Loading...
Sign in to edit your profile (add interests, mentoring, photo, etc.)

    Alessandro Sette

    TitleAdjunct Professor
    SchoolUniversity of California, San Diego
    DepartmentMedicine
    Address9500 Gilman Drive #0656
    CA La Jolla 92093
    vCardDownload vCard

      Collapse Bibliographic 
      Collapse Publications
      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.
      List All   |   Timeline
      1. Draheim M, Wlodarczyk MF, Crozat K, Saliou JM, Alayi TD, Tomavo S, Hassan A, Salvioni A, Demarta-Gatsi C, Sidney J, Sette A, Dalod M, Berry A, Silvie O, Blanchard N. Profiling MHC II immunopeptidome of blood-stage malaria reveals that cDC1 control the functionality of parasite-specific CD4 T cells. EMBO Mol Med. 2017 Sep 21. PMID: 28935714.
        View in: PubMed
      2. 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.
        View in: PubMed
      3. 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.
        View in: PubMed
      4. Lindestam Arlehamn CS, Paul S, Wang EHC, de Jong A, Christiano AM, Sette A. Large Scale Epitope Identification Screen and Its Potential Application to the Study of Alopecia Areata. J Invest Dermatol. 2017 Aug 29. PMID: 28864075.
        View in: PubMed
      5. 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.
        View in: PubMed
      6. 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 Sep; 14(9):729-736. PMID: 28756714.
        View in: PubMed
      7. 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.
        View in: PubMed
      8. Gu XX, Plotkin SA, Edwards KM, Sette A, Mills KHG, Levy O, Sant AJ, Mo A, Alexander W, Lu KT, Taylor CE. Waning Immunity and Microbial Vaccines-Workshop of the National Institute of Allergy and Infectious Diseases. Clin Vaccine Immunol. 2017 Jul; 24(7). PMID: 28490424.
        View in: PubMed
      9. Glanville J, Huang H, Nau A, Hatton O, Wagar LE, Rubelt F, Ji X, Han A, Krams SM, Pettus C, Haas N, Arlehamn CSL, Sette A, Boyd SD, Scriba TJ, Martinez OM, Davis MM. Identifying specificity groups in the T cell receptor repertoire. Nature. 2017 Jul 06; 547(7661):94-98. PMID: 28636589.
        View in: PubMed
      10. 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.
        View in: PubMed
      11. 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.
        View in: PubMed
      12. 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.
        View in: PubMed
      13. Ferlito C, Barnaba V, Abrignani S, Bombaci M, Sette A, Sidney J, Biselli R, Tomao E, Cattaruzza MS, Germano V, Biondo MI, Salerno G, Lulli P, Caporuscio S, Picchianti Diamanti A, Falco M, Biselli V, Cardelli P, Autore A, Lucertini E, De Cesare DP, Peragallo MS, Lista F, Martire C, Salemi S, Nisini R, D'Amelio R. Lack of evidence for post-vaccine onset of autoimmune/lymphoproliferative disorders, during a nine-month follow-up in multiply vaccinated Italian military personnel. Clin Immunol. 2017 Aug; 181:60-66. PMID: 28625884.
        View in: PubMed
      14. McElroy AK, Akondy RS, Harmon JR, Ellebedy AH, Cannon D, Klena JD, Sidney J, Sette A, Mehta AK, Kraft CS, Lyon MG, Varkey JB, Ribner BS, Nichol ST, Spiropoulou CF. A Case of Human Lassa Virus Infection With Robust Acute T-Cell Activation and Long-Term Virus-Specific T-Cell Responses. J Infect Dis. 2017 Jun 15; 215(12):1862-1872. PMID: 28863472.
        View in: PubMed
      15. Moguche AO, Musvosvi M, Penn-Nicholson A, Plumlee CR, Mearns H, Geldenhuys H, Smit E, Abrahams D, Rozot V, Dintwe O, Hoff ST, Kromann I, Ruhwald M, Bang P, Larson RP, Shafiani S, Ma S, Sherman DR, Sette A, Lindestam Arlehamn CS, McKinney DM, Maecker H, Hanekom WA, Hatherill M, Andersen P, Scriba TJ, Urdahl KB. Antigen Availability Shapes T Cell Differentiation and Function during Tuberculosis. Cell Host Microbe. 2017 Jun 14; 21(6):695-706.e5. PMID: 28618268.
        View in: PubMed
      16. 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.
        View in: PubMed
      17. Khan AA, Srivastava R, Chentoufi AA, Kritzer E, Chilukuri S, Garg S, Yu DC, Vahed H, Huang L, Syed SA, Furness JN, Tran TT, Anthony NB, McLaren CE, Sidney J, Sette A, Noelle RJ, BenMohamed L. Bolstering the Number and Function of HSV-1-Specific CD8+ Effector Memory T Cells and Tissue-Resident Memory T Cells in Latently Infected Trigeminal Ganglia Reduces Recurrent Ocular Herpes Infection and Disease. J Immunol. 2017 Jul 01; 199(1):186-203. PMID: 28539429.
        View in: PubMed
      18. 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.
        View in: PubMed
      19. Goel G, King T, Daveson AJ, Andrews JM, Krishnarajah J, Krause R, Brown GJE, Fogel R, Barish CF, Epstein R, Kinney TP, Miner PB, Tye-Din JA, Girardin A, Taavela J, Popp A, Sidney J, Mäki M, Goldstein KE, Griffin PH, Wang S, Dzuris JL, Williams LJ, Sette A, Xavier RJ, Sollid LM, Jabri B, Anderson RP. Epitope-specific immunotherapy targeting CD4-positive T cells in coeliac disease: two randomised, double-blind, placebo-controlled phase 1 studies. Lancet Gastroenterol Hepatol. 2017 Jul; 2(7):479-493. PMID: 28506538.
        View in: PubMed
      20. 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.
        View in: PubMed
      21. 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.
        View in: PubMed
      22. Sette A. Portrait of an optimist. Hum Vaccin Immunother. 2017 Jun 03; 13(6):1-3. PMID: 28350507.
        View in: PubMed
      23. Johnson AJ, Kennedy SC, Lindestam Arlehamn CS, Goldberg MF, Saini NK, Xu J, Paul S, Hegde SS, Blanchard JS, Chan J, Jacobs WR, Sette A, Porcelli SA. Identification of Mycobacterial RplJ/L10 and RpsA/S1 Proteins as Novel Targets for CD4+ T Cells. Infect Immun. 2017 Apr; 85(4). PMID: 28115505.
        View in: PubMed
      24. 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.
        View in: PubMed
      25. Arlehamn CS, Copin R, Leary S, Mack SJ, Phillips E, Mallal S, Sette A, Blatner G, Siefers H, Ernst JD. Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 100 Luo infants from the Boro area of Nyanza Province, Kenya. Hum Immunol. 2017 Apr; 78(4):325-326. PMID: 28315719.
        View in: PubMed
      26. 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.
        View in: PubMed
      27. Wen J, Tang WW, Sheets N, Ellison J, Sette A, Kim K, Shresta S. Identification of Zika virus epitopes reveals immunodominant and protective roles for dengue virus cross-reactive CD8+ T cells. Nat Microbiol. 2017 Mar 13; 2:17036. PMID: 28288094.
        View in: PubMed
      28. Nivarthi UK, Kose N, Sapparapu G, Widman D, Gallichotte E, Pfaff JM, Doranz BJ, Weiskopf D, Sette A, Durbin AP, Whitehead SS, Baric R, Crowe JE, de Silva AM. Mapping the Human Memory B Cell and Serum Neutralizing Antibody Responses to Dengue Virus Serotype 4 Infection and Vaccination. J Virol. 2017 Mar 01; 91(5). PMID: 28031369.
        View in: PubMed
      29. 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.
        View in: PubMed
      30. Picascia S, Sidney J, Camarca A, Mazzarella G, Giardullo N, Greco L, Auricchio R, Auricchio S, Troncone R, Sette A, Gianfrani C. Gliadin-Specific CD8+ T Cell Responses Restricted by HLA Class I A*0101 and B*0801 Molecules in Celiac Disease Patients. J Immunol. 2017 Mar 01; 198(5):1838-1845. PMID: 28148736.
        View in: PubMed
      31. Textor A, Schmidt K, Kloetzel PM, Weißbrich B, Perez C, Charo J, Anders K, Sidney J, Sette A, Schumacher TN, Keller C, Busch DH, Seifert U, Blankenstein T. Correction: Preventing tumor escape by targeting a post-proteasomal trimming independent epitope. J Exp Med. 2017 Feb; 214(2):567. PMID: 28096291.
        View in: PubMed
      32. Kimura T, Tse K, McArdle S, Gerhardt T, Miller J, Mikulski Z, Sidney J, Sette A, Wolf D, Ley K. Atheroprotective vaccination with MHC-II-restricted ApoB peptides induces peritoneal IL-10-producing CD4 T cells. Am J Physiol Heart Circ Physiol. 2017 Apr 01; 312(4):H781-H790. PMID: 28087520.
        View in: PubMed
      33. 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 Feb 15; 198(4):1748-1758. PMID: 28069807.
        View in: PubMed
      34. 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.
        View in: PubMed
      35. Sette A, Schulten V. It's a lot of work to be nonallergic. J Allergy Clin Immunol. 2017 Mar; 139(3):769-770. PMID: 27993537.
        View in: PubMed
      36. Tian Y, Sette A, Weiskopf D. Cytotoxic CD4 T Cells: Differentiation, Function, and Application to Dengue Virus Infection. Front Immunol. 2016; 7:531. PMID: 28003809.
        View in: PubMed
      37. 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.
        View in: PubMed
      38. 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.
        View in: PubMed
      39. 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.
        View in: PubMed
      40. Liepe J, Marino F, Sidney J, Jeko A, Bunting DE, Sette A, Kloetzel PM, Stumpf MP, Heck AJ, Mishto M. A large fraction of HLA class I ligands are proteasome-generated spliced peptides. Science. 2016 10 21; 354(6310):354-358. PMID: 27846572.
        View in: PubMed
      41. Singh SK, Andersson AM, Ellegård R, Lindestam Arlehamn CS, Sette A, Larsson M, Stendahl O, Blomgran R. HIV Interferes with Mycobacterium tuberculosis Antigen Presentation in Human Dendritic Cells. Am J Pathol. 2016 Dec; 186(12):3083-3093. PMID: 27746182.
        View in: PubMed
      42. Elong Ngono A, Chen HW, Tang WW, Joo Y, King K, Weiskopf D, Sidney J, Sette A, Shresta S. Protective Role of Cross-Reactive CD8 T Cells Against Dengue Virus Infection. EBioMedicine. 2016 Nov; 13:284-293. PMID: 27746192.
        View in: PubMed
      43. Dan JM, Havenar-Daughton C, Silvestri G, Sette A, Crotty S. Response to Comment on "A Cytokine-Independent Approach To Identify Antigen-Specific Human Germinal Center T Follicular Helper Cells and Rare Antigen-Specific CD4+ T Cells in Blood". J Immunol. 2016 Oct 01; 197(7):2558. PMID: 27638936.
        View in: PubMed
      44. El Bissati K, Chentoufi AA, Krishack PA, Zhou Y, Woods S, Dubey JP, Vang L, Lykins J, Broderick KE, Mui E, Suzuki Y, Sa Q, Bi S, Cardona N, Verma SK, Frazeck L, Reardon CA, Sidney J, Alexander J, Sette A, Vedvick T, Fox C, Guderian JA, Reed S, Roberts CW, McLeod R. Adjuvanted multi-epitope vaccines protect HLA-A*11:01 transgenic mice against Toxoplasma gondii. JCI Insight. 2016 Sep 22; 1(15):e85955. PMID: 27699241.
        View in: PubMed
      45. 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].
      46. Westernberg L, Schulten V, Sette A, Peters B. Reply. J Allergy Clin Immunol. 2016 Oct; 138(4):1237-1238. PMID: 27484034.
        View in: PubMed
      47. 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.
        View in: PubMed
      48. 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.
      49. Dan JM, Lindestam Arlehamn CS, Weiskopf D, da Silva Antunes R, Havenar-Daughton C, Reiss SM, Brigger M, Bothwell M, Sette A, Crotty S. A Cytokine-Independent Approach To Identify Antigen-Specific Human Germinal Center T Follicular Helper Cells and Rare Antigen-Specific CD4+ T Cells in Blood. J Immunol. 2016 Aug 01; 197(3):983-93. PMID: 27342848; PMCID: PMC4955771 [Available on 08/01/17].
      50. 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].
      51. 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; PMCID: PMC4899275 [Available on 06/01/17].
      52. 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].
      53. 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.
      54. 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].
      55. 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].
      56. 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; PMCID: PMC4754615 [Available on 03/01/17].
      57. 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.
      58. 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].
      59. 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.
      60. Sidney J, Schloss J, Moore C, Lindvall M, Wriston A, Hunt DF, Shabanowitz J, DiLorenzo TP, Sette A. Characterization of the peptide binding specificity of the HLA class I alleles B*38:01 and B*39:06. Immunogenetics. 2016 Mar; 68(3):231-6. PMID: 26754738; PMCID: PMC4760861 [Available on 03/01/17].
      61. 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.
      62. Sette A, Schenkelberg TR, Koff WC. Deciphering the human antigenome. Expert Rev Vaccines. 2016; 15(2):167-71. PMID: 26629807.
        View in: PubMed
      63. 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.
        View in: PubMed
      64. Textoris-Taube K, Keller C, Liepe J, Henklein P, Sidney J, Sette A, Kloetzel PM, Mishto M. The T210M Substitution in the HLA-a*02:01 gp100 Epitope Strongly Affects Overall Proteasomal Cleavage Site Usage and Antigen Processing. J Biol Chem. 2015 Dec 18; 290(51):30417-28. PMID: 26507656; PMCID: PMC4683264 [Available on 12/18/16].
      65. 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.
      66. 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.
      67. 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].
      68. Martini H, Citro A, Martire C, D'Ettorre G, Labbadia G, Accapezzato D, Piconese S, De Marzio P, Cavallari EN, Calvo L, Rizzo F, Severa M, Coccia EM, Grazi GL, Di Filippo S, Sidney J, Vullo V, Sette A, Barnaba V. Apoptotic Epitope-Specific CD8+ T Cells and Interferon Signaling Intersect in Chronic Hepatitis C Virus Infection. J Infect Dis. 2016 Feb 15; 213(4):674-83. PMID: 26386427.
        View in: PubMed
      69. Mothé BR, Lindestam Arlehamn CS, Dow C, Dillon MBC, Wiseman RW, Bohn P, Karl J, Golden NA, Gilpin T, Foreman TW, Rodgers MA, Mehra S, Scriba TJ, Flynn JL, Kaushal D, O'Connor DH, Sette A. The TB-specific CD4(+) T cell immune repertoire in both cynomolgus and rhesus macaques largely overlap with humans. Tuberculosis (Edinb). 2015 Dec; 95(6):722-735. PMID: 26526557; PMCID: PMC4773292 [Available on 12/01/16].
      70. Carpenter C, Sidney J, Kolla R, Nayak K, Tomiyama H, Tomiyama C, Padilla OA, Rozot V, Ahamed SF, Ponte C, Rolla V, Antas PR, Chandele A, Kenneth J, Laxmi S, Makgotlho E, Vanini V, Ippolito G, Kazanova AS, Panteleev AV, Hanekom W, Mayanja-Kizza H, Lewinsohn D, Saito M, McElrath MJ, Boom WH, Goletti D, Gilman R, Lyadova IV, Scriba TJ, Kallas EG, Murali-Krishna K, Sette A, Lindestam Arlehamn CS. A side-by-side comparison of T cell reactivity to fifty-nine Mycobacterium tuberculosis antigens in diverse populations from five continents. Tuberculosis (Edinb). 2015 Dec; 95(6):713-721. PMID: 26277695; PMCID: PMC4666753 [Available on 12/01/16].
      71. 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 04; 112(31):E4256-63. PMID: 26195744; PMCID: PMC4534238.
      72. Okada S, Markle JG, Deenick EK, Mele F, Averbuch D, Lagos M, Alzahrani M, Al-Muhsen S, Halwani R, Ma CS, Wong N, Soudais C, Henderson LA, Marzouqa H, Shamma J, Gonzalez M, Martinez-Barricarte R, Okada C, Avery DT, Latorre D, Deswarte C, Jabot-Hanin F, Torrado E, Fountain J, Belkadi A, Itan Y, Boisson B, Migaud M, Arlehamn CSL, Sette A, Breton S, McCluskey J, Rossjohn J, de Villartay JP, Moshous D, Hambleton S, Latour S, Arkwright PD, Picard C, Lantz O, Engelhard D, Kobayashi M, Abel L, Cooper AM, Notarangelo LD, Boisson-Dupuis S, Puel A, Sallusto F, Bustamante J, Tangye SG, Casanova JL. IMMUNODEFICIENCIES. Impairment of immunity to Candida and Mycobacterium in humans with bi-allelic RORC mutations. Science. 2015 Aug 07; 349(6248):606-613. PMID: 26160376; PMCID: PMC4668938.
      73. Caron E, Espona L, Kowalewski DJ, Schuster H, Ternette N, Alpízar A, Schittenhelm RB, Ramarathinam SH, Lindestam Arlehamn CS, Chiek Koh C, Gillet LC, Rabsteyn A, Navarro P, Kim S, Lam H, Sturm T, Marcilla M, Sette A, Campbell DS, Deutsch EW, Moritz RL, Purcell AW, Rammensee HG, Stevanovic S, Aebersold R. An open-source computational and data resource to analyze digital maps of immunopeptidomes. Elife. 2015 Jul 08; 4. PMID: 26154972; PMCID: PMC4507788.
      74. Citro A, Scrivo R, Martini H, Martire C, De Marzio P, Vestri AR, Sidney J, Sette A, Barnaba V, Valesini G. CD8+ T Cells Specific to Apoptosis-Associated Antigens Predict the Response to Tumor Necrosis Factor Inhibitor Therapy in Rheumatoid Arthritis. PLoS One. 2015; 10(6):e0128607. PMID: 26061065; PMCID: PMC4465029.
      75. 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].
      76. 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.
      77. 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].
      78. 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.
      79. Burns JC, Touma R, Song Y, Padilla RL, Tremoulet AH, Sidney J, Sette A, Franco A. Fine specificities of natural regulatory T cells after IVIG therapy in patients with Kawasaki disease. Autoimmunity. 2015 May; 48(3):181-8. PMID: 25822882; PMCID: PMC4784966.
      80. McElroy AK, Akondy RS, Davis CW, Ellebedy AH, Mehta AK, Kraft CS, Lyon GM, Ribner BS, Varkey J, Sidney J, Sette A, Campbell S, Ströher U, Damon I, Nichol ST, Spiropoulou CF, Ahmed R. Human Ebola virus infection results in substantial immune activation. Proc Natl Acad Sci U S A. 2015 Apr 14; 112(15):4719-24. PMID: 25775592; PMCID: PMC4403189.
      81. 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 01; 31(13):2174-81. PMID: 25717196; PMCID: PMC4481849.
      82. Kimura T, Tse K, Sette A, Ley K. Vaccination to modulate atherosclerosis. Autoimmunity. 2015 May; 48(3):152-60. PMID: 25683179; PMCID: PMC4429861.
      83. Ratto-Kim S, de Souza MS, Currier JR, Karasavvas N, Sidney J, Rolland M, Valencia-Micolta A, Madnote S, Sette A, Nitayaphan S, Pitisuttuthum P, Kaewkungwal J, Rerks-Ngarm S, O'Connell R, Michael N, Robb ML, Marovich M, Kim JH. Identification of immunodominant CD4-restricted epitopes co-located with antibody binding sites in individuals vaccinated with ALVAC-HIV and AIDSVAX B/E. PLoS One. 2015; 10(2):e0115582. PMID: 25665096; PMCID: PMC4321833.
      84. Cheloha RW, Sullivan JA, Wang T, Sand JM, Sidney J, Sette A, Cook ME, Suresh M, Gellman SH. Consequences of periodic a-to-ß(3) residue replacement for immunological recognition of peptide epitopes. ACS Chem Biol. 2015 Mar 20; 10(3):844-54. PMID: 25559929; PMCID: PMC4372116.
      85. 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.
      86. 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.
      87. 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.
      88. Ponomarenko J, Vaughan K, Sette A, Maurer-Stroh S. Conservancy of mAb Epitopes in Ebolavirus Glycoproteins of Previous and 2014 Outbreaks. PLoS Curr. 2014 Nov 03; 6. PMID: 25642381; PMCID: PMC4234462.
      89. 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.
      90. 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.
      91. 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.
      92. Duan F, Duitama J, Al Seesi S, Ayres CM, Corcelli SA, Pawashe AP, Blanchard T, McMahon D, Sidney J, Sette A, Baker BM, Mandoiu II, Srivastava PK. Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity. J Exp Med. 2014 Oct 20; 211(11):2231-48. PMID: 25245761; PMCID: PMC4203949.
      93. 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.
      94. Lucca LE, Desbois S, Ramadan A, Ben-Nun A, Eisenstein M, Carrié N, Guéry JC, Sette A, Nguyen P, Geiger TL, Mars LT, Liblau RS. Bispecificity for myelin and neuronal self-antigens is a common feature of CD4 T cells in C57BL/6 mice. J Immunol. 2014 Oct 01; 193(7):3267-77. PMID: 25135834.
        View in: PubMed
      95. 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.
      96. 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; 88(19):11383-94. PMID: 25056881; PMCID: PMC4178794.
      97. 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; PMCID: PMC4253970.
      98. 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.
      99. Siciliano NA, Hersperger AR, Lacuanan AM, Xu RH, Sidney J, Sette A, Sigal LJ, Eisenlohr LC. Impact of distinct poxvirus infections on the specificities and functionalities of CD4+ T cell responses. J Virol. 2014 Sep 01; 88(17):10078-91. PMID: 24965457; PMCID: PMC4136331.
      100. Lindestam Arlehamn CS, Lewinsohn D, Sette A, Lewinsohn D. Antigens for CD4 and CD8 T cells in tuberculosis. Cold Spring Harb Perspect Med. 2014 May 22; 4(7):a018465. PMID: 24852051; PMCID: PMC4066646.
      101. Gartland AJ, Li S, McNevin J, Tomaras GD, Gottardo R, Janes H, Fong Y, Morris D, Geraghty DE, Kijak GH, Edlefsen PT, Frahm N, Larsen BB, Tovanabutra S, Sanders-Buell E, deCamp AC, Magaret CA, Ahmed H, Goodridge JP, Chen L, Konopa P, Nariya S, Stoddard JN, Wong K, Zhao H, Deng W, Maust BS, Bose M, Howell S, Bates A, Lazzaro M, O'Sullivan A, Lei E, Bradfield A, Ibitamuno G, Assawadarachai V, O'Connell RJ, deSouza MS, Nitayaphan S, Rerks-Ngarm S, Robb ML, Sidney J, Sette A, Zolla-Pazner S, Montefiori D, McElrath MJ, Mullins JI, Kim JH, Gilbert PB, Hertz T. Analysis of HLA A*02 association with vaccine efficacy in the RV144 HIV-1 vaccine trial. J Virol. 2014 Aug; 88(15):8242-55. PMID: 24829343; PMCID: PMC4135964.
      102. 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.
      103. Lindestam Arlehamn CS, Sette A. Definition of CD4 Immunosignatures Associated with MTB. Front Immunol. 2014; 5:124. PMID: 24715893; PMCID: PMC3970006.
      104. Weiskopf D, Sette A. T-cell immunity to infection with dengue virus in humans. Front Immunol. 2014; 5:93. PMID: 24639680; PMCID: PMC3945531.
      105. 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.
      106. Tse K, Gonen A, Sidney J, Ouyang H, Witztum JL, Sette A, Tse H, Ley K. Atheroprotective Vaccination with MHC-II Restricted Peptides from ApoB-100. Front Immunol. 2013; 4:493. PMID: 24416033; PMCID: PMC3873602.
      107. 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.
      108. 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.
      109. Cannella AP, Arlehamn CS, Sidney J, Patra KP, Torres K, Tsolis RM, Liang L, Felgner PL, Saito M, Gotuzzo E, Gilman RH, Sette A, Vinetz JM. Brucella melitensis T cell epitope recognition in humans with brucellosis in Peru. Infect Immun. 2014 Jan; 82(1):124-31. PMID: 24126518; PMCID: PMC3911835.
      110. Nascimento EJ, Mailliard RB, Khan AM, Sidney J, Sette A, Guzman N, Paulaitis M, de Melo AB, Cordeiro MT, Gil LV, Lemonnier F, Rinaldo C, August JT, Marques ET. Identification of conserved and HLA promiscuous DENV3 T-cell epitopes. PLoS Negl Trop Dis. 2013; 7(10):e2497. PMID: 24130917; PMCID: PMC3794980.
      111. Chen S, Li Y, Depontieu FR, McMiller TL, English AM, Shabanowitz J, Kos F, Sidney J, Sette A, Rosenberg SA, Hunt DF, Mariuzza RA, Topalian SL. Structure-based design of altered MHC class II-restricted peptide ligands with heterogeneous immunogenicity. J Immunol. 2013 Nov 15; 191(10):5097-106. PMID: 24108701; PMCID: PMC3888030.
      112. 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.
      113. Dervillez X, Qureshi H, Chentoufi AA, Khan AA, Kritzer E, Yu DC, Diaz OR, Gottimukkala C, Kalantari M, Villacres MC, Scarfone VM, McKinney DM, Sidney J, Sette A, Nesburn AB, Wechsler SL, BenMohamed L. Asymptomatic HLA-A*02:01-restricted epitopes from herpes simplex virus glycoprotein B preferentially recall polyfunctional CD8+ T cells from seropositive asymptomatic individuals and protect HLA transgenic mice against ocular herpes. J Immunol. 2013 Nov 15; 191(10):5124-38. PMID: 24101547; PMCID: PMC4057607.
      114. Song H, Sidney J, Wiseman RW, Josleyn N, Cohen M, Blaney JE, Jahrling PB, Sette A. Characterizing monkeypox virus specific CD8+ T cell epitopes in rhesus macaques. Virology. 2013 Dec; 447(1-2):181-6. PMID: 24210113; PMCID: PMC4771384.
      115. Locci M, Havenar-Daughton C, Landais E, Wu J, Kroenke MA, Arlehamn CL, Su LF, Cubas R, Davis MM, Sette A, Haddad EK, Poignard P, Crotty S. Human circulating PD-1+CXCR3-CXCR5+ memory Tfh cells are highly functional and correlate with broadly neutralizing HIV antibody responses. Immunity. 2013 Oct 17; 39(4):758-69. PMID: 24035365; PMCID: PMC3996844.
      116. Dow C, Henderson R, Sette A, Mothé BR. CD4(+) T-cell inhibitory ligands: a tool for characterizing dysfunctional CD4(+) T cells during chronic infection. Immunology. 2013 Sep; 140(1):61-9. PMID: 23566283; PMCID: PMC3809706.
      117. Nitschke K, Barriga A, Schmidt J, Timm J, Viazov S, Kuntzen T, Kim AY, Lauer GM, Allen TM, Gaudieri S, Rauch A, Lange CM, Sarrazin C, Eiermann T, Sidney J, Sette A, Thimme R, López D, Neumann-Haefelin C. HLA-B*27 subtype specificity determines targeting and viral evolution of a hepatitis C virus-specific CD8+ T cell epitope. J Hepatol. 2014 Jan; 60(1):22-9. PMID: 23978718; PMCID: PMC3867523.
      118. Pratesi F, Petit Teixeira E, Sidney J, Michou L, Puxeddu I, Sette A, Cornelis F, Migliorini P. HLA shared epitope and ACPA: just a marker or an active player? Autoimmun Rev. 2013 Oct; 12(12):1182-7. PMID: 23958703.
        View in: PubMed
      119. Lolli F, Martini H, Citro A, Franceschini D, Portaccio E, Amato MP, Mechelli R, Annibali V, Sidney J, Sette A, Salvetti M, Barnaba V. Increased CD8+ T cell responses to apoptotic T cell-associated antigens in multiple sclerosis. J Neuroinflammation. 2013 Jul 27; 10:94. PMID: 23890271; PMCID: PMC3734107.
      120. Schussek S, Trieu A, Apte SH, Sidney J, Sette A, Doolan DL. Immunization with apical membrane antigen 1 confers sterile infection-blocking immunity against Plasmodium sporozoite challenge in a rodent model. Infect Immun. 2013 Oct; 81(10):3586-99. PMID: 23836827; PMCID: PMC3811765.
      121. Walsh KB, Sidney J, Welch M, Fremgen DM, Sette A, Oldstone MB. CD8+ T-cell epitope mapping for pneumonia virus of mice in H-2b mice. J Virol. 2013 Sep; 87(17):9949-52. PMID: 23824814; PMCID: PMC3754129.
      122. Ranasinghe S, Cutler S, Davis I, Lu R, Soghoian DZ, Qi Y, Sidney J, Kranias G, Flanders MD, Lindqvist M, Kuhl B, Alter G, Deeks SG, Walker BD, Gao X, Sette A, Carrington M, Streeck H. Association of HLA-DRB1-restricted CD4? T cell responses with HIV immune control. Nat Med. 2013 Jul; 19(7):930-3. PMID: 23793098; PMCID: PMC3974408.
      123. Youngblood B, Noto A, Porichis F, Akondy RS, Ndhlovu ZM, Austin JW, Bordi R, Procopio FA, Miura T, Allen TM, Sidney J, Sette A, Walker BD, Ahmed R, Boss JM, Sékaly RP, Kaufmann DE. Cutting edge: Prolonged exposure to HIV reinforces a poised epigenetic program for PD-1 expression in virus-specific CD8 T cells. J Immunol. 2013 Jul 15; 191(2):540-4. PMID: 23772031; PMCID: PMC3702641.
      124. 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.
      125. Vita R, Overton JA, Greenbaum JA, Sette A, Peters B. 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.
      126. Engels B, Engelhard VH, Sidney J, Sette A, Binder DC, Liu RB, Kranz DM, Meredith SC, Rowley DA, Schreiber H. Relapse or eradication of cancer is predicted by peptide-major histocompatibility complex affinity. Cancer Cell. 2013 Apr 15; 23(4):516-26. PMID: 23597565; PMCID: PMC3658176.
      127. 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; PMCID: PMC3670335.
      128. Gilchuk P, Spencer CT, Conant SB, Hill T, Gray JJ, Niu X, Zheng M, Erickson JJ, Boyd KL, McAfee KJ, Oseroff C, Hadrup SR, Bennink JR, Hildebrand W, Edwards KM, Crowe JE, Williams JV, Buus S, Sette A, Schumacher TN, Link AJ, Joyce S. Discovering naturally processed antigenic determinants that confer protective T cell immunity. J Clin Invest. 2013 May; 123(5):1976-87. PMID: 23543059; PMCID: PMC3635741.
      129. Xu W, Watts DM, Costanzo MC, Tang X, Venegas LA, Jiao F, Sette A, Sidney J, Sewell AK, Wooldridge L, Makino S, Morrill JC, Peters CJ, Kan-Mitchell J. The nucleocapsid protein of Rift Valley fever virus is a potent human CD8+ T cell antigen and elicits memory responses. PLoS One. 2013; 8(3):e59210. PMID: 23527138; PMCID: PMC3601065.
      130. Spencer CT, Dragovic SM, Conant SB, Gray JJ, Zheng M, Samir P, Niu X, Moutaftsi M, Van Kaer L, Sette A, Link AJ, Joyce S. Sculpting MHC class II-restricted self and non-self peptidome by the class I Ag-processing machinery and its impact on Th-cell responses. Eur J Immunol. 2013 May; 43(5):1162-72. PMID: 23386199; PMCID: PMC3798073.
      131. Mothé BR, Southwood S, Sidney J, English AM, Wriston A, Hoof I, Shabanowitz J, Hunt DF, Sette A. Peptide-binding motifs associated with MHC molecules common in Chinese rhesus macaques are analogous to those of human HLA supertypes and include HLA-B27-like alleles. Immunogenetics. 2013 May; 65(5):371-86. PMID: 23417323; PMCID: PMC3633659.
      132. 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; PMCID: PMC3587276.
      133. 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; PMCID: PMC3633633.
      134. Sidney J, Southwood S, Moore C, Oseroff C, Pinilla C, Grey HM, Sette A. Measurement of MHC/peptide interactions by gel filtration or monoclonal antibody capture. Curr Protoc Immunol. 2013 Feb; Chapter 18:Unit 18.3.. PMID: 23392640; PMCID: PMC3626435.
      135. de Melo AB, Nascimento EJ, Braga-Neto U, Dhalia R, Silva AM, Oelke M, Schneck JP, Sidney J, Sette A, Montenegro SM, Marques ET. T-cell memory responses elicited by yellow fever vaccine are targeted to overlapping epitopes containing multiple HLA-I and -II binding motifs. PLoS Negl Trop Dis. 2013; 7(1):e1938. PMID: 23383350; PMCID: PMC3561163.
      136. 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.
      137. 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; PMCID: PMC3554618.
      138. Mamone G, Camarca A, Fierro O, Sidney J, Mazzarella G, Addeo F, Auricchio S, Troncone R, Sette A, Gianfrani C. Immunogenic peptides can be detected in whole gluten by transamidating highly susceptible glutamine residues: implication in the search for gluten-free cereals. J Agric Food Chem. 2013 Jan 23; 61(3):747-54. PMID: 23244345.
        View in: PubMed
      139. 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.
        View in: PubMed
      140. Vaughan K, Kim Y, Sette A. A comparison of epitope repertoires associated with myasthenia gravis in humans and nonhuman hosts. Autoimmune Dis. 2012; 2012:403915. PMID: 23243503; PMCID: PMC3518085.
      141. 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; PMCID: PMC3629817.
      142. 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; PMCID: PMC3547526.
      143. 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.
      144. Almeida RR, Rosa DS, Ribeiro SP, Santana VC, Kallás EG, Sidney J, Sette A, Kalil J, Cunha-Neto E. Broad and cross-clade CD4+ T-cell responses elicited by a DNA vaccine encoding highly conserved and promiscuous HIV-1 M-group consensus peptides. PLoS One. 2012; 7(9):e45267. PMID: 23028895; PMCID: PMC3445454.
      145. 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; PMCID: PMC3422266.
      146. 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; PMCID: PMC3411923.
      147. Pratesi F, Petit-Teixeira E, Sidney J, Teixeira VH, Puxeddu I, Sette A, Cornelis F, Migliorini P. Effect of rheumatoid arthritis (RA) susceptibility genes on the immune response to viral citrullinated peptides in RA. J Rheumatol. 2012 Jul; 39(7):1490-3. PMID: 22753806.
        View in: PubMed
      148. Remakus S, Rubio D, Ma X, Sette A, Sigal LJ. Memory CD8+ T cells specific for a single immunodominant or subdominant determinant induced by peptide-dendritic cell immunization protect from an acute lethal viral disease. J Virol. 2012 Sep; 86(18):9748-59. PMID: 22740418; PMCID: PMC3446599.
      149. Franceschini D, Del Porto P, Piconese S, Trella E, Accapezzato D, Paroli M, Morrone S, Piccolella E, Spada E, Mele A, Sidney J, Sette A, Barnaba V. Polyfunctional type-1, -2, and -17 CD8? T cell responses to apoptotic self-antigens correlate with the chronic evolution of hepatitis C virus infection. PLoS Pathog. 2012; 8(6):e1002759. PMID: 22737070; PMCID: PMC3380931.
      150. 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; PMCID: PMC3392449.
      151. 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.
      152. 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.
      153. 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; PMCID: PMC3394288.
      154. Taniguchi RT, DeVoss JJ, Moon JJ, Sidney J, Sette A, Jenkins MK, Anderson MS. Detection of an autoreactive T-cell population within the polyclonal repertoire that undergoes distinct autoimmune regulator (Aire)-mediated selection. Proc Natl Acad Sci U S A. 2012 May 15; 109(20):7847-52. PMID: 22552229; PMCID: PMC3356674.
      155. Antal Z, Baker JC, Smith C, Jarchum I, Babad J, Mukherjee G, Yang Y, Sidney J, Sette A, Santamaria P, DiLorenzo TP. Beyond HLA-A*0201: new HLA-transgenic nonobese diabetic mouse models of type 1 diabetes identify the insulin C-peptide as a rich source of CD8+ T cell epitopes. J Immunol. 2012 Jun 01; 188(11):5766-75. PMID: 22539795; PMCID: PMC3358524.
      156. Burke KP, Munshaw S, Osburn WO, Levine J, Liu L, Sidney J, Sette A, Ray SC, Cox AL. Immunogenicity and cross-reactivity of a representative ancestral sequence in hepatitis C virus infection. J Immunol. 2012 May 15; 188(10):5177-88. PMID: 22508927; PMCID: PMC3345099.
      157. 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; PMCID: PMC3345088.
      158. Schreiber K, Arina A, Engels B, Spiotto MT, Sidney J, Sette A, Karrison TG, Weichselbaum RR, Rowley DA, Schreiber H. Spleen cells from young but not old immunized mice eradicate large established cancers. Clin Cancer Res. 2012 May 01; 18(9):2526-33. PMID: 22415314.
        View in: PubMed
      159. Sette A, Sidney J, Southwood S, Moore C, Berry J, Dow C, Bradley K, Hoof I, Lewis MG, Hildebrand WH, McMurtrey CP, Wilson NA, Watkins DI, Mothé BR. A shared MHC supertype motif emerges by convergent evolution in macaques and mice, but is totally absent in human MHC molecules. Immunogenetics. 2012 Jun; 64(6):421-34. PMID: 22322672; PMCID: PMC3349854.
      160. Cannella AP, Tsolis RM, Liang L, Felgner PL, Saito M, Sette A, Gotuzzo E, Vinetz JM. Antigen-specific acquired immunity in human brucellosis: implications for diagnosis, prognosis, and vaccine development. Front Cell Infect Microbiol. 2012; 2:1. PMID: 22919593; PMCID: PMC3417515.
      161. Moore C, Sidney J, English AM, Wriston A, Hunt DF, Shabanowitz J, Southwood S, Bradley K, Lafont BA, Mothé BR, Sette A. Identification of the peptide-binding motif recognized by the pigtail macaque class I MHC molecule Mane-A1*082:01 (Mane A*0301). Immunogenetics. 2012 Jun; 64(6):461-8. PMID: 22278177; PMCID: PMC3626442.
      162. 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.
      163. Cong H, Mui EJ, Witola WH, Sidney J, Alexander J, Sette A, Maewal A, El Bissati K, Zhou Y, Suzuki Y, Lee D, Woods S, Sommerville C, Henriquez FL, Roberts CW, McLeod R. Toxoplasma gondii HLA-B*0702-restricted GRA7(20-28) peptide with adjuvants and a universal helper T cell epitope elicits CD8(+) T cells producing interferon-? and reduces parasite burden in HLA-B*0702 mice. Hum Immunol. 2012 Jan; 73(1):1-10. PMID: 22027386; PMCID: PMC3246109.
      164. Neumann-Haefelin C, Oniangue-Ndza C, Kuntzen T, Schmidt J, Nitschke K, Sidney J, Caillet-Saguy C, Binder M, Kersting N, Kemper MW, Power KA, Ingber S, Reyor LL, Hills-Evans K, Kim AY, Lauer GM, Lohmann V, Sette A, Henn MR, Bressanelli S, Thimme R, Allen TM. Human leukocyte antigen B27 selects for rare escape mutations that significantly impair hepatitis C virus replication and require compensatory mutations. Hepatology. 2011 Oct; 54(4):1157-66. PMID: 22006856; PMCID: PMC3201753.
      165. 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; PMCID: PMC3186824.
      166. 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.
      167. Berger CT, Frahm N, Price DA, Mothe B, Ghebremichael M, Hartman KL, Henry LM, Brenchley JM, Ruff LE, Venturi V, Pereyra F, Sidney J, Sette A, Douek DC, Walker BD, Kaufmann DE, Brander C. High-functional-avidity cytotoxic T lymphocyte responses to HLA-B-restricted Gag-derived epitopes associated with relative HIV control. J Virol. 2011 Sep; 85(18):9334-45. PMID: 21752903; PMCID: PMC3165743.
      168. Reed JS, Sidney J, Piaskowski SM, Glidden CE, León EJ, Burwitz BJ, Kolar HL, Eernisse CM, Furlott JR, Maness NJ, Walsh AD, Rudersdorf RA, Bardet W, McMurtrey CP, O'Connor DH, Hildebrand WH, Sette A, Watkins DI, Wilson NA. The role of MHC class I allele Mamu-A*07 during SIV(mac)239 infection. Immunogenetics. 2011 Dec; 63(12):789-807. PMID: 21732180; PMCID: PMC3706270.
      169. Salek-Ardakani S, Moutaftsi M, Sette A, Croft M. Targeting OX40 promotes lung-resident memory CD8 T cell populations that protect against respiratory poxvirus infection. J Virol. 2011 Sep; 85(17):9051-9. PMID: 21715499; PMCID: PMC3165842.
      170. Wang P, Sidney J, Sette A, Peters B. A computational pipeline to generate MHC binding motifs. Immunome Res. 2011 May; 7(2). PMID: 28747991.
        View in: PubMed
      171. 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.
      172. 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; PMCID: PMC3042621.
      173. 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.
      174. 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.
      175. Cong H, Mui EJ, Witola WH, Sidney J, Alexander J, Sette A, Maewal A, McLeod R. Human immunome, bioinformatic analyses using HLA supermotifs and the parasite genome, binding assays, studies of human T cell responses, and immunization of HLA-A*1101 transgenic mice including novel adjuvants provide a foundation for HLA-A03 restricted CD8+T cell epitope based, adjuvanted vaccine protective against Toxoplasma gondii. Immunome Res. 2010 Dec 03; 6:12. PMID: 21129215; PMCID: PMC3009956.
      176. 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.
      177. Cong H, Mui EJ, Witola WH, Sidney J, Alexander J, Sette A, Maewal A, McLeod R. Towards an immunosense vaccine to prevent toxoplasmosis: protective Toxoplasma gondii epitopes restricted by HLA-A*0201. Vaccine. 2011 Jan 17; 29(4):754-62. PMID: 21095258; PMCID: PMC3014376.
      178. 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.
      179. Sette A, Rappuoli R. Reverse vaccinology: developing vaccines in the era of genomics. Immunity. 2010 Oct 29; 33(4):530-41. PMID: 21029963; PMCID: PMC3320742.
      180. 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; PMCID: PMC3013771.
      181. 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 01; 185(9):5405-16. PMID: 20870934; PMCID: PMC2962919.
      182. 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.
      183. 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.
      184. Botten J, Whitton JL, Barrowman P, Sidney J, Whitmire JK, Alexander J, Kotturi MF, Sette A, Buchmeier MJ. A multivalent vaccination strategy for the prevention of Old World arenavirus infection in humans. J Virol. 2010 Oct; 84(19):9947-56. PMID: 20668086; PMCID: PMC2937778.
      185. Tarosso LF, Sauer MM, Sanabani S, Giret MT, Tomiyama HI, Sidney J, Piaskowski SM, Diaz RS, Sabino EC, Sette A, Kalil-Filho J, Watkins DI, Kallas EG. Unexpected diversity of cellular immune responses against Nef and Vif in HIV-1-infected patients who spontaneously control viral replication. PLoS One. 2010 Jul 02; 5(7):e11436. PMID: 20625436; PMCID: PMC2896403.
      186. Schaubert KL, Price DA, Salkowitz JR, Sewell AK, Sidney J, Asher TE, Blondelle SE, Adams S, Marincola FM, Joseph A, Sette A, Douek DC, Ayyavoo V, Storkus W, Leung MY, Ng HL, Yang OO, Goldstein H, Wilson DB, Kan-Mitchell J. Generation of robust CD8+ T-cell responses against subdominant epitopes in conserved regions of HIV-1 by repertoire mining with mimotopes. Eur J Immunol. 2010 Jul; 40(7):1950-62. PMID: 20432235; PMCID: PMC3086652.
      187. 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; PMCID: PMC3310373.
      188. 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.
      189. 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.
      190. Cecconi V, Moro M, Del Mare S, Sidney J, Bachi A, Longhi R, Sette A, Protti MP, Dellabona P, Casorati G. The CD4+ T-cell epitope-binding register is a critical parameter when generating functional HLA-DR tetramers with promiscuous peptides. Eur J Immunol. 2010 Jun; 40(6):1603-16. PMID: 20306469.
        View in: PubMed
      191. 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.
      192. 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. PMID: 20478058; PMCID: PMC2880318.
      193. 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.
      194. Li Y, Depontieu FR, Sidney J, Salay TM, Engelhard VH, Hunt DF, Sette A, Topalian SL, Mariuzza RA. Structural basis for the presentation of tumor-associated MHC class II-restricted phosphopeptides to CD4+ T cells. J Mol Biol. 2010 Jun 18; 399(4):596-603. PMID: 20417641; PMCID: PMC2904831.
      195. 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.
      196. Tan TG, Mui E, Cong H, Witola WH, Montpetit A, Muench SP, Sidney J, Alexander J, Sette A, Grigg ME, Maewal A, McLeod R. Identification of T. gondii epitopes, adjuvants, and host genetic factors that influence protection of mice and humans. Vaccine. 2010 May 21; 28(23):3977-89. PMID: 20347630; PMCID: PMC2895808.
      197. Alexander J, Bilsel P, del Guercio MF, Marinkovic-Petrovic A, Southwood S, Stewart S, Ishioka G, Kotturi MF, Botten J, Sidney J, Newman M, Sette A. Identification of broad binding class I HLA supertype epitopes to provide universal coverage of influenza A virus. Hum Immunol. 2010 May; 71(5):468-74. PMID: 20156506; PMCID: PMC2856764.
      198. 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.
      199. 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. PMID: 20174654; PMCID: PMC2822856.
      200. 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.
      201. 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.
      202. 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; PMCID: PMC2928716.
      203. 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.
      204. 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.
      205. 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 01; 106(48):20365-70. PMID: 19918065; PMCID: PMC2777968.
      206. 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.
      207. Alexander J, Bilsel P, del Guercio MF, Stewart S, Marinkovic-Petrovic A, Southwood S, Crimi C, Vang L, Walker L, Ishioka G, Chitnis V, Sette A, Assarsson E, Hannaman D, Botten J, Newman MJ. Universal influenza DNA vaccine encoding conserved CD4+ T cell epitopes protects against lethal viral challenge in HLA-DR transgenic mice. Vaccine. 2010 Jan 08; 28(3):664-72. PMID: 19895924; PMCID: PMC3364000.
      208. Moyron-Quiroz JE, McCausland MM, Kageyama R, Sette A, Crotty S. The smallpox vaccine induces an early neutralizing IgM response. Vaccine. 2009 Dec 10; 28(1):140-7. PMID: 19822230; PMCID: PMC2788018.
      209. Walker LE, Vang L, Shen X, Livingston BD, Post P, Sette A, Godin CS, Newman MJ. Design and preclinical development of a recombinant protein and DNA plasmid mixed format vaccine to deliver HIV-derived T-lymphocyte epitopes. Vaccine. 2009 Nov 23; 27(50):7087-95. PMID: 19786132; PMCID: PMC2783266.
      210. 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.
      211. 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.
      212. Oswald-Richter K, Sato H, Hajizadeh R, Shepherd BE, Sidney J, Sette A, Newman LS, Drake WP. Mycobacterial ESAT-6 and katG are recognized by sarcoidosis CD4+ T cells when presented by the American sarcoidosis susceptibility allele, DRB1*1101. J Clin Immunol. 2010 Jan; 30(1):157-66. PMID: 19536643; PMCID: PMC2821522.
      213. 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.
      214. Li C, Goudy K, Hirsch M, Asokan A, Fan Y, Alexander J, Sun J, Monahan P, Seiber D, Sidney J, Sette A, Tisch R, Frelinger J, Samulski RJ. Cellular immune response to cryptic epitopes during therapeutic gene transfer. Proc Natl Acad Sci U S A. 2009 Jun 30; 106(26):10770-4. PMID: 19541644; PMCID: PMC2705599.
      215. Loffredo JT, Sidney J, Bean AT, Beal DR, Bardet W, Wahl A, Hawkins OE, Piaskowski S, Wilson NA, Hildebrand WH, Watkins DI, Sette A. Two MHC class I molecules associated with elite control of immunodeficiency virus replication, Mamu-B*08 and HLA-B*2705, bind peptides with sequence similarity. J Immunol. 2009 Jun 15; 182(12):7763-75. PMID: 19494300; PMCID: PMC2701622.
      216. Walsh SR, Gillis J, Peters B, Mothé BR, Sidney J, Sette A, Johnson RP. Diverse recognition of conserved orthopoxvirus CD8+ T cell epitopes in vaccinated rhesus macaques. Vaccine. 2009 Aug 06; 27(36):4990-5000. PMID: 19531389; PMCID: PMC2765250.
      217. 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; PMCID: PMC2674070.
      218. Camarca A, Anderson RP, Mamone G, Fierro O, Facchiano A, Costantini S, Zanzi D, Sidney J, Auricchio S, Sette A, Troncone R, Gianfrani C. Intestinal T cell responses to gluten peptides are largely heterogeneous: implications for a peptide-based therapy in celiac disease. J Immunol. 2009 Apr 01; 182(7):4158-66. PMID: 19299713; PMCID: PMC3306175.
      219. Muller WJ, Dong L, Vilalta A, Byrd B, Wilhelm KM, McClurkan CL, Margalith M, Liu C, Kaslow D, Sidney J, Sette A, Koelle DM. Herpes simplex virus type 2 tegument proteins contain subdominant T-cell epitopes detectable in BALB/c mice after DNA immunization and infection. J Gen Virol. 2009 May; 90(Pt 5):1153-63. PMID: 19264627; PMCID: PMC2675279.
      220. 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; PMCID: PMC2759087.
      221. Salek-Ardakani S, Arens R, Flynn R, Sette A, Schoenberger SP, Croft M. Preferential use of B7.2 and not B7.1 in priming of vaccinia virus-specific CD8 T cells. J Immunol. 2009 Mar 01; 182(5):2909-18. PMID: 19234186; PMCID: PMC2707928.
      222. Rutebemberwa A, Ray SC, Astemborski J, Levine J, Liu L, Dowd KA, Clute S, Wang C, Korman A, Sette A, Sidney J, Pardoll DM, Cox AL. High-programmed death-1 levels on hepatitis C virus-specific T cells during acute infection are associated with viral persistence and require preservation of cognate antigen during chronic infection. J Immunol. 2008 Dec 15; 181(12):8215-25. PMID: 19050238; PMCID: PMC2773824.
      223. 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 02; 9:514. PMID: 19055730; PMCID: PMC2607291.
      224. Salek-Ardakani S, Moutaftsi M, Crotty S, Sette A, Croft M. OX40 drives protective vaccinia virus-specific CD8 T cells. J Immunol. 2008 Dec 01; 181(11):7969-76. PMID: 19017988; PMCID: PMC2729132.
      225. 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.
      226. Wölfl M, Rutebemberwa A, Mosbruger T, Mao Q, Li HM, Netski D, Ray SC, Pardoll D, Sidney J, Sette A, Allen T, Kuntzen T, Kavanagh DG, Kuball J, Greenberg PD, Cox AL. Hepatitis C virus immune escape via exploitation of a hole in the T cell repertoire. J Immunol. 2008 Nov 01; 181(9):6435-46. PMID: 18941234; PMCID: PMC2742502.
      227. Kim M, Taylor J, Sidney J, Mikloska Z, Bodsworth N, Lagios K, Dunckley H, Byth-Wilson K, Denis M, Finlayson R, Khanna R, Sette A, Cunningham AL. Immunodominant epitopes in herpes simplex virus type 2 glycoprotein D are recognized by CD4 lymphocytes from both HSV-1 and HSV-2 seropositive subjects. J Immunol. 2008 Nov 01; 181(9):6604-15. PMID: 18941251; PMCID: PMC3312789.
      228. Assarsson E, Bui HH, Sidney J, Zhang Q, Glenn J, Oseroff C, Mbawuike IN, Alexander J, Newman MJ, Grey H, Sette A. Immunomic analysis of the repertoire of T-cell specificities for influenza A virus in humans. J Virol. 2008 Dec; 82(24):12241-51. PMID: 18842709; PMCID: PMC2593359.
      229. 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.
      230. Alvarez MG, Postan M, Weatherly DB, Albareda MC, Sidney J, Sette A, Olivera C, Armenti AH, Tarleton RL, Laucella SA. HLA Class I-T cell epitopes from trans-sialidase proteins reveal functionally distinct subsets of CD8+ T cells in chronic Chagas disease. PLoS Negl Trop Dis. 2008; 2(9):e288. PMID: 18846233; PMCID: PMC2565697.
      231. 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 01; 181(3):2124-33. PMID: 18641351; PMCID: PMC3319690.
      232. 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.
      233. Maciel M, Kellathur SN, Chikhlikar P, Dhalia R, Sidney J, Sette A, August TJ, Marques ET. Comprehensive analysis of T cell epitope discovery strategies using 17DD yellow fever virus structural proteins and BALB/c (H2d) mice model. Virology. 2008 Aug 15; 378(1):105-17. PMID: 18579176; PMCID: PMC2615555.
      234. 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.
      235. 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; PMCID: PMC2504733.
      236. 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.
      237. 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 01; 36(Web Server issue):W513-8. PMID: 18515843; PMCID: PMC2447801.
      238. 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; PMCID: PMC2587066.
      239. 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.
      240. Schneidewind A, Brockman MA, Sidney J, Wang YE, Chen H, Suscovich TJ, Li B, Adam RI, Allgaier RL, Mothé BR, Kuntzen T, Oniangue-Ndza C, Trocha A, Yu XG, Brander C, Sette A, Walker BD, Allen TM. Structural and functional constraints limit options for cytotoxic T-lymphocyte escape in the immunodominant HLA-B27-restricted epitope in human immunodeficiency virus type 1 capsid. J Virol. 2008 Jun; 82(11):5594-605. PMID: 18385228; PMCID: PMC2395179.
      241. Maness NJ, Yant LJ, Chung C, Loffredo JT, Friedrich TC, Piaskowski SM, Furlott J, May GE, Soma T, León EJ, Wilson NA, Piontkivska H, Hughes AL, Sidney J, Sette A, Watkins DI. Comprehensive immunological evaluation reveals surprisingly few differences between elite controller and progressor Mamu-B*17-positive simian immunodeficiency virus-infected rhesus macaques. J Virol. 2008 Jun; 82(11):5245-54. PMID: 18385251; PMCID: PMC2395202.
      242. Bergseng E, Sidney J, Sette A, Sollid LM. Analysis of the binding of gluten T-cell epitopes to various human leukocyte antigen class II molecules. Hum Immunol. 2008 Feb; 69(2):94-100. PMID: 18361933.
        View in: PubMed
      243. 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.
      244. 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.
      245. Benhnia MR, McCausland MM, Su HP, Singh K, Hoffmann J, Davies DH, Felgner PL, Head S, Sette A, Garboczi DN, Crotty S. Redundancy and plasticity of neutralizing antibody responses are cornerstone attributes of the human immune response to the smallpox vaccine. J Virol. 2008 Apr; 82(7):3751-68. PMID: 18234801; PMCID: PMC2268460.
      246. 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.
      247. 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.
      248. Ernst JD, Lewinsohn DM, Behar S, Blythe M, Schlesinger LS, Kornfeld H, Sette A. Meeting Report: NIH Workshop on the Tuberculosis Immune Epitope Database. Tuberculosis (Edinb). 2008 Jul; 88(4):366-70. PMID: 18068490; PMCID: PMC2504685.
      249. 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.
      250. Rawson PM, Molette C, Videtta M, Altieri L, Franceschini D, Donato T, Finocchi L, Propato A, Paroli M, Meloni F, Mastroianni CM, d'Ettorre G, Sidney J, Sette A, Barnaba V. Cross-presentation of caspase-cleaved apoptotic self antigens in HIV infection. Nat Med. 2007 Dec; 13(12):1431-9. PMID: 18026114.
        View in: PubMed
      251. Loffredo JT, Friedrich TC, León EJ, Stephany JJ, Rodrigues DS, Spencer SP, Bean AT, Beal DR, Burwitz BJ, Rudersdorf RA, Wallace LT, Piaskowski SM, May GE, Sidney J, Gostick E, Wilson NA, Price DA, Kallas EG, Piontkivska H, Hughes AL, Sette A, Watkins DI. CD8+ T cells from SIV elite controller macaques recognize Mamu-B*08-bound epitopes and select for widespread viral variation. PLoS One. 2007 Nov 14; 2(11):e1152. PMID: 18000532; PMCID: PMC2062500.
      252. Maness NJ, Valentine LE, May GE, Reed J, Piaskowski SM, Soma T, Furlott J, Rakasz EG, Friedrich TC, Price DA, Gostick E, Hughes AL, Sidney J, Sette A, Wilson NA, Watkins DI. AIDS virus specific CD8+ T lymphocytes against an immunodominant cryptic epitope select for viral escape. J Exp Med. 2007 Oct 29; 204(11):2505-12. PMID: 17954573; PMCID: PMC2118485.
      253. Depla E, Van der Aa A, Livingston BD, Crimi C, Allosery K, De Brabandere V, Krakover J, Murthy S, Huang M, Power S, Babé L, Dahlberg C, McKinney D, Sette A, Southwood S, Philip R, Newman MJ, Meheus L. Rational design of a multiepitope vaccine encoding T-lymphocyte epitopes for treatment of chronic hepatitis B virus infections. J Virol. 2008 Jan; 82(1):435-50. PMID: 17942551; PMCID: PMC2224390.
      254. Bui HH, Sidney J, Li W, Fusseder N, Sette A. Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. BMC Bioinformatics. 2007 Sep 26; 8:361. PMID: 17897458; PMCID: PMC2233646.
      255. Lewinsohn DA, Winata E, Swarbrick GM, Tanner KE, Cook MS, Null MD, Cansler ME, Sette A, Sidney J, Lewinsohn DM. Immunodominant tuberculosis CD8 antigens preferentially restricted by HLA-B. PLoS Pathog. 2007 Sep 21; 3(9):1240-9. PMID: 17892322; PMCID: PMC2323292.
      256. Frahm N, Yusim K, Suscovich TJ, Adams S, Sidney J, Hraber P, Hewitt HS, Linde CH, Kavanagh DG, Woodberry T, Henry LM, Faircloth K, Listgarten J, Kadie C, Jojic N, Sango K, Brown NV, Pae E, Zaman MT, Bihl F, Khatri A, John M, Mallal S, Marincola FM, Walker BD, Sette A, Heckerman D, Korber BT, Brander C. Extensive HLA class I allele promiscuity among viral CTL epitopes. Eur J Immunol. 2007 Sep; 37(9):2419-33. PMID: 17705138; PMCID: PMC2628559.
      257. 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.
      258. 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.
      259. Mothé BR, Stewart BS, Oseroff C, Bui HH, Stogiera S, Garcia Z, Dow C, Rodriguez-Carreno MP, Kotturi M, Pasquetto V, Botten J, Crotty S, Janssen E, Buchmeier MJ, Sette A. Chronic lymphocytic choriomeningitis virus infection actively down-regulates CD4+ T cell responses directed against a broad range of epitopes. J Immunol. 2007 Jul 15; 179(2):1058-67. PMID: 17617598.
        View in: PubMed
      260. 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.
        View in: PubMed
      261. 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 01; 178(11):6814-20. PMID: 17513729.
        View in: PubMed
      262. 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.
        View in: PubMed
      263. Terakura S, Murata M, Warren EH, Sette A, Sidney J, Naoe T, Riddell SR. A single minor histocompatibility antigen encoded by UGT2B17 and presented by human leukocyte antigen-A*2902 and -B*4403. Transplantation. 2007 May 15; 83(9):1242-8. PMID: 17496542.
        View in: PubMed
      264. Massa M, Passalia M, Manzoni SM, Campanelli R, Ciardelli L, Yung GP, Kamphuis S, Pistorio A, Meli V, Sette A, Prakken B, Martini A, Albani S. Differential recognition of heat-shock protein dnaJ-derived epitopes by effector and Treg cells leads to modulation of inflammation in juvenile idiopathic arthritis. Arthritis Rheum. 2007 May; 56(5):1648-57. PMID: 17469159.
        View in: PubMed
      265. 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.
        View in: PubMed
      266. 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.
      267. Bui HH, Botten J, Fusseder N, Pasquetto V, Mothe B, Buchmeier MJ, Sette A. Protein sequence database for pathogenic arenaviruses. Immunome Res. 2007 Feb 08; 3:1. PMID: 17288609; PMCID: PMC1803765.
      268. 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.
      269. Botten J, Whitton JL, Barrowman P, Sidney J, Whitmire JK, Alexander J, Ting JP, Bui HH, Sette A, Buchmeier MJ. HLA-A2-restricted protection against lethal lymphocytic choriomeningitis. J Virol. 2007 Mar; 81(5):2307-17. PMID: 17166907; PMCID: PMC1865925.
      270. Fonseca SG, Coutinho-Silva A, Fonseca LA, Segurado AC, Moraes SL, Rodrigues H, Hammer J, Kallás EG, Sidney J, Sette A, Kalil J, Cunha-Neto E. Identification of novel consensus CD4 T-cell epitopes from clade B HIV-1 whole genome that are frequently recognized by HIV-1 infected patients. AIDS. 2006 Nov 28; 20(18):2263-73. PMID: 17117012.
        View in: PubMed
      271. 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.
        View in: PubMed
      272. Cortez-Gonzalez X, Sidney J, Adotevi O, Sette A, Millard F, Lemonnier F, Langlade-Demoyen P, Zanetti M. Immunogenic HLA-B7-restricted peptides of hTRT. Int Immunol. 2006 Dec; 18(12):1707-18. PMID: 17077179.
        View in: PubMed
      273. Haveman LM, Bierings M, Legger E, Klein MR, de Jager W, Otten HG, Albani S, Kuis W, Sette A, Prakken BJ. Novel pan-DR-binding T cell epitopes of adenovirus induce pro-inflammatory cytokines and chemokines in healthy donors. Int Immunol. 2006 Nov; 18(11):1521-9. PMID: 16954167.
        View in: PubMed
      274. 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.
      275. Martin DL, Weatherly DB, Laucella SA, Cabinian MA, Crim MT, Sullivan S, Heiges M, Craven SH, Rosenberg CS, Collins MH, Sette A, Postan M, Tarleton RL. CD8+ T-Cell responses to Trypanosoma cruzi are highly focused on strain-variant trans-sialidase epitopes. PLoS Pathog. 2006 Aug; 2(8):e77. PMID: 16879036; PMCID: PMC1526708.
      276. 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 Jul 12; 7:341. PMID: 16836764; PMCID: PMC1534061.
      277. Tscharke DC, Woo WP, Sakala IG, Sidney J, Sette A, Moss DJ, Bennink JR, Karupiah G, Yewdell JW. Poxvirus CD8+ T-cell determinants and cross-reactivity in BALB/c mice. J Virol. 2006 Jul; 80(13):6318-23. PMID: 16775319; PMCID: PMC1488955.
      278. 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.
        View in: PubMed
      279. Lichterfeld M, Williams KL, Mui SK, Shah SS, Mothe BR, Sette A, Kim A, Johnston MN, Burgett N, Frahm N, Cohen D, Brander C, Rosenberg ES, Walker BD, Altfeld M, Yu XG. T cell receptor cross-recognition of an HIV-1 CD8+ T cell epitope presented by closely related alleles from the HLA-A3 superfamily. Int Immunol. 2006 Jul; 18(7):1179-88. PMID: 16772368.
        View in: PubMed
      280. 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 Biotechnol. 2006 Jul; 24(7):817-9. PMID: 16767078.
        View in: PubMed
      281. 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.
      282. Rosa DS, Iwai LK, Tzelepis F, Bargieri DY, Medeiros MA, Soares IS, Sidney J, Sette A, Kalil J, Mello LE, Cunha-Neto E, Rodrigues MM. Immunogenicity of a recombinant protein containing the Plasmodium vivax vaccine candidate MSP1(19) and two human CD4+ T-cell epitopes administered to non-human primates (Callithrix jacchus jacchus). Microbes Infect. 2006 Jul; 8(8):2130-7. PMID: 16797207.
        View in: PubMed
      283. Guyver CJ, Copland DA, Calder CJ, Sette A, Sidney J, Dick AD, Nicholson LB. Mapping immune responses to mRBP-3 1-16 peptide with altered peptide ligands. Invest Ophthalmol Vis Sci. 2006 May; 47(5):2027-35. PMID: 16639012.
        View in: PubMed
      284. Zhu S, Udaka K, Sidney J, Sette A, Aoki-Kinoshita KF, Mamitsuka H. Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules. Bioinformatics. 2006 Jul 01; 22(13):1648-55. PMID: 16613909.
        View in: PubMed
      285. Bihl F, Frahm N, Di Giammarino L, Sidney J, John M, Yusim K, Woodberry T, Sango K, Hewitt HS, Henry L, Linde CH, Chisholm JV, Zaman TM, Pae E, Mallal S, Walker BD, Sette A, Korber BT, Heckerman D, Brander C. Impact of HLA-B alleles, epitope binding affinity, functional avidity, and viral coinfection on the immunodominance of virus-specific CTL responses. J Immunol. 2006 Apr 01; 176(7):4094-101. PMID: 16547245.
        View in: PubMed
      286. Bui HH, Sidney J, Dinh K, Southwood S, Newman MJ, Sette A. Predicting population coverage of T-cell epitope-based diagnostics and vaccines. BMC Bioinformatics. 2006 Mar 17; 7:153. PMID: 16545123; PMCID: PMC1513259.
      287. Smith CL, Mirza F, Pasquetto V, Tscharke DC, Palmowski MJ, Dunbar PR, Sette A, Harris AL, Cerundolo V. Immunodominance of poxviral-specific CTL in a human trial of recombinant-modified vaccinia Ankara. J Immunol. 2005 Dec 15; 175(12):8431-7. PMID: 16339586.
        View in: PubMed
      288. Loffredo JT, Sidney J, Piaskowski S, Szymanski A, Furlott J, Rudersdorf R, Reed J, Peters B, Hickman-Miller 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 01; 175(9):5986-97. PMID: 16237093.
        View in: PubMed
      289. 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.
        View in: PubMed
      290. 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; PMCID: PMC1287064.
      291. 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.
      292. Schulze zur Wiesch J, Lauer GM, Day CL, Kim AY, Ouchi K, Duncan JE, Wurcel AG, Timm J, Jones AM, Mothe B, Allen TM, McGovern B, Lewis-Ximenez L, Sidney J, Sette A, Chung RT, Walker BD. Broad repertoire of the CD4+ Th cell response in spontaneously controlled hepatitis C virus infection includes dominant and highly promiscuous epitopes. J Immunol. 2005 Sep 15; 175(6):3603-13. PMID: 16148104.
        View in: PubMed
      293. Xu Y, Sette A, Sidney J, Gendler SJ, Franco A. Tumor-associated carbohydrate antigens: a possible avenue for cancer prevention. Immunol Cell Biol. 2005 Aug; 83(4):440-8. PMID: 16033540.
        View in: PubMed
      294. Sidney J, Southwood S, Sette A. Classification of A1- and A24-supertype molecules by analysis of their MHC-peptide binding repertoires. Immunogenetics. 2005 Jul; 57(6):393-408. PMID: 16003466.
        View in: PubMed
      295. Cox AL, Mosbruger T, Mao Q, Liu Z, Wang XH, Yang HC, Sidney J, Sette A, Pardoll D, Thomas DL, Ray SC. Cellular immune selection with hepatitis C virus persistence in humans. J Exp Med. 2005 Jun 06; 201(11):1741-52. PMID: 15939790; PMCID: PMC2213263.
      296. Peters B, Sette A. Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinformatics. 2005 May 31; 6:132. PMID: 15927070; PMCID: PMC1173087.
      297. 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):326-36. PMID: 15895191; PMCID: PMC4780685.
      298. 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.
        View in: PubMed
      299. Boggiano C, Moya R, Pinilla C, Bihl F, Brander C, Sidney J, Sette A, Blondelle SE. Discovery and characterization of highly immunogenic and broadly recognized mimics of the HIV-1 CTL epitope Gag77-85. Eur J Immunol. 2005 May; 35(5):1428-37. PMID: 15789356.
        View in: PubMed
      300. Pinchuk I, Starcher BC, Livingston B, Tvninnereim A, Wu S, Appella E, Sidney J, Sette A, Wizel B. A CD8+ T cell heptaepitope minigene vaccine induces protective immunity against Chlamydia pneumoniae. J Immunol. 2005 May 01; 174(9):5729-39. PMID: 15843575.
        View in: PubMed
      301. Altfeld M, Allen TM, Kalife ET, Frahm N, Addo MM, Mothe BR, Rathod A, Reyor LL, Harlow J, Yu XG, Perkins B, Robinson LK, Sidney J, Alter G, Lichterfeld M, Sette A, Rosenberg ES, Goulder PJ, Brander C, Walker BD. The majority of currently circulating human immunodeficiency virus type 1 clade B viruses fail to prime cytotoxic T-lymphocyte responses against an otherwise immunodominant HLA-A2-restricted epitope: implications for vaccine design. J Virol. 2005 Apr; 79(8):5000-5. PMID: 15795285; PMCID: PMC1069570.
      302. Fonseca SG, Moins-Teisserenc H, Clave E, Ianni B, Nunes VL, Mady C, Iwai LK, Sette A, Sidney J, Marin ML, Goldberg AC, Guilherme L, Charron D, Toubert A, Kalil J, Cunha-Neto E. Identification of multiple HLA-A*0201-restricted cruzipain and FL-160 CD8+ epitopes recognized by T cells from chronically Trypanosoma cruzi-infected patients. Microbes Infect. 2005 Apr; 7(4):688-97. PMID: 15848276.
        View in: PubMed
      303. Tangri S, Mothé BR, Eisenbraun J, Sidney J, Southwood S, Briggs K, Zinckgraf J, Bilsel P, Newman M, Chesnut R, Licalsi C, Sette A. Rationally engineered therapeutic proteins with reduced immunogenicity. J Immunol. 2005 Mar 15; 174(6):3187-96. PMID: 15749848.
        View in: PubMed
      304. Sette A, Sidney J, Bui HH, del Guercio MF, Alexander J, Loffredo J, Watkins DI, Mothé BR. Characterization of the peptide-binding specificity of Mamu-A*11 results in the identification of SIV-derived epitopes and interspecies cross-reactivity. Immunogenetics. 2005 Apr; 57(1-2):53-68. PMID: 15747117.
        View in: PubMed
      305. 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; PMCID: PMC1065705.
      306. 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.
        View in: PubMed
      307. Tscharke DC, Karupiah G, Zhou J, Palmore T, Irvine KR, Haeryfar SM, Williams S, Sidney J, Sette A, Bennink JR, Yewdell JW. Identification of poxvirus CD8+ T cell determinants to enable rational design and characterization of smallpox vaccines. J Exp Med. 2005 Jan 03; 201(1):95-104. PMID: 15623576; PMCID: PMC2212779.
      308. Mizukoshi E, Sidney J, Livingston B, Ghany M, Hoofnagle JH, Sette A, Rehermann B. Cellular immune responses to the hepatitis B virus polymerase. J Immunol. 2004 Nov 01; 173(9):5863-71. PMID: 15494540.
        View in: PubMed
      309. Loffredo JT, Sidney J, Wojewoda C, Dodds E, Reynolds MR, Napoé G, Mothé BR, O'Connor DH, Wilson NA, Watkins DI, Sette A. Identification of seventeen new simian immunodeficiency virus-derived CD8+ T cell epitopes restricted by the high frequency molecule, Mamu-A*02, and potential escape from CTL recognition. J Immunol. 2004 Oct 15; 173(8):5064-76. PMID: 15470050.
        View in: PubMed
      310. McKinney DM, Skvoretz R, Livingston BD, Wilson CC, Anders M, Chesnut RW, Sette A, Essex M, Novitsky V, Newman MJ. Recognition of variant HIV-1 epitopes from diverse viral subtypes by vaccine-induced CTL. J Immunol. 2004 Aug 01; 173(3):1941-50. PMID: 15265928.
        View in: PubMed
      311. Allen TM, Altfeld M, Yu XG, O'Sullivan KM, Lichterfeld M, Le Gall S, John M, Mothe BR, Lee PK, Kalife ET, Cohen DE, Freedberg KA, Strick DA, Johnston MN, Sette A, Rosenberg ES, Mallal SA, Goulder PJ, Brander C, Walker BD. Selection, transmission, and reversion of an antigen-processing cytotoxic T-lymphocyte escape mutation in human immunodeficiency virus type 1 infection. J Virol. 2004 Jul; 78(13):7069-78. PMID: 15194783; PMCID: PMC421658.
      312. Alexander J, del Guercio MF, Frame B, Maewal A, Sette A, Nahm MH, Newman MJ. Development of experimental carbohydrate-conjugate vaccines composed of Streptococcus pneumoniae capsular polysaccharides and the universal helper T-lymphocyte epitope (PADRE). Vaccine. 2004 Jun 23; 22(19):2362-7. PMID: 15193395.
        View in: PubMed
      313. Kaufmann DE, Bailey PM, Sidney J, Wagner B, Norris PJ, Johnston MN, Cosimi LA, Addo MM, Lichterfeld M, Altfeld M, Frahm N, Brander C, Sette A, Walker BD, Rosenberg ES. Comprehensive analysis of human immunodeficiency virus type 1-specific CD4 responses reveals marked immunodominance of gag and nef and the presence of broadly recognized peptides. J Virol. 2004 May; 78(9):4463-77. PMID: 15078927; PMCID: PMC387674.
      314. Lou Q, Kelleher RJ, Sette A, Loyall J, Southwood S, Bankert RB, Bernstein SH. Germ line tumor-associated immunoglobulin VH region peptides provoke a tumor-specific immune response without altering the response potential of normal B cells. Blood. 2004 Aug 01; 104(3):752-9. PMID: 15054043.
        View in: PubMed
      315. Vertuani S, Sette A, Sidney J, Southwood S, Fikes J, Keogh E, Lindencrona JA, Ishioka G, Levitskaya J, Kiessling R. Improved immunogenicity of an immunodominant epitope of the HER-2/neu protooncogene by alterations of MHC contact residues. J Immunol. 2004 Mar 15; 172(6):3501-8. PMID: 15004150.
        View in: PubMed
      316. Friedrich TC, Dodds EJ, Yant LJ, Vojnov L, Rudersdorf R, Cullen C, Evans DT, Desrosiers RC, Mothé BR, Sidney J, Sette A, Kunstman K, Wolinsky S, Piatak M, Lifson J, Hughes AL, Wilson N, O'Connor DH, Watkins DI. Reversion of CTL escape-variant immunodeficiency viruses in vivo. Nat Med. 2004 Mar; 10(3):275-81. PMID: 14966520.
        View in: PubMed
      317. Sette A. The immune epitope database and analysis resource: from vision to blueprint. Genome Inform. 2004; 15(2):299. PMID: 16312048.
        View in: PubMed
      318. Petersen TR, Bettelli E, Sidney J, Sette A, Kuchroo V, Bäckström BT. Characterization of MHC- and TCR-binding residues of the myelin oligodendrocyte glycoprotein 38-51 peptide. Eur J Immunol. 2004 Jan; 34(1):165-73. PMID: 14971042.
        View in: PubMed
      319. Shoukry NH, Sidney J, Sette A, Walker CM. Conserved hierarchy of helper T cell responses in a chimpanzee during primary and secondary hepatitis C virus infections. J Immunol. 2004 Jan 01; 172(1):483-92. PMID: 14688358.
        View in: PubMed
      320. Sidney J, Southwood S, Pasquetto V, Sette A. Simultaneous prediction of binding capacity for multiple molecules of the HLA B44 supertype. J Immunol. 2003 Dec 01; 171(11):5964-74. PMID: 14634108.
        View in: PubMed
      321. Wilson CC, McKinney D, Anders M, MaWhinney S, Forster J, Crimi C, Southwood S, Sette A, Chesnut R, Newman MJ, Livingston BD. Development of a DNA vaccine designed to induce cytotoxic T lymphocyte responses to multiple conserved epitopes in HIV-1. J Immunol. 2003 Nov 15; 171(10):5611-23. PMID: 14607970.
        View in: PubMed
      322. van der Most RG, Murali-Krishna K, Lanier JG, Wherry EJ, Puglielli MT, Blattman JN, Sette A, Ahmed R. Changing immunodominance patterns in antiviral CD8 T-cell responses after loss of epitope presentation or chronic antigenic stimulation. Virology. 2003 Oct 10; 315(1):93-102. PMID: 14592762.
        View in: PubMed
      323. Peters B, Tong W, Sidney J, Sette A, Weng Z. Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules. Bioinformatics. 2003 Sep 22; 19(14):1765-72. PMID: 14512347.
        View in: PubMed
      324. Fikes JD, Sette A. Design of multi-epitope, analogue-based cancer vaccines. Expert Opin Biol Ther. 2003 Sep; 3(6):985-93. PMID: 12943457.
        View in: PubMed
      325. Iwai LK, Yoshida M, Sidney J, Shikanai-Yasuda MA, Goldberg AC, Juliano MA, Hammer J, Juliano L, Sette A, Kalil J, Travassos LR, Cunha-Neto E. In silico prediction of peptides binding to multiple HLA-DR molecules accurately identifies immunodominant epitopes from gp43 of Paracoccidioides brasiliensis frequently recognized in primary peripheral blood mononuclear cell responses from sensitized individuals. Mol Med. 2003 Sep-Dec; 9(9-12):209-19. PMID: 15208742; PMCID: PMC1430984.
      326. Sette A, Fikes J. Epitope-based vaccines: an update on epitope identification, vaccine design and delivery. Curr Opin Immunol. 2003 Aug; 15(4):461-70. PMID: 12900280.
        View in: PubMed
      327. Doolan DL, Southwood S, Freilich DA, Sidney J, Graber NL, Shatney L, Bebris L, Florens L, Dobano C, Witney AA, Appella E, Hoffman SL, Yates JR, Carucci DJ, Sette A. Identification of Plasmodium falciparum antigens by antigenic analysis of genomic and proteomic data. Proc Natl Acad Sci U S A. 2003 Aug 19; 100(17):9952-7. PMID: 12886016; PMCID: PMC187898.
      328. Hill JA, Southwood S, Sette A, Jevnikar AM, Bell DA, Cairns E. Cutting edge: the conversion of arginine to citrulline allows for a high-affinity peptide interaction with the rheumatoid arthritis-associated HLA-DRB1*0401 MHC class II molecule. J Immunol. 2003 Jul 15; 171(2):538-41. PMID: 12847215.
        View in: PubMed
      329. Maverakis E, Beech J, Stevens DB, Ametani A, Brossay L, van den Elzen P, Mendoza R, Thai Q, Macias LH, Ethell D, Campagnoni CW, Campagnoni AT, Sette A, Sercarz EE. Autoreactive T cells can be protected from tolerance induction through competition by flanking determinants for access to class II MHC. Proc Natl Acad Sci U S A. 2003 Apr 29; 100(9):5342-7. PMID: 12707414; PMCID: PMC154347.
      330. Gianfrani C, Troncone R, Mugione P, Cosentini E, De Pascale M, Faruolo C, Senger S, Terrazzano G, Southwood S, Auricchio S, Sette A. Celiac disease association with CD8+ T cell responses: identification of a novel gliadin-derived HLA-A2-restricted epitope. J Immunol. 2003 Mar 01; 170(5):2719-26. PMID: 12594302.
        View in: PubMed
      331. Tatsumi T, Kierstead LS, Ranieri E, Gesualdo L, Schena FP, Finke JH, Bukowski RM, Brusic V, Sidney J, Sette A, Logan TF, Kasamon YL, Slingluff CL, Kirkwood JM, Storkus WJ. MAGE-6 encodes HLA-DRbeta1*0401-presented epitopes recognized by CD4+ T cells from patients with melanoma or renal cell carcinoma. Clin Cancer Res. 2003 Mar; 9(3):947-54. PMID: 12631591.
        View in: PubMed
      332. Sette A, Sidney J, Livingston BD, Dzuris JL, Crimi C, Walker CM, Southwood S, Collins EJ, Hughes AL. Class I molecules with similar peptide-binding specificities are the result of both common ancestry and convergent evolution. Immunogenetics. 2003 Mar; 54(12):830-41. PMID: 12671733.
        View in: PubMed
      333. Touloukian CE, Leitner WW, Schnur RE, Robbins PF, Li Y, Southwood S, Sette A, Rosenberg SA, Restifo NP. Normal tissue depresses while tumor tissue enhances human T cell responses in vivo to a novel self/tumor melanoma antigen, OA1. J Immunol. 2003 Feb 01; 170(3):1579-85. PMID: 12538723; PMCID: PMC2241741.
      334. Malhotra U, Holte S, Zhu T, Delpit E, Huntsberry C, Sette A, Shankarappa R, Maenza J, Corey L, McElrath MJ. Early induction and maintenance of Env-specific T-helper cells following human immunodeficiency virus type 1 infection. J Virol. 2003 Feb; 77(4):2663-74. PMID: 12552005; PMCID: PMC141076.
      335. Alexander J, Oseroff C, Sidney J, Sette A. Derivation of HLA-B*0702 transgenic mice: functional CTL repertoire and recognition of human B*0702-restricted CTL epitopes. Hum Immunol. 2003 Feb; 64(2):211-23. PMID: 12559623.
        View in: PubMed
      336. Boritz E, Palmer BE, Livingston B, Sette A, Wilson CC. Diverse repertoire of HIV-1 p24-specific, IFN-gamma-producing CD4+ T cell clones following immune reconstitution on highly active antiretroviral therapy. J Immunol. 2003 Jan 15; 170(2):1106-16. PMID: 12517980.
        View in: PubMed
      337. Vogel TU, Friedrich TC, O'Connor DH, Rehrauer W, Dodds EJ, Hickman H, Hildebrand W, Sidney J, Sette A, Hughes A, Horton H, Vielhuber K, Rudersdorf R, De Souza IP, Reynolds MR, Allen TM, Wilson N, Watkins DI. Escape in one of two cytotoxic T-lymphocyte epitopes bound by a high-frequency major histocompatibility complex class I molecule, Mamu-A*02: a paradigm for virus evolution and persistence? J Virol. 2002 Nov; 76(22):11623-36. PMID: 12388723; PMCID: PMC136802.
      338. Sidney J, del Guercio MF, Southwood S, Sette A. The HLA molecules DQA1*0501/B1*0201 and DQA1*0301/B1*0302 share an extensive overlap in peptide binding specificity. J Immunol. 2002 Nov 01; 169(9):5098-108. PMID: 12391226.
        View in: PubMed
      339. Allen TM, Jing P, Calore B, Horton H, O'Connor DH, Hanke T, Piekarczyk M, Ruddersdorf R, Mothé BR, Emerson C, Wilson N, Lifson JD, Belyakov IM, Berzofsky JA, Wang C, Allison DB, Montefiori DC, Desrosiers RC, Wolinsky S, Kunstman KJ, Altman JD, Sette A, McMichael AJ, Watkins DI. Effects of cytotoxic T lymphocytes (CTL) directed against a single simian immunodeficiency virus (SIV) Gag CTL epitope on the course of SIVmac239 infection. J Virol. 2002 Oct; 76(20):10507-11. PMID: 12239328; PMCID: PMC136573.
      340. Kakimi K, Isogawa M, Chung J, Sette A, Chisari FV. Immunogenicity and tolerogenicity of hepatitis B virus structural and nonstructural proteins: implications for immunotherapy of persistent viral infections. J Virol. 2002 Sep; 76(17):8609-20. PMID: 12163580; PMCID: PMC136410.
      341. Wizel B, Starcher BC, Samten B, Chroneos Z, Barnes PF, Dzuris J, Higashimoto Y, Appella E, Sette A. Multiple Chlamydia pneumoniae antigens prime CD8+ Tc1 responses that inhibit intracellular growth of this vacuolar pathogen. J Immunol. 2002 Sep 01; 169(5):2524-35. PMID: 12193722.
        View in: PubMed
      342. He XL, Radu C, Sidney J, Sette A, Ward ES, Garcia KC. Structural snapshot of aberrant antigen presentation linked to autoimmunity: the immunodominant epitope of MBP complexed with I-Au. Immunity. 2002 Jul; 17(1):83-94. PMID: 12150894.
        View in: PubMed
      343. Mothé BR, Sidney J, Dzuris JL, Liebl ME, Fuenger S, Watkins DI, Sette A. Characterization of the peptide-binding specificity of Mamu-B*17 and identification of Mamu-B*17-restricted epitopes derived from simian immunodeficiency virus proteins. J Immunol. 2002 Jul 01; 169(1):210-9. PMID: 12077247.
        View in: PubMed
      344. Alexander J, Oseroff C, Dahlberg C, Qin M, Ishioka G, Beebe M, Fikes J, Newman M, Chesnut RW, Morton PA, Fok K, Appella E, Sette A. A decaepitope polypeptide primes for multiple CD8+ IFN-gamma and Th lymphocyte responses: evaluation of multiepitope polypeptides as a mode for vaccine delivery. J Immunol. 2002 Jun 15; 168(12):6189-98. PMID: 12055232.
        View in: PubMed
      345. Livingston B, Crimi C, Newman M, Higashimoto Y, Appella E, Sidney J, Sette A. A rational strategy to design multiepitope immunogens based on multiple Th lymphocyte epitopes. J Immunol. 2002 Jun 01; 168(11):5499-506. PMID: 12023344.
        View in: PubMed
      346. Newman MJ, Livingston B, McKinney DM, Chesnut RW, Sette A. T-lymphocyte epitope identification and their use in vaccine development for HIV-1. Front Biosci. 2002 Jun 01; 7:d1503-15. PMID: 12048179.
        View in: PubMed
      347. Sundberg EJ, Sawicki MW, Southwood S, Andersen PS, Sette A, Mariuzza RA. Minor structural changes in a mutated human melanoma antigen correspond to dramatically enhanced stimulation of a CD4+ tumor-infiltrating lymphocyte line. J Mol Biol. 2002 May 31; 319(2):449-61. PMID: 12051920.
        View in: PubMed
      348. Sette A, Keogh E, Ishioka G, Sidney J, Tangri S, Livingston B, McKinney D, Newman M, Chesnut R, Fikes J. Epitope identification and vaccine design for cancer immunotherapy. Curr Opin Investig Drugs. 2002 Jan; 3(1):132-9. PMID: 12054064.
        View in: PubMed
      349. Sette A, Oseroff C, Sidney J, Alexander J, Chesnut RW, Kakimi K, Guidotti LG, Chisari FV. Overcoming T cell tolerance to the hepatitis B virus surface antigen in hepatitis B virus-transgenic mice. J Immunol. 2001 Jan 15; 166(2):1389-97. PMID: 11145724.
        View in: PubMed