerman, Simon Mallal. PLoS One, 4(8): e6687, August 2009.
• PhyloDet: a scalable visualization tool for mapping multiple traits to large evolutionary trees. Bongshin Lee, Lev Nachmanson , George Robertson , Jonathan M. Carlson and David Heckerman. Bioinformatics, 25(19): 2611-2612, July 2009.
• Estimating false discovery rates for contingency tables. Jonathan M. Carlson, David Heckerman, and Guy Shani, no. MSR-TR-2009-53, May 2009.
• 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 Carlson, David Heckerman, Thumbi Ndung'u, Bruce D Walker, Todd M Allen, Oliver G Pybus, and Philip J R Goulder. Journal of Virology, 83(9):4605-4615, May 2009.
• 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, and Todd M. Allen. Journal of Virology, 83(4):1845-1855, February 2009.

2008

• Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag. Jonathan M. Carlson, Zabrina Brumme, Christine Rousseau, Chanson Brumme, Philippa Matthews, Carl Kadie, James Mullins, Bruce D. Walker, P. Richard Harrigan, Philip J.R. Goulder, David Heckerman. PLoS Computational Biology, 4(11): e1000225, November 2008.    [cover feature]
• Protective HLA Class I Alleles Restricting Acute-Phase CD8+ T Cell Responses are Associated with Viral Escape Mutations Located in Highly Conserved Regions of HIV-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, doi:10.1128/JVI.01061-08, November 2008.
• 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 Brumme*, Chanson Brumme*, Jonathan M. Carlson*, Hendrick Streeck, Mina John, Quentin Eichbaum, Brian Block, Brett Baker, Carl Kadie, Martin Markowitz, Heiko Jessen, Anthony Kelleher, Eric Rosenberg, John Kaldor, Mary Carrington, Todd Allen, Simon Mallal, Marcus Altfeld, David Heckerman, Bruce D. Walker. Journal of Virology, 82(18)9216-9227, September 2008.
• Central role of reverting mutations in HLA associations with human immunodeficiency virus set point. Philippa Matthews, Andrew Prendergast, Alasdair Leslie, Hayley Crawford, Rebecca Payne, Christine Rousseau, Isobella Honeyborne, Jonathan M. Carlson, Carl Kadie, Christian Brander, Jamers Mullins, Hoosen Coovadia, Thumbi Nding.u, Bruce D. Walker, David Heckerman, Philip Goulder Journal of Virology, 82(17):8548-59, September 2008.
• 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 Brumme, Zabrina L. Brumme, Jonathan M. Carlson, Marcus Daniels, Florencia Pereyra, Alicia Trocha, Marylyn M. Addo, Brian Block, Alissa Rothchild, Brett Baker, Theresa Flynn1, Arne Schneidewind, Bin Li, Yaoyu Wang, Bette T. Korber, David Heckerman, Todd M.Allen, and Bruce D.Walker. Journal of Virology, 82(17):8422-30, September 2008.
• Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naive 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. Hepatology , 48(6) 1769-1778, Online July 2008.
• HIV evolution in response to HLA-restricted CTL selection pressures: a population-based perspective. Jonathan M. Carlson and Zabrina L. Brumme. (February 2008) Microbes and Infection, 10(5):455-61.
• 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, Haley Crawford, Andrew Prendergast, Philippa Matthews, Dana N. Raugi, Brandon S. Maust, Gerald H. Learn, David C. Nickle, Nicole Frahm, Christian Brander, Bruce D. Walker, Philip J. R. Goulder, Tanmoy Bhattacharya, David E. Heckerman, Bette T. Korber, James I. Mullins (2008) Journal of Virology, 82(13):6434-6446.
• HLA-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection.. Zabrina Brumme, Iris Tao, Sharon Szeto, Chanson Brumme, Jonathan M. Carlson, Dennison Chan, Carl Kadie, Nicole Frahm, Christian Brander, Bruce D. Walker, David Heckerman, P. Richard Harrigan. AIDS, 22(11):1277-1286, 2008.
• Transmission of HIV-1 Gag Immune Escape Mutations is Associated with Reduced Viral Load in Linked Recipients.. Paul 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 Goulder, Eric Hunter. Journal of Experimental Medicine, 205(5):1009-1017, May 2008.

2007

• Leveraging hierarchical population structure in discrete association studies.. Jonathan M. Carlson, Carl Kadie, Simon Mallal, David Heckerman. PLoS One, 2(7):e591, July 2007.
• Evidence of differential HLA class I-mediated viral evolution in functional and accessory/regulatory genes of Human Immunodeficiency Virus (HIV) type-1. Zabrina L. Brumme, Chanson J. Brumme, David Heckerman, Bette T. Korber, Marcus Daniels, Jonathan M. Carlson, 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. PLoS Pathogens, 3(7):e94, July 2007. [In the news: NewScientist, EurekAlert]
• 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 Gashen, Simon Mallal, James I. Mullins, David C. Nickle, Joshua Herbeck, Christine Rousseau, Gerald H. Learn, Toshiyuki Miura, Christian Brander, Bruce Walker, Bette Korber. Science, 315(5818):1583-1586, March 2007. [commentary] [In the news: MS release CNet ]
• A novel ensemble learning method for de novo computational identification DNA binding sites. Arijit Chakravarty, Jonatha M. Carlson, Rhadika S. Khetani and Robert H. Gross BMC Bioinformatics, 8:249, July 2007.
• SCOPE: A web server for practical de novo motif discovery. Jonathan M. Carlson, Arijit Chakravarty, Rhadika S. Khetani, Charles E. DeZiel and Robert H. Gross. Nucleic Acids Research, 35(Web Server issue):W259-264, July 2007.
• SPACER: Identification of cis-regulatory elements with non-contiguous critical residues. Arijit Chakravarty, Jonathan M. Carlson, Rhadika S. Khetani, Charles E. DeZiel, Robert H. Gross. Bioinformatics, 23(8):1029-1031, May 2007.