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.
.NET Bio: .NET Bio is a bioinformatics library for .NET. Upcoming versions of PhyloD will be available as part of the suite of tools packaged with .NET Bio.

Selected Videos

Lindau Nobel Laureates meeting opening ceremonies, with Bill Gates, Ada Yonath and Sandra Chishimba, July 2011.
[youtube, scientific american blogs, nature blog]
Health Tech Today, Microsoft technology helps unlock the mysteries of HIV, December 7, 2010.
Microsoft's Connected Health Conference, June 2010.
.NET Rocks Internet Audio Talk Show, Microsoft battles HIV!, September 10, 2009.
On10.NET, Microsoft Research: A look at tomorrow’s health solutions today - part II, August 25, 2008.

Publications

Selected Publications

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 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, and the International HIV Adaptation Collaborative Journal of Virology, 86(24):13187-13201, December 2012.
[Cover image]
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 and David Heckerman. PLoS Computational Biology, 4(11): e1000225, November 2008.
[Cover image]
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)

2013

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 and Mary Carrington. Science, 340(6128):87-91, April 2013. [MSR Blog]
Frequent and Variable Cytotoxic-T-Lymphocyte Escape-Associated Fitness Costs in the Human Immunodeficiency Virus Type 1 Subtype B Gag Proteins. Christian L Boutwell, Jonathan M Carlson, Tien-Ho Lin, Aaron Seese, Karen A Power, Jian Peng, Yanhua Tang, Zabrina L Brumme, David Heckerman, Arne Schneidewind and Todd M Allen. Journal of Virology, 87(7):3952-3965, March 2013.
HIV escape mutations occur preferentially at HLA-binding sites of CD8 T cell epitopes. Corine Bronke, Coral-Ann M Almeida, Elizabeth Mckinnon, Steven G Roberts, Niamh M Keane, Abha Chopra, Jonathan M Carlson, David Heckerman, Simon Mallal and Mina John. AIDS, 27(6):899-905, March 2013.
Distinct HIV-1 Escape Patterns Selected by Cytotoxic T Cells with Identical Epitope Specificity. Yuichi Yagitaa, Nozomi Kusea, Kimiko Kurokib, Hiroyuki Gatanagaa, Jonathan M. Carlsond, 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 and Masafumi Takiguchia. Journal of Virology, 87(4):2253-2263, February 2013.
Significant Reductions in Gag-Protease-Mediated HIV-1 Replication Capacity during the Course of the Epidemic in Japan. Shigeru Nomura, Noriaki Hosoya, Zabrina L Brumme, Mark A Brockman, Tadashi Kikuchi, Michiko Koga, Hitomi Nakamura, Tomohiko Koibuchi, Takeshi Fujii, Jonathan M Carlson, David Heckerman, Ai Kawana-Tachikawa, Aikichi Iwamoto and Toshiyuki Miura. Journal of Virology, 87(3):1465-1476, February 2013.

2012

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 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, and the International HIV Adaptation Collaborative. Journal of Virology, 86(24):13187-13201, December 2012.
[Cover image]
Role of transmitted Gag CTL escape mutations in defining replicative capacity and early HIV-1 pathogenesis. Daniel T. Claiborne*, Jessica L. Prince*, Jonathan M. Carlson, Malinda Schaefer, Tianwei Yu, Shabir Lahki, Heather A. Prentice, Ling Yue, Sundaram A. Vishwanathan, William Kilembe, Paul Goepfert, Matt Price, Joseph Mulenga, Cynthia A. Derdeyn, Jiaming Tang, David Heckerman, Richard A. Kaslow, Susan A. Allen, and Eric Hunter. Plos Pathogens, 8(11):e1003041, November 2012.
Increased HIV-1 vaccine efficacy against viruses with genetic signatures in Env V2. Morgane Rolland*, Paul T. Edlefsen*, Brendan B. Larsen, Sodsai Tovanabutra, Eric Sanders-Buell, Tomer Hertz, Allan C. de Camp, Chris Carrico, Sergey Menis, Craig A. Magaret, Hasan Ahmed, Michal Juraska, Lennie Chen, Philip Konopa, Snehal Nariya, Julia N. Stoddard, Kim Wong, Hong Zhao, Wenjie Deng, Brandon S. Maust, Meera Bose, Shana Howell, Adam Bates, Michelle Lazzaro, Annemarie O’Sullivan, Esther Lei, Andrea Bradfield, Grace Ibitamuno, Vatcharain Assawadarachai, Robert J. O’Connell, Mark S. deSouza, Sorachai Nitayaphan, Supachai Rerks-Ngarm, Merlin L. Robb, Jason S. McLellan, Ivelin Georgiev, Peter D. Kwong, Jonathan M. Carlson, Nelson L. Michael, William R. Schief, Peter B. Gilbert, James I. Mullins and Jerome H. Kim. Nature, 490(7420), 417-420, October 2012.
[In the news: Nature News, Nature News & Views, Infection Control Today, ScienceBlog, UW Today]
Co-Operative Additive Effects between HLA Alleles in Control of HIV-1. Philippa C. Matthews*, Jennifer Listgarten*, Jonathan M. Carlson, Rebecca Payne, Kuan-Hsiang Gary Huang, John Frater, Dominique Goedhals, Dewald Steyn, Cloete van Vuuren, Paolo Paioni, Pieter Jooste, Anthony Ogwu, Roger Shapiro, Zenele Mncube, Thumbi Ndung'u, Bruce D. Walker, David Heckerman and Philip J. R. Goulder PLoS One, 7(10):e47799, October 2012.
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 and the CAPRISA 002 Study Team Journal of Virology, doi:10.1128/JVI.02171-12, September 2012.
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. Kløverpris, 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 Shapiro, Christian Brander, Bruce Walker, Andrew K Sewell, Gustavo Reyes Teran,David Heckerman, Eric Hunter Søren Buus, Masafumi Takiguchi and Philip J. R. Goulder Journal of Virology, doi:10.1128/JVI.01381-12, September 2012.
HIV control through a single nucleotide on the HLA-B locus. Henrik N. Kløverpris, Mikkel Harndahl, Alasdair J. Leslie, Jonathan M. Carlson, Nasreen Ismail, Mary van der Stok, Kuan-Hsiang Gary Huang, Fabian Chen, Lynn Riddell, Dewald Steyn, Dominique Goedhals, Cloete van Vuuren, John Frater, Bruce D. Walker0, Mary Carrington, Thumbi Ndung'u, Søren Buus and Philip Goulder, Journal of Virology, 86(21)11493-11500, November 2012.
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 and Zabrina L Brumme. Journal of Virology, 86(12):6913-6923, June 2012.
Aminopeptidase Substrate Preference Affects HIV Epitope Presentation and Predicts Immune Escape Patterns in HIV-Infected Individuals. Shao Chong Zhang, Eric Martin, Mariko Shimada, Sasha Blue Godfrey, Jennifer Fricke, Shirley Locastro, Nicole Y Lai, Paul Liebesny, Jonathan M Carlson, Chanson J Brumme, Oluwatobi Awele Ogbechie, Huabiao Chen, Bruce D Walker, Zabrina L Brumme, Daniel G Kavanagh and Sylvie Le Gall. The Journal of Immunology, 188(12):5924-5934, June 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.
Minor contribution of HLA class I-associated selective pressure to the variability of HIV-1 accessory protein Vpu. Zafrul Hasan, Jonathan M Carlson, Hiroyuki Gatanaga, Anh Le, Chanson J Brumme, Shinichi Oka, Zabrina L Brumme and Takamasa Ueno. Biochemical and Biophysical Research Communications, 421(2):291-295, April 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. Journal 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 image]
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. [pdf]
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, Jonathan 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.

2006

Bounded search for de novo identification of degenerate cis-regulatory elements. Jonathan M. Carlson*, Arijit Chakravarty*, Robert S. Khetani and Robert H. Gross BMC Bioinformatics, 7(1):254, May 2006.
BEAM: A beam search algorithm for the identification of cis-regulatory elements in groups of genes. Jonathan M. Carlson*, Arijit Chakravarty* and Robert H. Gross. Journal of Computational Biology, 13(3):686-701, April 2006.

Theses

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)]
Creation of a Relational Database for Identifying Functional DNA Sequence Motifs in A. thaliana and Other Genomes. Jonathan M. Carlson. Undergraduate Honors thesis, Dept. Biology, Dartmouth College, June 2003.
Dartmouth Kemeny Computing prize and Reed Biology Award
[pdf]

Contact

Microsoft Research
1100 Glendon Ave PH-1
Los Angeles, CA 90024
Tel: (425) 704-8906
Fax: (425) 936-7329
carlson@microsoft.com