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    Bjoern Peters

    Address9500 Gilman Drive #0912
    CA La Jolla 92093
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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Scriba TJ, Carpenter C, Pro SC, Sidney J, Musvosvi M, Rozot V, Seumois G, Rosales SL, Vijayanand P, Goletti D, Makgotlho E, Hanekom W, Hatherill M, Peters B, Sette A, Arlehamn CSL. Differential Recognition of Mycobacterium tuberculosis-Specific Epitopes as a Function of Tuberculosis Disease History. Am J Respir Crit Care Med. 2017 Sep 15; 196(6):772-781. PMID: 28759253.
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      2. Sulzer D, Alcalay RN, Garretti F, Cote L, Kanter E, Agin-Liebes J, Liong C, McMurtrey C, Hildebrand WH, Mao X, Dawson VL, Dawson TM, Oseroff C, Pham J, Sidney J, Dillon MB, Carpenter C, Weiskopf D, Phillips E, Mallal S, Peters B, Frazier A, Arlehamn CSL, Sette A. Erratum: T cells from patients with Parkinson's disease recognize a-synuclein peptides. Nature. 2017 Sep 13; 549(7671):292. PMID: 28905919.
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      3. Dhanda SK, Grifoni A, Pham J, Vaughan K, Sidney J, Peters B, Sette A. Development of a strategy and computational application to select candidate protein analogs with reduced HLA binding and immunogenicity. Immunology. 2017 Aug 22. PMID: 28833085.
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      4. Vaughan K, Xu X, Caron E, Peters B, Sette A. Deciphering the MHC-associated peptidome: a review of naturally processed ligand data. Expert Rev Proteomics. 2017 Aug 11; 1-8. PMID: 28756714.
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      5. Verma S, Weiskopf D, Gupta A, McDonald B, Peters B, Sette A, Benedict CA. Erratum for Verma et al., "Cytomegalovirus-Specific CD4 T Cells Are Cytolytic and Mediate Vaccine Protection". J Virol. 2017 Sep 01; 91(17). PMID: 28798100.
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      6. Paul S, Arlehamn CSL, Schulten V, Westernberg L, Sidney J, Peters B, Sette A. Experimental validation of the RATE tool for inferring HLA restrictions of T cell epitopes. BMC Immunol. 2017 Jun 21; 18(Suppl 1):20. PMID: 28681704.
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      7. Sulzer D, Alcalay RN, Garretti F, Cote L, Kanter E, Agin-Liebes J, Liong C, McMurtrey C, Hildebrand WH, Mao X, Dawson VL, Dawson TM, Oseroff C, Pham J, Sidney J, Dillon MB, Carpenter C, Weiskopf D, Phillips E, Mallal S, Peters B, Frazier A, Lindestam Arlehamn CS, Sette A. T cells from patients with Parkinson's disease recognize a-synuclein peptides. Nature. 2017 Jun 29; 546(7660):656-661. PMID: 28636593.
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      8. Andreatta M, Jurtz VI, Kaever T, Sette A, Peters B, Nielsen M. Machine learning reveals a non-canonical mode of peptide binding to MHC class II molecules. Immunology. 2017 Oct; 152(2):255-264. PMID: 28542831.
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      9. Fleri W, Vaughan K, Salimi N, Vita R, Peters B, Sette A. The Immune Epitope Database: How Data Are Entered and Retrieved. J Immunol Res. 2017; 2017:5974574. PMID: 28634590.
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      10. Schulten V, Tripple V, Seumois G, Qian Y, Scheuermann RH, Fu Z, Locci M, Rosales S, Vijayanand P, Sette A, Alam R, Crotty S, Peters B. Allergen-specific immunotherapy modulates the balance of circulating Tfh and Tfr cells. J Allergy Clin Immunol. 2017 May 12. PMID: 28506846.
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      11. Sidney J, Becart S, Zhou M, Duffy K, Lindvall M, Moore EC, Moore EL, Rao T, Rao N, Nielsen M, Peters B, Sette A. Citrullination only infrequently impacts peptide binding to HLA class II MHC. PLoS One. 2017; 12(5):e0177140. PMID: 28481943.
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      12. Jespersen MC, Peters B, Nielsen M, Marcatili P. BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Res. 2017 May 02. PMID: 28472356.
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      13. Grifoni A, Angelo M, Sidney J, Paul S, Peters B, de Silva AD, Phillips E, Mallal S, Diehl SA, Botten J, Boyson J, Kirkpatrick BD, Whitehead SS, Durbin AP, Sette A, Weiskopf D. Patterns of Cellular Immunity Associated with Experimental Infection with rDEN2?30 (Tonga/74) Support Its Suitability as a Human Dengue Virus Challenge Strain. J Virol. 2017 Apr 15; 91(8). PMID: 28148797.
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      14. Bergmann T, Lindvall M, Moore E, Moore E, Sidney J, Miller D, Tallmadge RL, Myers PT, Malaker SA, Shabanowitz J, Osterrieder N, Peters B, Hunt DF, Antczak DF, Sette A. Peptide-binding motifs of two common equine class I MHC molecules in Thoroughbred horses. Immunogenetics. 2017 May; 69(5):351-358. PMID: 28315936.
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      15. Fleri W, Paul S, Dhanda SK, Mahajan S, Xu X, Peters B, Sette A. The Immune Epitope Database and Analysis Resource in Epitope Discovery and Synthetic Vaccine Design. Front Immunol. 2017; 8:278. PMID: 28352270.
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      16. Angelo MA, Grifoni A, O'Rourke PH, Sidney J, Paul S, Peters B, de Silva AD, Phillips E, Mallal S, Diehl SA, Kirkpatrick BD, Whitehead SS, Durbin AP, Sette A, Weiskopf D. Human CD4+ T Cell Responses to an Attenuated Tetravalent Dengue Vaccine Parallel Those Induced by Natural Infection in Magnitude, HLA Restriction, and Antigen Specificity. J Virol. 2017 Mar 01; 91(5). PMID: 27974563.
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      17. Remesh SG, Andreatta M, Ying G, Kaever T, Nielsen M, McMurtrey C, Hildebrand W, Peters B, Zajonc DM. Unconventional Peptide Presentation by Major Histocompatibility Complex (MHC) Class I Allele HLA-A*02:01: BREAKING CONFINEMENT. J Biol Chem. 2017 Mar 31; 292(13):5262-5270. PMID: 28179428.
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      18. Burel JG, Qian Y, Lindestam Arlehamn C, Weiskopf D, Zapardiel-Gonzalo J, Taplitz R, Gilman RH, Saito M, de Silva AD, Vijayanand P, Scheuermann RH, Sette A, Peters B. An Integrated Workflow To Assess Technical and Biological Variability of Cell Population Frequencies in Human Peripheral Blood by Flow Cytometry. J Immunol. 2017 Jan 09. PMID: 28069807.
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      19. Vita R, Overton JA, Sette A, Peters B. Better living through ontologies at the Immune Epitope Database. Database (Oxford). 2017 Jan 01; 2017(1). PMID: 28365732.
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      20. Oseroff C, Pham J, Frazier A, Hinz D, Sidney J, Paul S, Greenbaum JA, Vita R, Peters B, Schulten V, Sette A. Immunodominance in allergic T-cell reactivity to Japanese cedar in different geographic cohorts. Ann Allergy Asthma Immunol. 2016 Dec; 117(6):680-689.e1. PMID: 27979027.
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      21. Schmiedel BJ, Seumois G, Samaniego-Castruita D, Cayford J, Schulten V, Chavez L, Ay F, Sette A, Peters B, Vijayanand P. 17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells. Nat Commun. 2016 Nov 16; 7:13426. PMID: 27848966.
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      22. Xu X, Vaughan K, Weiskopf D, Grifoni A, Diamond MS, Sette A, Peters B. Identifying Candidate Targets of Immune Responses in Zika Virus Based on Homology to Epitopes in Other Flavivirus Species. PLoS Curr. 2016 Nov 15; 8. PMID: 28018746.
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      23. Paul S, Sidney J, Sette A, Peters B. TepiTool: A Pipeline for Computational Prediction of T Cell Epitope Candidates. Curr Protoc Immunol. 2016 Aug 01; 114:18.19.1-18.19.24. PMID: 27479659; PMCID: PMC4981331 [Available on 08/01/17].
      24. Westernberg L, Schulten V, Sette A, Peters B. Reply. J Allergy Clin Immunol. 2016 Oct; 138(4):1237-1238. PMID: 27484034.
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      25. Weiskopf D, Angelo MA, Grifoni A, O'Rourke PH, Sidney J, Paul S, De Silva AD, Phillips E, Mallal S, Premawansa S, Premawansa G, Wijewickrama A, Peters B, Sette A. HLA-DRB1 Alleles Are Associated With Different Magnitudes of Dengue Virus-Specific CD4+ T-Cell Responses. J Infect Dis. 2016 Oct 01; 214(7):1117-24. PMID: 27443615.
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      26. Lindestam Arlehamn CS, McKinney DM, Carpenter C, Paul S, Rozot V, Makgotlho E, Gregg Y, van Rooyen M, Ernst JD, Hatherill M, Hanekom WA, Peters B, Scriba TJ, Sette A. A Quantitative Analysis of Complexity of Human Pathogen-Specific CD4 T Cell Responses in Healthy M. tuberculosis Infected South Africans. PLoS Pathog. 2016 Jul; 12(7):e1005760. PMID: 27409590; PMCID: PMC4943605.
      27. Seumois G, Zapardiel-Gonzalo J, White B, Singh D, Schulten V, Dillon M, Hinz D, Broide DH, Sette A, Peters B, Vijayanand P. Transcriptional Profiling of Th2 Cells Identifies Pathogenic Features Associated with Asthma. J Immunol. 2016 Jul 15; 197(2):655-64. PMID: 27271570; PMCID: PMC4936908 [Available on 07/15/17].
      28. Bancroft T, Dillon MB, da Silva Antunes R, Paul S, Peters B, Crotty S, Lindestam Arlehamn CS, Sette A. Th1 versus Th2 T cell polarization by whole-cell and acellular childhood pertussis vaccines persists upon re-immunization in adolescence and adulthood. Cell Immunol. 2016 Jun-Jul; 304-305:35-43. PMID: 27212461.
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      29. Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J. The Ontology for Biomedical Investigations. PLoS One. 2016; 11(4):e0154556. PMID: 27128319.
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      30. Kaever T, Matho MH, Meng X, Crickard L, Schlossman A, Xiang Y, Crotty S, Peters B, Zajonc DM. Linear Epitopes in Vaccinia Virus A27 Are Targets of Protective Antibodies Induced by Vaccination against Smallpox. J Virol. 2016 May 1; 90(9):4334-45. PMID: 26889021.
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      31. de Alwis R, Bangs DJ, Angelo MA, Cerpas C, Fernando A, Sidney J, Peters B, Gresh L, Balmaseda A, de Silva AD, Harris E, Sette A, Weiskopf D. Immunodominant Dengue Virus-Specific CD8+ T Cell Responses Are Associated with a Memory PD-1+ Phenotype. J Virol. 2016 May; 90(9):4771-9. PMID: 26912627; PMCID: PMC4836325 [Available on 10/14/16].
      32. Jozwik A, Habibi MS, Paras A, Zhu J, Guvenel A, Dhariwal J, Almond M, Wong EH, Sykes A, Maybeno M, Del Rosario J, Trujillo-Torralbo MB, Mallia P, Sidney J, Peters B, Kon OM, Sette A, Johnston SL, Openshaw PJ, Chiu C. Erratum: RSV-specific airway resident memory CD8+ T cells and differential disease severity after experimental human infection. Nat Commun. 2016 Mar 09; 7:11011. PMID: 26957359; PMCID: PMC4786878.
      33. Westernberg L, Schulten V, Greenbaum JA, Natali S, Tripple V, McKinney DM, Frazier A, Hofer H, Wallner M, Sallusto F, Sette A, Peters B. T-cell epitope conservation across allergen species is a major determinant of immunogenicity. J Allergy Clin Immunol. 2016 Aug; 138(2):571-578.e7. PMID: 26883464; PMCID: PMC4975972 [Available on 08/01/17].
      34. Bresciani A, Paul S, Schommer N, Dillon MB, Bancroft T, Greenbaum J, Sette A, Nielsen M, Peters B. T-cell recognition is shaped by epitope sequence conservation in the host proteome and microbiome. Immunology. 2016 May; 148(1):34-9. PMID: 26789414; PMCID: PMC4819143 [Available on 05/01/17].
      35. Vita R, Vasilevsky N, Bandrowski A, Haendel M, Sette A, Peters B. Reproducibility and conflicts in immune epitope data. Immunology. 2016 Mar; 147(3):349-54. PMID: 26678806.
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      36. McMurtrey C, Trolle T, Sansom T, Remesh SG, Kaever T, Bardet W, Jackson K, McLeod R, Sette A, Nielsen M, Zajonc DM, Blader IJ, Peters B, Hildebrand W. Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove. Elife. 2016 Jan 29; 5. PMID: 26824387; PMCID: PMC4775218.
      37. Trolle T, McMurtrey CP, Sidney J, Bardet W, Osborn SC, Kaever T, Sette A, Hildebrand WH, Nielsen M, Peters B. The Length Distribution of Class I-Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele-Specific Binding Preference. J Immunol. 2016 Feb 15; 196(4):1480-7. PMID: 26783342; PMCID: PMC4744552 [Available on 02/15/17].
      38. Vita R, Overton JA, Seymour E, Sidney J, Kaufman J, Tallmadge RL, Ellis S, Hammond J, Butcher GW, Sette A, Peters B. An ontology for major histocompatibility restriction. J Biomed Semantics. 2016; 7:1. PMID: 26759709; PMCID: PMC4709943.
      39. Jozwik A, Habibi MS, Paras A, Zhu J, Guvenel A, Dhariwal J, Almond M, Wong EH, Sykes A, Maybeno M, Del Rosario J, Trujillo-Torralbo MB, Mallia P, Sidney J, Peters B, Kon OM, Sette A, Johnston SL, Openshaw PJ, Chiu C. RSV-specific airway resident memory CD8+ T cells and differential disease severity after experimental human infection. Nat Commun. 2015 Dec 21; 6:10224. PMID: 26687547; PMCID: PMC4703893.
      40. Sette A, Paul S, Vaughan K, Peters B. The Use of the Immune Epitope Database to Study Autoimmune Epitope Data Related to Alopecia Areata. J Investig Dermatol Symp Proc. 2015 Nov; 17(2):36-41. PMID: 26551944.
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      41. Verma S, Weiskopf D, Gupta A, McDonald B, Peters B, Sette A, Benedict CA. Cytomegalovirus-Specific CD4 T Cells Are Cytolytic and Mediate Vaccine Protection. J Virol. 2015 Oct 21; 90(2):650-8. PMID: 26491148; PMCID: PMC4702662.
      42. Carrasco Pro S, Sidney J, Paul S, Lindestam Arlehamn C, Weiskopf D, Peters B, Sette A. Automatic Generation of Validated Specific Epitope Sets. J Immunol Res. 2015; 2015:763461. PMID: 26568965; PMCID: PMC4629045.
      43. Bergmann T, Moore C, Sidney J, Miller D, Tallmadge R, Harman RM, Oseroff C, Wriston A, Shabanowitz J, Hunt DF, Osterrieder N, Peters B, Antczak DF, Sette A. The common equine class I molecule Eqca-1*00101 (ELA-A3.1) is characterized by narrow peptide binding and T cell epitope repertoires. Immunogenetics. 2015 Nov; 67(11-12):675-89. PMID: 26399241; PMCID: PMC4783141 [Available on 11/01/16].
      44. Matho MH, Schlossman A, Meng X, Benhnia MR, Kaever T, Buller M, Doronin K, Parker S, Peters B, Crotty S, Xiang Y, Zajonc DM. Structural and Functional Characterization of Anti-A33 Antibodies Reveal a Potent Cross-Species Orthopoxviruses Neutralizer. PLoS Pathog. 2015 Sep; 11(9):e1005148. PMID: 26325270.
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      45. Weiskopf D, Bangs DJ, Sidney J, Kolla RV, De Silva AD, de Silva AM, Crotty S, Peters B, Sette A. Dengue virus infection elicits highly polarized CX3CR1+ cytotoxic CD4+ T cells associated with protective immunity. Proc Natl Acad Sci U S A. 2015 Aug 4; 112(31):E4256-63. PMID: 26195744.
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      46. Metushi IG, Wriston A, Banerjee P, Gohlke BO, English AM, Lucas A, Moore C, Sidney J, Buus S, Ostrov DA, Mallal S, Phillips E, Shabanowitz J, Hunt DF, Preissner R, Peters B. Acyclovir Has Low but Detectable Influence on HLA-B*57:01 Specificity without Inducing Hypersensitivity. PLoS One. 2015; 10(5):e0124878. PMID: 26024233.
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      47. McKinney DM, Fu Z, Le L, Greenbaum JA, Peters B, Sette A. Development and validation of a sample sparing strategy for HLA typing utilizing next generation sequencing. Hum Immunol. 2015 Dec; 76(12):917-22. PMID: 26027778; PMCID: PMC4662932 [Available on 12/01/16].
      48. Vaughan K, Ponomarenko J, Peters B, Sette A. Analysis of Human RSV Immunity at the Molecular Level: Learning from the Past and Present. PLoS One. 2015; 10(5):e0127108. PMID: 26001197; PMCID: PMC4441423.
      49. Weiskopf D, Cerpas C, Angelo MA, Bangs DJ, Sidney J, Paul S, Peters B, Sanches FP, Silvera CG, Costa PR, Kallas EG, Gresh L, de Silva AD, Balmaseda A, Harris E, Sette A. Human CD8+ T-Cell Responses Against the 4 Dengue Virus Serotypes Are Associated With Distinct Patterns of Protein Targets. J Infect Dis. 2015 Dec 01; 212(11):1743-51. PMID: 25980035; PMCID: PMC4633759 [Available on 12/01/16].
      50. Paul S, Lindestam Arlehamn CS, Scriba TJ, Dillon MB, Oseroff C, Hinz D, McKinney DM, Carrasco Pro S, Sidney J, Peters B, Sette A. Development and validation of a broad scheme for prediction of HLA class II restricted T cell epitopes. J Immunol Methods. 2015 Jul; 422:28-34. PMID: 25862607; PMCID: PMC4458426.
      51. Sela-Culang I, Ofran Y, Peters B. Antibody specific epitope prediction-emergence of a new paradigm. Curr Opin Virol. 2015 Apr; 11:98-102. PMID: 25837466; PMCID: PMC4456244.
      52. Trolle T, Metushi IG, Greenbaum JA, Kim Y, Sidney J, Lund O, Sette A, Peters B, Nielsen M. Automated benchmarking of peptide-MHC class I binding predictions. Bioinformatics. 2015 Jul 1; 31(13):2174-81. PMID: 25717196.
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      53. Lindestam Arlehamn CS, Paul S, Mele F, Huang C, Greenbaum JA, Vita R, Sidney J, Peters B, Sallusto F, Sette A. Immunological consequences of intragenus conservation of Mycobacterium tuberculosis T-cell epitopes. Proc Natl Acad Sci U S A. 2015 Jan 13; 112(2):E147-55. PMID: 25548174; PMCID: PMC4299226.
      54. Matho MH, de Val N, Miller GM, Brown J, Schlossman A, Meng X, Crotty S, Peters B, Xiang Y, Hsieh-Wilson LC, Ward AB, Zajonc DM. Murine Anti-vaccinia Virus D8 Antibodies Target Different Epitopes and Differ in Their Ability to Block D8 Binding to CS-E. PLoS Pathog. 2014 Dec; 10(12):e1004495. PMID: 25474621.
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      55. Sela-Culang I, Ashkenazi S, Peters B, Ofran Y. PEASE: predicting B-cell epitopes utilizing antibody sequence. Bioinformatics. 2015 Apr 15; 31(8):1313-5. PMID: 25432167.
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      56. Schulten V, Peters B, Sette A. New strategies for allergen T cell epitope identification: going beyond IgE. Int Arch Allergy Immunol. 2014; 165(2):75-82. PMID: 25402674; PMCID: PMC4315360.
      57. Freeman ML, Burkum CE, Cookenham T, Roberts AD, Lanzer KG, Huston GE, Jensen MK, Sidney J, Peters B, Kohlmeier JE, Woodland DL, van Dyk LF, Sette A, Blackman MA. CD4 T cells specific for a latency-associated ?-herpesvirus epitope are polyfunctional and cytotoxic. J Immunol. 2014 Dec 15; 193(12):5827-34. PMID: 25378595; PMCID: PMC4301266.
      58. Frazier A, Schulten V, Hinz D, Oseroff C, Sidney J, Peters B, Sette A. Allergy-associated T cell epitope repertoires are surprisingly diverse and include non-IgE reactive antigens. World Allergy Organ J. 2014; 7(1):26. PMID: 25352946; PMCID: PMC4210551.
      59. Weiskopf D, Angelo MA, Bangs DJ, Sidney J, Paul S, Peters B, de Silva AD, Lindow JC, Diehl SA, Whitehead S, Durbin A, Kirkpatrick B, Sette A. The human CD8+ T cell responses induced by a live attenuated tetravalent dengue vaccine are directed against highly conserved epitopes. J Virol. 2015 Jan; 89(1):120-8. PMID: 25320311; PMCID: PMC4301095.
      60. Vita R, Overton JA, Greenbaum JA, Ponomarenko J, Clark JD, Cantrell JR, Wheeler DK, Gabbard JL, Hix D, Sette A, Peters B. The immune epitope database (IEDB) 3.0. Nucleic Acids Res. 2015 Jan; 43(Database issue):D405-12. PMID: 25300482; PMCID: PMC4384014.
      61. Sedegah M, Hollingdale MR, Farooq F, Ganeshan H, Belmonte M, Kim Y, Peters B, Sette A, Huang J, McGrath S, Abot E, Limbach K, Shi M, Soisson L, Diggs C, Chuang I, Tamminga C, Epstein JE, Villasante E, Richie TL. Sterile immunity to malaria after DNA prime/adenovirus boost immunization is associated with effector memory CD8+T cells targeting AMA1 class I epitopes. PLoS One. 2014; 9(9):e106241. PMID: 25211344; PMCID: PMC4161338.
      62. Arlehamn CL, Seumois G, Gerasimova A, Huang C, Fu Z, Yue X, Sette A, Vijayanand P, Peters B. Transcriptional profile of tuberculosis antigen-specific T cells reveals novel multifunctional features. J Immunol. 2014 Sep 15; 193(6):2931-40. PMID: 25092889; PMCID: PMC4157075.
      63. Weiskopf D, Angelo MA, Sidney J, Peters B, Shresta S, Sette A. Immunodominance Changes as a Function of the Infecting Dengue Virus Serotype and Primary versus Secondary Infection. J Virol. 2014 Oct 1; 88(19):11383-94. PMID: 25056881.
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      64. Kaever T, Meng X, Matho MH, Schlossman A, Li S, Sela-Culang I, Ofran Y, Buller M, Crump RW, Parker S, Frazier A, Crotty S, Zajonc DM, Peters B, Xiang Y. Potent neutralization of vaccinia virus by divergent murine antibodies targeting a common site of vulnerability in l1 protein. J Virol. 2014 Oct 1; 88(19):11339-55. PMID: 25031354.
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      65. Schulten V, Tripple V, Sidney J, Greenbaum J, Frazier A, Alam R, Broide D, Peters B, Sette A. Association between specific timothy grass antigens and changes in TH1- and TH2-cell responses following specific immunotherapy. J Allergy Clin Immunol. 2014 Nov; 134(5):1076-83. PMID: 25042980.
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      66. Kim Y, Sidney J, Buus S, Sette A, Nielsen M, Peters B. Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions. BMC Bioinformatics. 2014 Jul 14; 15:241. PMID: 25017736; PMCID: PMC4111843.
      67. Chiu C, McCausland M, Sidney J, Duh FM, Rouphael N, Mehta A, Mulligan M, Carrington M, Wieland A, Sullivan NL, Weinberg A, Levin MJ, Pulendran B, Peters B, Sette A, Ahmed R. Broadly reactive human CD8 T cells that recognize an epitope conserved between VZV, HSV and EBV. PLoS Pathog. 2014 Mar; 10(3):e1004008. PMID: 24675761; PMCID: PMC3968128.
      68. Sela-Culang I, Benhnia MR, Matho MH, Kaever T, Maybeno M, Schlossman A, Nimrod G, Li S, Xiang Y, Zajonc D, Crotty S, Ofran Y, Peters B. Using a combined computational-experimental approach to predict antibody-specific B cell epitopes. Structure. 2014 Apr 8; 22(4):646-57. PMID: 24631463.
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      69. Vaughan K, Seymour E, Peters B, Sette A. Substantial gaps in knowledge of Bordetella pertussis antibody and T cell epitopes relevant for natural immunity and vaccine efficacy. Hum Immunol. 2014 May; 75(5):440-51. PMID: 24530743; PMCID: PMC4792526.
      70. Vaughan K, Peters B, O'Connor KC, Martin R, Sette A. A molecular view of multiple sclerosis and experimental autoimmune encephalitis: what can we learn from the epitope data? J Neuroimmunol. 2014 Feb 15; 267(1-2):73-85. PMID: 24365494; PMCID: PMC4784960.
      71. Sarikonda G, Pettus J, Sachithanantham S, Phatak S, Miller JF, Ganesan L, Chae J, Mallios R, Edelman S, Peters B, von Herrath M. Temporal intra-individual variation of immunological biomarkers in type 1 diabetes patients: implications for future use in cross-sectional assessment. PLoS One. 2013; 8(11):e79383. PMID: 24223938.
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      72. Calis JJ, Maybeno M, Greenbaum JA, Weiskopf D, De Silva AD, Sette A, Kesmir C, Peters B. Properties of MHC class I presented peptides that enhance immunogenicity. PLoS Comput Biol. 2013 Oct; 9(10):e1003266. PMID: 24204222; PMCID: PMC3808449.
      73. Paul S, Kolla RV, Sidney J, Weiskopf D, Fleri W, Kim Y, Peters B, Sette A. Evaluating the immunogenicity of protein drugs by applying in vitro MHC binding data and the immune epitope database and analysis resource. Clin Dev Immunol. 2013; 2013:467852. PMID: 24222776; PMCID: PMC3816028.
      74. Sedegah M, Kim Y, Ganeshan H, Huang J, Belmonte M, Abot E, Banania JG, Farooq F, McGrath S, Peters B, Sette A, Soisson L, Diggs C, Doolan DL, Tamminga C, Villasante E, Hollingdale MR, Richie TL. Identification of minimal human MHC-restricted CD8+ T-cell epitopes within the Plasmodium falciparum circumsporozoite protein (CSP). Malar J. 2013 Jun 05; 12:185. PMID: 23738590; PMCID: PMC3683343.
      75. Vita R, Overton JA, Greenbaum JA, Sette A. Query enhancement through the practical application of ontology: the IEDB and OBI. J Biomed Semantics. 2013 Apr 15; 4 Suppl 1:S6. PMID: 23734660; PMCID: PMC3633001.
      76. Weiskopf D, Angelo MA, de Azeredo EL, Sidney J, Greenbaum JA, Fernando AN, Broadwater A, Kolla RV, De Silva AD, de Silva AM, Mattia KA, Doranz BJ, Grey HM, Shresta S, Peters B, Sette A. Comprehensive analysis of dengue virus-specific responses supports an HLA-linked protective role for CD8+ T cells. Proc Natl Acad Sci U S A. 2013 May 28; 110(22):E2046-53. PMID: 23580623.
        View in: PubMed
      77. Schulten V, Greenbaum JA, Hauser M, McKinney DM, Sidney J, Kolla R, Lindestam Arlehamn CS, Oseroff C, Alam R, Broide DH, Ferreira F, Ferreira-Briza F, Grey HM, Sette A, Peters B. Previously undescribed grass pollen antigens are the major inducers of T helper 2 cytokine-producing T cells in allergic individuals. Proc Natl Acad Sci U S A. 2013 Feb 26; 110(9):3459-64. PMID: 23401558.
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      78. McKinney DM, Southwood S, Hinz D, Oseroff C, Arlehamn CS, Schulten V, Taplitz R, Broide D, Hanekom WA, Scriba TJ, Wood R, Alam R, Peters B, Sidney J, Sette A. A strategy to determine HLA class II restriction broadly covering the DR, DP, and DQ allelic variants most commonly expressed in the general population. Immunogenetics. 2013 May; 65(5):357-70. PMID: 23392739.
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      79. Gerasimova A, Chavez L, Li B, Seumois G, Greenbaum J, Rao A, Vijayanand P, Peters B. Predicting cell types and genetic variations contributing to disease by combining GWAS and epigenetic data. PLoS One. 2013; 8(1):e54359. PMID: 23382893; PMCID: PMC3559682.
      80. Kim Y, Yewdell JW, Sette A, Peters B. Positional bias of MHC class I restricted T-cell epitopes in viral antigens is likely due to a bias in conservation. PLoS Comput Biol. 2013; 9(1):e1002884. PMID: 23357871; PMCID: PMC3554532.
      81. Lindestam Arlehamn CS, Gerasimova A, Mele F, Henderson R, Swann J, Greenbaum JA, Kim Y, Sidney J, James EA, Taplitz R, McKinney DM, Kwok WW, Grey H, Sallusto F, Peters B, Sette A. Memory T cells in latent Mycobacterium tuberculosis infection are directed against three antigenic islands and largely contained in a CXCR3+CCR6+ Th1 subset. PLoS Pathog. 2013 Jan; 9(1):e1003130. PMID: 23358848.
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      82. Vaughan K, Peters B, Mallone R, von Herrath M, Roep BO, Sette A. Navigating diabetes-related immune epitope data: resources and tools provided by the Immune Epitope Database (IEDB). Immunome Res. 2013; 9(1). PMID: 25140192.
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      83. Vaughan K, Peters B, Larche M, Pomes A, Broide D, Sette A. Strategies to query and display allergy-derived epitope data from the immune epitope database. Int Arch Allergy Immunol. 2013; 160(4):334-45. PMID: 23172234.
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      84. Schulten V, Oseroff C, Alam R, Broide D, Vijayanand P, Peters B, Sette A. The identification of potentially pathogenic and therapeutic epitopes from common human allergens. Ann Allergy Asthma Immunol. 2013 Jan; 110(1):7-10. PMID: 23244651.
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      85. Benhnia MR, Maybeno M, Blum D, Aguilar-Sino R, Matho M, Meng X, Head S, Felgner PL, Zajonc DM, Koriazova L, Kato S, Burton DR, Xiang Y, Crowe JE, Peters B, Crotty S. Unusual features of vaccinia virus extracellular virion form neutralization resistance revealed in human antibody responses to the smallpox vaccine. J Virol. 2013 Feb; 87(3):1569-85. PMID: 23152530.
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      86. Salimi N, Fleri W, Peters B, Sette A. The immune epitope database: a historical retrospective of the first decade. Immunology. 2012 Oct; 137(2):117-23. PMID: 22681406; PMCID: PMC3461392.
      87. Maybeno M, Redeker A, Welten SP, Peters B, Loughhead SM, Schoenberger SP, Sette A, Arens R. Polyfunctional CD4+ T cell responses to immunodominant epitopes correlate with disease activity of virulent Salmonella. PLoS One. 2012; 7(8):e43481. PMID: 22912884.
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      88. Oseroff C, Sidney J, Vita R, Tripple V, McKinney DM, Southwood S, Brodie TM, Sallusto F, Grey H, Alam R, Broide D, Greenbaum JA, Kolla R, Peters B, Sette A. T cell responses to known allergen proteins are differently polarized and account for a variable fraction of total response to allergen extracts. J Immunol. 2012 Aug 15; 189(4):1800-11. PMID: 22786768.
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      89. Oseroff C, Sidney J, Tripple V, Grey H, Wood R, Broide DH, Greenbaum J, Kolla R, Peters B, Pomés A, Sette A. Analysis of T cell responses to the major allergens from German cockroach: epitope specificity and relationship to IgE production. J Immunol. 2012 Jul 15; 189(2):679-88. PMID: 22706084.
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      90. Kim Y, Vaughan K, Greenbaum J, Peters B, Law M, Sette A. A meta-analysis of the existing knowledge of immunoreactivity against hepatitis C virus (HCV). PLoS One. 2012; 7(5):e38028. PMID: 22675428; PMCID: PMC3364976.
      91. Ostrov DA, Grant BJ, Pompeu YA, Sidney J, Harndahl M, Southwood S, Oseroff C, Lu S, Jakoncic J, de Oliveira CA, Yang L, Mei H, Shi L, Shabanowitz J, English AM, Wriston A, Lucas A, Phillips E, Mallal S, Grey HM, Sette A, Hunt DF, Buus S, Peters B. Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire. Proc Natl Acad Sci U S A. 2012 Jun 19; 109(25):9959-64. PMID: 22645359; PMCID: PMC3382472.
      92. Matho MH, Maybeno M, Benhnia MR, Becker D, Meng X, Xiang Y, Crotty S, Peters B, Zajonc DM. Structural and biochemical characterization of the vaccinia virus envelope protein D8 and its recognition by the antibody LA5. J Virol. 2012 Aug; 86(15):8050-8. PMID: 22623786.
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      93. Kim Y, Ponomarenko J, Zhu Z, Tamang D, Wang P, Greenbaum J, Lundegaard C, Sette A, Lund O, Bourne PE, Nielsen M, Peters B. Immune epitope database analysis resource. Nucleic Acids Res. 2012 Jul; 40(Web Server issue):W525-30. PMID: 22610854.
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      94. Arlehamn CS, Sidney J, Henderson R, Greenbaum JA, James EA, Moutaftsi M, Coler R, McKinney DM, Park D, Taplitz R, Kwok WW, Grey H, Peters B, Sette A. Dissecting mechanisms of immunodominance to the common tuberculosis antigens ESAT-6, CFP10, Rv2031c (hspX), Rv2654c (TB7.7), and Rv1038c (EsxJ). J Immunol. 2012 May 15; 188(10):5020-31. PMID: 22504645.
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      95. Seymour E, Damle R, Sette A, Peters B. Cost sensitive hierarchical document classification to triage PubMed abstracts for manual curation. BMC Bioinformatics. 2011 Dec 19; 12:482. PMID: 22182279; PMCID: PMC3314711.
      96. Weiskopf D, Yauch LE, Angelo MA, John DV, Greenbaum JA, Sidney J, Kolla RV, De Silva AD, de Silva AM, Grey H, Peters B, Shresta S, Sette A. Insights into HLA-restricted T cell responses in a novel mouse model of dengue virus infection point toward new implications for vaccine design. J Immunol. 2011 Oct 15; 187(8):4268-79. PMID: 21918184.
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      97. Kotturi MF, Swann JA, Peters B, Arlehamn CL, Sidney J, Kolla RV, James EA, Akondy RS, Ahmed R, Kwok WW, Buchmeier MJ, Sette A. Human CD8? and CD4? T cell memory to lymphocytic choriomeningitis virus infection. J Virol. 2011 Nov; 85(22):11770-80. PMID: 21900169; PMCID: PMC3209290.
      98. Wang P, Sidney J, Sette A, Peters B. A computational pipeline to generate MHC binding motifs. Immunome Res. 2011 May; 7(2). PMID: 28747991.
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      99. St Leger AJ, Peters B, Sidney J, Sette A, Hendricks RL. Defining the herpes simplex virus-specific CD8+ T cell repertoire in C57BL/6 mice. J Immunol. 2011 Apr 01; 186(7):3927-33. PMID: 21357536; PMCID: PMC3308013.
      100. Vaughan K, Greenbaum J, Kim Y, Vita R, Chung J, Peters B, Broide D, Goodman R, Grey H, Sette A. Towards defining molecular determinants recognized by adaptive immunity in allergic disease: an inventory of the available data. J Allergy (Cairo). 2010; 2010:628026. PMID: 21403821.
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      101. Greenbaum J, Sidney J, Chung J, Brander C, Peters B, Sette A. Functional classification of class II human leukocyte antigen (HLA) molecules reveals seven different supertypes and a surprising degree of repertoire sharing across supertypes. Immunogenetics. 2011 Jun; 63(6):325-35. PMID: 21305276; PMCID: PMC3626422.
      102. Southwood S, Solomon C, Hoof I, Rudersdorf R, Sidney J, Peters B, Wahl A, Hawkins O, Hildebrand W, Mothé BR, Sette A. 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. Immunogenetics. 2011 May; 63(5):275-90. PMID: 21274527; PMCID: PMC3068250.
      103. Wang P, Sidney J, Kim Y, Sette A, Lund O, Nielsen M, Peters B. Peptide binding predictions for HLA DR, DP and DQ molecules. BMC Bioinformatics. 2010 Nov 22; 11:568. PMID: 21092157; PMCID: PMC2998531.
      104. Kim Y, Sette A, Peters B. Applications for T-cell epitope queries and tools in the Immune Epitope Database and Analysis Resource. J Immunol Methods. 2011 Nov 30; 374(1-2):62-9. PMID: 21047510; PMCID: PMC3041860.
      105. Ponomarenko J, Papangelopoulos N, Zajonc DM, Peters B, Sette A, Bourne PE. IEDB-3D: structural data within the immune epitope database. Nucleic Acids Res. 2011 Jan; 39(Database issue):D1164-70. PMID: 21030437.
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      106. 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 Nov 1; 185(9):5405-16. PMID: 20870934.
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      107. 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 Oct 01; 185(7):4189-98. PMID: 20810981; PMCID: PMC3307390.
      108. 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; 9:241. PMID: 20735847; PMCID: PMC2939619.
      109. 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):943-55. PMID: 20554959.
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      110. 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):157-70. PMID: 20508245; PMCID: PMC2884409.
      111. 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):259-84. PMID: 20565291; PMCID: PMC2942863.
      112. 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):451-64. PMID: 20480161; PMCID: PMC2890073.
      113. 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. PMID: 20490281; PMCID: PMC2871663.
      114. 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; 6:4. PMID: 20478058.
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      115. 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 01; 5(4):e9993. PMID: 20376318; PMCID: PMC2848623.
      116. Salimi N, Fleri W, Peters B, Sette A. Design and utilization of epitope-based databases and predictive tools. Immunogenetics. 2010 Apr; 62(4):185-96. PMID: 20213141; PMCID: PMC2843836.
      117. 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; 5(2):e9272. PMID: 20174654.
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      118. 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 01; 184(5):2492-503. PMID: 20139279; PMCID: PMC2935290.
      119. 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. 2011 Feb; 44(1):75-9. PMID: 20123131.
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      120. 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):2881-92. PMID: 20053740; PMCID: PMC2826075.
      121. 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:G21-6. PMID: 20006135.
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      122. 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 Pathog. 2009 Dec; 5(12):e1000695. PMID: 20019801; PMCID: PMC2787016.
      123. 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 Bioinformatics. 2009 Nov 30; 10:394. PMID: 19948066; PMCID: PMC2790471.
      124. 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):707-19. PMID: 19933168.
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      125. 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 Natl Acad Sci U S A. 2009 Dec 1; 106(48):20365-70. PMID: 19918065.
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      126. Vita R, 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 Jan; 38(Database issue):D854-62. PMID: 19906713; PMCID: PMC2808938.
      127. 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. PMID: 19774228; PMCID: PMC2747625.
      128. 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, McMichael A, Yewdell JW. Quantitating T cell cross-reactivity for unrelated peptide antigens. J Immunol. 2009 Oct 01; 183(7):4337-45. PMID: 19734234; PMCID: PMC2762195.
      129. 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. PMID: 19534819; PMCID: PMC2702351.
      130. Yauch LE, Zellweger RM, Kotturi MF, Qutubuddin A, 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):4865-73. PMID: 19342665.
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      131. 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):717-22. PMID: 19224639.
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      132. 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; 9:514. PMID: 19055730.
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      133. 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):1-13. PMID: 19002680; PMCID: PMC3319061.
      134. 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):11734-41. PMID: 18829752; PMCID: PMC2583689.
      135. 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):2124-33. PMID: 18641351.
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      136. 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 04; 4(7):e1000107. PMID: 18604266; PMCID: PMC2430535.
      137. 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. PMID: 18545702; PMCID: PMC2408963.
      138. 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 01; 180(11):7193-202. PMID: 18490718; PMCID: PMC2533852.
      139. Sette A, Moutaftsi M, Moyron-Quiroz J, McCausland MM, Davies DH, Johnston RJ, Peters B, Rafii-El-Idrissi 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):847-58. PMID: 18549802.
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      140. 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. PMID: 18515843.
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      141. 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):6472-6. PMID: 18453564.
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      142. 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 04; 4(4):e1000048. PMID: 18389056; PMCID: PMC2267221.
      143. 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):2140-5. PMID: 18245380; PMCID: PMC2542872.
      144. 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):55-74. PMID: 18251694; PMCID: PMC3319117.
      145. 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. PMID: 18221540; PMCID: PMC2248166.
      146. Sidney J, Peters B, Frahm N, Brander C, Sette A. HLA class I supertypes: a revised and updated classification. BMC Immunol. 2008 Jan 22; 9:1. PMID: 18211710; PMCID: PMC2245908.
      147. Blythe MJ, Zhang Q, Vaughan K, de Castro R, Salimi N, Bui HH, Lewinsohn DM, Ernst JD, Peters B, Sette A. An analysis of the epitope knowledge related to Mycobacteria. Immunome Res. 2007 Dec 14; 3:10. PMID: 18081934; PMCID: PMC2228276.
      148. Nielsen M, Lundegaard C, Blicher T, Lamberth K, Harndahl M, Justesen S, Røder 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. PMID: 17726526; PMCID: PMC1949492.
      149. Wang P, Morgan AA, Zhang Q, Sette A, Peters B. Automating document classification for the Immune Epitope Database. BMC Bioinformatics. 2007 Jul 26; 8:269. PMID: 17655769; PMCID: PMC1965490.
      150. 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):7890-901. PMID: 17548627.
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      151. Peters B, Sette A. Integrating epitope data into the emerging web of biomedical knowledge resources. Nat Rev Immunol. 2007 Jun; 7(6):485-90. PMID: 17479127.
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      152. 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):6814-20. PMID: 17513729.
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      153. 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 Mar-Apr; 20(2):75-82. PMID: 17205610.
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      154. Kotturi MF, Peters B, Buendia-Laysa F, Sidney J, Oseroff C, Botten J, Grey H, Buchmeier MJ, Sette A. The CD8+ T-cell response to lymphocytic choriomeningitis virus involves the L antigen: uncovering new tricks for an old virus. J Virol. 2007 May; 81(10):4928-40. PMID: 17329346; PMCID: PMC1900207.
      155. 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 U S A. 2007 Jan 02; 104(1):246-51. PMID: 17200302; PMCID: PMC1765443.
      156. Sette A, Peters B. Immune epitope mapping in the post-genomic era: lessons for vaccine development. Curr Opin Immunol. 2007 Feb; 19(1):106-10. PMID: 17113275.
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      157. 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):8351-61. PMID: 16912286; PMCID: PMC1563871.
      158. 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, Chan RK, Sidney J, Wilson SS, Stewart S, Way S, Peters B, Sette A. Curation of complex, context-dependent immunological data. BMC Bioinformatics. 2006; 7:341. PMID: 16836764.
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      159. 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):559-70. PMID: 16791621.
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      161. Peters B, Bui HH, Frankild S, Nielson M, Lundegaard C, Kostem E, Basch D, Lamberth K, Harndahl M, Fleri W, Wilson SS, Sidney J, Lund O, Buus S, Sette A. A community resource benchmarking predictions of peptide binding to MHC-I molecules. PLoS Comput Biol. 2006 Jun 09; 2(6):e65. PMID: 16789818; PMCID: PMC1475712.
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      163. 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):5504-15. PMID: 16210659.
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      164. 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. PMID: 16305755.
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      165. 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 U S A. 2005 Sep 27; 102(39):13980-5. PMID: 16172378; PMCID: PMC1236582.
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      168. Bui HH, Sidney J, Peters B, Sathiamurthy M, Sinichi A, Purton KA, Mothé 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):304-14. PMID: 15868141.
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      169. 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. PMID: 15760272.
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      170. 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):155-61. PMID: 15773067.
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