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Volumn 5251 LNBI, Issue , 2008, Pages 210-221

Multiple instance learning allows MHC class II epitope predictions across alleles

Author keywords

[No Author keywords available]

Indexed keywords

AMINES; BIOINFORMATICS; DATA STRUCTURES; EDUCATION; IMMUNOLOGY; LEARNING SYSTEMS; PEPTIDES; PROTEINS; ROBOT LEARNING; STANDARDIZATION; TECHNICAL PRESENTATIONS;

EID: 56649091109     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-87361-7_18     Document Type: Conference Paper
Times cited : (25)

References (37)
  • 1
    • 0028003924 scopus 로고
    • MHC class II restricted tumor antigens and the role of CD4+ T cells in cancer immunotherapy
    • Topalian, S.L.: MHC class II restricted tumor antigens and the role of CD4+ T cells in cancer immunotherapy. Curr. Opin. Immunol. 6(5), 741-745 (1994)
    • (1994) Curr. Opin. Immunol , vol.6 , Issue.5 , pp. 741-745
    • Topalian, S.L.1
  • 2
    • 0037246882 scopus 로고    scopus 로고
    • IMGT/HLA and IMGT/MHC: Sequence databases for the study of the major histocompatibility complex
    • Robinson, J., Waller, M.J., Parham, P., Groot, N.d., et al.: IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex. Nucleic Acids Res. 31(1), 311-314 (2003)
    • (2003) Nucleic Acids Res , vol.31 , Issue.1 , pp. 311-314
    • Robinson, J.1    Waller, M.J.2    Parham, P.3    Groot, N.D.4
  • 3
    • 20944447214 scopus 로고    scopus 로고
    • The immune epitope database and analysis resource: From vision to blueprint
    • Peters, B., Sidney, J., Bourne, P., Bui, H.H., Buus, S., et al.: The immune epitope database and analysis resource: from vision to blueprint. PLoS Biol. 3(3), 91 (2005)
    • (2005) PLoS Biol , vol.3 , Issue.3 , pp. 91
    • Peters, B.1    Sidney, J.2    Bourne, P.3    Bui, H.H.4    Buus, S.5
  • 4
    • 21344466799 scopus 로고    scopus 로고
    • Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications
    • Bui, H.H., Sidney, J., Peters, B., Sathiamurthy, M., Asabe, S., et al.: Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications. Immunogenetics 57(5), 304-314 (2005)
    • (2005) Immunogenetics , vol.57 , Issue.5 , pp. 304-314
    • Bui, H.H.1    Sidney, J.2    Peters, B.3    Sathiamurthy, M.4    Asabe, S.5
  • 5
    • 34547778364 scopus 로고    scopus 로고
    • Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method
    • Nielsen, M., Lundegaard, C., Lund, O.: Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinformatics 8, 238 (2007)
    • (2007) BMC Bioinformatics , vol.8 , pp. 238
    • Nielsen, M.1    Lundegaard, C.2    Lund, O.3
  • 6
    • 0028985984 scopus 로고
    • MHC ligands and peptide motifs: First listing
    • Rammensee, H.G., Friede, T., Stevanović, S.: MHC ligands and peptide motifs: first listing. Immunogenetics 41(4), 178-228 (1995)
    • (1995) Immunogenetics , vol.41 , Issue.4 , pp. 178-228
    • Rammensee, H.G.1    Friede, T.2    Stevanović, S.3
  • 7
    • 5444249860 scopus 로고    scopus 로고
    • Enhancement to the RANKPEP resource for the prediction of peptide binding to MHC molecules using profiles
    • Reche, P.A., Glutting, J.P., Zhang, H., Reinherz, E.L.: Enhancement to the RANKPEP resource for the prediction of peptide binding to MHC molecules using profiles. Immunogenetics 56(6), 405-419 (2004)
    • (2004) Immunogenetics , vol.56 , Issue.6 , pp. 405-419
    • Reche, P.A.1    Glutting, J.P.2    Zhang, H.3    Reinherz, E.L.4
  • 8
    • 0036137241 scopus 로고    scopus 로고
    • ProPred: Prediction of HLA-DR binding sites
    • Singh, H., Raghava, G.P.: ProPred: prediction of HLA-DR binding sites. Bioinformatics 17(12), 1236-1237 (2001)
    • (2001) Bioinformatics , vol.17 , Issue.12 , pp. 1236-1237
    • Singh, H.1    Raghava, G.P.2
  • 9
    • 0033021020 scopus 로고    scopus 로고
    • Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices
    • Sturniolo, T., Bono, E., Ding, J., Raddrizzani, L., Tuereci, O., et al.: Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices. Nat. Biotechnol. 17(6), 555-561 (1999)
    • (1999) Nat. Biotechnol , vol.17 , Issue.6 , pp. 555-561
    • Sturniolo, T.1    Bono, E.2    Ding, J.3    Raddrizzani, L.4    Tuereci, O.5
  • 10
    • 2442499729 scopus 로고    scopus 로고
    • Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach
    • Nielsen, M., Lundegaard, C., Worning, P., Hvid, C.S., 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 20(9), 1388-1397 (2004)
    • (2004) Bioinformatics , vol.20 , Issue.9 , pp. 1388-1397
    • Nielsen, M.1    Lundegaard, C.2    Worning, P.3    Hvid, C.S.4    Lamberth, K.5    Buus, S.6    Brunak, S.7    Lund, O.8
  • 11
    • 0036399733 scopus 로고    scopus 로고
    • Hidden markov model-based prediction of antigenic peptides that interact with MHC class II molecules
    • Noguchi, H., Kato, R., Hanai, T., Matsubara, Y., Honda, H., Brusic, V., Kobayashi, T.: Hidden markov model-based prediction of antigenic peptides that interact with MHC class II molecules. J. Biosci. Bioeng. 94(3), 264-270 (2002)
    • (2002) J. Biosci. Bioeng , vol.94 , Issue.3 , pp. 264-270
    • Noguchi, H.1    Kato, R.2    Hanai, T.3    Matsubara, Y.4    Honda, H.5    Brusic, V.6    Kobayashi, T.7
  • 12
    • 24144463821 scopus 로고    scopus 로고
    • Prediction of MHC class II binders using the ant colony search strategy
    • Karpenko, O., Shi, J., Dai, Y.: Prediction of MHC class II binders using the ant colony search strategy. Artif. Intell. Med. 35(1-2), 147-156 (2005)
    • (2005) Artif. Intell. Med , vol.35 , Issue.1-2 , pp. 147-156
    • Karpenko, O.1    Shi, J.2    Dai, Y.3
  • 13
    • 0031825709 scopus 로고    scopus 로고
    • Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network
    • Brusic, V., Rudy, G., Honeyman, G., Hammer, J., Harrison, L.: Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network. Bioinformatics 14(2), 121-130 (1998)
    • (1998) Bioinformatics , vol.14 , Issue.2 , pp. 121-130
    • Brusic, V.1    Rudy, G.2    Honeyman, G.3    Hammer, J.4    Harrison, L.5
  • 14
    • 0041620259 scopus 로고    scopus 로고
    • MHCPred: A server for quantitative prediction of peptide-MHC binding
    • Guan, P., Doytchinova, I.A., Zygouri, C., Flower, D.R.: MHCPred: A server for quantitative prediction of peptide-MHC binding. Nucleic Acids Res. 31(13), 3621-3624 (2003)
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3621-3624
    • Guan, P.1    Doytchinova, I.A.2    Zygouri, C.3    Flower, D.R.4
  • 15
    • 33747839161 scopus 로고    scopus 로고
    • Dönnes, P., Kohlbacher, O.: SVMHC: a server for prediction of MHC-binding peptides. Nucleic Acids Res. 34, 194-197 (Web Server issue) (2006)
    • Dönnes, P., Kohlbacher, O.: SVMHC: a server for prediction of MHC-binding peptides. Nucleic Acids Res. 34, 194-197 (Web Server issue) (2006)
  • 16
    • 33845240573 scopus 로고    scopus 로고
    • Predicting class 11 MHC-peptide binding: A, kernel based approach using similarity scores
    • Salomon, J., Flower, D.: Predicting class 11 MHC-peptide binding: a, kernel based approach using similarity scores. BMC Bioinformatics 7(1), 501 (2006)
    • (2006) BMC Bioinformatics , vol.7 , Issue.1 , pp. 501
    • Salomon, J.1    Flower, D.2
  • 18
    • 42949139524 scopus 로고    scopus 로고
    • 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. 4(4), 1000048 (2008)
    • 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. 4(4), 1000048 (2008)
  • 19
    • 34547404661 scopus 로고    scopus 로고
    • Zaitlen, N., Reyes-Gomez, M., Heckerman, D., Jojic, N.: Shift-invariant adaptive double threading: Learning MHC II - peptide binding. In: Speed, T., Huang, H. (eds.) RECOMB 2007. LNCS (LNBI), 4453, pp. 181-195. Springer, Heidelberg (2007)
    • Zaitlen, N., Reyes-Gomez, M., Heckerman, D., Jojic, N.: Shift-invariant adaptive double threading: Learning MHC II - peptide binding. In: Speed, T., Huang, H. (eds.) RECOMB 2007. LNCS (LNBI), vol. 4453, pp. 181-195. Springer, Heidelberg (2007)
  • 20
    • 33845790971 scopus 로고    scopus 로고
    • A modular concept of hla for comprehensive peptide binding prediction
    • DeLuca, D., Khattab, B., Blasczyk, R..: A modular concept of hla for comprehensive peptide binding prediction. Immunogenetics 59(1), 25-35 (2007)
    • (2007) Immunogenetics , vol.59 , Issue.1 , pp. 25-35
    • DeLuca, D.1    Khattab, B.2    Blasczyk, R.3
  • 21
    • 38849139819 scopus 로고    scopus 로고
    • Efficient peptide-MHC-I binding prediction for alleles with few known binders
    • Jacob, L., Vert, J.P.: Efficient peptide-MHC-I binding prediction for alleles with few known binders. Bioinformatics 24(3), 358-366 (2008)
    • (2008) Bioinformatics , vol.24 , Issue.3 , pp. 358-366
    • Jacob, L.1    Vert, J.P.2
  • 23
    • 56649108194 scopus 로고    scopus 로고
    • Gärtner, T., Flach, P.A., Kowalczyk, A., Smola, A.J.: Multi-instance kernels. In: Sammut, C., Hoffmann, A.G. (eds.) ICML, pp. 179-186. Morgan Kaufmann, San Francisco (2002)
    • Gärtner, T., Flach, P.A., Kowalczyk, A., Smola, A.J.: Multi-instance kernels. In: Sammut, C., Hoffmann, A.G. (eds.) ICML, pp. 179-186. Morgan Kaufmann, San Francisco (2002)
  • 24
    • 0030649484 scopus 로고    scopus 로고
    • Solving the multiple instance problem with axis-parallel rectangles
    • Dietterich, T.G., Lathrop, R.H., Lozano-Pérez, T.: Solving the multiple instance problem with axis-parallel rectangles. Artif. Intell. 89(1-2), 31-71 (1997)
    • (1997) Artif. Intell , vol.89 , Issue.1-2 , pp. 31-71
    • Dietterich, T.G.1    Lathrop, R.H.2    Lozano-Pérez, T.3
  • 29
    • 0035789124 scopus 로고    scopus 로고
    • New quantitative descriptors of amino acids based on multidimensional scaling of a large number of physical-chemical properties
    • Venkatarajan, M.S., Braun, W.: New quantitative descriptors of amino acids based on multidimensional scaling of a large number of physical-chemical properties. Journal of Molecular Modeling 7(12), 445-453 (2001)
    • (2001) Journal of Molecular Modeling , vol.7 , Issue.12 , pp. 445-453
    • Venkatarajan, M.S.1    Braun, W.2
  • 30
  • 31
    • 33947372576 scopus 로고    scopus 로고
    • Pepdist: A new framework for protein-peptide binding prediction based on learning peptide distance functions
    • S
    • Hertz, T., Yanover, C: Pepdist: A new framework for protein-peptide binding prediction based on learning peptide distance functions. BMC Bioinformatics 7 (suppl. 1), S3 (2006)
    • (2006) BMC Bioinformatics , vol.7 , Issue.SUPPL. 1 , pp. 3
    • Hertz, T.1    Yanover, C.2
  • 33
    • 2442587564 scopus 로고    scopus 로고
    • A class of edit kernels for SVMs to predict translation initiation sites in eukaryotic mRNAs
    • Li, H., Jiang, T.: A class of edit kernels for SVMs to predict translation initiation sites in eukaryotic mRNAs. In: RECOMB, pp. 262-271 (2004)
    • (2004) RECOMB , pp. 262-271
    • Li, H.1    Jiang, T.2
  • 34
    • 84968492782 scopus 로고
    • Metric spaces and positive definite functions
    • Schoenberg, I.J.: Metric spaces and positive definite functions. Trans. Amer. Math. Soc. 44(3), 522-536 (1938)
    • (1938) Trans. Amer. Math. Soc , vol.44 , Issue.3 , pp. 522-536
    • Schoenberg, I.J.1
  • 35
    • 0037305578 scopus 로고    scopus 로고
    • Identification of immunodominant regions among promiscuous HLA-DR,-restricted CD4+ T-cell epitopes on the tumor antigen MAGE-3
    • Consogno, G., Manici, S., Facchinetti, V., Bachi, A., Hammer, J., et al: Identification of immunodominant regions among promiscuous HLA-DR,-restricted CD4+ T-cell epitopes on the tumor antigen MAGE-3. Blood 101(3), 1038-1044 (2003)
    • (2003) Blood , vol.101 , Issue.3 , pp. 1038-1044
    • Consogno, G.1    Manici, S.2    Facchinetti, V.3    Bachi, A.4    Hammer, J.5
  • 37
    • 48449105929 scopus 로고    scopus 로고
    • Feldhahn, M., Thiel, P., Schiller, M.M., Hillen, N., Stevanovic̈, S., et al: EpiToolKit-a web server for computational immunomics. Nucleic Acids Res. (2008) (advanced access, doi:10.1093/nar/gkn229)
    • Feldhahn, M., Thiel, P., Schiller, M.M., Hillen, N., Stevanovic̈, S., et al: EpiToolKit-a web server for computational immunomics. Nucleic Acids Res. (2008) (advanced access, doi:10.1093/nar/gkn229)


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