Research Topics
| John SidneySummaryAffiliation: La Jolla Institute for Allergy and Immunology Country: USA Publications
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Detail Information
Publications
Five HLA-DP molecules frequently expressed in the worldwide human population share a common HLA supertypic binding specificityJohn 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...- 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 CHua 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.... - Curation of complex, context-dependent immunological dataRandi 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... - HLA class I supertypes: a revised and updated classificationJohn 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... - Dissociation between epitope hierarchy and immunoprevalence in CD8 responses to vaccinia virus western reserveCarla 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... 
A quantitative analysis of the variables affecting the repertoire of T cell specificities recognized after vaccinia virus infectionErika 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...- A multivalent and cross-protective vaccine strategy against arenaviruses associated with human diseaseMaya 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... - HLA-A2-restricted protection against lethal lymphocytic choriomeningitisJason 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.... - 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 pathogensAlessandro 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... - Correlates of protection efficacy induced by vaccinia virus-specific CD8+ T-cell epitopes in the murine intranasal challenge modelMagdalini 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... - A shared MHC supertype motif emerges by convergent evolution in macaques and mice, but is totally absent in human MHC moleculesAlessandro 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... - Vaccinia virus-specific CD4+ T cell responses target a set of antigens largely distinct from those targeted by CD8+ T cell responsesMagdalini 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... - Derivation of an amino acid similarity matrix for peptide: MHC binding and its application as a Bayesian priorYohan 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... - Molecular determinants of T cell epitope recognition to the common Timothy grass allergenCarla 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... - Immunomic analysis of the repertoire of T-cell specificities for influenza A virus in humansErika 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... - The CD8+ T-cell response to lymphocytic choriomeningitis virus involves the L antigen: uncovering new tricks for an old virusMaya 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... - Naive precursor frequencies and MHC binding rather than the degree of epitope diversity shape CD8+ T cell immunodominanceMaya 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... - Polyfunctional CD4+ T cell responses to a set of pathogenic arenaviruses provide broad population coverageMaya 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.... - Lymphocytic choriomeningitis virus infection yields overlapping CD4+ and CD8+ T-cell responsesCourtney 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... - T cell responses to known allergen proteins are differently polarized and account for a variable fraction of total response to allergen extractsCarla 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)... - Analysis of T cell responses to the major allergens from German cockroach: epitope specificity and relationship to IgE productionCarla 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... 
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....- Peptide binding predictions for HLA DR, DP and DQ moleculesPeng 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... - Divergent motifs but overlapping binding repertoires of six HLA-DQ molecules frequently expressed in the worldwide human populationJohn 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... - Functional classification of class II human leukocyte antigen (HLA) molecules reveals seven different supertypes and a surprising degree of repertoire sharing across supertypesJason 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... - 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... - Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccinesHuynh 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... - A protective role for dengue virus-specific CD8+ T cellsLauren E Yauch
Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
J Immunol 182:4865-73. 2009.... - Cutting edge: murine cytomegalovirus induces a polyfunctional CD4 T cell responseRamon 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... - 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 specificitiesScott Southwood
Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
Immunogenetics 63:275-90. 2011.... - Insights into HLA-restricted T cell responses in a novel mouse model of dengue virus infection point toward new implications for vaccine designDaniela 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... - IMMUNOCAT-a data management system for epitope mapping studiesJo 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... - Characterization of the peptide-binding specificity of the chimpanzee class I alleles A 0301 and A 0401 using a combinatorial peptide libraryJohn Sidney
La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
Immunogenetics 59:745-51. 2007.... - Immunogenic HLA-B7-restricted peptides of hTRTXochitl 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.... - Identification of protective Lassa virus epitopes that are restricted by HLA-A2Jason Botten
Molecular and Integrative Neurosciences Department, The Scripps Research Institute, La Jolla, CA 92037, USA
J Virol 80:8351-61. 2006.... - Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applicationsHuynh-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... - Analysis of epitope information related to Bacillus anthracis and Clostridium botulinumLaura 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... - A community resource benchmarking predictions of peptide binding to MHC-I moleculesBjoern Peters
La Jolla Institute for Allergy and Immunology, San Diego, California, USA
PLoS Comput Biol 2:e65. 2006.... - Classification of A1- and A24-supertype molecules by analysis of their MHC-peptide binding repertoiresJohn Sidney
La Jolla Institute for Allergy and Immunology, 3030 Bunker Hill St, Ste 326, San Diego, CA, 92109, USA
Immunogenetics 57:393-408. 2005.... - Class I molecules with similar peptide-binding specificities are the result of both common ancestry and convergent evolutionAlessandro Sette
La Jolla Institute for Allergy and Immunology, San Diego, CA 92121, USA
Immunogenetics 54:830-41. 2003.... - Predicting population coverage of T-cell epitope-based diagnostics and vaccinesHuynh 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... - A computational pipeline to generate MHC binding motifsPenny 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... - Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genesErika 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... - Analysis of the binding of gluten T-cell epitopes to various human leukocyte antigen class II moleculesElin 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... - Comprehensive analysis of T cell epitope discovery strategies using 17DD yellow fever virus structural proteins and BALB/c (H2d) mice modelMilton 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... - Extensive HLA class I allele promiscuity among viral CTL epitopesNicole 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... - Immunodominant tuberculosis CD8 antigens preferentially restricted by HLA-BDeborah 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... - A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approachPeng 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... - 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 SIVmac239John 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... - Conserved hierarchy of helper T cell responses in a chimpanzee during primary and secondary hepatitis C virus infectionsNaglaa 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... - Identification of poxvirus CD8+ T cell determinants to enable rational design and characterization of smallpox vaccinesDavid 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... - Cellular immune responses to the hepatitis B virus polymeraseEishiro 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... - 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 indLeo 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... - Comprehensive analysis of human immunodeficiency virus type 1-specific CD4 responses reveals marked immunodominance of gag and nef and the presence of broadly recognized peptidesDaniel 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... - Improved immunogenicity of an immunodominant epitope of the HER-2/neu protooncogene by alterations of MHC contact residuesSimona 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... - Characterization of MHC- and TCR-binding residues of the myelin oligodendrocyte glycoprotein 38-51 peptideTroels 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... - Reversion of CTL escape-variant immunodeficiency viruses in vivoThomas 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... - Simultaneous prediction of binding capacity for multiple molecules of the HLA B44 supertypeJohn 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... - Examining the independent binding assumption for binding of peptide epitopes to MHC-I moleculesBjorn 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... - Identification of Plasmodium falciparum antigens by antigenic analysis of genomic and proteomic dataDenise 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... - MAGE-6 encodes HLA-DRbeta1*0401-presented epitopes recognized by CD4+ T cells from patients with melanoma or renal cell carcinomaTomohide 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... - Derivation of HLA-B*0702 transgenic mice: functional CTL repertoire and recognition of human B*0702-restricted CTL epitopesJeff Alexander
Epimmune Inc, San Diego, California 92121, USA
Hum Immunol 64:211-23. 2003.... - The HLA molecules DQA1*0501/B1*0201 and DQA1*0301/B1*0302 share an extensive overlap in peptide binding specificityJohn 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... - 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... - Structural snapshot of aberrant antigen presentation linked to autoimmunity: the immunodominant epitope of MBP complexed with I-AuXiao-lin He
Department of Microbiology and Immunology, Stanford University School of Medicine, CA 94305, USA
Immunity 17:83-94. 2002.... - Characterization of the peptide-binding specificity of Mamu-B*17 and identification of Mamu-B*17-restricted epitopes derived from simian immunodeficiency virus proteinsBianca 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... - Characterization of the peptide-binding specificity of Mamu-A*11 results in the identification of SIV-derived epitopes and interspecies cross-reactivityAlessandro 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... - Impact of HLA-B alleles, epitope binding affinity, functional avidity, and viral coinfection on the immunodominance of virus-specific CTL responsesFlorian 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... - HLA-A*0201, HLA-A*1101, and HLA-B*0702 transgenic mice recognize numerous poxvirus determinants from a wide variety of viral gene productsValerie 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... - HLA class I-restricted responses to vaccinia recognize a broad array of proteins mainly involved in virulence and viral gene regulationCarla 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... - Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC moleculesShanfeng Zhu
Bioinformatics Center, Institute for Chemical Research, Kyoto University Gokasho, Uji 611-0011, Japan
Bioinformatics 22:1648-55. 2006..Our approach can thus be used to help find new binders for MHC molecules... - A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virusMagdalini 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... - Tumor-associated carbohydrate antigens: a possible avenue for cancer preventionYanfei 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... - Poxvirus CD8+ T-cell determinants and cross-reactivity in BALB/c miceDavid 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... - The design and implementation of the immune epitope database and analysis resourceBjoern Peters
La Jolla Institute of Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA 92109, USA
Immunogenetics 57:326-36. 2005..quot; 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... - Detailed characterization of the peptide binding specificity of five common Patr class I MHC moleculesJohn 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... - Identification of multiple HLA-A*0201-restricted cruzipain and FL-160 CD8+ epitopes recognized by T cells from chronically Trypanosoma cruzi-infected patientsSimone 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... - A CD8+ T cell heptaepitope minigene vaccine induces protective immunity against Chlamydia pneumoniaeIrina 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.... - Identification of novel consensus CD4 T-cell epitopes from clade B HIV-1 whole genome that are frequently recognized by HIV-1 infected patientsSimone G Fonseca
Division of Clinical Immunology and Allergy, Department of Medicine, , Brazil
AIDS 20:2263-73. 2006..This combination of CD4 T-cell epitopes - 11 of them not described before - may have the potential for inclusion in a vaccine against HIV-1, allowing the immunization of genetically distinct populations... - Cross-presentation of caspase-cleaved apoptotic self antigens in HIV infectionPisana 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... - Rationally engineered therapeutic proteins with reduced immunogenicityShabnam 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... - Comprehensive immunological evaluation reveals surprisingly few differences between elite controller and progressor Mamu-B*17-positive simian immunodeficiency virus-infected rhesus macaquesNicholas 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... - A rational strategy to design multiepitope immunogens based on multiple Th lymphocyte epitopesBrian 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... - Broad repertoire of the CD4+ Th cell response in spontaneously controlled hepatitis C virus infection includes dominant and highly promiscuous epitopesJulian 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... - Cellular immune selection with hepatitis C virus persistence in humansAndrea 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... - 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 recognitionJohn 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... - 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 designMarcus Altfeld
Partners AIDS Research Center, Massachusetts General Hospital, 149 13th St, Boston, MA 02129, USA
J Virol 79:5000-5. 2005.... - A single minor histocompatibility antigen encoded by UGT2B17 and presented by human leukocyte antigen-A*2902 and -B*4403Seitaro Terakura
Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
Transplantation 83:1242-8. 2007....