Heeney JL: Zoonotic viral diseases and the frontier of early diagnosis, control and prevention. J Intern Med. 2006, 260: 399-408. 10.1111/j.1365-2796.2006.01711.x.
CAS
PubMed
Google Scholar
White PJ, Norman RA, Trout RC, Gould EA, Hudson PJ: The emergence of rabbit haemorrhagic disease virus: will a non-pathogenic strain protect the UK?. Philos Trans R Soc Lond B Biol Sci. 2001, 356: 1087-1095. 10.1098/rstb.2001.0897.
PubMed Central
CAS
PubMed
Google Scholar
Perlman S, Netland J: Coronaviruses post-SARS: update on replication and pathogenesis. Nat Rev Microbiol. 2009, 7: 439-450. 10.1038/nrmicro2147.
PubMed Central
CAS
PubMed
Google Scholar
de Wit E, Kawaoka Y, de Jong MD, Fouchier RAM: Pathogenicity of highly pathogenic avian influenza virus in mammals. Vaccine. 2008, 26 (Suppl 4): D54-D58. 10.1016/j.vaccine.2008.07.072.
PubMed Central
CAS
PubMed
Google Scholar
Lister P, Reynolds F, Parslow R, Chan A, Cooper M, Plunkett A, Riphagen S, Peters M: Swine-origin influenza virus H1N1, seasonal influenza virus, and critical illness in children. Lancet. 2009, 374: 605-607. 10.1016/S0140-6736(09)61512-9.
PubMed
Google Scholar
Boni MF, Manh BH, Thai PQ, Farrar J, Hien TT, Hien NT, Kinh NV, Horby P: Modelling the progression of pandemic influenza A (H1N1) in Vietnam and the opportunities for reassortment with other influenza viruses. BMC Med. 2009, 7: 43-10.1186/1741-7015-7-43.
PubMed Central
PubMed
Google Scholar
Akira S, Uematsu S, Takeuchi O: Pathogen recognition and innate immunity. Cell. 2006, 124: 783-801. 10.1016/j.cell.2006.02.015.
CAS
PubMed
Google Scholar
Ellis RW: New technologies for making vaccines. Vaccine. 1999, 17: 1596-1604. 10.1016/S0264-410X(98)00416-2.
CAS
PubMed
Google Scholar
Hutchings CL, Gilbert SC, Hill AV, Moore AC: Novel protein and poxvirus-based vaccine combinations for simultaneous induction of humoral and cell-mediated immunity. J Immunol. 2005, 175: 599-606.
CAS
PubMed
Google Scholar
Janeway C: . Immunobiology : the immune system in health and disease. 2005, New York: Garland Science
Google Scholar
Loureiroa J, Ploegha HL: Antigen Presentation and the Ubiquitin-Proteasome System in Host–Pathogen Interactions. Advances in Immunology. 2006, 92: 225-305. full_text.
Google Scholar
Rock KL, Gramm C, Rothstein L, Clark K, Stein R, Dick L, Hwang D, Goldberg AL: Inhibitors of the proteasome block the degradation of most cell proteins and the generation of peptides presented on MHC class I molecules. Cell. 1994, 78: 761-771. 10.1016/S0092-8674(94)90462-6.
CAS
PubMed
Google Scholar
Kelly A, Powis SH, Kerr LA, Mockridge I, Elliott T, Bastin J, Uchanska-Ziegler B, Ziegler A, Trowsdale J, Townsend A: Assembly and function of the two ABC transporter proteins encoded in the human major histocompatibility complex. 1992
Google Scholar
Lautscham G, Rickinson A, Blake N: TAP-independent antigen presentation on MHC class I molecules: Lessons from Epstein--Barr virus. Microbes and Infection. 2003, 5: 291-299. 10.1016/S1286-4579(03)00031-5.
CAS
PubMed
Google Scholar
Hansen TH, Bouvier M: MHC class I antigen presentation: learning from viral evasion strategies. Nat Rev Immunol. 2009, 9: 503-513. 10.1038/nri2575.
CAS
PubMed
Google Scholar
Seliger B, Ritz U, Abele R, Bock M, Tampé R, Sutter G, Drexler I, Huber C, Ferrone S: Immune escape of melanoma: first evidence of structural alterations in two distinct components of the MHC class I antigen processing pathway. Cancer Res. 2001, 61: 8647-8650.
CAS
PubMed
Google Scholar
Larsen MV, Nielsen M, Weinzierl A, Lund O: TAP-Independent MHC Class I Presentation. Current Immunology Reviews. 2006, 2: 233-245. 10.2174/157339506778018550.
CAS
Google Scholar
Stoltze L, Schirle M, Schwarz G, Schroter C, Thompson MW, Hersh LB, Kalbacher H, Stevanovic S, Rammensee HG, Schild H: Two new proteases in the MHC class I processing pathway. Nat. Immunol. 2000, 1: 413-418. 10.1038/80852.
CAS
PubMed
Google Scholar
Zhang GL, Petrovsky N, Kwoh CK, August JT, Brusic V: PRED(TAP): a system for prediction of peptide binding to the human transporter associated with antigen processing. Immunome Res. 2006, 2: 3-10.1186/1745-7580-2-3.
PubMed Central
PubMed
Google Scholar
Chen M, Bouvier M: Analysis of interactions in a tapasin/class I complex provides a mechanism for peptide selection. EMBO J. 2007, 26: 1681-1690. 10.1038/sj.emboj.7601624.
PubMed Central
CAS
PubMed
Google Scholar
Schoenhals GJ, Krishna RM, Grandea AG: Retention of empty MHC class I molecules by tapasin is essential to reconstitute antigen presentation in invertebrate cells. EMBO J. 1999, 18: 743-10.1093/emboj/18.3.743. others
PubMed Central
CAS
PubMed
Google Scholar
Yewdell JW, Bennink JR: Immunodominance in major histocompatibility complex class I-restricted T lymphocyte responses. Annu Rev Immunol. 1999, 17: 51-88. 10.1146/annurev.immunol.17.1.51.
CAS
PubMed
Google Scholar
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, 24: 817-819. 10.1038/nbt1215.
CAS
PubMed
Google Scholar
Burrows SR, Rossjohn J, McCluskey J: Have we cut ourselves too short in mapping CTL epitopes?. Trends Immunol. 2006, 27: 11-16. 10.1016/j.it.2005.11.001.
CAS
PubMed
Google Scholar
Rammensee H, Bachmann J, Emmerich NP, Bachor OA, Stevanovic S: SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics. 1999, 50: 213-219. 10.1007/s002510050595.
CAS
PubMed
Google Scholar
Falk K, Rotzschke O, Rammensee HG: Cellular peptide composition governed by major histocompatibility complex class I molecules. Nature. 1990, 348: 248-251. 10.1038/348248a0.
CAS
PubMed
Google Scholar
Kondo A, Sidney J, Southwood S, del Guercio MF, Appella E, Sakamoto H, Grey HM, Celis E, Chesnut RW, Kubo RT, Sette A: Two distinct HLA-A*0101-specific submotifs illustrate alternative peptide binding modes. Immunogenetics. 1997, 45: 249-258. 10.1007/s002510050200.
CAS
PubMed
Google Scholar
Kubo RT, Sette A, Grey HM, Appella E, Sakaguchi K, Zhu NZ, Arnott D, Sherman N, Shabanowitz J, Michel H: Definition of specific peptide motifs for four major HLA-A alleles. J Immunol. 1994, 152: 3913-3924.
CAS
PubMed
Google Scholar
Pamer EG, Davis CE, So M: Expression and deletion analysis of the Trypanosoma brucei rhodesiense cysteine protease in Escherichia coli. Infect Immun. 1991, 59: 1074-1078.
PubMed Central
CAS
PubMed
Google Scholar
Rotzschke O, Falk K, Stevanovic S, Jung G, Walden P, Rammensee HG: Exact prediction of a natural T cell epitope. Eur J Immunol. 1991, 21: 2891-2894. 10.1002/eji.1830211136.
CAS
PubMed
Google Scholar
Sette A, Buus S, Appella E, Smith JA, Chesnut R, Miles C, Colon SM, Grey HM: Prediction of major histocompatibility complex binding regions of protein antigens by sequence pattern analysis. Proc Natl Acad Sci U S A. 1989, 86: 3296-3300. 10.1073/pnas.86.9.3296.
PubMed Central
CAS
PubMed
Google Scholar
Meister GE, Roberts CG, Berzofsky JA, De Groot AS: Two novel T cell epitope prediction algorithms based on MHC-binding motifs; comparison of predicted and published epitopes from Mycobacterium tuberculosis and HIV protein sequences. Vaccine. 1995, 13: 581-591. 10.1016/0264-410X(94)00014-E.
CAS
PubMed
Google Scholar
Parker KC, Bednarek MA, Coligan JE: Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains. J Immunol. 1994, 152: 163-175.
CAS
PubMed
Google Scholar
Stryhn A, Pedersen LO, Romme T, Holm CB, Holm A, Buus S: Peptide binding specificity of major histocompatibility complex class I resolved into an array of apparently independent subspecificities: quantitation by peptide libraries and improved prediction of binding. Eur J Immunol. 1996, 26: 1911-1918. 10.1002/eji.1830260836.
CAS
PubMed
Google Scholar
Schafer JR, Jesdale BM, George JA, Kouttab NM, De Groot AS: Prediction of well-conserved HIV-1 ligands using a matrix-based algorithm, EpiMatrix. Vaccine. 1998, 16: 1880-1884. 10.1016/S0264-410X(98)00173-X.
CAS
PubMed
Google Scholar
Rammensee HG, Bachmann J, Stevanovic S: . MHC ligands and Peptide Motifs. 1997, New York: Chapman & Hall
Google Scholar
Reche PA, Glutting JP, Reinherz EL: Prediction of MHC class I binding peptides using profile motifs. Hum Immunol. 2002, 63: 701-709. 10.1016/S0198-8859(02)00432-9.
CAS
PubMed
Google Scholar
Nielsen M, Lundegaard C, Worning P, Hvid CS, Lamberth K, Buus S, Brunak S, Lund O: Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. Bioinformatics. 2004, 20: 1388-1397. 10.1093/bioinformatics/bth100.
CAS
PubMed
Google Scholar
Peters B, Sette A: Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinformatics. 2005, 6: 132-10.1186/1471-2105-6-132.
PubMed Central
PubMed
Google Scholar
Bui HH, Sidney J, Peters B, Sathiamurthy M, Sinichi A, Purton KA, Mothe BR, Chisari FV, Watkins DI, Sette A: Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications. Immunogenetics. 2005, 57: 304-314. 10.1007/s00251-005-0798-y.
CAS
PubMed
Google Scholar
Lin HH, Ray S, Tongchusak S, Reinherz EL, Brusic V: Evaluation of MHC class I peptide binding prediction servers: applications for vaccine research. BMC Immunol. 2008, 9: 8-10.1186/1471-2172-9-8.
PubMed Central
PubMed
Google Scholar
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, 2: e65-10.1371/journal.pcbi.0020065.
PubMed Central
PubMed
Google Scholar
Adams HP, Koziol JA: Prediction of binding to MHC class I molecules. J Immunol Methods. 1995, 185: 181-190. 10.1016/0022-1759(95)00111-M.
CAS
PubMed
Google Scholar
Brusic V, Rudy G, Harrison LC: Prediction of MHC binding peptides using artificial neural networks. Complex systems: mechanism of adaptation. Edited by: Stonier RJ, Yu XS. 1994, Amsterdam: IOS Press, 253-260.
Google Scholar
Buus S, Lauemoller SL, Worning P, Kesmir C, Frimurer T, Corbet S, Fomsgaard A, Hilden J, Holm A, Brunak S: Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach. Tissue Antigens. 2003, 62: 378-384. 10.1034/j.1399-0039.2003.00112.x.
CAS
PubMed
Google Scholar
Gulukota K, Sidney J, Sette A, DeLisi C: Two complementary methods for predicting peptides binding major histocompatibility complex molecules. J Mol Biol. 1997, 267: 1258-1267. 10.1006/jmbi.1997.0937.
CAS
PubMed
Google Scholar
Nielsen M, Lundegaard C, Worning P, Lauemøller SL, Lamberth K, Buus S, Brunak S, Lund O: Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci. 2003, 12: 1007-1017. 10.1110/ps.0239403.
PubMed Central
CAS
PubMed
Google Scholar
Dönnes P, Kohlbacher O: SVMHC: a server for prediction of MHC-binding peptides. Nucleic Acids Res. 2006, 34: W194-W197. 10.1093/nar/gkl284.
PubMed Central
PubMed
Google Scholar
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, 38: D854-D862. 10.1093/nar/gkp1004.
PubMed Central
CAS
PubMed
Google Scholar
Sette A, Fleri W, Peters B, Sathiamurthy M, Bui HH, Wilson S: A roadmap for the immunomics of category A-C pathogens. Immunity. 2005, 22: 155-161. 10.1016/j.immuni.2005.01.009.
CAS
PubMed
Google Scholar
Lundegaard C, Lund O, Buus S, Nielsen M: Major histocompatibility complex class I binding predictions as a tool in epitope discovery. Immunology. 2010, 130: 309-318. 10.1111/j.1365-2567.2010.03300.x.
PubMed Central
CAS
PubMed
Google Scholar
Lundegaard C, Lamberth K, Harndahl M, Buus S, Lund O, Nielsen M: NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11. Nucleic Acids Res. 2008, 36: W509-W512. 10.1093/nar/gkn202.
PubMed Central
CAS
PubMed
Google Scholar
Lundegaard C, Lund O, Kesmir C, Brunak S, Nielsen M: Modeling the adaptive immune system: predictions and simulations. Bioinformatics. 2007, 23: 3265-3275. 10.1093/bioinformatics/btm471.
CAS
PubMed
Google Scholar
Toussaint NC, Kohlbacher O: Towards in silico design of epitope-based vaccines. Expert Opin. Drug Discov. 2009, 4697-
Google Scholar
Lundegaard C, Lund O, Nielsen M: Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers. Bioinformatics. 2008, 24: 1397-1398. 10.1093/bioinformatics/btn128.
CAS
PubMed
Google Scholar
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, 4: e1000048-10.1371/journal.pcbi.1000048.
PubMed Central
PubMed
Google Scholar
Sidney J, del Guercio MF, Southwood S, Engelhard VH, Appella E, Rammensee HG, Falk K, Rötzschke O, Takiguchi M, Kubo RT: Several HLA alleles share overlapping peptide specificities. J Immunol. 1995, 154: 247-259.
CAS
PubMed
Google Scholar
Lund O, Nielsen M, Kesmir C, Petersen AG, Lundegaard C, Worning P, Sylvester-Hvid C, Lamberth K, Røder G, Justesen S, Buus S, Brunak S: Definition of supertypes for HLA molecules using clustering of specificity matrices. Immunogenetics. 2004, 55: 797-810. 10.1007/s00251-004-0647-4.
CAS
PubMed
Google Scholar
Doytchinova IA, Guan P, Flower DR: Identifiying human MHC supertypes using bioinformatic methods. J Immunol. 2004, 172: 4314-4323.
CAS
PubMed
Google Scholar
Reche PA, Reinherz EL: Definition of MHC supertypes through clustering of MHC peptide binding repertoires. Artificial Immune Systems, Proceedings. 2004, Berlin: Springer Verlag, 189-196. full_text.
Google Scholar
Reche PA, Reinherz EL: Definition of MHC supertypes through clustering of MHC peptide-binding repertoires. Methods Mol Biol. 2007, 409: 163-173. full_text.
CAS
PubMed
Google Scholar
Sidney J, Grey HM, Southwood S, Celis E, Wentworth PA, del Guercio MF, Kubo RT, Chesnut RW, Sette A: Definition of an HLA-A3-like supermotif demonstrates the overlapping peptide-binding repertoires of common HLA molecules. Hum Immunol. 1996, 45: 79-93. 10.1016/0198-8859(95)00173-5.
CAS
PubMed
Google Scholar
Sidney J, Peters B, Frahm N, Brander C, Sette A: HLA class I supertypes: a revised and updated classification. BMC Immunol. 2008, 9: 1-10.1186/1471-2172-9-1.
PubMed Central
PubMed
Google Scholar
Buus S, Stryhn A, Winther K, Kirkby N, Pedersen LO: Receptor-ligand interactions measured by an improved spun column chromatography technique. A high efficiency and high throughput size separation method. Biochim Biophys Acta. 1995, 1243: 453-460.
PubMed
Google Scholar
Harndahl M, Justesen S, Lamberth K, Røder G, Nielsen M, Buus S: Peptide binding to HLA class I molecules: homogenous, high-throughput screening, and affinity assays. J Biomol Screen. 2009, 14: 173-180. 10.1177/1087057108329453.
CAS
PubMed
Google Scholar
Sidney J, Southwood S, Oseroff C, del Guercio MF, Sette A, Grey HM: Measurement of MHC/peptide interactions by gel filtration. Curr Protoc Immunol. 2001, Chapter 18:Unit 18.3
Google Scholar
Sylvester-Hvid C, Kristensen N, Blicher T, Ferre H, Lauemoller SL, Wolf XA, Lamberth K, Nissen MH, Pedersen LO, Buus S: Establishment of a quantitative ELISA capable of determining peptide-MHC class I interaction. Tissue Antigens. 2002, 59: 251-258. 10.1034/j.1399-0039.2002.590402.x.
CAS
PubMed
Google Scholar
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, 36: W513-W518. 10.1093/nar/gkn254.
PubMed Central
CAS
PubMed
Google Scholar
Zhang GL, Khan AM, Srinivasan KN, August JT, Brusic V: MULTIPRED: a computational system for prediction of promiscuous HLA binding peptides. Nucleic Acids Res. 2005, 33: W172-W179. 10.1093/nar/gki452.
PubMed Central
CAS
PubMed
Google Scholar
Jacob L, Vert JP: Efficient peptide-MHC-I binding prediction for alleles with few known binders. Bioinformatics. 2008, 24: 358-366. 10.1093/bioinformatics/btm611.
CAS
PubMed
Google Scholar
Jojic N, Reyes-Gomez M, Heckerman D, Kadie C, Schueler-Furman O: Learning MHC I--peptide binding. Bioinformatics. 2006, 22: e227-e235. 10.1093/bioinformatics/btl255.
CAS
PubMed
Google Scholar
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, 2: e796-10.1371/journal.pone.0000796.
PubMed Central
PubMed
Google Scholar
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, 61: 1-13. 10.1007/s00251-008-0341-z.
PubMed Central
CAS
PubMed
Google Scholar
Zhang H, Lundegaard C, Nielsen M: Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods. Bioinformatics. 2009, 25: 83-89. 10.1093/bioinformatics/btn579.
PubMed Central
PubMed
Google Scholar
Kloetzel PM: The proteasome and MHC class I antigen processing. Biochim Biophys Acta. 2004, 1695: 225-233. 10.1016/j.bbamcr.2004.10.004.
CAS
PubMed
Google Scholar
Kloetzel PM: Generation of major histocompatibility complex class I antigens: functional interplay between proteasomes and TPPII. Nat Immunol. 2004, 5: 661-669. 10.1038/ni1090.
CAS
PubMed
Google Scholar
Nielsen M, Lundegaard C, Lund O, Keşmir C: The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics. 2005, 57: 33-41. 10.1007/s00251-005-0781-7.
CAS
PubMed
Google Scholar
Holzhutter HG, Frommel C, Kloetzel PM: A theoretical approach towards the identification of cleavage-determining amino acid motifs of the 20 S proteasome. J. Mol. Biol. 1999, 286: 1251-1265. 10.1006/jmbi.1998.2530.
CAS
PubMed
Google Scholar
Holzhutter HG, Kloetzel PM: A kinetic model of vertebrate 20S proteasome accounting for the generation of major proteolytic fragments from oligomeric peptide substrates. Biophys J. 2000, 79: 1196-1205. 10.1016/S0006-3495(00)76374-0.
PubMed Central
CAS
PubMed
Google Scholar
Kuttler C, Nussbaum AK, Dick TP, Rammensee HG, Schild H, Hadeler KP: An Algorithm for the Prediction of Proteasomal Cleavages. J. Mol. Biol. 2000, 298: 417-429. 10.1006/jmbi.2000.3683.
CAS
PubMed
Google Scholar
Nussbaum AK, Kuttler C, Hadeler KP, Rammensee HG, Schild H: PAProC: a prediction algorithm for proteasomal cleavages available on the WWW. Immunogenetics. 2001, 53: 87-94. 10.1007/s002510100300.
CAS
PubMed
Google Scholar
Tenzer S, Stoltze L, Schonfisch B, Dengjel J, Muller M, Stevanovic S, Rammensee HG, Schild H: Quantitative analysis of prion-protein degradation by constitutive and immuno-20S proteasomes indicates differences correlated with disease susceptibility. J Immunol. 2004, 172: 1083-1091.
CAS
PubMed
Google Scholar
Kesmir C, Nussbaum AK, Schild H, Detours V, Brunak S: Prediction of proteasome cleavage motifs by neural networks. Protein Eng. 2002, 15: 287-296. 10.1093/protein/15.4.287.
CAS
PubMed
Google Scholar
Saxová P, Buus S, Brunak S, Kesmir C: Predicting proteasomal cleavage sites: a comparison of available methods. Int. Immunol. 2003, 15: 781-787. 10.1093/intimm/dxg084.
PubMed
Google Scholar
Bhasin M, Raghava GPS: Pcleavage: an SVM based method for prediction of constitutive proteasome and immunoproteasome cleavage sites in antigenic sequences. Nucleic Acids Research. 2005, 33: W202-W207. 10.1093/nar/gki587.
PubMed Central
CAS
PubMed
Google Scholar
Liu T, Liu W, Song Z, Jiao C, Zhu M, Wang X: Computational prediction of the specificities of proteasome interaction with antigen protein. Cell Mol Immunol. 2009, 6: 135-142. 10.1038/cmi.2009.19.
PubMed Central
CAS
PubMed
Google Scholar
Hanley JA, McNeil BJ: The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology. 1982, 143: 29-36.
CAS
PubMed
Google Scholar
Ginodi I, Vider-Shalit T, Tsaban L, Louzoun Y: Precise score for the prediction of peptides cleaved by the proteasome. Bioinformatics. 2008, 24: 477-483. 10.1093/bioinformatics/btm616.
CAS
PubMed
Google Scholar
Daniel S, Brusic V, Caillat-Zucman S, Petrovsky N, Harrison L, Riganelli D, Sinigaglia F, Gallazzi F, Hammer J, van Endert PM: Relationship between peptide selectivities of human transporters associated with antigen processing and HLA class I molecules. J Immunol. 1998, 161: 617-624.
CAS
PubMed
Google Scholar
Fruci D, Niedermann G, Butler RH, van Endert PM: Efficient MHC class I-independent amino-terminal trimming of epitope precursor peptides in the endoplasmic reticulum. Immunity. 2001, 15: 467-476. 10.1016/S1074-7613(01)00203-5.
CAS
PubMed
Google Scholar
Peters B, Bulik S, Tampe R, Van Endert PM, Holzhütter HG: Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors. J Immunol. 2003, 171: 1741-1749.
CAS
PubMed
Google Scholar
Lafuente EM, Reche PA: Prediction of MHC-peptide binding: a systematic and comprehensive overview. Curr Pharm Des. 2009, 15: 3209-3220. 10.2174/138161209789105162.
CAS
PubMed
Google Scholar
Diez-Rivero CM, Chenlo B, Zuluaga P, Reche PA: Quantitative modeling of peptide binding to TAP using support vector machine. Proteins. 2010, 78: 63-72. 10.1002/prot.22535.
CAS
PubMed
Google Scholar
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, 28: 3977-3989. 10.1016/j.vaccine.2010.03.028.
PubMed Central
CAS
PubMed
Google Scholar
Lankat-Buttgereit B, Tampe R: The transporter associated with antigen processing TAP: structure and function. FEBS Lett. 1999, 464: 108-112. 10.1016/S0014-5793(99)01676-2.
CAS
PubMed
Google Scholar
Sieker F, Straatsma TP, Springer S, Zacharias M: Differential tapasin dependence of MHC class I molecules correlates with conformational changes upon peptide dissociation: a molecular dynamics simulation study. Mol Immunol. 2008, 45: 3714-3722. 10.1016/j.molimm.2008.06.009.
CAS
PubMed
Google Scholar
Lundegaard C, Nielsen M, Lund O: The validity of predicted T-cell epitopes. Trends Biotechnol. 2006, 24: 537-538. 10.1016/j.tibtech.2006.10.001.
CAS
PubMed
Google Scholar
Stranzl T, Larsen MV, Lundegaard C, Nielsen M: NetCTLpan: pan-specific MHC class I pathway epitope predictions. Immunogenetics. 2010, 62: 357-368. 10.1007/s00251-010-0441-4.
PubMed Central
CAS
PubMed
Google Scholar
Hakenberg J, Nussbaum AK, Schild H, Rammensee HG, Kuttler C, Holzhutter HG, Kloetzel PM, Kaufmann SH, Mollenkopf HJ: MAPPP: MHC class I antigenic peptide processing prediction. Appl Bioinformatics. 2003, 2: 155-158.
CAS
PubMed
Google Scholar
Larsen MV, Lundegaard C, Lamberth K, Buus S, Brunak S, Lund O, Nielsen M: 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. 2005, 35: 2295-2303. 10.1002/eji.200425811.
CAS
PubMed
Google Scholar
Tenzer S, Peters B, Bulik S, Schoor O, Lemmel C, Schatz MM, Kloetzel PM, Rammensee HG, Schild H, Holzhutter HG: Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class I binding. Cell Mol Life Sci. 2005, 62: 1025-1037. 10.1007/s00018-005-4528-2.
CAS
PubMed
Google Scholar
Doytchinova IA, Guan P, Flower DR: EpiJen: a server for multistep T cell epitope prediction. BMC Bioinformatics. 2006, 7: 131-10.1186/1471-2105-7-131.
PubMed Central
PubMed
Google Scholar
Donnes P, Kohlbacher O: Integrated modeling of the major events in the MHC class I antigen processing pathway. Protein Sci. 2005, 14: 2132-2140. 10.1110/ps.051352405.
PubMed Central
PubMed
Google Scholar
Larsen MV, Lundegaard C, Lamberth K, Buus S, Lund O, Nielsen M: Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinformatics. 2007, 8: 424-10.1186/1471-2105-8-424.
PubMed Central
PubMed
Google Scholar
Perez CL, Larsen MV, Gustafsson R, Norstrom MM, Atlas A, Nixon DF, Nielsen M, Lund O, Karlsson AC: Broadly immunogenic HLA class I supertype-restricted elite CTL epitopes recognized in a diverse population infected with different HIV-1 subtypes. J Immunol. 2008, 180: 5092-5100.
CAS
PubMed
Google Scholar
Wang M, Lamberth K, Harndahl M, Røder G, Stryhn A, Larsen MV, Nielsen M, Lundegaard C, Tang ST, Dziegiel MH, Rosenkvist J, Pedersen AE, Buus S, Claesson MH, Lund O: CTL epitopes for influenza A including the H5N1 bird flu; genome-, pathogen-, and HLA-wide screening. Vaccine. 2007, 25: 2823-2831. 10.1016/j.vaccine.2006.12.038.
CAS
PubMed
Google Scholar
Cohen S: Cell mediated immunity and the inflammatory system. Human pathology. 1976, 7: 249-10.1016/S0046-8177(76)80036-6.
CAS
PubMed
Google Scholar
Castellino F, Zhong G, Germain RN: Antigen presentation by MHC class II molecules: invariant chain function, protein trafficking, and the molecular basis of diverse determinant capture. Hum Immunol. 1997, 54: 159-169. 10.1016/S0198-8859(97)00078-5.
CAS
PubMed
Google Scholar
Nielsen M, Lund O, Buus S, Lundegaard C: MHC Class II epitope predictive algorithms. Immunology. 2010, 130: 319-328. 10.1111/j.1365-2567.2010.03268.x.
PubMed Central
CAS
PubMed
Google Scholar
Stern LJ, Brown JH, Jardetzky TS, Gorga JC, Urban RG, Strominger JL, Wiley DC: Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide. Nature. 1994, 368: 215-221. 10.1038/368215a0.
CAS
PubMed
Google Scholar
Rudensky AY, Preston-Hurlburt P, Hong SC, Barlow A, Janeway CA: Sequence analysis of peptides bound to MHC class II molecules. Nature. 1991, 353: 622-627. 10.1038/353622a0.
CAS
PubMed
Google Scholar
Hammer J, Bono E, Gallazzi F, Belunis C, Nagy Z, Sinigaglia F: Precise prediction of major histocompatibility complex class II-peptide interaction based on peptide side chain scanning. J Exp Med. 1994, 180: 2353-2358. 10.1084/jem.180.6.2353.
CAS
PubMed
Google Scholar
Singh H, Raghava GP: ProPred: prediction of HLA-DR binding sites. Bioinformatics. 2001, 17: 1236-1237. 10.1093/bioinformatics/17.12.1236.
CAS
PubMed
Google Scholar
Bhasin M, Raghava GP: SVM based method for predicting HLA-DRB1*0401 binding peptides in an antigen sequence. Bioinformatics. 2004, 20: 421-423. 10.1093/bioinformatics/btg424.
CAS
PubMed
Google Scholar
Godkin AJ, Smith KJ, Willis A, Tejada-Simon MV, Zhang J, Elliott T, Hill AV: Naturally processed HLA class II peptides reveal highly conserved immunogenic flanking region sequence preferences that reflect antigen processing rather than peptide-MHC interactions. J Immunol. 2001, 166: 6720-6727.
CAS
PubMed
Google Scholar
Chang ST, Ghosh D, Kirschner DE, Linderman JJ: Peptide length-based prediction of peptide-MHC class II binding. Bioinformatics. 2006, 22: 2761-2767. 10.1093/bioinformatics/btl479.
CAS
PubMed
Google Scholar
Nielsen M, Lundegaard C, Lund O: Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinformatics. 2007, 8: 238-10.1186/1471-2105-8-238.
PubMed Central
PubMed
Google Scholar
Lin HH, Zhang GL, Tongchusak S, Reinherz EL, Brusic V: Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research. BMC Bioinformatics. 2008, 9 (Suppl 12): S22-10.1186/1471-2105-9-S12-S22.
PubMed Central
PubMed
Google Scholar
Nielsen M, Lund O: NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction. BMC Bioinformatics. 2009, 10: 296-10.1186/1471-2105-10-296.
PubMed Central
PubMed
Google Scholar
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, 4: e1000107-10.1371/journal.pcbi.1000107.
PubMed Central
PubMed
Google Scholar
Rosa DS, Ribeiro SP, Cunha-Neto E: CD4+ T cell epitope discovery and rational vaccine design. Arch Immunol Ther Exp (Warsz). 2010, 58: 121-130. 10.1007/s00005-010-0067-0.
CAS
Google Scholar
Mustafa AS: Th1 cell reactivity and HLA-DR binding prediction for promiscuous recognition of MPT63 (Rv1926c), a major secreted protein of Mycobacterium tuberculosis. Scand J Immunol. 2009, 69: 213-222. 10.1111/j.1365-3083.2008.02221.x.
CAS
PubMed
Google Scholar
Fischer W, Perkins S, Theiler J, Bhattacharya T, Yusim K, Funkhouser R, Kuiken C, Haynes B, Letvin NL, Walker BD, Hahn BH, Korber BT: Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variants. Nat Med. 2007, 13: 100-106. 10.1038/nm1461.
CAS
PubMed
Google Scholar
Toussaint NC, Dönnes P, Kohlbacher O: A mathematical framework for the selection of an optimal set of peptides for epitope-based vaccines. PLoS Comput Biol. 2008, 4: e1000246-10.1371/journal.pcbi.1000246.
PubMed Central
PubMed
Google Scholar
Toussaint NC, Kohlbacher O: OptiTope--a web server for the selection of an optimal set of peptides for epitope-based vaccines. Nucleic Acids Res. 2009, 37: W617-W622. 10.1093/nar/gkp293.
PubMed Central
CAS
PubMed
Google Scholar
Hildner K, Edelson BT, Purtha WE, Diamond M, Matsushita H, Kohyama M, Calderon B, Schraml BU, Unanue ER, Diamond MS: Batf3 deficiency reveals a critical role for CD8 alpha}+ dendritic cells in cytotoxic T cell immunity. Science. 2008, 322: 1097-10.1126/science.1164206. others
PubMed Central
CAS
PubMed
Google Scholar
Lamberth K, Røder G, Harndahl M, Nielsen M, Lundegaard C, Schafer-Nielsen C, Lund O, Buus S: The peptide-binding specificity of HLA-A*3001 demonstrates membership of the HLA-A3 supertype. Immunogenetics. 2008, 60: 633-643. 10.1007/s00251-008-0317-z.
CAS
PubMed
Google Scholar
Hoof I, Pérez CL, Buggert M, Gustafsson RK, Nielsen M, Lund O, Karlsson AC: Interdisciplinary Analysis of HIV-Specific CD8+ T Cell Responses against Variant Epitopes Reveals Restricted TCR Promiscuity. J Immunol. 2010
Google Scholar
Rapin N, Hoof I, Lund O, Nielsen M: MHC motif viewer. Immunogenetics. 2008, 60: 759-765. 10.1007/s00251-008-0330-2.
PubMed Central
CAS
PubMed
Google Scholar