Kim, Yohan, Sidney, John, Pinilla, Clemencia, Sette, Alessandro, Peters, Bjoern
Abstract Background Experts in peptide:MHC binding studies are often able to estimate the impact of a single residue substitution based on a heuristic understanding of amino acid similarity in an...
Mapping Immune Responses to mRBP-3 1-16 Peptide with Altered Peptide Ligands (2008)
Carly J. Guyver, David A. Copl, Claudia J. Calder, Ro Sette, John Sidney, Andrew D. Dick, ...
PURPOSE. Experimental autoimmune uveoretinitis (EAU) can be induced in C57BL/6 mice (I-A b) using human retinoid-binding protein-3 (hRBP-3, previously IRBP) residues 1-20. This study of a truncated...
Rutebemberwa, Alleluiah, Ray, Stuart C., Astemborski, Jacqueline A., Levine, Jordana, Liu, Lin, Dowd, Kimberly A., ...
Hepatitis C virus (HCV) is an important human pathogen that represents a model for chronic infection given that the majority of infected individuals fail to clear the infection despite generation of...
Improving MHC binding peptide prediction by incorporating binding data of auxiliary (2008)
Shanfeng Zhu, Keiko Udaka, John Sidney, Ro Sette, Kiyoko F. Aoki-kinoshita, Satoru Miyano
doi:10.1093/bioinformatics/btl141
DOI 10.1007/s00251-005-0803-5 ORIGINAL PAPER (2008)
Bjoern Peters, John Sidney, Phil Bourne, Huynh-hoa Bui, Soeren Buus, David Nemazee, ...
The design and implementation of the immune epitope database and analysis resource
HLA class I supertypes: a revised and updated classification (2008)
John Sidney, Bjoern Peters, Nicole Frahm, Christian Brander, Alessandro Sette
Background: Class I major histocompatibility complex (MHC) molecules bind, and present to T cells, short peptides derived from intracellular processing of proteins. The peptide repertoire of a...
John Sidney, Erika Assarsson, Carrie Moore, Y Ngo, Clemencia Pinilla, Ro Sette, ...
Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries
Cross-presentation of caspase-cleaved apoptotic self antigens in HIV infection (2007)
Pisana Moroni Rawson, Caroline Molette, Melissa Videtta, Laura Altieri, Debora Franceschini, Tiziana Donato, ...
Immunodominant Tuberculosis CD8 Antigens Preferentially Restricted by HLA-B (2007)
Deborah A. Lewinsohn, Ervina Winata, Gwendolyn M. Swarbrick, Katie E. Tanner, Matthew S. Cook, Megan D. Null, ...
CD8+ T cells are essential for host defense to intracellular bacterial pathogens such as Mycobacterium tuberculosis (Mtb), Salmonella species, and Listeria monocytogenes, yet the repertoire and...
Magdalini Moutaftsi, Bjoern Peters, Valerie Pasquetto, David C Tscharke, John Sidney, Huynh-Hoa Bui, ...
A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I Molecules (2006)
Bjoern Peters, Huynh-Hoa Bui, Sune Frankild, Morten Nielsen, Claus Lundegaard, Emrah Kostem, ...
Recognition of peptides bound to major histocompatibility complex (MHC) class I molecules by T lymphocytes is an essential part of immune surveillance. Each MHC allele has a characteristic peptide...
I Vita, Kerrie Vaughan, Laura Zarebski, Nima Salimi, Ward Fleri, Howard Grey, ...
© 2006 Vita et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
falciparum antigens by antigenic analysis of genomic and proteomic (2006)
Z. Bozdech, M. Llinas, B. L. Pulliam, E. D. Wong, J. Zhu, Z. Bozdech, ...
plasmodium
Immunogenic HLA-B7-restricted peptides of hTRT (2006)
Cortez-Gonzalez, Xochitl, Sidney, John, Adotevi, Olivier, Sette, Alessandro, Millard, Frederick, Lemonnier, Francois, ...
Telomerase reverse transcriptase (TRT) is the first bona fide common tumor antigen. While several 9mer peptides of the human TRT have been identified for HLA-A2, little information exists on peptides...
Immunogenic HLA-B7-restricted peptides of hTRT (2006)
Cortez-Gonzalez, Xochitl, Sidney, John, Adotevi, Olivier, Sette, Alessandro, Millard, Frederick, Lemonnier, Francois, ...
Telomerase reverse transcriptase (TRT) is the first bona fide common tumor antigen. While several 9mer peptides of the human TRT have been identified for HLA-A2, little information exists on peptides...
Zhu, Shanfeng, Udaka, Keiko, Sidney, John, Sette, Alessandro, Aoki-Kinoshita, Kiyoko F., Mamitsuka, Hiroshi
Motivation: Various computational methods have been proposed to tackle the problem of predicting the peptide binding ability for a specific MHC molecule. These methods are based on known binding...
Zhu, Shanfeng, Udaka, Keiko, Sidney, John, Sette, Alessandro, Aoki-Kinoshita, Kiyoko F., Mamitsuka, Hiroshi
Motivation: Various computational methods have been proposed to tackle the problem of predicting the peptide binding ability for a specific MHC molecule. These methods are based on known binding...
Tumor-associated carbohydrate antigens: A possible avenue for cancer prevention (2005)
Yanfei Xu, Alessandro Sette, John Sidney, Sandra J Gendler, Alessandra Franco
The Immune Epitope Database and Analysis Resource: From Vision to Blueprint (2005)
Bjoern Peters, John Sidney, Phil Bourne, Huynh-Hoa Bui, Soeren Buus, Grace Doh, ...
Reversion of CTL escape–variant immunodeficiency viruses in vivo (2004)
Thomas C Friedrich, Elizabeth J Dodds, Levi J Yant, Lara Vojnov, Richard Rudersdorf, Candice Cullen, ...
Peters, Björn, Tong, Weiwei, Sidney, John, Sette, Alessandro, Weng, Zhiping
Motivation: Various methods have been proposed to predict the binding affinities of peptides to Major Histocompatibility Complex class I (MHC-I) molecules based on experimental binding data. They can...
Wentworth, Peggy A., Sette, Alessandro, Celis, Esteban, Sidney, John, Southwood, Scott, Crimi, Claire, ...
We have focused on conserved regions of the hepatitis C Virus (HCV) genome to identify viral peptides that contain HLA class I binding motifs and bind with high affinity to the corresponding purified...
Sette, Alessandro, Sidney, John, Gaeta, Federico C. A, Appella, Ettore, Colón, Sonia M., Guercio, Marie-France Del, ...
Synthetic peptides spanning the entire sequence of both human and mouse β2-microglobulin (β2M) have been tested for their capacity to bind to three different mouse (I-Ad, I-Ed, and I-Ak) or human...
Wall, Mellssa, Southwood, Scott, Sidney, John, Oseroff, Carla, Guericio, Marie-France Del, Lamont, Alan G., ...
A direct binding assay specific for IAs molecules has been developed and Its immunological relevance validated by examining, for a panel of nine different synthetic peptides, the correlation between...
Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes
Assarsson, Erika, Greenbaum, Jason A., Sundström, Magnus, Schaffer, Lana, Hammond, Jennifer A., Pasquetto, Valerie, ...
Vaccinia virus is the prototypic orthopoxvirus and was the vaccine used to eradicate smallpox, yet the expression profiles of many of its genes remain unknown. Using a genome tiling array approach,...
Alvarez, María G., Postan, Miriam, Weatherly, D. Brent, Albareda, María C., Sidney, John, Sette, Alessandro, ...
At present, 16–20 million people in Central and South America are infected with Trypanosoma cruzi, the causative agent of Chagas disease in humans. The primary clinical consequence of the infection...
Schneidewind, Arne, Brockman, Mark A., Sidney, John, Wang, Yaoyu E., Chen, Huabiao, Suscovich, Todd J., ...
Control of human immunodeficiency virus type 1 (HIV-1) by HLA-B27-positive subjects has been linked to an immunodominant CD8+ cytotoxic T-lymphocyte (CTL) response targeting the conserved KK10...
Maness, Nicholas J., Yant, Levi J., Chung, Chungwon, Loffredo, John T., Friedrich, Thomas C., Piaskowski, Shari M., ...
The association between particular major histocompatibility complex class I (MHC-I) alleles and control of human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) replication...
Reply to Satheshkumar and Moss: Poxvirus transcriptome analysis
Assarsson, Erika, Greenbaum, Jason A., Sundström, Magnus, Schaffer, Lana, Hammond, Jennifer A., Pasquetto, Valerie, ...
Lymphocytic Choriomeningitis Virus Infection Yields Overlapping CD4+ and CD8+ T-Cell Responses▿
Dow, Courtney, Oseroff, Carla, Peters, Bjoern, Nance-Sotelo, Courtney, Sidney, John, Buchmeier, Michael, ...
Activation of CD4+ T cells helps establish and sustain other immune responses. We have previously shown that responses against a broad set of nine CD4+ T-cell epitopes were present in the setting of...
Immunomic Analysis of the Repertoire of T-Cell Specificities for Influenza A Virus in Humans ▿ † ‡
Assarsson, Erika, Bui, Huynh-Hoa, Sidney, John, Zhang, Qing, Glenn, Jean, Oseroff, Carla, ...
Continuing antigenic drift allows influenza viruses to escape antibody-mediated recognition, and as a consequence, the vaccine currently in use needs to be altered annually. Highly conserved epitopes...
Kotturi, Maya F., Botten, Jason, Sidney, John, Bui, Huynh-Hoa, Giancola, Lori, Maybeno, Matt, ...
Arenaviruses are the causative pathogens of severe hemorrhagic fever and aseptic meningitis in humans, for which no licensed vaccines are currently available. Pathogen heterogeneity within the...
Cellular immune response to cryptic epitopes during therapeutic gene transfer
Li, Chengwen, Goudy, Kevin, Hirsch, Matt, Asokan, Aravind, Fan, Yun, Alexander, Jeff, ...
The immune response has been implicated as a critical factor in determining the success or failure of clinical gene therapy trials. Generally, such a response is elicited by the desired transgene...