* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Curriculum Vitae
Sociality and disease transmission wikipedia , lookup
Vaccination wikipedia , lookup
Adoptive cell transfer wikipedia , lookup
Monoclonal antibody wikipedia , lookup
Immunocontraception wikipedia , lookup
Gluten immunochemistry wikipedia , lookup
Human leukocyte antigen wikipedia , lookup
Social immunity wikipedia , lookup
Adaptive immune system wikipedia , lookup
Immune system wikipedia , lookup
Major histocompatibility complex wikipedia , lookup
Cancer immunotherapy wikipedia , lookup
Innate immune system wikipedia , lookup
DNA vaccination wikipedia , lookup
Hygiene hypothesis wikipedia , lookup
Immunosuppressive drug wikipedia , lookup
Psychoneuroimmunology wikipedia , lookup
Curriculum Vitae NAME POSITION TITLE Bjoern Peters Assistant Member and Head of the LIAI Bioinformatics and Statistics Core eRA COMMONS USER NAME (credential, e.g., agency login) BJPETERS EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) INSTITUTION AND LOCATION University of Hamburg, Hamburg, Germany Humboldt University, Berlin, Germany La Jolla Institute for Allergy and Immunology DEGREE (if applicable) Diploma (summa cum laude) Ph.D. (summa cum laude) Postdoctoral Fellow YEAR(s) FIELD OF STUDY 2000 2003 2004-6 Physics Biophysics/Bioinformatics Bioinformatics/Immunology A. Positions and Honors 2002 Visiting Research Assistant, Boston University, Boston, MA, Dr. Zhiping Weng 2003 Visiting Postdoctoral Fellow, University of Thübingen, Germany, Drs. Hans-Georg Rammensee and Hans-Jörg Schild 07/06–12/07 Research Scientist, La Jolla Institute for Allergy and Immunology, San Diego, CA 01/08Assistant Member, La Jolla Institute for Allergy and Immunology, San Diego, CA 01/08Head, Statistics and Bioinformatics Core, La Jolla Institute for Allergy and Immunology B. Membership and Activities International Society for Computational Biology – Member since 2006 American Association of Immunology – Member since 2007 Ontology for Biomedical Investigations (OBI) - Coordinating committee member since 2006 and elected OBI representative in the Open Biomedical Ontology (OBO) foundry Member of the Data Interoperability Steering Committee of the Division of Allergy, Infectious Disease and Transplantation, (NIAID, NIH) Advisory Board member for multi-center research grant ‘Therapeutic Systems Immunology’ (BMBF funded, Berlin, Germany) NIAID external advisory council, ad hoc member (09/2009) Grant application reviews for: o National Institute of Allergy and Infectious Diseases (NIAID), Special Emphasis Panel o Dutch National Science Foundation (NWO) o Israel Science Foundation (ISF) Manuscript reviews for: Bioinformatics, BioSystems, BMC Bioinformatics, FEBS Letters, Human Immunology, Immunome Research, Journal of Biomedical Informatics, Journal of Genetics and Genomics, Journal of Immunology, Journal of Molecular Recognition, Leukemia Research, Nature Biotechnology, Nucleic Acids Research, PLoS Computational Biology, PLoS ONE, Protein Science, Proteomics, Tissue Antigens, Vaccine. C. Peer-reviewed journal publications (reverse chronological order) 1. Yauch LE, Prestwood TR, May MM, Morar MM, Zellweger RM, Peters B, Sette A, Shresta S. 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. J Immunol. 2010 Sep 24. [Epub ahead of print] PubMed PMID:20870934. 2. Sidney J, Steen A, Moore C, Ngo S, Chung J, Peters B, Sette A. Divergent motifs but overlapping binding repertoires of six HLA-DQ molecules frequently expressed in the worldwide human population. J Immunol. 2010 Sep 1. [Epub ahead of print] PMCID: PMC Journal – In Process 3. Sedegah M, Kim Y, Peters B, McGrath S, Ganeshan H, Lejano J, Abot E, Banania G, Belmonte M, Sayo R, Farooq F, Doolan DL, Regis D, Tamminga C, Chuang I, Bruder JT, King CR, Ockenhouse CF, Faber B, Remarque E, Hollingdale MR, Richie TL, Sette A. Identification and localization of minimal MHC-restricted CD8+ T cell epitopes within the Plasmodium falciparum AMA1 protein. Malar J. 2010 Aug 24;9(1):241. PMCID: PMC Journal – In Process 4. Oseroff C, Sidney J, Kotturi MF, Kolla R, Alam R, Broide DH, Wasserman SI, Weiskopf D, McKinney DM, Chung JL, Petersen A, Grey H, Peters B, Sette A. Molecular determinants of T cell epitope recognition to the common Timothy grass allergen. J Immunol. 2010 Jul 15;185(2):943. PMCID: PMC Journal – In Process 5. Chung JL, Sun J, Sidney J, Sette A, Peters B. IMMUNOCAT-a data management system for epitope mapping studies. J Biomed Biotechnol. 2010;2010:856842. PMCID: PMC2871663 6. Solomon C, Southwood S, Hoof I, Rudersdorf R, Peters B, Sidney J, Pinilla C, Marcondes MC, Ling B, Marx P, Sette A, Mothé BR. The most common Chinese rhesus macaque MHC class I molecule shares peptide binding repertoire with the HLA-B7 supertype. Immunogenetics. 2010 Jul;62(7):451. Epub 2010 May 18. PMCID: PMC2890073 7. Vaughan K, Greenbaum J, Blythe M, Peters B, Sette A. 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. Viral Immunol. 2010 Jun;23(3):259. PMCID: PMC Journal – In Process 8. Botten J, Sidney J, Mothé BR, Peters B, Sette A, Kotturi MF. Coverage of related pathogenic species by multivalent and cross-protective vaccine design: arenaviruses as a model system. Microbiol Mol Biol Rev. 2010 Jun;74(2):157. PMCID: PMC Journal – In Process 9. Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, RoccaSerra P, Ruttenberg A, Sansone SA, Soldatova LN, Stoeckert CJ Jr, Turner JA, Zheng J; OBI consortium. Modeling biomedical experimental processes with OBI. J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S7. PubMed PMID:20626927; PubMed Central PMCID: PMC2903726 10. Kotturi MF, Botten J, Maybeno M, Sidney J, Glenn J, Bui HH, Oseroff C, Crotty S, Peters B, Grey H, Altmann DM, Buchmeier MJ, Sette A. Polyfunctional CD4+ T cell responses to a set of pathogenic arenaviruses provide broad population coverage. Immunome Res. 2010 May 17;6:4. PMCID: PMC2880318 11. Greenbaum JA, Assarsson E, Chung JL, Head S, Sette A, Peters B. TiArA: a virtual appliance for the analysis of tiling array data. PLoS One. 2010 Apr 1;5(4):e9993. PMCID: PMC2848623 12. Salimi N, Fleri W, Peters B, Sette A. Design and utilization of epitope-based databases and predictive tools. Immunogenetics. 2010 Apr;62(4):185. PMCID: PMC2843836 13. Sidney J, Steen A, Moore C, Ngo S, Chung J, Peters B, Sette A. Five HLA-DP molecules frequently expressed in the worldwide human population share a common HLA supertypic binding specificity. J Immunol. 2010 Mar 1;184(5):2492. PMCID: PMC2935290 14. Freeman ML, Lanzer KG, Cookenham T, Peters B, Sidney J, Wu TT, Sun R, Woodland DL, Sette A, Blackman MA. Two kinetic patterns of epitope-specific CD8 T-cell responses following murine gammaherpesvirus 68 infection. J Virol. 2010 Mar;84(6):2881. PMCID: PMC2826075 15. Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondr√©-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ. Hematopoietic cell types: Prototype for a revised cell ontology. J Biomed Inform. 2010 Feb 1. [Epub ahead of print] PubMed PMID: PMC Journal – In Progress 16. 20123131; PubMed Central PMCID: PMC2892030.Zhang H, Wang P, Papangelopoulos N, Xu Y, Sette A, Bourne PE, Lund O, Ponomarenko J, Nielsen M, Peters B. Limitations of Ab initio predictions of peptide binding to MHC class II molecules. PLoS One. 2010 Feb 17;5(2):e9272. PMCID: PMC2822856 17. Moutaftsi M, Tscharke DC, Vaughan K, Koelle DM, Stern L, Calvo-Calle M, Ennis F, Terajima M, Sutter G, Crotty S, Drexler I, Franchini G, Yewdell JW, Head SR, Blum J, Peters B, Sette A. Uncovering the interplay between CD8, CD4 and antibody responses to complex pathogens. Future Microbiol. 2010 Feb;5(2):221. PMCID: PMC Journal – In Process 18. Vita Randi, Zarebski L, Greenbaum JA, Emami H, Hoof I, Salimi N, Damle R, Sette A, Peters B. The Immune Epitope Database 2.0. Nucleic Acids Res. 2010 January; 38(Database issue):D854–D862. PMCID: PMC2808938 19. Sette A, Grey H, Oseroff C, Peters B, Moutaftsi M, Crotty S, Assarsson E, Greenbaum J, Kim Y, Kolla R, Tscharke D, Koelle D, Johnson RP, Blum J, Head S, Sidney J. 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. Vaccine. 2009 Dec 30;27 Suppl 6:G21. PMCID: PMC Journal – In Progress 20. Greenbaum JA, Kotturi MF, Kim Y, Oseroff C, Vaughan K, Salimi N, Vita R, Ponomarenko J, Scheuermann RH, Sette A, Peters B. Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population. Proc Nat Acad Sci USA. 2009 Dec 1;106(48):20365. PMCID: PMC2777968 21. Kotturi MF, Botten J, Sidney J, Bui HH, Giancola L, Maybeno M, Babin J, Oseroff C, Pasquetto V, Greenbaum JA, Peters B, Ting J, Do D, Vang L, Alexander J, Grey H, Buchmeier MJ, Sette A. A multivalent and cross-protective vaccine strategy against arenaviruses associated with human disease. PLoS Path. 2009 Dec;5(12):e1000695. PMCID: PMC2787016 22. Greenbaum JA, Vita R, Zarebski LM, Sette A, Peters B. Ontology development for The Immune Epitope Database. In: Bioinformatic for Immunomics 2009 3:47. PMCID: PMC Journal – In Progress 23. Kim Y, Sidney J, Pinilla C, Sette A, Peters B. Derivation of an amino acid similarity matrix for peptide: MHC binding and its application as a bayesian prior. BMC Bioinfo. 2009 Nov 30;10:394. PMCID: PMC2790471 24. Karp DR, Marthandan N, Marsh SG, Ahn C, Arnett FC, Deluca DS, Diehl AD, Dunivin R, Eilbeck K, Feolo M, Guidry PA, Helmberg W, Lewis S, Mayes MD, Mungall C, Natale DA, Peters B, Petersdorf E, Reveille JD, Smith B, Thomson G, Waller MJ, Scheuermann RH. Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis. Hum Mol Genet. 2010 Feb 15;19(4):707. PMCID: PMC Journal – In Progress 25. Ishizuka J, Grebe K, Shenderov E, Peters B, Chen Q, Peng Y, Wang L, Dong T, Pasquetto V, Oseroff C, Sidney J, Hickman H, Cerundolo V, Sette A, Bennink JR, McMchael A, Yewdell JW. Quantitating T cell cross-reactivity for unrelated peptide antigens. J Immunol. 2009 Oct 1;183(7):4337. PMCID: PMC Journal – In Progress 26. Davies V, Vaughan K, Damle R, Peters B, Sette A. Classification of the universe of immune epitope literature: representation and knowledge gaps. PLoS One. 2009 Sep 14;4(9):e6948. PMCID: PMC2747625 27. Kotturi MF, Assarsson E, Peters B, Grey H, Oseroff C, Pasquetto V, Sette A. Of mice and humans: how good are HLA transgenic mice as a model of human immune responses? Immunome Res. 2009 Jun 17;5:3. PMCID: PMC2702351 28. Walsh SR, Gillis J, Peters B, Mothe BR, Sidney J, Sette A, Johnson RP. Diverse recognition of conserved orthopoxvirus CD8+ T cell epitopes in vaccinated rhesus macaques. Vaccine. 2009 Aug 6;27(36):49905000. PMCID: PMC2765250 29. Yauch LE, Zellweger RM, Kotturi MF, Qutubuddin S, Sidney J, Peters B, Prestwood TR, Sette A, Shresta S. A protective role for dengue virus-specific CD8+ T cells. J Immunol. 2009 Apr 15;182(8):4865. PMCID: PMC2765250 30. Chen C, Bouman TJ, Beare PA, Mertens K, Zhang GQ, Russell-Lodrigue KE, Hogaboam JP, Peters B, Felgner PL, Brown WC, Heinzen RA, Hendrix LR, Samuel JE. A systematic approach to evaluate humoral and cellular immune responses to Coxiella burnetii immunoreactive antigens. Clin Microbiol Infect. 2009 Mar 11. PMCID: PMC2916703 31. Moutaftsi M, Salek-Ardakani S, Croft M, Peters B, Sidney J, Grey H, Sette A. Correlates of protection efficacy induced by vaccinia virus-specific CD8+ T-cell epitopes in the murine intranasal challenge model. Eur J Immunol. 2009 Mar;39(3):717. PMCID: PMC2759087 32. Vaughan K, Blythe M, Greenbaum J, Zhang Q, Peters B, Doolan DL, Sette A. Meta-analysis of immune epitope data for all plasmodia: overview and applications for malarial immunobiology and vaccine-related issues. Parasite Immunol. 2009 Feb;31(2):78. PMCID: PMC Journal – In Process 33. Hoof I, Peters B, Sidney J, Pedersen LE, Sette A, Lund O, Buus S, Nielsen M. NetMHCpan, A method for MHC class I binding prediction beyond humans. Immunogenetics. 2009 Jan;61(1):1. NIHMS138465 PMCID: PMC Journal – In Progress 34. Schatz MM, Peters B, Akkad N, Ullrich N, Martinez AN, Carroll O, Bulik S, Rammensee HG, van Endert P, Holzhütter HG, Tenzer S, Schild H. Characterizing the N-terminal processing motif of MHC class I ligands. J Immunol. 2008 180:3210. PMCID: PMC Journal – In Progress 35. Ponomarenko J, Bui HH, Li W, Fusseder N, Bourne PE, Sette A, Peters B. ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics. 2008 Dec 2;9:514. PMCID: PMC2607291 36. Dow C, Oseroff C, Peters B, Nance-Sotelo C, Sidney J, Buchmeier M, Sette A, Mothé BR. Lymphocytic choriomeningitis virus infection yields overlapping CD4+ and CD8+ T-cell responses. J Virol. 2008 Dec;82(23):11734. Epub 2008 Oct 1. PMC2583689 37. Vita R, Peters B, Sette A. The curation guidelines of the immune epitope database and analysis resource. Cytometry A. 2008 Nov;73(11):1066. PMCID: PMC2597159 38. Kotturi MF, Scott I, Wolfe T, Peters B, Sidney J, Cheroutre H, von Herrath MG, Buchmeier MJ, Grey H, Sette A. Naive precursor frequencies and MHC binding rather than the degree of epitope diversity shape CD8+ T cell immunodominance. J Immunol. 2008 Aug 1;181(3):2124. PMCID: PMC Journal – In Progress 39. Nielsen M, Lundegaard C, Blicher T, Peters B, Sette A, Justesen S, Buus S, Lund O. Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan. PLoS Comput Biol. 2008 Jul 4;4(7):e1000107. PMC2430535 40. Zhang Q, Wang P, Kim Y, Haste-Andersen P, Beaver J, Bourne PE, Bui HH, Buus S, Frankild S, Greenbaum J, Lund O, Lundegaard C, Nielsen M, Ponomarenko J, Sette A, Zhu Z, Peters B. Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W513-8. Epub 2008 May 31. PMC2447801 41. Burgevin A, Saveanu L, Kim Y, Barilleau E, Kotturi M, Sette A, van Endert P, Peters B. A detailed analysis of the murine TAP transporter substrate specificity. PLoS One. 2008 Jun 11;3(6):e2402. PMCID: PMC2408963 42. Oseroff C, Peters B, Pasquetto V, Moutaftsi M, Sidney J, Panchanathan V, Tscharke DC, Maillere B, Grey H, Sette A. Dissociation between epitope hierarchy and immunoprevalence in CD8 responses to vaccinia virus western reserve. J Immunol. 2008 Jun 1;180(11):7193. PMCID: PMC2533852 43. Sette A, Moutaftsi M, Moyron-Quiroz J, McCausland MM, Davies DH, Johnston RJ, Peters B, Rafii-ElIdrissi Benhnia M, Hoffmann J, Su HP, Singh K, Garboczi DN, Head S, Grey H, Felgner PL, Crotty S. Selective CD4+ T cell help for antibody responses to a large viral pathogen: deterministic linkage of specificities. Immunity. 2008 Jun;28(6):847. PMCID: PMC2504733 44. Arens R, Wang P, Sidney J, Loewendorf A, Sette A, Schoenberger SP, Peters B, Benedict CA. Cutting edge: murine cytomegalovirus induces a polyfunctional CD4 T cell response. J Immunol. 2008 May 15;180(10):6472. PMCID: PMC2587066 45. Wang P, Sidney J, Dow C, Mothé B, Sette A, Peters B. A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PLoS Comput Biol. 2008 Apr 4;4(4):e1000048. PMCID: PMC2267221 46. Assarsson E, Greenbaum JA, Sundström M, Schaffer L, Hammond JA, Pasquetto V, Oseroff C, Hendrickson RC, Lefkowitz EJ, Tscharke DC, Sidney J, Grey HM, Head SR, Peters B, Sette A. Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes. Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):2140-2145. Epub 2008 Feb 1. Erratum in: Proc Natl Acad Sci. 2008 May 6;105(18):6787. PMCID: PMC2542872 47. Zarebski LM, Vaughan K, Sidney J, Peters B, Grey H, Janda KD, Casadevall A, Sette A. Analysis of epitope information related to Bacillus anthracis and Clostridium botulinum. Expert Rev Vaccines. 2008 Feb;7(1):55. Review. PMCID: PMC Journal – In Progress 48. Sidney J, Assarsson E, Moore C, Ngo S, Pinilla C, Sette A, Peters B. Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries. Immunome Res. 2008 Jan 25;4:2. PMCID: PMC2248166 49. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ. The OBI Consortium, Leontis N, Rocca-Serra P, Alan Ruttenberg A, SansoneS S-A, Scheuermann RH, Shah N, Whetzel PL, Lewis S. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotech. 2007 25:1251. 50. Sidney J, Peters B, Moore C, Pencille TJ, Ngo S, Masterman KA, Asabe S, Pinilla C, Chisari FV, Sette A. Characterization of the peptide-binding specificity of the chimpanzee class I alleles A*0301 and A*0401 using a combinatorial peptide library. Immunogenetics. 2007 Sep;59(9):745. 51. Nielsen M, Lundegaard C, Blicher T, Lamberth K, Harndahl M, Justesen S, Roder G, Peters B, Sette A, Lund O, Buus S. NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and B locus protein of known sequence. PLoS ONE. 2007 Aug 29;2(8):e796. PMCID: PMC1949492 52. Wang P, Morgan AA, Zhang Q, Sette A, Peters B. Automating document classification for the Immune Epitope Database. BMC Bioinf. 2007 Jul 26;8:269. PMCID: PMC1965490 53. Assarsson E, Sidney J, Oseroff C, Pasquetto V, Bui HH, Frahm N, Brander C, Peters B, Grey H, Sette A. A quantitative analysis of the variables affecting the repertoire of T cell specificities recognized after vaccinia virus infection. J Immunol. 2007 Jun 15;178(12):7890. 54. Moutaftsi M, Bui HH, Peters B, Sidney J, Salek-Ardakani S, Oseroff C, Pasquetto V, Crotty S, Croft M, Lefkowitz EJ, Grey H, Sette A. Vaccinia virus-specific CD4+ T cell responses target a set of antigens largely distinct from those targeted by CD8+ T cell responses. J Immunol. 2007 Jun 1;178(11):6814. 55. Peters B, Sette A. Integrating epitope data into the emerging web of biomedical knowledge resources. Nat Rev Immunol. 2007 7:485. 56. Kotturi MF, Peters B, Buendia-Laysa F Jr, Sidney J, Oseroff C, Botten J, Grey H, Buchmeier MJ, Sette A. Uncovering new tricks for an old virus: CD8+ T cell response to LCMV involves the L antigen. J Virol. 2007 Feb 28, 81:4928. 57. Greenbaum JA, Andersen PH, Blythe M, Bui HH, Cachau RE, Crowe J, Davies M, Kolaskar AS, Lund O, Morrison S, Mumey B, Ofran Y, Pellequer JL, Pinilla C, Ponomarenko JV, Raghava GP, van Regenmortel MH, Roggen EL, Sette A, Schlessinger A, Sollner J, Zand M, Peters B. Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. J Mol Recognit. 2007 Jan 5, 20:75. 58. Bui HH, Peters B, Assarsson E, Mbawuike I, Sette A. Ab and T cell epitopes of influenza A virus, knowledge and opportunities. Proc Natl Acad Sci. 2007 Jan 2;104(1):246. PMCID: PMC1765443 59. Sette A, Peters B. Immune epitope mapping in the post-genomic era: lessons for vaccine development. Curr Opin Immunol. 2007 Feb;19(1):106. 60. Sette A, Bui HH, Sidney J, Bourne P, Buus S, Fleri W, Kubo R, Lund O, Nemazee D, Ponomarenko JV, Sathiamurthy M, Stewart S, Way S, Wilson SS, Peters B. The immune epitope database and analysis resource. Book Chapter in: Pattern Recognition in Bioinformatics, Springer, 2006. 61. Botten J, Alexander J, Pasquetto V, Sidney J, Barrowman P, Ting J, Peters B, Southwood S, Stewart B, Rodriguez-Carreno MP, Mothe B, Whitton JL, Sette A, Buchmeier MJ. Identification of protective Lassa virus epitopes that are restricted by HLA-A2. J Virol. 2006 Sep;80(17):8351. PMCID: PMC1563871 62. Vita R, Vaughan K, Zarebski L, Salimi N, Fleri W, Grey H, Sathiamurthy M, Mokili J, Bui HH, Bourne PE, Ponomarenko J, de Castro R Jr, Chan RK, Sidney J, Wilson SS, Stewart S, Way S, Peters B, Sette A. Curation of complex, context-dependent immunological data. BMC Bioinf. 2006 Jul 12;7:341. PMCID: PMC1534061 63. Sidney J, Asabe S, Peters B, Purton KA, Chung J, Pencille TJ, Purcell R, Walker CM, Chisari FV, Sette A. Detailed characterization of the peptide binding specificity of five common Patr class I MHC molecules. Immunogenetics. 2006 Jul;58(7):559. 64. Moutaftsi M, Peters B, Pasquetto V, Tscharke DC, Sidney J, Bui HH, Grey H, Sette A. A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus. Nat Biotech. 2006 Jul;24(7):817. 65. Peters B, Bui HH, Frankild S, Nielsen M, Lundegaard C, Kostem E, Basch D, Lamberth K, Harndahl M, Fleri W, Wilson SS, Sidney J, Lund O, Buus S and Sette A. A community resource benchmarking predictions of peptide binding to MHC-I molecules. PLoS Comput Biol. 2006 Jun 9;2(6):e65. PMCID: PMC1475712 66. Bulik S, Peters B, Holzhutter HG. Quantifying the contribution of defective ribosomal products to antigen production: a model-based computational analysis. J Immunol. 2005 Dec 15;175(12):7957. 67. Peters B, Bui HH, Sidney J, Weng Z, Loffredo JT, Watkins DI, Mothe BR, Sette A. A computational resource for the prediction of peptide binding to Indian rhesus macaque MHC class I molecules. Vaccine. 2005 Nov 1;23(45):5212. 68. Loffredo JT, Sidney J, Piaskowski S, Szymanski A, Furlott J, Rudersdorf R, Reed J, Peters B, HickmanMiller HD, Bardet W, Rehrauer WM, O'Connor DH, Wilson NA, Hildebrand WH, Sette A, Watkins DI. 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. J Immunol. 2005 Nov 1;175(9):5986. 69. Pasquetto V, Bui HH, Giannino R, Banh C, Mirza F, Sidney J, Oseroff C, Tscharke DC, Irvine K, Bennink JR, Peters B, Southwood S, Cerundolo V, Grey H, Yewdell JW, Sette A. HLA-A*0201, HLA-A*1101, and HLA-B*0702 transgenic mice recognize numerous poxvirus determinants from a wide variety of viral gene products. J Immunol. 2005 Oct 15;175(8):5504. 70. Oseroff C, Kos F, Bui HH, Peters B, Pasquetto V, Glenn J, Palmore T, Sidney J, Tscharke DC, Bennink JR, Southwood S, Grey HM, Yewdell JW, Sette A. HLA class I-restricted responses to vaccinia recognize a broad array of proteins mainly involved in virulence and viral gene regulation. Proc Natl Acad Sci. 2005 Sep 27;102(39):13980. 71. Sathiamurthy M, Peters B, Bui HH, Sidney J, Mokili J, Wilson SS, Fleri W, McGuinness DL, Bourne PE, Sette A. An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities. Immunome Res. 2005 Sep 20;1(1):2. 72. Peters B, Sidney J, Bourne P, Bui HH, Buus S, Doh G, Fleri W, Kronenberg M, Kubo R, Lund O, Nemazee D, Ponomarenko JV, Sathiamurthy M, Schoenberger SP, Stewart S, Surko P, Way S, Wilson S, Sette A. The design and implementation of the immune epitope database and analysis resource. Immunogenetics. 2005 Jun;57(5):326. 73. Bui HH, Sidney J, Peters B, Sathiamurthy M, Sinichi A, Purton KA, Mothe BR, Chisari FV, Watkins DI, Sette A. Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications. Immunogenetics. 2005 Jun;57(5):304. 74. Peters B, Sette A. Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinf. 2005 May 31;6(1):132. 75. Tenzer S, Peters B, Bulik S, Schoor O, Lemmel C, Schatz MM, Kloetzel PM, Rammensee HG, Schild H, Holzhutter HG. Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class I binding. Cell Mol Life Sci. 2005 May;62(9):1025. 76. Peters B, Sidney J, Bourne P, Bui HH, Buus S, Doh G, Fleri W, Kronenberg M, Kubo R, Lund O, Nemazee D, Ponomarenko JV, Sathiamurthy M, Schoenberger S, Stewart S, Surko P, Way S, Wilson S, Sette A. The immune epitope database and analysis resource: from vision to blueprint. PLoS Biol. 2005 Mar;3(3):e91. 77. Lorenzen S, Peters B, Goede A, Preissner R, Frommel C. Conservation of cis prolyl bonds in proteins during evolution. Proteins. 2005 Feb 15;58(3):589. 78. Sette A, Fleri W, Peters B, Sathiamurthy M, Bui HH, Wilson S. A roadmap for the immunomics of category A-C pathogens. Immunity. 2005 Feb;22(2):155. 79. Peters B, Tong W, Sidney J, Sette A and Weng Z. Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules. Bioinf. 200319(14):1765. 80. Peters B, Bulik S, Tampe R, van Endert PM, Holzhütter HG. Identifying MHC-I epitopes by predicting the TAP transport efficiency of epitope precursors. J Immunol. 2002 171(4):1741. 81. Peters B, Janek K, Kuckelkorn U, Holzhütter HG. Assessment of proteasomal cleavage probabilities from kinetic analysis of time-dependent product formation. J Mol Biol. 2002 2002318:847. 82. Peters B, Holzhütter HG. In vitro phototoxicity testing: Development and validation of a new concentration response analysis software and biostatistical analyses relates to the use of various prediction models. ATLA. 2002 30:415. 83. Peters B, Hünkemeier J, Baev VM, Khanin YI. Low-frequency dynamics of a Nd-doped glass laser. Phys Rev A. 2001 64:23816. D. Book chapters 1. Jason A. Greenbaum, Randi Vita, Laura M. Zarebski, Alessandro Sette and Bjoern Peters. Ontology Development for the Immune Epitope Database. In: Bioinformatics for Immunomics, Immunomics Reviews, 2010, Volume 3, 47-56, DOI: 10.1007/978-1-4419-0540-6_4 2. Magdalini Moutaftsi, Bjoern Peters, Valerie Pasquetto, Carla Oseroff, John Sidney, Huynh Hoa-Bui, Howard Grey and Alessandro Sette. Immunomic and Bioinformatics Analysis of Host Immunity in the Vaccinia Virus and Influenza A Systems. National Institute of Allergy and Infectious Diseases, NIH. Infectious Disease, 2008, IV, Part 9, 429-434, DOI: 10.1007/978-1-59745-569-5_46 3. Sette A, Bui HH, Sidney J, Bourne P, Buus S, Fleri W, Kubo R, Lund O, Nemazee D and Ponomarenko JV, Sathiamurthy M, Stewart S, Way S, Wilson SS, Peters B. The Immune Epitope Database and Analysis Resource. In: Pattern Recognition in Bioinformatics. Lecture Notes in Computer Science, 2006, Volume 4146/2006, 126-132, DOI: 10.1007/11818564_14 E. Presentations 08/02/2010, ACM International Conference on Bioinformatics and Computational Biology, Buffalo, NY “An automatic computational pipeline to display MHC binding motifs in the Immune Epitope Database (IEDB)” 06/17/2010, NIAID workshop on IEDB content, Bethesda “The Immune Epitope Database and Analysis Resource” 06/08/2010, Aegean conference on molecular recognition, Crete, Greece “Representing B cell epitopes in the Immune Epitope Database (IEDB)” 02/15/2010, OBO foundry meeting, EBI, Cambridge, UK. “Ontology of biomedical investigations (OBI)” 09/16/2009, NCBO seminar series (webinar) “Representing the Immune Epitope Database in OWL” 09/14/2009, DAIT council meeting (NIAID, NIH) “The Design of the Immune Epitope Database and Associated Analysis Resource” 07/26/2009, International Conference on Biomedical Ontology, University of Buffalo, NY. “Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates” 07/22/2009, NIAID mycobacterial ‘omics’ meeting, Sterling, Virginia “Mycobacterial epitopes in the Immune Epitope Database” 06/28/2009, ISMB 2009, Bioontologies SIG, Stockholm, Sweden “Representing the Immune Epitope Database in OWL” 06/17/2009, Denmark Technical University, Copenhagen. “Using the Immune Epitope Database to predict epitopes conserved in swine flu” 05/09/2009, Seattle, AAI 2009. IEDB workshop “The Immune Epitope Database and Analysis Resource” 02/25/2009, UCSD Extension course “Immune Epitopes – Prediction and Vaccine Design” 01/07/2009, Freie Universitaet Berlin, Germany. Seminar series. “Immune Epitopes – Prediction and Analysis” 09/28/2008, Pittsburgh. Vaccine Development 2008 “Divide and conquer: New approaches to predicting antibody epitope subsets: 09/16/2008, University of Buffalo, New York. Infectious Disease Ontology 2008 “Ontology development for the Immune Epitope Database” 04/08/2008, San Diego, AAI 2008. IEDB workshop “The Immune Epitope Database and Analysis Resource” 04/04/2008, LIAI, Allergy symposium “Allergen Epitopes in the Immune Epitope Database” 01/08/08, San Diego, PAG - Plant and Animal Genome Conference “OBI - The Ontology for Biomedical Investigations” 12/06/07, San Diego, Antibody Engineering Conference “Evaluating B cell Epitope Prediction Tools - Datasets and Metrics” 11/2/07, San Diego, UCSD, CTBP seminar. "Predicting MHC class I binding peptides with machine learning methods" 07/10/07, Oakland, PSWRCE annual meeting. “Mapping targets of T-cell responses in Coxiella burnetii" 05/19/07, Miami, AAI 2007, NIH sponsored symposium. "Immunology Ontology 101: Who Cares and Why You Should" 05/07/07, Washington, Bioinformatics Resource Summit. "HLA data interoperability" 04/16/07, St. Louis, National RCE Meeting. "Mapping targets of T cell responses in C. burnetii" 03/27/07, Washington, DARPA Workshop on Controlling Pathogen Evolution. "Predicting the Interplay of Epitope Recognition and Evolution in RNA Viruses under Immune Pressure" 12/11/06, Newark, DIMACS Workshop on Immuno-Epidemiology. "Defining and characterizing epitopes in infectious pathogens – from prediction to protection" 12/07/06, Birmingham, Alabama, 4th Bioinformatics Resource Centers Meeting. "The Immune Epitope Database - Updates, Links and Outreach" 11/07/06, Washington, Immune Epitope Database and Epitope Discovery contract annual meeting. "The Immune Epitope Database and Analysis Resource" 09/12/06, La Jolla, Joint LIAI and Kirin workshop. "Analysis of Antibody and T Cell Epitopes of Influenza A – Knowledge Gaps and Opportunities" 09/11/06, Texas A&M, seminar presentation. "Identifying T cell epitopes in complex pathogens - From Prediction to Protection" 09/07/06, Washington, NIH Antibody Epitope Tools Meeting. "Antibody Epitopes and Prediction Tools in the IEDB" 06/24/06, Cambridge, UK, Functional Genomics Ontology Workshop. “Ontology for Immune Epitopes” 03/22/06, Washington, NIAID Immune Ontology Meeting. “Ontology Development for the Immune Epitope Database” 02/16/06, Washington, DAIT / NIAID Bioinformatics Summit. “The Immune Epitope Database” 02/06/06, Philadelphia, 3rd Bioinformatics Resource Centers & Inter-Operability Working Group Meeting. “Immune Epitope Database Tools” F. Research Support Ongoing Research Support HHSN272200900048C (B. Peters, P.I.) 09/30/09-09/29/14 NIH/NIAID “Discovering Targets of Antibody Responses in Vaccinia Virus and Their Mechanism of Protection” The major goals of this project are to use combine immunological, structural, and bioinformatic techniques to ascertain protective B cell epitopes against Vaccinia viruses. As part of this study, we will concurrently perform crystallography to determine antibody-epitope specificity, generate new Vaccinia specific monoclonal antibodies, and develop bioinformatic tools to predict antibody epitopes to assist in future vaccine development. HHSN26620040006C (A. Sette, PI) 12/15/03-12/14/10 NIH/NIAID “Immune Epitope Database and Analysis Program” Specific tasks and objectives: 1) Establish and maintain a web-based relational database populated with antibody epitope and T cell epitope information, 2) establish and maintain and analysis resource for the immune epitope database, 3) maintain close ties to the scientific community, 4) submit a proposed transition plan, to allow the NIAID to operate the database independent of the contractors, and 5) submit a proposed implementation plan. 1P01AI089624-01 (M. Kronenberg, PI) 07/16/10-06/30/15 NIH/NIAID “Induction and Maintenance of Regulatory T Cells” Core B: Bioinformatics Core. The specific aims of this core are to 1) analyze and compare the data derived from ChIP-seq direct sequencing experiments performed. 2) Perform statistic analysis of the experimental data from both in vitro and in vivo studies including those from various mouse models including asthma, colitis, and viral infection. 3) To measure and analyze cytokine production and protein phosphorylation using the BioPlex system. HHSN272200700048C (A. Sette, P.I.) 09/28/07-09/27/12 NIH/NIAID “The Identification of Potentially Pathogenic and Therapeutic Epitopes from Common Human Allergens” Specific Aims: 1) Develop human subjects protocols and conduct clinical research, 2) identify and validate allergen-specific T cell epitopes, 3) develop and operate a database management system, and submit data to the Immune Epitope Database and Analysis Resource, 4) establish an external scientific advisory group and conduct scientific meetings and, 5) make cell lines available to the scientific community. HHSN272200900042C (A. Sette, P.I.) 09/30/09-09/29/14 NIH/NIAID “The Identification of HLA Class I and Class II T Cell Epitopes from Dengue Virus” The major goals are to define potentially protective or diagnostic T cell epitopes derived from Dengue viruses. We will perform bioinformatic peptide predictions to synthesize peptides which we will then test in healthy individuals once exposed to Dengue virus. The identified epitopes will then be tested in a murine model of Dengue infection to test protection and discover mechanisms behind the development of Dengue Fever and Hemorrhagic fever pathogenesis. HHSN272200900044C (A. Sette, P.I.) 09/30/09-09/29/14 NIH/NIAID “The Identification of HLA Class II T Cell Epitopes from Mycobacterium Tuberculosis” The major goals are to define potentially protective or diagnostic T cell epitopes derived from mycobacterium tuberculosis. We will perform bioinformatic peptide predictions to synthesize peptides which we will then test for recognition in donors with various clinical manifestations of TB infection. The identified epitopes tested will also be tested in donor cohorts from volunteers in Brazil. Completed Research Support U54 AI065359 (B. Peters, PI) 05/01/06-04/30/08 Pacific Southwest RCE Developmental Grant “Mapping Targets of T-cell Responses in Coxiella Burnetii” Specific Aims: 1) Establish the presence and magnitude of CD8+ vs. CD4+ T-cell responses in infected mice, 2) Identify a set of candidate peptides by applying state of the art computational T-cell probability of being antigenic, 3) Test the top 400 peptides for recognition by T-cells from C. burnetii infected mice, and 4) Determine the ability of recognized peptides to convey protective immunity against challenge. Overlap: There is no scientific or budgetary overlap. DARPA FY06-0026 (Peters, PI) 01/01/07-10/31/07 DARPA “Predicting the Interplay of Epitope Recognition and Evolution in RNA Viruses under Immune Pressure” Specific Aims: 1. Build a theoretical framework to specifically predict the likelihood that certain viral mutations will emerge 2. Test its performance in a model system of RNA viral infection and immune pressure, namely the murine model of LCMV infection 3. Generate a revised predictor based on the results obtained and select model systems and targets for more advanced studies.