T-Cell Epitope Prediction: Rescaling Can Mask Biological Variation between MHC Molecules

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  1. Yewdell JW, Bennink JR (1999) Immunodominance in major histocompatibility complex class I-restricted T lymphocyte responses.. Annu Rev Immunol 17: 51-88.
  2. Assarsson E, Sidney J, Oseroff C, Pasquetto V, Bui HH (2007) A quantitative analysis of the variables affecting the repertoire of T cell specificities recognized after vaccinia virus infection.. J Immunol 178: 7890-7901.
  3. Larsen MV, Lundegaard C, Lamberth K, Buus S, Brunak S (2005) An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions.. Eur J Immunol 35: 2295-2303.
  4. Carrington M, Nelson GW, Martin MP, Kissner T, Vlahov D (1999) HLA and HIV-1: heterozygote advantage and B*35-Cw*04 disadvantage.. Science 283: 1748-1752.
  5. Bangham CRM, Osame M (2005) Cellular immune response to HTLV-1.. Oncogene 24: 6035-6046.
  6. Bui HH, Sidney J, Dinh K, Southwood S, Newman MJ (2006) Predicting population coverage of T-cell epitope-based diagnostics and vaccines.. BMC Bioinformatics 7: 153.
  7. Sette A, Fleri W, Peters B, Sathiamurthy M, Bui HH (2005) A roadmap for the immunomics of category A-C pathogens.. Immunity 22: 155-161.
  8. Sette A, Peters B (2007) Immune epitope mapping in the post-genomic era: lessons for vaccine development.. Curr Opin Immunol 19: 106-110.
  9. Snyder JT, Belyakov IM, Dzutsev A, Lemonnier F, Berzofsky JA (2004) Protection against lethal vaccinia virus challenge in HLA-A2 transgenic mice by immunization with a single CD8+ T-cell peptide epitope of vaccinia and variola viruses.. J Virol 78: 7052-7060.
  10. Drexler I, Staib C, Kastenmuller W, Stevanović S, Schmidt B (2003) Identification of vaccinia virus epitope-specific HLA-A*0201-restricted T cells and comparative analysis of smallpox vaccines.. Proc Natl Acad Sci U S A 100: 217-222.
  11. Oseroff C, Kos F, Bui HH, Peters B, Pasquetto V (2005) 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 102: 13980-13985.
  12. Pasquetto V, Bui HH, Giannino R, Banh C, Mirza F (2005) 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 175: 5504-5515.
  13. Wang M, Johansen B, Nissen MH, Thorn M, Kløverpris H (2007) Identification of an HLA-A*0201 restricted Bcl2-derived epitope expressed on tumors.. Cancer Lett 251: 86-95.
  14. Thorn M, Wang M, Kløverpris H, Schmidt EGW, Fomsgaard A (2007) Identification of a new hTERT-derived HLA-A*0201 restricted, naturally processed CTL epitope.. Cancer Immunol Immunother 56: 1755-1763.
  15. Wang M, Lamberth K, Harndahl M, Røder G, Stryhn A (2007) CTL epitopes for influenza A including the H5N1 bird flu; genome-, pathogen-, and HLA-wide screening.. Vaccine 25: 2823-2831.
  16. Moutaftsi M, Peters B, Pasquetto V, Tscharke DC, Sidney J (2006) A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus.. Nat Biotechnol 24: 817-819.
  17. Brumme ZL, Brumme CJ, Heckerman D, Korber BT, Daniels M (2007) Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1.. PLoS Pathog 3: e94doi:10.1371/journal.ppat.0030094.
  18. Borghans JAM, Mølgaard A, de Boer RJ, Keşmir C (2007) HLA Alleles Associated with Slow Progression to AIDS Truly Prefer to Present HIV-1 p24.. PLoS ONE 2: e920doi:10.1371/journal.pone.1000920.
  19. Rolland M, Heckerman D, Deng W, Rousseau CM, Coovadia H (2008) Broad and Gag-Biased HIV-1 Epitope Repertoires Are Associated with Lower Viral Loads.. PLoS ONE 3: e1424doi:10.1371/journal.pone.1001424.
  20. Rammensee H, Bachmann J, Emmerich NP, Bachor OA, Stevanović S (1999) SYFPEITHI: database for MHC ligands and peptide motifs.. Immunogenetics 50: 213-219.
  21. Nielsen M, Lundegaard C, Worning P, Hvid CS, Lamberth K (2004) Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach.. Bioinformatics 20: 1388-1397.
  22. Bui HH, Sidney J, Peters B, Sathiamurthy M, Sinichi A (2005) Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications.. Immunogenetics 57: 304-314.
  23. Peters B, Sette A (2005) Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method.. BMC Bioinformatics 6: 132.
  24. Heckerman D, Kadie C, Listgarten J (2007) Leveraging information across HLA alleles/supertypes improves epitope prediction.. J Comput Biol 14: 736-746.
  25. Buus S, Lauemøller SL, Worning P, Kesmir C, Frimurer T (2003) Sensitive quantitative predictions of peptide-MHC binding by a ‘Query by Committee’ artificial neural network approach.. Tissue Antigens 62: 378-384.
  26. Nielsen M, Lundegaard C, Worning P, Lauemøller SL, Lamberth K (2003) Reliable prediction of T-cell epitopes using neural networks with novel sequence representations.. Protein Sci 12: 1007-1017.
  27. Peters B, Bui HH, Sidney J, Weng Z, Loffredo JT (2005) A computational resource for the prediction of peptide binding to Indian rhesus macaque MHC class I molecules.. Vaccine 23: 5212-5224.
  28. Sturniolo T, Bono E, Ding J, Raddrizzani L, Tuereci O (1999) Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices.. Nat Biotechnol 17: 555-561.
  29. George AJT, Stark J, Chan C (2005) Understanding specificity and sensitivity of T-cell recognition.. Trends Immunol 26: 653-659.
  30. Elliott T (2006) The ‘chop-and-change’ of MHC class I assembly.. Nat Immunol 7: 7-9.
  31. Williams AP, Peh CA, Purcell AW, McCluskey J, Elliott T (2002) Optimization of the MHC class I peptide cargo is dependent on tapasin.. Immunity 16: 509-520.
  32. Sette A, Sidney J (1999) Nine major HLA class I supertypes account for the vast preponderance of HLA-A and -B polymorphism.. Immunogenetics 50: 201-212.
  33. Korber BTM, Brander C, Haynes BF, Koup R, Moore JP (2005) . HIV Molecular Immunology 2005Los Alamos National Laboratory, Theoretical Biology and Biophysics. Los Alamos, New Mexico.
  34. Peters B, Bui HH, Frankild S, Nielson M, Lundegaard C (2006) A community resource benchmarking predictions of peptide binding to MHC-I molecules.. PLoS Comput Biol 2: e65doi:10.1371/journal.pcbi.0020065.
  35. Larsen M, Lundegaard C, Lamberth K, Buus S, Lund O (2007) Large-Scale validation of methods for cytotoxic T-lymphocyte epitope prediction.. BMC Bioinformatics 8: 424.
  36. Engelhard VH (1994) Structure of peptides associated with class I and class II MHC molecules.. Annu Rev Immunol 12: 181-207.
  37. Frahm N, Yusim K, Suscovich TJ, Adams S, Sidney J (2007) Extensive HLA class I allele promiscuity among viral CTL epitopes.. Eur J Immunol 37: 2419-2433.
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