Bjoern Peters

Summary

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

Publications

  1. ncbi Classification of the universe of immune epitope literature: representation and knowledge gaps
    Vince Davies
    La Jolla Institute for Allergy and Immunology, Vaccine Discovery, La Jolla, California, United States of America
    PLoS ONE 4:e6948. 2009
  2. ncbi Cost sensitive hierarchical document classification to triage PubMed abstracts for manual curation
    Emily Seymour
    The La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
    BMC Bioinformatics 12:482. 2011
  3. ncbi Identification and localization of minimal MHC-restricted CD8+ T cell epitopes within the Plasmodium falciparum AMA1 protein
    Martha Sedegah
    USMMVP, Malaria Department, NMRC, Silver Spring, MD 20910, USA
    Malar J 9:241. 2010
  4. ncbi Modeling biomedical experimental processes with OBI
    Ryan R Brinkman
    British Columbia Cancer Agency, Vancouver, Canada
    J Biomed Semantics 1:S7. 2010
  5. ncbi 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
  6. ncbi 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
  7. ncbi The immune epitope database 2.0
    Randi Vita
    La Jolla Institute for Allergy and Immunology, Center for Infectious Disease, Allergy and Asthma Research, 9420 Athena Circle, La Jolla, CA 92037, USA
    Nucleic Acids Res 38:D854-62. 2010
  8. ncbi 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
  9. ncbi CD4+ T cells are not required for the induction of dengue virus-specific CD8+ T cell or antibody responses but contribute to protection after vaccination
    Lauren E Yauch
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    J Immunol 185:5405-16. 2010
  10. ncbi 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

Detail Information

Publications66

  1. ncbi Classification of the universe of immune epitope literature: representation and knowledge gaps
    Vince Davies
    La Jolla Institute for Allergy and Immunology, Vaccine Discovery, La Jolla, California, United States of America
    PLoS ONE 4:e6948. 2009
    ..The IEDB is maintained and continually updated by monitoring PubMed for new, potentially relevant references...
  2. ncbi Cost sensitive hierarchical document classification to triage PubMed abstracts for manual curation
    Emily Seymour
    The La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
    BMC Bioinformatics 12:482. 2011
    ..abstract:..
  3. ncbi Identification and localization of minimal MHC-restricted CD8+ T cell epitopes within the Plasmodium falciparum AMA1 protein
    Martha Sedegah
    USMMVP, Malaria Department, NMRC, Silver Spring, MD 20910, USA
    Malar J 9:241. 2010
    ..Since CD8+ T cell responses have been implicated in protection against pre-erythrocytic stage malaria, this study was designed to identify MHC class I-restricted epitopes within AMA1...
  4. ncbi Modeling biomedical experimental processes with OBI
    Ryan R Brinkman
    British Columbia Cancer Agency, Vancouver, Canada
    J Biomed Semantics 1:S7. 2010
    ..AVAILABILITY : OBI is available at http://purl.obolibrary.org/obo/obi/2009-11-02/obi.owl...
  5. ncbi 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...
  6. ncbi 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
    ....
  7. ncbi The immune epitope database 2.0
    Randi Vita
    La Jolla Institute for Allergy and Immunology, Center for Infectious Disease, Allergy and Asthma Research, 9420 Athena Circle, La Jolla, CA 92037, USA
    Nucleic Acids Res 38:D854-62. 2010
    ..The database structure, as well as its querying, browsing and reporting interfaces, was completely redesigned for the IEDB 2.0 release, which became publicly available in early 2009...
  8. ncbi 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...
  9. ncbi CD4+ T cells are not required for the induction of dengue virus-specific CD8+ T cell or antibody responses but contribute to protection after vaccination
    Lauren E Yauch
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    J Immunol 185:5405-16. 2010
    ..These findings suggest inducing anti-DENV CD4(+) T cell responses by vaccination may be beneficial...
  10. ncbi 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...
  11. ncbi 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...
  12. ncbi 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...
  13. ncbi Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population
    Jason A Greenbaum
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 106:20365-70. 2009
    ..These results are consistent with reports about disease incidence, severity, and mortality rates associated with human S-OIV...
  14. ncbi Immune epitope database analysis resource (IEDB-AR)
    Qing Zhang
    Immune Epitope Database and Analysis Resource IEDB AR, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
    Nucleic Acids Res 36:W513-8. 2008
    ..New functionalities have been added to most of the previously implemented tools, and a total of eight new tools were added, including two B-cell epitope prediction tools, four T-cell epitope prediction tools and two analysis tools...
  15. ncbi 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...
  16. ncbi Selective CD4+ T cell help for antibody responses to a large viral pathogen: deterministic linkage of specificities
    Alessandro Sette
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology LIAI, La Jolla, CA 92037, USA
    Immunity 28:847-58. 2008
    ..Therefore, MHC restriction is a key selective event for the antiviral antibody response and is probably important for vaccine development to large pathogens...
  17. ncbi 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...
  18. ncbi 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...
  19. ncbi 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...
  20. ncbi 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...
  21. ncbi ElliPro: a new structure-based tool for the prediction of antibody epitopes
    Julia Ponomarenko
    San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
    BMC Bioinformatics 9:514. 2008
    ..The aim of this work was to implement that method as a web-tool and evaluate its performance on discontinuous epitopes known from the structures of antibody-protein complexes...
  22. ncbi 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...
  23. ncbi 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. ncbi 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...
  25. ncbi 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
    ..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...
  26. ncbi 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...
  27. ncbi 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...
  28. ncbi 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...
  29. ncbi 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...
  30. ncbi 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...
  31. ncbi 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...
  32. ncbi 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...
  33. ncbi 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...
  34. ncbi 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
    ....
  35. ncbi 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
    ....
  36. ncbi 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...
  37. ncbi 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...
  38. ncbi Design and utilization of epitope-based databases and predictive tools
    Nima Salimi
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
    Immunogenetics 62:185-96. 2010
    ..Taken together, the results highlight the growing impact and utility of immunological databases for the scientific community...
  39. ncbi 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
    ....
  40. ncbi 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...
  41. ncbi 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...
  42. ncbi Uncovering the interplay between CD8, CD4 and antibody responses to complex pathogens
    Magdalini Moutaftsi
    Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
    Future Microbiol 5:221-39. 2010
    ..This review summarizes and highlights key findings based on identification of VACV antigens targeted by the immune system (CD4, CD8 and antibodies) and the complex interplay between responses...
  43. ncbi 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...
  44. ncbi 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
    ....
  45. ncbi TiArA: a virtual appliance for the analysis of Tiling Array data
    Jason A Greenbaum
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
    PLoS ONE 5:e9993. 2010
    ..Genomic tiling arrays have been described in the scientific literature since 2003, yet there is a shortage of user-friendly applications available for their analysis...
  46. ncbi 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
    ....
  47. ncbi Automating document classification for the Immune Epitope Database
    Peng Wang
    The La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    BMC Bioinformatics 8:269. 2007
    ..Like similar projects in other knowledge domains, significant effort is spent on identifying which articles are relevant for this purpose...
  48. ncbi Of mice and humans: how good are HLA transgenic mice as a model of human immune responses?
    Maya F Kotturi
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
    Immunome Res 5:3. 2009
    ....
  49. ncbi 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...
  50. ncbi Human CD8? and CD4? T cell memory to lymphocytic choriomeningitis virus infection
    Maya F Kotturi
    Pfizer Inc, Vaccine Research West, 10777 Science Center Drive, San Diego, CA 92121, USA
    J Virol 85:11770-80. 2011
    ..These data demonstrate for the first time LCMV-specific CD8(+) and CD4(+) T cells in infected humans and begin to provide new insights into memory T cell responses following an acute virus infection...
  51. ncbi Towards defining molecular determinants recognized by adaptive immunity in allergic disease: an inventory of the available data
    Kerrie Vaughan
    The Immune Epitope Database IEDB, La Jolla Institute for Allergy and Immunology LIAI, La Jolla, CA 92037, USA
    J Allergy (Cairo) 2010:628026. 2010
    ..Finally, our analysis also underscores that only a handful of epitopes have thus far been investigated for their immunotherapeutic potential...
  52. ncbi Meta-analysis of all immune epitope data in the Flavivirus genus: inventory of current immune epitope data status in the context of virus immunity and immunopathology
    Kerrie Vaughan
    La Jolla Institute of Allergy and Immunology, La Jolla, CA 92037, USA
    Viral Immunol 23:259-84. 2010
    ..Through this work we hope to provide useful data to those working in the area of Flavivirus research...
  53. ncbi Integrating epitope data into the emerging web of biomedical knowledge resources
    Bjoern Peters
    La Jolla Institute for Allergy and Immunology, Division of Vaccine Discovery, 9420 Athena Circle, La Jolla, California 92037, USA
    Nat Rev Immunol 7:485-90. 2007
    ....
  54. ncbi Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method
    Bjoern Peters
    La Jolla Institute for Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA 92109, USA
    BMC Bioinformatics 6:132. 2005
    ..This method has been successfully applied to predicting peptide binding to MHC molecules, peptide transport by the transporter associated with antigen presentation (TAP) and proteasomal cleavage of protein sequences...
  55. ncbi 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...
  56. ncbi Ab and T cell epitopes of influenza A virus, knowledge and opportunities
    Huynh Hoa Bui
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 104:246-51. 2007
    ..At the same time, the analysis illustrates gaps in our collective knowledge that should inspire directions for further study of immunity against the influenza A virus...
  57. ncbi 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...
  58. ncbi A roadmap for the immunomics of category A-C pathogens
    Alessandro Sette
    La Jolla Institute for Allegy and Immunology, San Diego, CA 92121, USA
    Immunity 22:155-61. 2005
    ..Herein is an account of the meeting and its results...
  59. ncbi A Model for Collaborative Curation, The IEDB and ChEBI Curation of Non-peptidic Epitopes
    Randi Vita
    La Jolla Institute for Allergy and Immunology, Vaccine Discovery, La Jolla, California, USA
    Immunome Res 7:1-8. 2011
    ..This project has resulted in the comprehensive inventory and curation of immune epitope data related to non-peptidic structures and serves as a model for successful collaborative curation between established resources...
  60. ncbi Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools
    Jason A Greenbaum
    Immune Epitope Database and Analysis Resource IEDB, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
    J Mol Recognit 20:75-82. 2007
    ..By developing common datasets, standardized data formats, and the means with which to consolidate information, we hope to greatly enhance the development of B-cell epitope prediction tools...
  61. ncbi Immune epitope mapping in the post-genomic era: lessons for vaccine development
    Alessandro Sette
    La Jolla Institute for Allergy and Immunology, Division of Vaccine Discovery, 9420 Athena Circle, La Jolla, CA 92037, USA
    Curr Opin Immunol 19:106-10. 2007
    ..However, they raise the question if vaccines, which try to emulate protective natural immune responses, should elicit an equally broad range of responses to efficiently convey protection...
  62. ncbi Applications for T-cell epitope queries and tools in the Immune Epitope Database and Analysis Resource
    Yohan Kim
    La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
    J Immunol Methods 374:62-9. 2011
    ..We address common questions and concerns faced by users, and identify patterns of usage that have proven successful...
  63. ncbi The immune epitope database and analysis resource: from vision to blueprint
    Bjoern Peters
    La Jolla Institute of Allergy and Immunology, San Diego, California, USA
    PLoS Biol 3:e91. 2005
  64. ncbi 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...
  65. ncbi Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan
    Morten Nielsen
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
    PLoS Comput Biol 4:e1000107. 2008
    ....
  66. ncbi Quantifying the contribution of defective ribosomal products to antigen production: a model-based computational analysis
    Sascha Bulik
    , Charite, , Berlin, Germany
    J Immunol 175:7957-64. 2005
    ..g., virus derived) protein, and 3) inhibition of protein synthesis by the translation inhibitor cycloheximide appears to be paralleled with an instantaneous decrease of protein degradation down to approximately 1/3 of the normal value...