Bounded search for de novo identification of degenerate cis-regulatory elements

door Khetani Radhika S, Chakravarty Arijit, Carlson Jonathan M, Gross Robert H
Gepubliceerd in 2006-05-01

Bounded search for de novo identification of degenerate cis-regulatory elements

door Carlson, Jonathan M, Chakravarty, Arijit, Khetani, Radhika S, Gross, Robert H
Gepubliceerd in 2006

A novel ensemble learning method for de novo computational identification of DNA binding sites

door Chakravarty, Arijit, Carlson, Jonathan M, Khetani, Radhika S, Gross, Robert H
Gepubliceerd in 2007

PhyloDet: a scalable visualization tool for mapping multiple traits to large evolutionary trees

door Lee, Bongshin, Nachmanson, Lev, Robertson, George, Carlson, Jonathan M., Heckerman, David
Gepubliceerd in 2009

SCOPE: a web server for practical de novo motif discovery

door Carlson, Jonathan M., Chakravarty, Arijit, DeZiel, Charles E., Gross, Robert H.
Gepubliceerd in 2007

Clinical and evolutionary consequences of HIV adaptation to HLA: implications for vaccine and cure

door Avila-Rios, Santiago, Carlson, Jonathan M., John, Mina, Mallal, Simon, Brumme, Zabrina L.
Gepubliceerd in Curr Opin HIV AIDS (2019)

Enhanced recognition of HIV-1 Cryptic Epitopes Restricted by HLA-Class I alleles Associated with a Favorable Clinical Outcome

door Bansal, Anju, Mann, Tiffanie, Sterrett, Sarah, Peng, Binghao J., Bet, Anne, Carlson, Jonathan M., Goepfert, Paul A.
Gepubliceerd in J Acquir Immune Defic Syndr (2015)

Brief Report: Selection of HIV-1 Variants With Higher Transmission Potential by 1% Tenofovir Gel Microbicide

door Ngandu, Nobubelo K., Carlson, Jonathan M., Chopera, Denis R., Ndabambi, Nonkululeko, Abdool Karim, Quarraisha, Abdool Karim, Salim, Williamson, Carolyn
Gepubliceerd in J Acquir Immune Defic Syndr (2017)

Increased Sequence Coverage through Combined Targeting of Variant and Conserved Epitopes Correlates with Control of HIV Replication

door Sunshine, Justine, Kim, Moon, Carlson, Jonathan M., Heckerman, David, Czartoski, Julie, Migueles, Stephen A., Maenza, Janine, McElrath, M. Juliana, Mullins, James I., Frahm, Nicole
Gepubliceerd in 2014

Elevated HIV Infection of CD4 T Cells in MRKAd5 Vaccine Recipients Due to CD8 T Cells Targeting Adapted Epitopes

door Qin, Kai, Boppana, Sushma, Carlson, Jonathan M., Fiore-Gartland, Andrew, Files, Jacob, Zeng, Jie, Edberg, Jeffrey, Mailliard, Robbie B., Ochsenbauer, Christina, Bansal, Anju, Goepfert, Paul
Gepubliceerd in J Virol (2021)

HIV escape mutations occur preferentially at HLA-binding sites of CD8 T-cell epitopes

door Bronke, Corine, Almeida, Coral-Ann M., McKinnon, Elizabeth, Roberts, Steven G., Keane, Niamh M., Chopra, Abha, Carlson, Jonathan M., Heckerman, David, Mallal, Simon, John, Mina
Gepubliceerd in 2013

The Hypervariable HIV-1 Capsid Protein Residues Comprise HLA-Driven CD8(+) T-Cell Escape Mutations and Covarying HLA-Independent Polymorphisms

door Crawford, Hayley, Matthews, Philippa C., Schaefer, Malinda, Carlson, Jonathan M., Leslie, Alasdair, Kilembe, William, Allen, Susan, Ndung'u, Thumbi, Heckerman, David, Hunter, Eric, Goulder, Philip J. R.
Gepubliceerd in 2011

Immune Screening Identifies Novel T Cell Targets Encoded by Antisense Reading Frames of HIV-1

door Berger, Christoph T., Llano, Anuska, Carlson, Jonathan M., Brumme, Zabrina L., Brockman, Mark A., Cedeño, Samandhy, Harrigan, P. Richard, Kaufmann, Daniel E., Heckerman, David, Meyerhans, Andreas, Brander, Christian
Gepubliceerd in J Virol (2015)

Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein

door Van Egeren, Debra, Novokhodko, Alexander, Stoddard, Madison, Tran, Uyen, Zetter, Bruce, Rogers, Michael, Pentelute, Bradley L., Carlson, Jonathan M., Hixon, Mark, Joseph-McCarthy, Diane, Chakravarty, Arijit
Gepubliceerd in PLoS One (2021)

Additive Contribution of HLA Class I Alleles in the Immune Control of HIV-1 Infection

door Leslie, Alasdair, Matthews, Philippa C., Listgarten, Jennifer, Carlson, Jonathan M., Kadie, Carl, Ndung'u, Thumbi, Brander, Christian, Coovadia, Hoosen, Walker, Bruce D., Heckerman, David, Goulder, Philip J. R.
Gepubliceerd in 2010

Adaptive interactions between HLA and HIV-1: Highly divergent selection imposed by HLA class I molecules with common supertype motifs

door John, Mina, Heckerman, David, James, Ian, Park, Lawrence P., Carlson, Jonathan M., Chopra, Abha, Gaudieri, Silvana, Nolan, David, Haas, David W., Riddler, Sharon A., Haubrich, Richard, Mallal, Simon
Gepubliceerd in 2010

Frequent and Variable Cytotoxic-T-Lymphocyte Escape-Associated Fitness Costs in the Human Immunodeficiency Virus Type 1 Subtype B Gag Proteins

door Boutwell, Christian L., Carlson, Jonathan M., Lin, Tien-Ho, Seese, Aaron, Power, Karen A., Peng, Jian, Tang, Yanhua, Brumme, Zabrina L., Heckerman, David, Schneidewind, Arne, Allen, Todd M.
Gepubliceerd in 2013

CD8 T cells targeting adapted epitopes in chronic HIV infection promote dendritic cell maturation and CD4 T cell trans-infection

door Qin, Kai, Boppana, Sushma, Du, Victor Y., Carlson, Jonathan M., Yue, Ling, Dilernia, Dario A., Hunter, Eric, Mailliard, Robbie B., Mallal, Simon A., Bansal, Anju, Goepfert, Paul A.
Gepubliceerd in PLoS Pathog (2019)

HLA-A*68:02-restricted Gag-specific CTL responses can drive selection pressure on HIV but are subdominant and ineffective

door Kløverpris, Henrik N., Stryhn, Anette, Harndahl, Mikkel, Carlson, Jonathan M., Leslie, Alasdair J, Chen, Fabian, Riddell, Lynn, Mulenga, Joseph, Walker, Bruce D., Ndung’u, Thumbi, Buus, Søren, Goulder, Philip
Gepubliceerd in AIDS (2013)

Widespread Impact of HLA Restriction on Immune Control and Escape Pathways of HIV-1

door Carlson, Jonathan M., Listgarten, Jennifer, Pfeifer, Nico, Tan, Vincent, Kadie, Carl, Walker, Bruce D., Ndung'u, Thumbi, Shapiro, Roger, Frater, John, Brumme, Zabrina L., Goulder, Philip J. R., Heckerman, David
Gepubliceerd in 2012