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Transcript
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, Gondré-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.