TY - JOUR AU - Blythe, M. J. AU - Flower, D. R. PY - 2005 DA - 2005// TI - Benchmarking B cell epitope prediction: underperformance of existing methods JO - Protein Sci VL - 14 UR - https://doi.org/10.1110/ps.041059505 DO - 10.1110/ps.041059505 ID - Blythe2005 ER - TY - CHAP AU - Flower, D. R. AU - Doytchinova, I. A. AU - Paine, K. AU - P., T. AU - Blythe, M. J. AU - Lamponi, D. AU - Zygouri, C. AU - Guan, P. AU - McSparron, H. AU - H., K. ED - Flower, D. R. PY - 2002 DA - 2002// TI - Computational Vaccine Design BT - Drug Design: Cutting Edge Approaches PB - Cambridge CY - Royal Society of Chemisty UR - https://doi.org/10.1039/9781847550705 DO - 10.1039/9781847550705 ID - Flower2002 ER - TY - JOUR AU - Sette, A. AU - Buus, S. AU - Appella, E. AU - Smith, J. A. AU - Chesnut, R. AU - Miles, C. AU - Colon, S. M. AU - Grey, H. M. PY - 1989 DA - 1989// TI - Prediction of major histocompatibility complex binding regions of protein antigens by sequence pattern analysis JO - Proc Natl Acad Sci U S A VL - 86 UR - https://doi.org/10.1073/pnas.86.9.3296 DO - 10.1073/pnas.86.9.3296 ID - Sette1989 ER - TY - JOUR AU - Nielsen, M. AU - Lundegaard, C. AU - Worning, P. AU - Hvid, C. S. AU - Lamberth, K. AU - Buus, S. AU - Brunak, S. AU - Lund, O. PY - 2004 DA - 2004// TI - Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth100 DO - 10.1093/bioinformatics/bth100 ID - Nielsen2004 ER - TY - JOUR AU - Rammensee, H. AU - Bachmann, J. AU - Emmerich, N. P. AU - Bachor, O. A. AU - Stevanovic, S. PY - 1999 DA - 1999// TI - SYFPEITHI: database for MHC ligands and peptide motifs JO - Immunogenetics VL - 50 UR - https://doi.org/10.1007/s002510050595 DO - 10.1007/s002510050595 ID - Rammensee1999 ER - TY - JOUR AU - Parker, K. C. AU - Bednarek, M. A. AU - Coligan, J. E. PY - 1994 DA - 1994// TI - Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains JO - J Immunol VL - 152 ID - Parker1994 ER - TY - JOUR AU - Reche, P. A. AU - Glutting, J. P. AU - Reinherz, E. L. PY - 2002 DA - 2002// TI - Prediction of MHC class I binding peptides using profile motifs JO - Hum Immunol VL - 63 UR - https://doi.org/10.1016/S0198-8859(02)00432-9 DO - 10.1016/S0198-8859(02)00432-9 ID - Reche2002 ER - TY - JOUR AU - Nielsen, M. AU - Lundegaard, C. AU - Worning, P. AU - Lauemoller, S. L. AU - Lamberth, K. AU - Buus, S. AU - Brunak, S. AU - Lund, O. PY - 2003 DA - 2003// TI - Reliable prediction of T-cell epitopes using neural networks with novel sequence representations JO - Protein Sci VL - 12 UR - https://doi.org/10.1110/ps.0239403 DO - 10.1110/ps.0239403 ID - Nielsen2003 ER - TY - JOUR AU - Brusic, V. AU - Rudy, G. AU - Honeyman, G. AU - Hammer, J. AU - Harrison, L. PY - 1998 DA - 1998// TI - Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network JO - Bioinformatics VL - 14 UR - https://doi.org/10.1093/bioinformatics/14.2.121 DO - 10.1093/bioinformatics/14.2.121 ID - Brusic1998 ER - TY - JOUR AU - Honeyman, M. C. AU - Brusic, V. AU - Stone, N. L. AU - Harrison, L. C. PY - 1998 DA - 1998// TI - Neural network-based prediction of candidate T-cell epitopes JO - Nat Biotechnol VL - 16 UR - https://doi.org/10.1038/nbt1098-966 DO - 10.1038/nbt1098-966 ID - Honeyman1998 ER - TY - JOUR AU - Mamitsuka, H. PY - 1998 DA - 1998// TI - Predicting peptides that bind to MHC molecules using supervised learning of hidden Markov models JO - Proteins VL - 33 UR - https://doi.org/3.0.CO;2-M DO - 3.0.CO;2-M ID - Mamitsuka1998 ER - TY - JOUR AU - Donnes, P. AU - Elofsson, A. PY - 2002 DA - 2002// TI - Prediction of MHC class I binding peptides, using SVMHC JO - BMC Bioinformatics VL - 3 UR - https://doi.org/10.1186/1471-2105-3-25 DO - 10.1186/1471-2105-3-25 ID - Donnes2002 ER - TY - JOUR AU - Bhasin, M. AU - Raghava, G. P. PY - 2004 DA - 2004// TI - SVM based method for predicting HLA-DRB1*0401 binding peptides in an antigen sequence JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/btg424 DO - 10.1093/bioinformatics/btg424 ID - Bhasin2004 ER - TY - JOUR AU - Doytchinova, I. A. AU - Blythe, M. J. AU - Flower, D. R. PY - 2002 DA - 2002// TI - Additive method for the prediction of protein-peptide binding affinity. Application to the MHC class I molecule HLA-A*0201 JO - J Proteome Res VL - 1 UR - https://doi.org/10.1021/pr015513z DO - 10.1021/pr015513z ID - Doytchinova2002 ER - TY - CHAP AU - Hattotuwagama, C. K. AU - Toseland, C. P. AU - Guan, P. AU - Taylor, D. L. AU - Hemsley, S. L. AU - Doytchinova, I. A. AU - Flower, D. R. PY - 2005 DA - 2005// TI - Class II Mouse Major Histocompatibility Complex Peptide Binding Affinity: In Silico bioinformatic prediction using robust multivariate statistics. BT - J Chem Inf Mod (in press) ID - Hattotuwagama2005 ER - TY - JOUR AU - Doytchinova, I. A. AU - Flower, D. R. PY - 2003 DA - 2003// TI - Towards the in silico identification of class II restricted T-cell epitopes: a partial least squares iterative self-consistent algorithm for affinity prediction JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg312 DO - 10.1093/bioinformatics/btg312 ID - Doytchinova2003 ER - TY - JOUR AU - Hattotuwagama, C. K. AU - Guan, P. AU - Doytchinova, I. A. AU - Flower, D. R. PY - 2004 DA - 2004// TI - New horizons in mouse immunoinformatics: reliable in silico prediction of mouse class I histocompatibility major complex peptide binding affinity JO - Org Biomol Chem VL - 2 UR - https://doi.org/10.1039/b409656h DO - 10.1039/b409656h ID - Hattotuwagama2004 ER - TY - CHAP AU - Cristianini, N. AU - Shawe-Taylor, J. PY - 2000 DA - 2000// BT - An introduction to support vector machines and other kernel-based learning methods PB - Cambridge University Press CY - Cambridge, UK UR - https://doi.org/10.1017/CBO9780511801389 DO - 10.1017/CBO9780511801389 ID - Cristianini2000 ER - TY - STD TI - SVRMHC supplementary web site [http://SVRMHC.umn.edu/SVRMHC] ID - ref19 ER - TY - JOUR AU - Xue, C. X. AU - Zhang, R. S. AU - Liu, H. X. AU - Liu, M. C. AU - Hu, Z. D. AU - Fan, B. T. PY - 2004 DA - 2004// TI - Support vector machines-based quantitative structure-property relationship for the prediction of heat capacity JO - J Chem Inf Comput Sci VL - 44 UR - https://doi.org/10.1021/ci049934n DO - 10.1021/ci049934n ID - Xue2004 ER - TY - JOUR AU - Yao, X. J. AU - Panaye, A. AU - Doucet, J. P. AU - Zhang, R. S. AU - Chen, H. F. AU - Liu, M. C. AU - Hu, Z. D. AU - Fan, B. T. PY - 2004 DA - 2004// TI - Comparative study of QSAR/QSPR correlations using support vector machines, radial basis function neural networks, and multiple linear regression JO - J Chem Inf Comput Sci VL - 44 UR - https://doi.org/10.1021/ci049965i DO - 10.1021/ci049965i ID - Yao2004 ER - TY - JOUR AU - Cherkassky, V. AU - Ma, Y. PY - 2004 DA - 2004// TI - Practical selection of SVM parameters and noise estimation for SVM regression JO - Neural Netw VL - 17 UR - https://doi.org/10.1016/S0893-6080(03)00169-2 DO - 10.1016/S0893-6080(03)00169-2 ID - Cherkassky2004 ER - TY - JOUR AU - Liu, H. X. AU - Zhang, R. S. AU - Yao, X. J. AU - Liu, M. C. AU - Hu, Z. D. AU - Fan, B. T. PY - 2004 DA - 2004// TI - Prediction of the isoelectric point of an amino acid based on GA-PLS and SVMs JO - J Chem Inf Comput Sci VL - 44 UR - https://doi.org/10.1021/ci034173u DO - 10.1021/ci034173u ID - Liu2004 ER - TY - JOUR AU - Huang, Y. AU - Fayad, R. AU - Smock, A. AU - Ullrich, A. M. AU - Qiao, L. PY - 2005 DA - 2005// TI - Induction of mucosal and systemic immune responses against human carcinoembryonic antigen by an oral vaccine JO - Cancer Res VL - 65 UR - https://doi.org/10.1158/0008-5472.CAN-04-3669 DO - 10.1158/0008-5472.CAN-04-3669 ID - Huang2005 ER - TY - JOUR AU - Saren, A. AU - Pascolo, S. AU - Stevanovic, S. AU - Dumrese, T. AU - Puolakkainen, M. AU - Sarvas, M. AU - Rammensee, H. G. AU - Vuola, J. M. PY - 2002 DA - 2002// TI - Identification of Chlamydia pneumoniae-derived mouse CD8 epitopes JO - Infect Immun VL - 70 UR - https://doi.org/10.1128/IAI.70.7.3336-3343.2002 DO - 10.1128/IAI.70.7.3336-3343.2002 ID - Saren2002 ER - TY - JOUR AU - Jaimes, M. C. AU - Feng, N. AU - Greenberg, H. B. PY - 2005 DA - 2005// TI - Characterization of homologous and heterologous rotavirus-specific T-cell responses in infant and adult mice JO - J Virol VL - 79 UR - https://doi.org/10.1128/JVI.79.8.4568-4579.2005 DO - 10.1128/JVI.79.8.4568-4579.2005 ID - Jaimes2005 ER - TY - JOUR AU - Wrightsman, R. A. AU - Luhrs, K. A. AU - Fouts, D. AU - Manning, J. E. PY - 2002 DA - 2002// TI - Paraflagellar rod protein-specific CD8+ cytotoxic T lymphocytes target Trypanosoma cruzi-infected host cells JO - Parasite Immunol VL - 24 UR - https://doi.org/10.1046/j.1365-3024.2002.00479.x DO - 10.1046/j.1365-3024.2002.00479.x ID - Wrightsman2002 ER - TY - JOUR AU - Peng, S. AU - Ji, H. AU - Trimble, C. AU - He, L. AU - Tsai, Y. C. AU - Yeatermeyer, J. AU - Boyd, D. A. AU - Hung, C. F. AU - Wu, T. C. PY - 2004 DA - 2004// TI - Development of a DNA vaccine targeting human papillomavirus type 16 oncoprotein E6 JO - J Virol VL - 78 UR - https://doi.org/10.1128/JVI.78.16.8468-8476.2004 DO - 10.1128/JVI.78.16.8468-8476.2004 ID - Peng2004 ER - TY - JOUR AU - Zhi, Y. AU - Kobinger, G. P. AU - Jordan, H. AU - Suchma, K. AU - Weiss, S. R. AU - Shen, H. AU - Schumer, G. AU - Gao, G. AU - Boyer, J. L. AU - Crystal, R. G. AU - Wilson, J. M. PY - 2005 DA - 2005// TI - Identification of murine CD8 T cell epitopes in codon-optimized SARS-associated coronavirus spike protein JO - Virology VL - 335 UR - https://doi.org/10.1016/j.virol.2005.01.050 DO - 10.1016/j.virol.2005.01.050 ID - Zhi2005 ER - TY - JOUR AU - Schueler-Furman, O. AU - Altuvia, Y. AU - Sette, A. AU - Margalit, H. PY - 2000 DA - 2000// TI - Structure-based prediction of binding peptides to MHC class I molecules: application to a broad range of MHC alleles JO - Protein Sci VL - 9 UR - https://doi.org/10.1110/ps.9.9.1838 DO - 10.1110/ps.9.9.1838 ID - Schueler-Furman2000 ER - TY - JOUR AU - Doytchinova, I. AU - Hemsley, S. AU - Flower, D. R. PY - 2004 DA - 2004// TI - Transporter associated with antigen processing preselection of peptides binding to the MHC: a bioinformatic evaluation JO - J Immunol VL - 173 UR - https://doi.org/10.4049/jimmunol.173.11.6813 DO - 10.4049/jimmunol.173.11.6813 ID - Doytchinova2004 ER - TY - JOUR AU - Bhasin, M. AU - Singh, H. AU - Raghava, G. P. PY - 2003 DA - 2003// TI - MHCBN: a comprehensive database of MHC binding and non-binding peptides JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg055 DO - 10.1093/bioinformatics/btg055 ID - Bhasin2003 ER - TY - JOUR AU - Doytchinova, I. A. AU - Flower, D. R. PY - 2001 DA - 2001// TI - Toward the quantitative prediction of T-cell epitopes: coMFA and coMSIA studies of peptides with affinity for the class I MHC molecule HLA-A*0201 JO - J Med Chem VL - 44 UR - https://doi.org/10.1021/jm010021j DO - 10.1021/jm010021j ID - Doytchinova2001 ER - TY - JOUR AU - Doytchinova, I. A. AU - Flower, D. R. PY - 2002 DA - 2002// TI - Physicochemical explanation of peptide binding to HLA-A*0201 major histocompatibility complex: a three-dimensional quantitative structure-activity relationship study JO - Proteins VL - 48 UR - https://doi.org/10.1002/prot.10154 DO - 10.1002/prot.10154 ID - Doytchinova2002 ER - TY - CHAP AU - Vapnik, V. PY - 1998 DA - 1998// BT - Statistical Learning Theory PB - New York CY - Sons ID - Vapnik1998 ER - TY - JOUR AU - Zhao, Y. AU - Pinilla, C. AU - Valmori, D. AU - Martin, R. AU - Simon, R. PY - 2003 DA - 2003// TI - Application of support vector machines for T-cell epitopes prediction JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg255 DO - 10.1093/bioinformatics/btg255 ID - Zhao2003 ER - TY - JOUR AU - Guan, P. AU - Doytchinova, I. A. AU - Zygouri, C. AU - Flower, D. R. PY - 2003 DA - 2003// TI - MHCPred: A server for quantitative prediction of peptide-MHC binding JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg510 DO - 10.1093/nar/gkg510 ID - Guan2003 ER - TY - JOUR AU - Toseland, C. P. AU - Clayton, D. J. AU - McSparron, H. AU - Hemsley, S. L. AU - Blythe, M. J. AU - Paine, K. AU - Doytchinova, I. A. AU - Guan, P. AU - Hattotuwagama, C. K. AU - Flower, D. R. PY - 2005 DA - 2005// TI - AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data JO - Immunome Res VL - 1 UR - https://doi.org/10.1186/1745-7580-1-4 DO - 10.1186/1745-7580-1-4 ID - Toseland2005 ER - TY - CHAP AU - Chang, C. C. AU - Lin, C. J. PY - 2004 DA - 2004// BT - A practical guide to SVM classification, LibSVM documentation ID - Chang2004 ER - TY - CHAP AU - Baldi, P. AU - Brunak, S. PY - 2001 DA - 2001// BT - Bioinformatics: the machine learning approach PB - The MIT Press CY - Cambridge, MA ID - Baldi2001 ER - TY - JOUR AU - Kawashima, S. AU - Ogata, H. AU - Kanehisa, M. PY - 1999 DA - 1999// TI - AAindex: Amino Acid Index Database JO - Nucleic Acids Res VL - 27 UR - https://doi.org/10.1093/nar/27.1.368 DO - 10.1093/nar/27.1.368 ID - Kawashima1999 ER - TY - STD TI - MHCPred [http://www.jenner.ac.uk/MHCPred/] ID - ref42 ER - TY - STD TI - SYFPEITHI [http://www.syfpeithi.de/Scripts/MHCServer.dll/EpitopePrediction.htm] ID - ref43 ER - TY - STD TI - BIMAS [http://thr.cit.nih.gov/molbio/hla_bind/] ID - ref44 ER - TY - STD TI - RANKPEP [http://www.mifoundation.org/Tools/rankpep.html] ID - ref45 ER - TY - STD TI - SVMHC [http://www-bs.informatik.uni-tuebingen.de/SVMHC] ID - ref46 ER -