John Sidney

Summary

Affiliation: La Jolla Institute for Allergy and Immunology
Country: USA

Publications

  1. pmc Five HLA-DP molecules frequently expressed in the worldwide human population share a common HLA supertypic binding specificity
    John Sidney
    La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    J Immunol 184:2492-503. 2010
  2. pmc Increased CD8+ T cell responses to apoptotic T cell-associated antigens in multiple sclerosis
    Francesco Lolli
    Dipartimento di Scienze Biomediche, Sperimentali e Cliniche and Neurofarba, Università of Firenze, Azienda Ospedaliera di Careggi, Largo Brambilla 6, 50134 Firenze, Italy
    J Neuroinflammation 10:94. 2013
  3. pmc Human immunome, bioinformatic analyses using HLA supermotifs and the parasite genome, binding assays, studies of human T cell responses, and immunization of HLA-A*1101 transgenic mice including novel adjuvants provide a foundation for HLA-A03 restricted C
    Hua Cong
    Departments of Surgery Ophthalmology and Visual Sciences and Pediatrics Infectious Disease, Committees on Immunology, Molecular Medicine, and Genetics, Institute of Genomics and Systems Biology, and The College, The University of Chicago, Chicago, Illinois 60637, USA
    Immunome Res 6:12. 2010
  4. pmc Curation of complex, context-dependent immunological data
    Randi Vita
    La Jolla Institute for Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, California, USA
    BMC Bioinformatics 7:341. 2006
  5. pmc HLA class I supertypes: a revised and updated classification
    John Sidney
    Division of Vaccine Discovery, The La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
    BMC Immunol 9:1. 2008
  6. pmc Dissociation between epitope hierarchy and immunoprevalence in CD8 responses to vaccinia virus western reserve
    Carla Oseroff
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    J Immunol 180:7193-202. 2008
  7. pmc Peptide-binding motifs associated with MHC molecules common in Chinese rhesus macaques are analogous to those of human HLA supertypes and include HLA-B27-like alleles
    Bianca R Mothe
    Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    Immunogenetics 65:371-86. 2013
  8. ncbi request reprint A quantitative analysis of the variables affecting the repertoire of T cell specificities recognized after vaccinia virus infection
    Erika Assarsson
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
    J Immunol 178:7890-901. 2007
  9. pmc A multivalent and cross-protective vaccine strategy against arenaviruses associated with human disease
    Maya F Kotturi
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
    PLoS Pathog 5:e1000695. 2009
  10. pmc Correlates of protection efficacy induced by vaccinia virus-specific CD8+ T-cell epitopes in the murine intranasal challenge model
    Magdalini Moutaftsi
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
    Eur J Immunol 39:717-22. 2009

Collaborators

Detail Information

Publications99

  1. pmc Five HLA-DP molecules frequently expressed in the worldwide human population share a common HLA supertypic binding specificity
    John Sidney
    La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    J Immunol 184:2492-503. 2010
    ..Taken together, these DP supertype molecules are found in >90% of the human population. Thus, these findings have important implications for epitope-identification studies and monitoring of human class II-restricted immune responses...
  2. pmc Increased CD8+ T cell responses to apoptotic T cell-associated antigens in multiple sclerosis
    Francesco Lolli
    Dipartimento di Scienze Biomediche, Sperimentali e Cliniche and Neurofarba, Università of Firenze, Azienda Ospedaliera di Careggi, Largo Brambilla 6, 50134 Firenze, Italy
    J Neuroinflammation 10:94. 2013
    ..Here, we evaluated the hypothesis that CD8+ T cell responses to caspase-cleaved antigens derived from effector T cells undergoing apoptosis, may contribute to multiple sclerosis (MS) immunopathology...
  3. pmc Human immunome, bioinformatic analyses using HLA supermotifs and the parasite genome, binding assays, studies of human T cell responses, and immunization of HLA-A*1101 transgenic mice including novel adjuvants provide a foundation for HLA-A03 restricted C
    Hua Cong
    Departments of Surgery Ophthalmology and Visual Sciences and Pediatrics Infectious Disease, Committees on Immunology, Molecular Medicine, and Genetics, Institute of Genomics and Systems Biology, and The College, The University of Chicago, Chicago, Illinois 60637, USA
    Immunome Res 6:12. 2010
    ....
  4. pmc Curation of complex, context-dependent immunological data
    Randi Vita
    La Jolla Institute for Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, California, USA
    BMC Bioinformatics 7:341. 2006
    ..The Immune Epitope Database and Analysis Resource (IEDB) is dedicated to capturing, housing and analyzing complex immune epitope related data http://www.immuneepitope.org...
  5. pmc HLA class I supertypes: a revised and updated classification
    John Sidney
    Division of Vaccine Discovery, The La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
    BMC Immunol 9:1. 2008
    ..The utility of this original supertype classification, as well several other subsequent arrangements derived by others, has been demonstrated in a large number of epitope identification studies...
  6. pmc Dissociation between epitope hierarchy and immunoprevalence in CD8 responses to vaccinia virus western reserve
    Carla Oseroff
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    J Immunol 180:7193-202. 2008
    ..Together, these findings have clear implications for the design of CD8(+) T cell subunit vaccines and in particular raise the exciting prospect of being able to choose subunits without reference to MHC restriction...
  7. pmc Peptide-binding motifs associated with MHC molecules common in Chinese rhesus macaques are analogous to those of human HLA supertypes and include HLA-B27-like alleles
    Bianca R Mothe
    Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    Immunogenetics 65:371-86. 2013
    ....
  8. ncbi request reprint A quantitative analysis of the variables affecting the repertoire of T cell specificities recognized after vaccinia virus infection
    Erika Assarsson
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
    J Immunol 178:7890-901. 2007
    ..This suggested that additional factors, including immunoregulatory mechanisms, restrict the repertoire of T cell specificities after vaccinia infection by a factor of at least 10...
  9. pmc A multivalent and cross-protective vaccine strategy against arenaviruses associated with human disease
    Maya F Kotturi
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
    PLoS Pathog 5:e1000695. 2009
    ..In conclusion, the set of identified epitopes allows broad, non-ethnically biased coverage of all 7 viral species targeted by our studies...
  10. pmc Correlates of protection efficacy induced by vaccinia virus-specific CD8+ T-cell epitopes in the murine intranasal challenge model
    Magdalini Moutaftsi
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
    Eur J Immunol 39:717-22. 2009
    ..However, binding affinity partially predicted protection efficacy and ultimately epitope immunogenicity and recognition of infected cells offered the best correlation...
  11. pmc HLA-A2-restricted protection against lethal lymphocytic choriomeningitis
    Jason Botten
    Molecular and Integrative Neurosciences Department, The Scripps Research Institute, SP30 2020, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Virol 81:2307-17. 2007
    ....
  12. pmc Definition of epitopes and antigens recognized by vaccinia specific immune responses: their conservation in variola virus sequences, and use as a model system to study complex pathogens
    Alessandro Sette
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
    Vaccine 27:G21-6. 2009
    ..Finally, we find that the vast majority of VACV epitopes are conserved in variola virus (VARV), thus suggesting that the epitopes defined herein also have relevance for the efficacy of VACV as a smallpox vaccine...
  13. pmc HLA class I alleles are associated with peptide-binding repertoires of different size, affinity, and immunogenicity
    Sinu Paul
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
    J Immunol 191:5831-9. 2013
    ..Finally, we investigated the genetic and structural basis of the phenomenon. Although no stringent correlate was defined, on average HLA B alleles are associated with significantly narrower repertoires than are HLA A alleles...
  14. pmc The CD8+ T-cell response to lymphocytic choriomeningitis virus involves the L antigen: uncovering new tricks for an old virus
    Maya F Kotturi
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
    J Virol 81:4928-40. 2007
    ..Taken together, these findings illustrate that the LCMV-specific CD8(+) T-cell response is more complex than previously appreciated...
  15. pmc Previously undescribed grass pollen antigens are the major inducers of T helper 2 cytokine-producing T cells in allergic individuals
    Véronique Schulten
    La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 110:3459-64. 2013
    ..The discovery of proteins that induce Th2 cells but are not IgE reactive may allow the development of safer immunotherapeutic strategies...
  16. pmc A shared MHC supertype motif emerges by convergent evolution in macaques and mice, but is totally absent in human MHC molecules
    Alessandro Sette
    Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    Immunogenetics 64:421-34. 2012
    ..This is the first detailed characterization of the pocket residues yielding this specific motif in nonhuman primates and mice, revealing a new supertype motif not present in humans...
  17. pmc Evaluating the immunogenicity of protein drugs by applying in vitro MHC binding data and the immune epitope database and analysis resource
    Sinu Paul
    La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, San Diego, CA 92037, USA
    Clin Dev Immunol 2013:467852. 2013
    ..Finally the use, advantages, and limitations of the methodology will be demonstrated in a review of two previous studies investigating the immunogenicity of erythropoietin and timothy grass pollen. ..
  18. ncbi request reprint Vaccinia virus-specific CD4+ T cell responses target a set of antigens largely distinct from those targeted by CD8+ T cell responses
    Magdalini Moutaftsi
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    J Immunol 178:6814-20. 2007
    ..Taken together, these results highlight fundamental differences in immunodominance of CD4(+) and CD8(+) T cell responses to a complex pathogen...
  19. pmc Lymphocytic choriomeningitis virus infection yields overlapping CD4+ and CD8+ T-cell responses
    Courtney Dow
    The La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, USA
    J Virol 82:11734-41. 2008
    ..These findings demonstrate that immunodominance is a complex phenomenon in the context of helper responses...
  20. pmc Comprehensive analysis of dengue virus-specific responses supports an HLA-linked protective role for CD8+ T cells
    Daniela Weiskopf
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 110:E2046-53. 2013
    ....
  21. pmc A strategy to determine HLA class II restriction broadly covering the DR, DP, and DQ allelic variants most commonly expressed in the general population
    Denise M McKinney
    La Jolla Institute for Allergy and Immunology, La Jolla, San Diego, CA 92037, USA
    Immunogenetics 65:357-70. 2013
    ..This panel of lines will enable high throughput determination of HLA restriction, enabling better characterization of HLA class II-restricted T cell responses and facilitating the development of HLA tetrameric staining reagents...
  22. pmc Derivation of an amino acid similarity matrix for peptide: MHC binding and its application as a Bayesian prior
    Yohan Kim
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
    BMC Bioinformatics 10:394. 2009
    ..Our aim is to quantify this measure of similarity to improve peptide:MHC binding prediction methods. This should help compensate for holes and bias in the sequence space coverage of existing peptide binding datasets...
  23. pmc Naive precursor frequencies and MHC binding rather than the degree of epitope diversity shape CD8+ T cell immunodominance
    Maya F Kotturi
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    J Immunol 181:2124-33. 2008
    ..Thus, our results indicate that an intrinsic property of the epitope (MHC binding affinity) and an intrinsic property of the host (naive precursor frequency) jointly dictate the immunodominance hierarchy of CD8(+) T cell responses...
  24. pmc Immunomic analysis of the repertoire of T-cell specificities for influenza A virus in humans
    Erika Assarsson
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
    J Virol 82:12241-51. 2008
    ..These results enable further functional studies of T-cell responses during influenza virus infection and provide a potential base for the development of a universal influenza vaccine...
  25. pmc Molecular determinants of T cell epitope recognition to the common Timothy grass allergen
    Carla Oseroff
    La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    J Immunol 185:943-55. 2010
    ..Consistent with this notion, different Phl p Ags were associated with distinct patterns of IL-5, IFN-gamma, IL-10, and IL-17 production...
  26. pmc Polyfunctional CD4+ T cell responses to a set of pathogenic arenaviruses provide broad population coverage
    Maya F Kotturi
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, California, 92037 USA
    Immunome Res 6:4. 2010
    ....
  27. pmc Measurement of MHC/peptide interactions by gel filtration or monoclonal antibody capture
    John Sidney
    La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
    Curr Protoc Immunol . 2013
    ..Three methods for separation are described, two utilizing size-exclusion gel-filtration chromatography and a third using monoclonal antibody capture of MHC. Data analysis for each method is also explained...
  28. pmc T cell responses to known allergen proteins are differently polarized and account for a variable fraction of total response to allergen extracts
    Carla Oseroff
    La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    J Immunol 189:1800-11. 2012
    ..These epitopes might be used to characterize T cell phenotype/T cell plasticity as a function of seasonality, or as a result of specific immunotherapy treatment or varying disease severity (asthma or rhinitis)...
  29. pmc Analysis of T cell responses to the major allergens from German cockroach: epitope specificity and relationship to IgE production
    Carla Oseroff
    La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    J Immunol 189:679-88. 2012
    ..Monitoring these responses may therefore yield important information relevant to understanding cockroach allergies and their treatment...
  30. pmc Identification of the peptide-binding motif recognized by the pigtail macaque class I MHC molecule Mane-A1*082:01 (Mane A*0301)
    Carrie Moore
    La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    Immunogenetics 64:461-8. 2012
    ....
  31. pmc Peptide binding predictions for HLA DR, DP and DQ molecules
    Peng Wang
    La Jolla Institute for Allergy and Immunology, La Jolla, USA
    BMC Bioinformatics 11:568. 2010
    ..This reflects a significant gap in knowledge as HLA DP and DQ molecules are presumably equally important, and have only been studied less because they are more difficult to handle experimentally...
  32. pmc Divergent motifs but overlapping binding repertoires of six HLA-DQ molecules frequently expressed in the worldwide human population
    John Sidney
    La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    J Immunol 185:4189-98. 2010
    ..Because the DQ molecules studied are found in >85% of the general human population, these findings have important implications for epitope identification studies and monitoring of DQ-restricted immune responses...
  33. pmc Functional classification of class II human leukocyte antigen (HLA) molecules reveals seven different supertypes and a surprising degree of repertoire sharing across supertypes
    Jason Greenbaum
    La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
    Immunogenetics 63:325-35. 2011
    ..This fundamental difference between HLA class I and class II would not have been predicted on the basis of analysis of either binding motifs or the sequence/predicted structures of the HLA molecules...
  34. pmc Dissecting mechanisms of immunodominance to the common tuberculosis antigens ESAT-6, CFP10, Rv2031c (hspX), Rv2654c (TB7.7), and Rv1038c (EsxJ)
    Cecilia S Lindestam Arlehamn
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    J Immunol 188:5020-31. 2012
    ..In conclusion, these results highlight the feasibility of more clearly defined TB diagnostic reagent...
  35. pmc Cutting edge: murine cytomegalovirus induces a polyfunctional CD4 T cell response
    Ramon Arens
    Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    J Immunol 180:6472-6. 2008
    ..In total, this study reveals that the MCMV-specific CD4 T cell response is complex and functionally diverse, highlighting its important role in controlling this persistent pathogen...
  36. pmc A protective role for dengue virus-specific CD8+ T cells
    Lauren E Yauch
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    J Immunol 182:4865-73. 2009
    ....
  37. pmc Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines
    Huynh Hoa Bui
    La Jolla Institute for Allergy and Immunology, Division of Vaccine Discovery, 9420 Athena Circle, La Jolla, CA 92037, USA
    BMC Bioinformatics 8:361. 2007
    ..In both cases, concrete information pertaining to the degree of conservancy of the epitope(s) considered is crucial...
  38. pmc Insights into HLA-restricted T cell responses in a novel mouse model of dengue virus infection point toward new implications for vaccine design
    Daniela Weiskopf
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    J Immunol 187:4268-79. 2011
    ..Our results provide new insights into HLA-restricted T cell responses against DENV, and we describe in this study a novel murine model that allows the investigation of T cell-mediated immune mechanisms relevant to vaccine design...
  39. pmc Functional analysis of frequently expressed Chinese rhesus macaque MHC class I molecules Mamu-A1*02601 and Mamu-B*08301 reveals HLA-A2 and HLA-A3 supertypic specificities
    Scott Southwood
    Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    Immunogenetics 63:275-90. 2011
    ....
  40. pmc IMMUNOCAT-a data management system for epitope mapping studies
    Jo L Chung
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    J Biomed Biotechnol 2010:856842. 2010
    ..This provides a case study for the use of bioinformatics and information management techniques to track and analyze data produced in a translational research study aimed at epitope identification...
  41. ncbi request reprint Immunogenic HLA-B7-restricted peptides of hTRT
    Xochitl Cortez-Gonzalez
    Laboratory of Immunology, Department of Medicine and Moores Cancer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0837, USA
    Int Immunol 18:1707-18. 2006
    ....
  42. ncbi request reprint Characterization of the peptide-binding specificity of the chimpanzee class I alleles A 0301 and A 0401 using a combinatorial peptide library
    John Sidney
    La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
    Immunogenetics 59:745-51. 2007
    ....
  43. pmc Identification of protective Lassa virus epitopes that are restricted by HLA-A2
    Jason Botten
    Molecular and Integrative Neurosciences Department, The Scripps Research Institute, La Jolla, CA 92037, USA
    J Virol 80:8351-61. 2006
    ....
  44. pmc Analysis of epitope information related to Bacillus anthracis and Clostridium botulinum
    Laura M Zarebski
    Immune Epitope Database and Analysis Resource, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 9203, 7 USA
    Expert Rev Vaccines 7:55-74. 2008
    ..Despite this, several distinct structures at the epitope and fragment level are described herein, which could be potential additions to future vaccines or targets of novel immunotherapeutics and diagnostic reagents...
  45. ncbi request reprint Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications
    Huynh Hoa Bui
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA 92109, USA
    Immunogenetics 57:304-14. 2005
    ..MHC binding predictions based on ARB matrices were made available at http://epitope.liai.org:8080/matrix web server...
  46. ncbi request reprint Class I molecules with similar peptide-binding specificities are the result of both common ancestry and convergent evolution
    Alessandro Sette
    La Jolla Institute for Allergy and Immunology, San Diego, CA 92121, USA
    Immunogenetics 54:830-41. 2003
    ....
  47. ncbi request reprint Classification of A1- and A24-supertype molecules by analysis of their MHC-peptide binding repertoires
    John Sidney
    La Jolla Institute for Allergy and Immunology, 3030 Bunker Hill St, Ste 326, San Diego, CA, 92109, USA
    Immunogenetics 57:393-408. 2005
    ....
  48. pmc A community resource benchmarking predictions of peptide binding to MHC-I molecules
    Bjoern Peters
    La Jolla Institute for Allergy and Immunology, San Diego, California, USA
    PLoS Comput Biol 2:e65. 2006
    ....
  49. pmc Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes
    Erika Assarsson
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 105:2140-5. 2008
    ..Additionally, genes within each kinetic class were spatially grouped together in the genome. This genome-wide picture of transcription alters our understanding of how orthopoxviruses regulate gene expression...
  50. pmc CD8+ T-cell epitope mapping for pneumonia virus of mice in H-2b mice
    Kevin B Walsh
    Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA
    J Virol 87:9949-52. 2013
    ..These data open the door for using widely profiled, genetically manipulated C57BL/6 mice to study the contribution of epitope-specific CD8(+) T cells to PVM pathogenesis. ..
  51. pmc Brucella melitensis T cell epitope recognition in humans with brucellosis in Peru
    Anthony P Cannella
    Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, California, USA
    Infect Immun 82:124-31. 2014
    ....
  52. pmc Predicting population coverage of T-cell epitope-based diagnostics and vaccines
    Huynh Hoa Bui
    La Jolla Institute for Allergy and Immunology, Division of Vaccine Discovery, 3030 Bunker Hill Street, Suite 326, San Diego, CA 92109, USA
    BMC Bioinformatics 7:153. 2006
    ..Thus, without careful consideration, a vaccine or diagnostic with ethnically biased population coverage could result...
  53. ncbi request reprint A computational pipeline to generate MHC binding motifs
    Penny Wang
    La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
    Immunome Res 7:16. 2011
    ..The pipeline has been incorporated into the immune epitope database and analysis resource (IEDB) and motifs can be visualized while browsing MHC alleles in the IEDB...
  54. doi request reprint Analysis of the binding of gluten T-cell epitopes to various human leukocyte antigen class II molecules
    Elin Bergseng
    Centre for Immune Regulation and Institute of Immunology, Rikshospitalet University Hospital, N 0027 Oslo, Norway
    Hum Immunol 69:94-100. 2008
    ..The results demonstrate that the gluten T-cell epitopes mainly bind to the DQ2 molecule...
  55. pmc A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach
    Peng Wang
    La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
    PLoS Comput Biol 4:e1000048. 2008
    ..We show that this consensus approach achieved best overall performance. Finally, we make the large datasets used publicly available as a benchmark to facilitate further development of MHC class II binding peptide prediction methods...
  56. pmc Comprehensive analysis of T cell epitope discovery strategies using 17DD yellow fever virus structural proteins and BALB/c (H2d) mice model
    Milton Maciel
    Johns Hopkins University, School of Medicine, Pharmacology Department, Baltimore, USA
    Virology 378:105-17. 2008
    ..The results allowed the characterization of 2 MHC class I and 17 class II epitopes in the envelope protein of the YF virus in BALB/c (H2d) mice...
  57. ncbi request reprint Reversion of CTL escape-variant immunodeficiency viruses in vivo
    Thomas C Friedrich
    Wisconsin National Primate Research Center, Madison, Wisconsin 53715, USA
    Nat Med 10:275-81. 2004
    ..In the absence of selective pressure upon transmission to new hosts, these original escape mutations can be lost. This suggests that some HIV CTL epitopes will be maintained in human populations...
  58. ncbi request reprint Impact of HLA-B alleles, epitope binding affinity, functional avidity, and viral coinfection on the immunodominance of virus-specific CTL responses
    Florian Bihl
    Partners AIDS Research Center, Massachusetts General Hospital, Charlestown, 02129, USA
    J Immunol 176:4094-101. 2006
    ..The data support the important role of HLA-B alleles in antiviral immunity and afford a better understanding of the factors contributing to inter- and intraindividual immunodominance...
  59. ncbi request reprint The design and implementation of the immune epitope database and analysis resource
    Bjoern Peters
    La Jolla Institute of Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA 92109, USA
    Immunogenetics 57:326-36. 2005
    ..We describe how we plan to capture, structure, and store this information, what query interfaces we will make available to the public, and what additional predictive and analytical tools we will provide...
  60. ncbi request reprint The HLA molecules DQA1*0501/B1*0201 and DQA1*0301/B1*0302 share an extensive overlap in peptide binding specificity
    John Sidney
    Epimmune, Inc, San Diego, CA 92121, USA
    J Immunol 169:5098-108. 2002
    ..In light of the known linkage of both HLA-DQ2.3 and -DQ3.2 with insulin-dependent diabetes mellitus and celiac disease, these results might have important implications for understanding HLA class II autoimmune disease associations...
  61. ncbi request reprint A CD8+ T cell heptaepitope minigene vaccine induces protective immunity against Chlamydia pneumoniae
    Irina Pinchuk
    Center for Pulmonary and Infectious Disease Control, Department of Microbiology and Immunology, University of Texas Health Center, Tyler, TX 75708, USA
    J Immunol 174:5729-39. 2005
    ....
  62. ncbi request reprint MAGE-6 encodes HLA-DRbeta1*0401-presented epitopes recognized by CD4+ T cells from patients with melanoma or renal cell carcinoma
    Tomohide Tatsumi
    Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
    Clin Cancer Res 9:947-54. 2003
    ..These data suggest that MAGE-6-derived epitopes could serve as useful vaccine candidate components and may provide an immune-monitoring index of clinically important Th1-type immunity in patients with renal cell carcinoma or melanoma...
  63. ncbi request reprint Characterization of the peptide-binding specificity of Mamu-A*11 results in the identification of SIV-derived epitopes and interspecies cross-reactivity
    Alessandro Sette
    La Jolla Institute for Allergy and Immunology, San Diego, CA 92121, USA
    Immunogenetics 57:53-68. 2005
    ..This is the first detailed description of mouse-macaque interspecies cross-reactivity, potentially useful in testing novel vaccines in mice and macaques...
  64. pmc Identification of poxvirus CD8+ T cell determinants to enable rational design and characterization of smallpox vaccines
    David C Tscharke
    Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    J Exp Med 201:95-104. 2005
    ..These findings have important implications for understanding poxvirus immunity in animal models and bench-marking immune responses to poxvirus vaccines in humans...
  65. ncbi request reprint Cellular immune responses to the hepatitis B virus polymerase
    Eishiro Mizukoshi
    Liver Diseases Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
    J Immunol 173:5863-71. 2004
    ..These newly described HBV polymerase epitopes could be a valuable component of a therapeutic vaccine for a large and ethnically diverse patient population...
  66. pmc Identification of Plasmodium falciparum antigens by antigenic analysis of genomic and proteomic data
    Denise L Doolan
    Malaria Program, Naval Medical Research Center, Silver Spring, MD 20910 7500, USA
    Proc Natl Acad Sci U S A 100:9952-7. 2003
    ..The data suggest that immune responses to Plasmodium are dispersed on a relatively large number of parasite antigens. These studies have implications for our understanding of immunodominance and breadth of responses to complex pathogens...
  67. pmc In silico prediction of peptides binding to multiple HLA-DR molecules accurately identifies immunodominant epitopes from gp43 of Paracoccidioides brasiliensis frequently recognized in primary peripheral blood mononuclear cell responses from sensitized ind
    Leo Kei Iwai
    Laboratory of Immunology, Heart Institute InCor, Millenium Institutes, Brazil
    Mol Med 9:209-19. 2003
    ..brasiliensis. The combination of several such epitopes may increase the frequency of positive responses and allow the immunization of genetically distinct populations...
  68. pmc Comprehensive analysis of human immunodeficiency virus type 1-specific CD4 responses reveals marked immunodominance of gag and nef and the presence of broadly recognized peptides
    Daniel E Kaufmann
    Partners AIDS Research Center and Infectious Disease Unit, Howard Hughes Medical Institute, Massachusetts General Hospital, and Division of AIDS, Boston, Massachusetts 02114, USA
    J Virol 78:4463-77. 2004
    ..These findings have implications for the design of immunotherapeutic strategies and for testing candidate HIV vaccines...
  69. ncbi request reprint Improved immunogenicity of an immunodominant epitope of the HER-2/neu protooncogene by alterations of MHC contact residues
    Simona Vertuani
    Cancer Center Karolinska, Karolinska Hospital, Stockholm, Sweden
    J Immunol 172:3501-8. 2004
    ..369 epitope and the V2V9 analogue. Our results indicate that the high biological activity of the HER-2.369 V2V9 epitope is associated with a slower dissociation kinetic profile, resulting in an epitope with greater HLA-A2 stability...
  70. ncbi request reprint Characterization of MHC- and TCR-binding residues of the myelin oligodendrocyte glycoprotein 38-51 peptide
    Troels R Petersen
    Malaghan Institute of Medical Research, Wellington South, New Zealand
    Eur J Immunol 34:165-73. 2004
    ..Our results could be useful to design peptides with altered agretopes and epitopes of the MOG(38-51) peptide to study their therapeutic potential in the EAE model...
  71. ncbi request reprint Conserved hierarchy of helper T cell responses in a chimpanzee during primary and secondary hepatitis C virus infections
    Naglaa H Shoukry
    Center for Vaccines and Immunity, Columbus Children s Research Institute, 700 Children s Drive, Columbus, OH 43205, USA
    J Immunol 172:483-92. 2004
    ..The hierarchial nature of the CD4+ T cell response, if broadly applicable to other HCV-infected chimpanzees and humans, could be a factor governing the outcome of HCV infection...
  72. ncbi request reprint Simultaneous prediction of binding capacity for multiple molecules of the HLA B44 supertype
    John Sidney
    Division of Translational Immunology and Biodefense, La Jolla Institute for Allergy and Immunology, San Diego, CA 92121, USA
    J Immunol 171:5964-74. 2003
    ..Taken together, these findings have important implications for epitope-based approaches to vaccination, immunotherapy, and the monitoring of immune responses...
  73. pmc Escape in one of two cytotoxic T-lymphocyte epitopes bound by a high-frequency major histocompatibility complex class I molecule, Mamu-A*02: a paradigm for virus evolution and persistence?
    Thorsten U Vogel
    Wisconsin Regional Primate Research Center, University of Wisconsin, Madison, Wisconsin 53715, USA
    J Virol 76:11623-36. 2002
    ..Differential selection by CTL may therefore be a paradigm of immunodeficiency virus infection...
  74. ncbi request reprint Tumor-associated carbohydrate antigens: a possible avenue for cancer prevention
    Yanfei Xu
    Torrey Pines Institute for Molecular Studies, San Diego, California, USA
    Immunol Cell Biol 83:440-8. 2005
    ..Our results have suggested that CTL derived from normal donors respond with high efficiency to glycopeptides in vitro, opening a new avenue for the design of prospective vaccines for cancer prevention...
  75. pmc Immunodominant tuberculosis CD8 antigens preferentially restricted by HLA-B
    Deborah A Lewinsohn
    Department of Pediatrics, Oregon Health and Sciences University, Portland, Oregon, USA
    PLoS Pathog 3:1240-9. 2007
    ..These findings provide an improved understanding of immunodominance in humans and may contribute to a development of an effective TB vaccine and improved immunodiagnostics...
  76. ncbi request reprint Identification of multiple HLA-A*0201-restricted cruzipain and FL-160 CD8+ epitopes recognized by T cells from chronically Trypanosoma cruzi-infected patients
    Simone G Fonseca
    Laboratorio de Imunologia, Heart Institute, Instituto do Coração InCor, Faculdade de Medicina da Universidade de Sao Paulo, Av Dr Eneas de Carvalho Aguiar, 44 BL 2, 9 andar, São Paulo SP 05403 000, Brazil
    Microbes Infect 7:688-97. 2005
    ..Thus, our results suggest that the recognition of CD8+ T cell epitopes in cruzipain and FL-160 may have a pathogenic or protective role in chronic Chagas disease...
  77. pmc Extensive HLA class I allele promiscuity among viral CTL epitopes
    Nicole Frahm
    Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
    Eur J Immunol 37:2419-33. 2007
    ..These data have significant implications for the understanding of MHC class I-restricted antigen presentation and vaccine development...
  78. ncbi request reprint A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus
    Magdalini Moutaftsi
    La Jolla Institute for Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, California 92109, USA
    Nat Biotechnol 24:817-9. 2006
    ..This approach reveals the breadth of T-cell responses to vaccinia, a widely studied murine viral infection model, and may provide a tool for developing comprehensive antigenic maps of any complex pathogen...
  79. ncbi request reprint Derivation of HLA-B*0702 transgenic mice: functional CTL repertoire and recognition of human B*0702-restricted CTL epitopes
    Jeff Alexander
    Epimmune Inc, San Diego, California 92121, USA
    Hum Immunol 64:211-23. 2003
    ....
  80. ncbi request reprint Identification of novel consensus CD4 T-cell epitopes from clade B HIV-1 whole genome that are frequently recognized by HIV-1 infected patients
    Simone G Fonseca
    Division of Clinical Immunology and Allergy, Department of Medicine, University of Sao Paulo School of Medicine, Brazil
    AIDS 20:2263-73. 2006
    ..To identify promiscuous and potentially protective human CD4 T-cell epitopes in most conserved regions within the protein-coding genome of HIV-1 clade B consensus sequence...
  81. ncbi request reprint Detailed characterization of the peptide binding specificity of five common Patr class I MHC molecules
    John Sidney
    La Jolla Institute for Allergy and Immunology, 3030 Bunker Hill St, Ste 326, San Diego, CA 92109, USA
    Immunogenetics 58:559-70. 2006
    ..Because the Patr alleles studied herein were found to be very common in two different chimpanzee populations, the present data should facilitate the use of chimpanzees for immunological studies...
  82. pmc Poxvirus CD8+ T-cell determinants and cross-reactivity in BALB/c mice
    David C Tscharke
    Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases NIH, Bethesda, MD 20892, USA
    J Virol 80:6318-23. 2006
    ..We then use these determinants to test if predicted conservation across orthopoxvirus species matches experimental observation and find an unexpectedly cross-reactive variant peptide encoded by ectromelia (mousepox) virus...
  83. ncbi request reprint Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules
    Shanfeng Zhu
    Bioinformatics Center, Institute for Chemical Research, Kyoto University Gokasho, Uji 611 0011, Japan
    Bioinformatics 22:1648-55. 2006
    ....
  84. ncbi request reprint Characterization of the peptide-binding specificity of Mamu-B*17 and identification of Mamu-B*17-restricted epitopes derived from simian immunodeficiency virus proteins
    Bianca R Mothe
    Wisconsin Regional Primate Research Center, University of Wisconsin, Madison, WI 53715, USA
    J Immunol 169:210-9. 2002
    ..Furthermore, it is an important step toward the design of a multiepitope vaccine for SIV and HIV...
  85. ncbi request reprint The high frequency Indian rhesus macaque MHC class I molecule, Mamu-B*01, does not appear to be involved in CD8+ T lymphocyte responses to SIVmac239
    John T Loffredo
    Wisconsin National Primate Research Center WNPRC, University of Wisconsin, Madison, WI 53715, USA
    J Immunol 175:5986-97. 2005
    ..Our results suggest that the high frequency MHC class I molecule, Mamu-B*01, is not involved in SIV-specific CD8+ T lymphocyte responses...
  86. ncbi request reprint HLA-A*0201, HLA-A*1101, and HLA-B*0702 transgenic mice recognize numerous poxvirus determinants from a wide variety of viral gene products
    Valerie Pasquetto
    La Jolla Institute for Allergy and Immunology, San Diego, CA 92109, USA
    J Immunol 175:5504-15. 2005
    ..These findings have implications for the design of new smallpox vaccines and the understanding of immune responses to large DNA viruses in general...
  87. pmc HLA class I-restricted responses to vaccinia recognize a broad array of proteins mainly involved in virulence and viral gene regulation
    Carla Oseroff
    La Jolla Institute for Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA 92109, USA
    Proc Natl Acad Sci U S A 102:13980-5. 2005
    ..Finally, most epitopes were highly conserved among vaccinia virus Western Reserve, variola major and modified vaccinia Ankara, supporting their potential use in vaccine and diagnostic applications...
  88. ncbi request reprint Structural snapshot of aberrant antigen presentation linked to autoimmunity: the immunodominant epitope of MBP complexed with I-Au
    Xiao lin He
    Department of Microbiology and Immunology, Stanford University School of Medicine, CA 94305, USA
    Immunity 17:83-94. 2002
    ....
  89. ncbi request reprint Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules
    Bjorn Peters
    Institut fur Biochemie, Charite, Humboldt Universitat Berlin, Monbijoustr 2, 10117 Berlin, Germany
    Bioinformatics 19:1765-72. 2003
    ..g. artificial neural networks). We aim to compare the prediction accuracies of these methods, and quantify the impact of interactions between peptide positions...
  90. ncbi request reprint A single minor histocompatibility antigen encoded by UGT2B17 and presented by human leukocyte antigen-A*2902 and -B*4403
    Seitaro Terakura
    Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
    Transplantation 83:1242-8. 2007
    ....
  91. ncbi request reprint Identification of seventeen new simian immunodeficiency virus-derived CD8+ T cell epitopes restricted by the high frequency molecule, Mamu-A*02, and potential escape from CTL recognition
    John T Loffredo
    National Primate Research Center, University of Wisconsin WPRC, Madison 53715, USA
    J Immunol 173:5064-76. 2004
    ..This work enhances the use of the SIV-infected macaque model for HIV and increases our understanding of the breadth of CD8+ T cell responses in SIV infection...
  92. ncbi request reprint Rationally engineered therapeutic proteins with reduced immunogenicity
    Shabnam Tangri
    Epimmune, San Diego, CA 92121, USA
    J Immunol 174:3187-96. 2005
    ..These findings support our hypothesis and demonstrate that immunogenicity of protein drugs can be reduced in a systematic and predictable manner...
  93. pmc The majority of currently circulating human immunodeficiency virus type 1 clade B viruses fail to prime cytotoxic T-lymphocyte responses against an otherwise immunodominant HLA-A2-restricted epitope: implications for vaccine design
    Marcus Altfeld
    Partners AIDS Research Center, Massachusetts General Hospital, 149 13th St, Boston, MA 02129, USA
    J Virol 79:5000-5. 2005
    ....
  94. ncbi request reprint A rational strategy to design multiepitope immunogens based on multiple Th lymphocyte epitopes
    Brian Livingston
    Epimmune, San Diego, CA 92121, USA
    J Immunol 168:5499-506. 2002
    ..Finally, we demonstrate that a GPGPG spacer construct can be used to induce HTL responses by either polypeptide or DNA immunization, highlighting the flexibility of the approach...
  95. pmc Cellular immune selection with hepatitis C virus persistence in humans
    Andrea L Cox
    Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
    J Exp Med 201:1741-52. 2005
    ..015). These findings reveal two distinct mechanisms of sequence evolution involved in HCV persistence: viral escape from CD8+ T cell responses and optimization of replicative capacity...
  96. ncbi request reprint Broad repertoire of the CD4+ Th cell response in spontaneously controlled hepatitis C virus infection includes dominant and highly promiscuous epitopes
    Julian Schulze zur Wiesch
    Partners AIDS Research Center and Infectious Disease Division, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
    J Immunol 175:3603-13. 2005
    ..This comprehensive characterization of CD4(+) T cell epitopes in resolved HCV infection provides important information to facilitate studies of immunopathogenesis and HCV vaccine design and evaluation...
  97. ncbi request reprint Cross-presentation of caspase-cleaved apoptotic self antigens in HIV infection
    Pisana Moroni Rawson
    Fondazione Andrea Cesalpino Dipartimento di Medicina Interna, Sapienza Universita di Roma, 00161 Rome, Italy
    Nat Med 13:1431-9. 2007
    ..These findings demonstrate a previously undescribed role for caspases in immunopathology...
  98. pmc Comprehensive immunological evaluation reveals surprisingly few differences between elite controller and progressor Mamu-B*17-positive simian immunodeficiency virus-infected rhesus macaques
    Nicholas J Maness
    Wisconsin National Primate Research Center, University of Wisconsin Madison, Madison, Wisconsin 53711, USA
    J Virol 82:5245-54. 2008
    ..Most importantly, our data indicate that the important differences between Mamu-B*17-positive ECs and progressors are not readily discernible using standard assays to measure immune responses...