2009

• Jonathan M. Carlson, David Heckerman, and Guy Shani, Estimating false discovery rates for contingency tables, no. MSR-TR-2009-53, May 2009
• 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, HLA footprints on HIV-1 are associated with inter-clade polymorphisms and intra-clade phylogenetic clustering, in Journal of Virology, pp. JVI.02017-08, 2009
• 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, 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, in Journal of Virology, vol. 83, no. 4, pp. 1845-1855, 2009

2008

• 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, and David Heckerman, Phylogenetic Dependency Networks: inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag, in PLoS Computational Biology, vol. 4, no. 11, pp. e1000225, PLoS Computational Biology (Public Library of Science Computational Biology), , November 2008
• Paul A. 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 J. R. Goulder, and Eric Hunter, Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients, in Journal of Experimental Medicine, vol. 205, no. 5, pp. 1009-1017, 2008
• Zabrina L Brumme, Iris Tao, Sharon Szeto, Chanson J Brumme, Christian Brander, Bruce Walker, David Heckerman, P Richard Harrigan, Jonathan M Carlson, Dennison Chan, Carl Kadie, and Nicole Frahm, Human leukocyte antigen-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection, in AIDS, vol. 22, no. 11, pp. 1277–1286, 2008
• 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, and Todd M. Allen, Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients, in Hepatology, vol. 48, no. 6, pp. 1769–1778, 2008
• 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, and Bruce D. Walker, 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, in Journal of Virology, vol. 82, no. 18, pp. 9216-9227, 2008
• Jonathan M. Carlson and Zabrina L. Brumme, HIV evolution in response to HLA-restricted CTL selection pressures: a population-based perspective, in Microbes and Infection, vol. 10, no. 5, pp. 455–461, Elsevier, 2008
• Philippa C. Matthews, Andrew Prendergast, Alasdair Leslie, Hayley Crawford, Rebecca Payne, Christine Rousseau, Morgane Rolland, Isobella Honeyborne, Jonathan Carlson, Carl Kadie, Christian Brander, Karen Bishop, Nonkululeko Mlotshwa, James I. Mullins, Hoosen Coovadia, Thumbi Ndung'u, Bruce D. Walker, David Heckerman, and Philip J. R. Goulder, Central role of reverting mutations in HLA associations with Human Immunodeficiency Virus set point, in Journal of Virology, vol. 82, no. 17, pp. 8548-8559, 2008
• 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 E. Heckerman, Bette T. Korber, and James I. Mullins, HLA Class I-Driven Evolution of Human Immunodeficiency Virus Type 1 Subtype C Proteome: immune Escape and Viral Load, in Journal of Virology, vol. 82, no. 13, pp. 6434-6446, 2008
• 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, and Bruce D. Walker, Genetic Characterization of Human Immunodeficiency Virus type 1 in Elite Controllers: Lack of gross genetic defects or common amino acid changes, in Journal of Virology, pp. JVI.00535-08, 2008

2007

• Zabrina L Brumme, Chanson J Brumme, David Heckerman, Bette T Korber, Marcus Daniels, Jonathan 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, and P. Richard Harrigan, Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1, in PLoS Pathogens, vol. 3, no. 7, pp. e94, July 2007
• Arijit Chakravarty, Jonathan M. Carlson, Radhika S. Khetani, Charles E. DeZiel, and Robert H. Gross, SPACER: identification of cis-regulatory elements with non-contiguous critical residues, in Bioinformatics, vol. 23, no. 8, pp. 1029-1031, 2007
• Arijit Chakravarty, Jonathan Carlson, Radhika Khetani, and Robert Gross, A novel ensemble learning method for de novo computational identification of DNA binding sites, in BMC Bioinformatics, vol. 8, no. 1, pp. 249, 2007
• Jonathan Carlson, Carl Kadie, Simon Mallal, and David Heckerman, Leveraging Hierarchical Population Structure in Discrete Association Studies, in PLoS One, vol. 2, no. 7, pp. e591, Public Library of Science San Francisco, USA, 2007
• 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, and Bette Korber, Founder Effects in the Assessment of HIV Polymorphisms and HLA Allele Associations, in Science, vol. 315, no. 5818, pp. 1583-1586, American Association for the Advancement of Science, 2007

2006

• Jonathan Carlson*, Arijit Chakravarty*, Radhika Khetani, and Robert Gross, Bounded search for de novo identification of degenerate cis-regulatory elements, in BMC Bioinformatics, vol. 7, no. 1, pp. 254, 2006
• Jonathan M. Carlson*, Arijit Chakravarty*, and Robert H. Gross, BEAM: A Beam Search Algorithm for the Identification of Cis-Regulatory Elements in Groups of Genes, in Journal of Computational Biology, vol. 13, no. 3, pp. 686-701, 2006