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Volumn 89, Issue 1, 2011, Pages 81-89

Innovative bioinformatic approaches for developing peptide-based vaccines against hypervariable viruses

Author keywords

epitope mapping; HIV; hypervariable viruses; peptide vaccines; vaccinomics

Indexed keywords

ANTIGEN; AVIAN INFLUENZA VACCINE; HUMAN IMMUNODEFICIENCY VIRUS VACCINE; INFLUENZA VACCINE; PEPTIDE VACCINE; SWINE INFLUENZA VACCINE; VIRUS VACCINE;

EID: 78651096072     PISSN: 08189641     EISSN: 14401711     Source Type: Journal    
DOI: 10.1038/icb.2010.65     Document Type: Review
Times cited : (60)

References (107)
  • 3
    • 7944235807 scopus 로고    scopus 로고
    • From genome to vaccine-new immunoinformatics tools for vaccine design
    • De Groot AS, Berzofsky JA. From genome to vaccine-new immunoinformatics tools for vaccine design. Methods 2004; 34: 425-428.
    • (2004) Methods , vol.34 , pp. 425-428
    • De Groot, A.S.1    Berzofsky, J.A.2
  • 4
    • 33645356185 scopus 로고    scopus 로고
    • Immunomics: Discovering new targets for vaccines and therapeutics
    • De Groot AS. Immunomics: discovering new targets for vaccines and therapeutics. Drug Discov Today 2006; 11: 203-209.
    • (2006) Drug. Discov. Today , vol.11 , pp. 203-209
    • De Groot, A.S.1
  • 6
    • 0142174642 scopus 로고    scopus 로고
    • Prediction of MHC class I binding peptides using SVMHC
    • Donnes P, Elofsson A. Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinformatics 2002; 3: 25.
    • (2002) BMC Bioinformatics , vol.3 , pp. 25
    • Donnes, P.1    Elofsson, A.2
  • 7
    • 33746352651 scopus 로고    scopus 로고
    • Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression SVR models
    • Liu W, Meng X, Xu Q, Flower DR, Li T. Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression (SVR) models. BMC Bioinformatics 2006; 7: 182.
    • (2006) BMC Bioinformatics , vol.7 , pp. 182
    • Liu, W.1    Meng, X.2    Xu, Q.3    Flower, D.R.4    Li, T.5
  • 9
    • 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 et al. Hidden Markov model-based prediction of antigenic peptides that interact with MHC class II molecules. J Biosci Bioeng 2002; 94: 264-270.
    • (2002) J. Biosci. Bioeng. , vol.94 , pp. 264-270
    • Noguchi, H.1    Kato, R.2    Hanai, T.3    Matsubara, Y.4    Honda, H.5    Brusic, V.6
  • 10
    • 20444386168 scopus 로고    scopus 로고
    • Predictive Bayesian neural network models of MHC class II peptide binding
    • Burden FR, Winkler DA. Predictive Bayesian neural network models of MHC class II peptide binding. J Mol Graph Model 2005; 23: 481-489.
    • (2005) J. Mol. Graph. Model. , vol.23 , pp. 481-489
    • Burden, F.R.1    Winkler, D.A.2
  • 11
    • 23144443082 scopus 로고    scopus 로고
    • PEPVAC: A web server for multi-epitope vaccine development based on the prediction of supertypic MHC ligands
    • Reche PA, Reinherz EL. PEPVAC: a web server for multi-epitope vaccine development based on the prediction of supertypic MHC ligands. Nucleic Acids Res 2005; 33: W138-W142.
    • (2005) Nucleic. Acids Res. , vol.33
    • Reche, P.A.1    Reinherz, E.L.2
  • 13
    • 22144474037 scopus 로고    scopus 로고
    • Towards the chemometric dissection of peptide-HLA-A*0201 binding affinity: Comparison of local and global QSAR models
    • Doytchinova IA, Walshe V, Borrow P, Flower DR. Towards the chemometric dissection of peptide-HLA-A*0201 binding affinity: comparison of local and global QSAR models. J Comput Aided Mol Des 2005; 19: 203-212.
    • (2005) J. Comput. Aided. Mol. Des. , vol.19 , pp. 203-212
    • Doytchinova, I.A.1    Walshe, V.2    Borrow, P.3    Flower, D.R.4
  • 14
    • 33751120934 scopus 로고    scopus 로고
    • Immunogenicity of a polyvalent HIV-1 candidate vaccine based on fourteen wild type gp120 proteins in golden hamsters
    • Azizi A, Anderson DE, Ghorbani M, Gee K, Diaz-Mitoma F. Immunogenicity of a polyvalent HIV-1 candidate vaccine based on fourteen wild type gp120 proteins in golden hamsters. BMC Immunol 2006; 7: 25.
    • (2006) BMC Immunol. , vol.7 , pp. 25
    • Azizi, A.1    Anderson, D.E.2    Ghorbani, M.3    Gee, K.4    Diaz-Mitoma, F.5
  • 15
    • 0037189323 scopus 로고    scopus 로고
    • Diversity considerations in HIV-1 vaccine selection
    • Gaschen B, Taylor J, Yusim K, Foley B, Gao F, Lang D et al. Diversity considerations in HIV-1 vaccine selection. Science 2002; 296: 2354-2360.
    • (2002) Science , vol.296 , pp. 2354-2360
    • Gaschen, B.1    Taylor, J.2    Yusim, K.3    Foley, B.4    Gao, F.5    Lang, D.6
  • 16
    • 23044441689 scopus 로고    scopus 로고
    • Characterization of liver histopathology in a transgenic mouse model expressing genotype 1a hepatitis C virus core and envelope proteins 1 and 2
    • Naas T, Ghorbani M, varez-Maya I, Lapner M, Kothary R, De Repentigny Y et al. Characterization of liver histopathology in a transgenic mouse model expressing genotype 1a hepatitis C virus core and envelope proteins 1 and 2. J Gen Virol 2005; 86: 2185-2196.
    • (2005) J. Gen. Virol. , vol.86 , pp. 2185-2196
    • Naas, T.1    Ghorbani, M.2    Varez-Maya, I.3    Lapner, M.4    Kothary, R.5    De Repentigny, Y.6
  • 17
    • 70349303282 scopus 로고    scopus 로고
    • The remarkable frequency of human immunodeficiency virus type 1 genetic recombination
    • Table
    • Onafuwa-Nuga A, Telesnitsky A. The remarkable frequency of human immunodeficiency virus type 1 genetic recombination. Microbiol Mol Biol Rev 2009; 73: 451-480, Table.
    • (2009) Microbiol. Mol. Biol. Rev. , vol.73 , pp. 451-480
    • Onafuwa-Nuga, A.1    Telesnitsky, A.2
  • 18
    • 0031743285 scopus 로고    scopus 로고
    • An isolate of human immunodeficiency virus type 1 originally classified as subtype I represents a complex mosaic comprising three different group M subtypes A G and I
    • Gao F, Robertson DL, Carruthers CD, Li Y, Bailes E, Kostrikis LG et al. An isolate of human immunodeficiency virus type 1 originally classified as subtype I represents a complex mosaic comprising three different group M subtypes (A, G, and I). J Virol 1998; 72: 10234-10241.
    • (1998) J. Virol. , vol.72 , pp. 10234-10241
    • Gao, F.1    Robertson, D.L.2    Carruthers, C.D.3    Li, Y.4    Bailes, E.5    Kostrikis, L.G.6
  • 20
    • 0036909589 scopus 로고    scopus 로고
    • Reverse vaccinology: A genome-based approach for vaccine development
    • DOI 10.1517/14712598.2.8.895
    • Masignani V, Rappuoli R, Pizza M. Reverse vaccinology: a genome-based approach for vaccine development. Expert Opin Biol Ther 2002; 2: 895-905. (Pubitemid 36033255)
    • (2002) Expert Opinion on Biological Therapy , vol.2 , Issue.8 , pp. 895-905
    • Masignani, V.1    Rappuoli, R.2    Pizza, M.3
  • 21
    • 0142147304 scopus 로고    scopus 로고
    • Reverse vaccinology and genomics
    • Rappuoli R, Covacci A. Reverse vaccinology and genomics. Science 2003; 302: 602.
    • (2003) Science , vol.302 , pp. 602
    • Rappuoli, R.1    Covacci, A.2
  • 22
    • 77958162748 scopus 로고    scopus 로고
    • Live attenuated vaccines for pandemic influenza
    • Chen GL, Subbarao K. Live attenuated vaccines for pandemic influenza. Curr Top Microbiol Immunol 2009; 333: 109-132.
    • (2009) Curr. Top Microbiol. Immunol. , vol.333 , pp. 109-132
    • Chen, G.L.1    Subbarao, K.2
  • 23
    • 0035987429 scopus 로고    scopus 로고
    • Principles underlying the development and use of live attenuated cold-adapted influenza A and B virus vaccines
    • Murphy BR, Coelingh K. Principles underlying the development and use of live attenuated cold-adapted influenza A and B virus vaccines. Viral Immunol 2002; 15: 295-323.
    • (2002) Viral. Immunol. , vol.15 , pp. 295-323
    • Murphy, B.R.1    Coelingh, K.2
  • 26
    • 37349026910 scopus 로고    scopus 로고
    • Viral peptide immunogens: Current challenges and opportunities
    • Azizi A, Diaz-Mitoma F. Viral peptide immunogens: current challenges and opportunities. J Pept Sci 2007; 13: 776-786.
    • (2007) J. Pept. Sci. , vol.13 , pp. 776-786
    • Azizi, A.1    Diaz-Mitoma, F.2
  • 27
    • 32444446673 scopus 로고    scopus 로고
    • Involvement of multiple epitope-specific cytotoxic T-lymphocyte responses in vaccine-based control of simian immunodeficiency virus replication in rhesus macaques
    • Kawada M, Igarashi H, Takeda A, Tsukamoto T, Yamamoto H, Dohki S et al. Involvement of multiple epitope-specific cytotoxic T-lymphocyte responses in vaccine- based control of simian immunodeficiency virus replication in rhesus macaques. J Virol 2006; 80: 1949-1958.
    • (2006) J. Virol. , vol.80 , pp. 1949-1958
    • Kawada, M.1    Igarashi, H.2    Takeda, A.3    Tsukamoto, T.4    Yamamoto, H.5    Dohki, S.6
  • 28
    • 0038617573 scopus 로고    scopus 로고
    • Dissecting the role of peptides in the immune response: Theory practice and the application to vaccine design
    • Purcell AW, Zeng W, Mifsud NA, Ely LK, Macdonald WA, Jackson DC. Dissecting the role of peptides in the immune response: theory, practice and the application to vaccine design. J Pept Sci 2003; 9: 255-281.
    • (2003) J. Pept. Sci. , vol.9 , pp. 255-281
    • Purcell, A.W.1    Zeng, W.2    Mifsud, N.A.3    Ely, L.K.4    Macdonald, W.A.5    Jackson, D.C.6
  • 29
    • 34247891741 scopus 로고    scopus 로고
    • More than one reason to rethink the use of peptides in vaccine design
    • Purcell AW, McCluskey J, Rossjohn J. More than one reason to rethink the use of peptides in vaccine design. Nat Rev Drug Discov 2007; 6: 404-414.
    • (2007) Nat. Rev. Drug. Discov. , vol.6 , pp. 404-414
    • Purcell, A.W.1    McCluskey, J.2    Rossjohn, J.3
  • 30
    • 12444268257 scopus 로고    scopus 로고
    • Prototype alzheimers disease vaccine using the immunodominant B cell epitope from beta-amyloid and promiscuous T cell epitope pan HLA DR-binding peptide
    • Agadjanyan MG, Ghochikyan A, Petrushina I, Vasilevko V, Movsesyan N, Mkrtichyan M et al. Prototype Alzheimers disease vaccine using the immunodominant B cell epitope from beta-amyloid and promiscuous T cell epitope pan HLA DR-binding peptide. J Immunol 2005; 174: 1580-1586.
    • (2005) J. Immunol. , vol.174 , pp. 1580-1586
    • Agadjanyan, M.G.1    Ghochikyan, A.2    Petrushina, I.3    Vasilevko, V.4    Movsesyan, N.5    Mkrtichyan, M.6
  • 31
    • 0029031039 scopus 로고
    • Identification of T and B cell epitopes recognized by humans in the C-terminal 42- kDa domain of the plasmodium falciparum merozoite surface protein MSP-1
    • Udhayakumar V, Anyona D, Kariuki S, Shi YP, Bloland PB, Branch OH et al. Identification of T and B cell epitopes recognized by humans in the C-terminal 42- kDa domain of the plasmodium falciparum merozoite surface protein (MSP)-1. J Immunol 1995; 154: 6022-6030.
    • (1995) J. Immunol. , vol.154 , pp. 6022-6030
    • Udhayakumar, V.1    Anyona, D.2    Kariuki, S.3    Shi, Y.P.4    Bloland, P.B.5    Branch, O.H.6
  • 33
    • 0027958005 scopus 로고
    • A speculative view of immune recognition
    • Lu NQ. A speculative view of immune recognition. Immunol Invest 1994; 23: 53-71.
    • (1994) Immunol. Invest. , vol.23 , pp. 53-71
    • Lu, N.Q.1
  • 35
    • 70349119901 scopus 로고    scopus 로고
    • In vivo enhancement of peptide display by MHC class II molecules with small molecule catalysts of peptide exchange
    • Call MJ, Xing X, Cuny GD, Seth NP, Altmann DM, Fugger L et al. In vivo enhancement of peptide display by MHC class II molecules with small molecule catalysts of peptide exchange. J Immunol 2009; 182: 6342-6352.
    • (2009) J. Immunol. , vol.182 , pp. 6342-6352
    • Call, M.J.1    Xing, X.2    Cuny, G.D.3    Seth, N.P.4    Altmann, D.M.5    Fugger, L.6
  • 37
    • 0037029939 scopus 로고    scopus 로고
    • HIV vaccine strategies
    • Nabel GJ. HIV vaccine strategies. Vaccine 2002; 20: 1945-1947.
    • (2002) Vaccine , vol.20 , pp. 1945-1947
    • Nabel, G.J.1
  • 38
    • 0027406672 scopus 로고
    • Immune response of chimpanzees after immunization with the inactivated whole immunodeficiency virus HIV-1 three different adjuvants and challenge
    • Niedrig M, Gregersen JP, Fultz PN, Broker M, Mehdi S, Hilfenhaus J. Immune response of chimpanzees after immunization with the inactivated whole immunodeficiency virus (HIV-1), three different adjuvants and challenge. Vaccine 1993; 11: 67-74.
    • (1993) Vaccine , vol.11 , pp. 67-74
    • Niedrig, M.1    Gregersen, J.P.2    Fultz, P.N.3    Broker, M.4    Mehdi, S.5    Hilfenhaus, J.6
  • 40
    • 23244434512 scopus 로고    scopus 로고
    • Human immunodeficiency virus type 1 env clones from acute and early subtype B infections for standardized assessments of vaccine-elicited neutralizing antibodies
    • Li M, Gao F, Mascola JR, Stamatatos L, Polonis VR, Koutsoukos M et al. Human immunodeficiency virus type 1 env clones from acute and early subtype B infections for standardized assessments of vaccine-elicited neutralizing antibodies. J Virol 2005; 79: 10108-10125.
    • (2005) J. Virol. , vol.79 , pp. 10108-10125
    • Li, M.1    Gao, F.2    Mascola, J.R.3    Stamatatos, L.4    Polonis, V.R.5    Koutsoukos, M.6
  • 41
    • 0032787513 scopus 로고    scopus 로고
    • Antibody and cellular immune responses in breakthrough infection subjects after HIV type 1 glycoprotein 120 vaccination
    • Locher CP, Grant RM, Collisson EA, Reyes-Terán G, Elbeik T, Kahn JO et al. Antibody and cellular immune responses in breakthrough infection subjects after HIV type 1 glycoprotein 120 vaccination. AIDS Res Hum Retroviruses 1999; 15: 1685-1689.
    • (1999) AIDS Res. Hum. Retroviruses , vol.15 , pp. 1685-1689
    • Locher, C.P.1    Grant, R.M.2    Collisson, E.A.3    Reyes-Terán, G.4    Elbeik, T.5    Kahn, J.O.6
  • 42
    • 0034968106 scopus 로고    scopus 로고
    • Neutralizing antibodies against autologous human immunodeficiency virus type 1 isolates in patients with increasing CD4 cell counts despite incomplete virus suppression during antiretroviral treatment
    • Sarmati L, dEttorre G, Nicastri E, Ercoli L, Uccella I, Massetti P et al. Neutralizing antibodies against autologous human immunodeficiency virus type 1 isolates in patients with increasing CD4 cell counts despite incomplete virus suppression during antiretroviral treatment. Clin Diagn Lab Immunol 2001; 8: 822-824.
    • (2001) Clin. Diagn. Lab Immunol. , vol.8 , pp. 822-824
    • Sarmati, L.1    D Ettorre, G.2    Nicastri, E.3    Ercoli, L.4    Uccella, I.5    Massetti, P.6
  • 43
    • 4344573018 scopus 로고    scopus 로고
    • Neutralizing antibody responses to HIV: Role in protective immunity and challenges for vaccine design
    • Srivastava IK, Ulmer JB, Barnett SW. Neutralizing antibody responses to HIV: role in protective immunity and challenges for vaccine design. Expert Rev Vaccines 2004; 3: S33-S52.
    • (2004) Expert Rev. Vaccines , vol.3
    • Srivastava, I.K.1    Ulmer, J.B.2    Barnett, S.W.3
  • 44
    • 33746598200 scopus 로고    scopus 로고
    • HIV vaccines: New frontiers in vaccine development
    • Duerr A, Wasserheit JN, Corey L. HIV vaccines: new frontiers in vaccine development. Clin Infect Dis 2006; 43: 500-511.
    • (2006) Clin. Infect. Dis. , vol.43 , pp. 500-511
    • Duerr, A.1    Wasserheit, J.N.2    Corey, L.3
  • 45
    • 34248382494 scopus 로고    scopus 로고
    • Effect of plasmid DNA vaccine design and in vivo electroporation on the resulting vaccinespecific immune responses in rhesus macaques
    • Luckay A, Sidhu MK, Kjeken R, Megati S, Chong SY, Roopchand V et al. Effect of plasmid DNA vaccine design and in vivo electroporation on the resulting vaccinespecific immune responses in rhesus macaques. J Virol 2007; 81: 5257-5269.
    • (2007) J. Virol. , vol.81 , pp. 5257-5269
    • Luckay, A.1    Sidhu, M.K.2    Kjeken, R.3    Megati, S.4    Chong, S.Y.5    Roopchand, V.6
  • 46
    • 33750579820 scopus 로고    scopus 로고
    • Potency of cellmediated immune responses to different combined HIV-1 immunogens in a humanized murine model
    • Azizi A, Ghorbani M, Kryworuchko M, Aucoin S, Diaz-Mitoma F. Potency of cellmediated immune responses to different combined HIV-1 immunogens in a humanized murine model. Hum Vaccin 2005; 1: 170-176.
    • (2005) Hum. Vaccin , vol.1 , pp. 170-176
    • Azizi, A.1    Ghorbani, M.2    Kryworuchko, M.3    Aucoin, S.4    Diaz-Mitoma, F.5
  • 48
    • 32844462280 scopus 로고    scopus 로고
    • Preclinical evaluation of cellular immune responses elicited by a polyvalent DNA prime/protein boost HIV-1 vaccine
    • Cristillo AD, Wang S, Caskey MS, Unangst T, Hocker L, He L et al. Preclinical evaluation of cellular immune responses elicited by a polyvalent DNA prime/protein boost HIV-1 vaccine. Virology 2006; 346: 151-168.
    • (2006) Virology , vol.346 , pp. 151-168
    • Cristillo, A.D.1    Wang, S.2    Caskey, M.S.3    Unangst, T.4    Hocker, L.5    He, L.6
  • 50
    • 18344418801 scopus 로고    scopus 로고
    • Cytotoxic T cell responses to multiple conserved HIV epitopes in HIV-resistant prostitutes in Nairobi
    • Rowland-Jones SL, Dong T, Fowke KR, Fowke KR, Kimani J, Krausa P et al. Cytotoxic T cell responses to multiple conserved HIV epitopes in HIV-resistant prostitutes in Nairobi. J Clin Invest 1998; 102: 1758-1765.
    • (1998) J. Clin. Invest. , vol.102 , pp. 1758-1765
    • Rowland-Jones, S.L.1    Dong, T.2    Fowke, K.R.3    Fowke, K.R.4    Kimani, J.5    Krausa, P.6
  • 53
    • 70649093803 scopus 로고    scopus 로고
    • Discovery of naturally processed and HLA-presented class I peptides from vaccinia virus infection using mass spectrometry for vaccine development
    • Johnson KL, Ovsyannikova IG, Mason CJ, Bergen III HR, Poland GA. Discovery of naturally processed and HLA-presented class I peptides from vaccinia virus infection using mass spectrometry for vaccine development. Vaccine 2009; 28: 38-47.
    • (2009) Vaccine , vol.28 , pp. 38-47
    • Johnson, K.L.1    Ovsyannikova, I.G.2    Mason, C.J.3    Bergen III, H.R.4    Poland, G.A.5
  • 54
    • 34247388467 scopus 로고    scopus 로고
    • Harnessing bioinformatics to discover new vaccines
    • Davies MN, Flower DR. Harnessing bioinformatics to discover new vaccines. Drug Discov Today 2007; 12: 389-395.
    • (2007) Drug. Discov. Today , vol.12 , pp. 389-395
    • Davies, M.N.1    Flower, D.R.2
  • 55
    • 20344405720 scopus 로고    scopus 로고
    • 3D-Epitope-explorer 3DEX: Localization of conformational epitopes within three-dimensional structures of proteins
    • Schreiber A, Humbert M, Benz A, Dietrich U. 3D-Epitope-Explorer (3DEX): localization of conformational epitopes within three-dimensional structures of proteins. J Comput Chem 2005; 26: 879-887.
    • (2005) J. Comput. Chem. , vol.26 , pp. 879-887
    • Schreiber, A.1    Humbert, M.2    Benz, A.3    Dietrich, U.4
  • 57
    • 33751099863 scopus 로고    scopus 로고
    • Prediction of residues in discontinuous B-cell epitopes using protein 3D structures
    • Haste AP, Nielsen M, Lund O. Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci 2006; 15: 2558-2567.
    • (2006) Protein. Sci. , vol.15 , pp. 2558-2567
    • Haste, A.P.1    Nielsen, M.2    Lund, O.3
  • 58
  • 59
    • 0033567326 scopus 로고    scopus 로고
    • Prediction of three-dimensional structure and mapping of conformational epitopes of envelope glycoprotein of Japanese encephalitis virus
    • Kolaskar AS, Kulkarni-Kale U. Prediction of three-dimensional structure and mapping of conformational epitopes of envelope glycoprotein of Japanese encephalitis virus. Virology 1999; 261: 31-42.
    • (1999) Virology , vol.261 , pp. 31-42
    • Kolaskar, A.S.1    Kulkarni-Kale, U.2
  • 61
    • 31144436591 scopus 로고    scopus 로고
    • An in silico method using an epitope motif database for predicting the location of antigenic determinants on proteins in a structural context
    • Batori V, Friis EP, Nielsen H, Roggen EL. An in silico method using an epitope motif database for predicting the location of antigenic determinants on proteins in a structural context. J Mol Recognit 2006; 19: 21-29.
    • (2006) J. Mol. Recognit. , vol.19 , pp. 21-29
    • Batori, V.1    Friis, E.P.2    Nielsen, H.3    Roggen, E.L.4
  • 62
    • 11144246404 scopus 로고    scopus 로고
    • Benchmarking B cell epitope prediction: Underperformance of existing methods
    • Blythe MJ, Flower DR. Benchmarking B cell epitope prediction: underperformance of existing methods. Protein Sci 2005; 14: 246-248.
    • (2005) Protein. Sci. , vol.14 , pp. 246-248
    • Blythe, M.J.1    Flower, D.R.2
  • 63
    • 37749042370 scopus 로고    scopus 로고
    • Antibody-protein interactions: Benchmark datasets and prediction tools evaluation
    • Ponomarenko JV, Bourne PE. Antibody-protein interactions: benchmark datasets and prediction tools evaluation. BMC Struct Biol 2007; 7: 64.
    • (2007) BMC Struct. Biol. , vol.7 , pp. 64
    • Ponomarenko, J.V.1    Bourne, P.E.2
  • 64
    • 34248581488 scopus 로고    scopus 로고
    • Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools
    • Greenbaum JA, Andersen PH, Blythe M, Bui HH, Cachau RE, Crowe J et al. Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. J Mol Recognit 2007; 20: 75-82.
    • (2007) J. Mol. Recognit , vol.20 , pp. 75-82
    • Greenbaum, J.A.1    Andersen, P.H.2    Blythe, M.3    Bui, H.H.4    Cachau, R.E.5    Crowe, J.6
  • 65
    • 45449086674 scopus 로고    scopus 로고
    • PEPITO: Improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure
    • Sweredoski MJ, Baldi P. PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure. Bioinformatics 2008; 24: 1459-1460.
    • (2008) Bioinformatics , vol.24 , pp. 1459-1460
    • Sweredoski, M.J.1    Baldi, P.2
  • 66
    • 0025605617 scopus 로고
    • A semi-empirical method for prediction of antigenic determinants on protein antigens
    • Kolaskar AS, Tongaonkar PC. A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Lett 1990; 276: 172-174.
    • (1990) FEBS Lett.. , vol.276 , pp. 172-174
    • Kolaskar, A.S.1    Tongaonkar, P.C.2
  • 67
    • 74449091535 scopus 로고    scopus 로고
    • In silico predicted conserved B-cell epitopes in the merozoite surface antigen-2 family of B bovis are neutralization sensitive
    • Dominguez M, Echaide I, Echaide ST, Mosqueda J, Cetrá B, Suarez CE et al. In silico predicted conserved B-cell epitopes in the merozoite surface antigen-2 family of B. bovis are neutralization sensitive. Vet Parasitol 2010; 167: 216-226.
    • (2010) Vet. Parasitol. , vol.167 , pp. 216-226
    • Dominguez, M.1    Echaide, I.2    Echaide, S.T.3    Mosqueda, J.4    Cetrá, B.5    Suarez, C.E.6
  • 69
    • 73049097456 scopus 로고    scopus 로고
    • Detection of influenza A and B neutralizing antibodies in vaccinated ferrets and macaques using specific biotin-streptavidin conjugated antibodies
    • Sirskyj D, Weltzin R, Golshani A, Anderson D, Bozic J, Diaz-Mitoma F et al. Detection of influenza A and B neutralizing antibodies in vaccinated ferrets and macaques using specific biotin-streptavidin conjugated antibodies. J Virol Methods 2010; 163: 459-464.
    • (2010) J. Virol. Methods. , vol.163 , pp. 459-464
    • Sirskyj, D.1    Weltzin, R.2    Golshani, A.3    Anderson, D.4    Bozic, J.5    Diaz-Mitoma, F.6
  • 70
    • 0032169271 scopus 로고    scopus 로고
    • Conservation of gene order: A fingerprint of proteins that physically interact
    • Dandekar T, Snel B, Huynen M, Bork P. Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci 1998; 23: 324-328.
    • (1998) Trends. Biochem. Sci. , vol.23 , pp. 324-328
    • Dandekar, T.1    Snel, B.2    Huynen, M.3    Bork, P.4
  • 72
    • 0037110589 scopus 로고    scopus 로고
    • MULTIPROSPECTOR: An algorithm for the prediction of protein-protein interactions by multimeric threading
    • Lu L, Lu H, Skolnick J. MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins 2002; 49: 350-364.
    • (2002) Proteins , vol.49 , pp. 350-364
    • Lu, L.1    Lu, H.2    Skolnick, J.3
  • 73
    • 13444301479 scopus 로고    scopus 로고
    • PreSPI: A domain combination based prediction system for protein-protein interaction
    • Han DS, Kim HS, Jang WH, Lee SD, Suh JK. PreSPI: a domain combination based prediction system for protein-protein interaction. Nucleic Acids Res 2004; 32: 6312-6320.
    • (2004) Nucleic. Acids Res. , vol.32 , pp. 6312-6320
    • Han, D.S.1    Kim, H.S.2    Jang, W.H.3    Lee, S.D.4    Suh, J.K.5
  • 75
    • 34248371273 scopus 로고    scopus 로고
    • Predicting protein-protein interactions based only on sequences information
    • USA
    • Shen J, Zhang J, Luo X, Zhu W, Yu K, Chen K et al. Predicting protein-protein interactions based only on sequences information. Proc Natl Acad Sci USA 2007; 104: 4337-4341.
    • (2007) Proc. Natl. Acad. Sci. , vol.104 , pp. 4337-4341
    • Shen, J.1    Zhang, J.2    Luo, X.3    Zhu, W.4    Yu, K.5    Chen, K.6
  • 76
    • 33748135657 scopus 로고    scopus 로고
    • PIPE: A protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs
    • Pitre S, Dehne F, Chan A, Cheetham J, Duong A, Emili A et al. PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs. BMC Bioinformatics 2006; 7: 365.
    • (2006) BMC Bioinformatics , vol.7 , pp. 365
    • Pitre, S.1    Dehne, F.2    Chan, A.3    Cheetham, J.4    Duong, A.5    Emili, A.6
  • 77
    • 48349125978 scopus 로고    scopus 로고
    • Global investigation of protein-protein interactions in yeast saccharomyces cerevisiae using re-occurring short polypeptide sequences
    • Pitre S, North C, Alamgir M, Jessulat M, Chan A, Luo X et al. Global investigation of protein-protein interaction in yeast saccharomyces cerevisiae using re-occurring short polypeptide sequences. Nucleic Acids Res 2008; 36: 4286-4294.
    • (2008) Nucleic. Acids Res. , vol.36 , pp. 4286-4294
    • Pitre, S.1    North, C.2    Alamgir, M.3    Jessulat, M.4    Chan, A.5    Luo, X.6
  • 78
  • 79
    • 68049124726 scopus 로고    scopus 로고
    • Mucosal vaccines: Novel advances in technology and delivery
    • Yuki Y, Kiyono H. Mucosal vaccines: novel advances in technology and delivery. Expert Rev Vaccines 2009; 8: 1083-1097.
    • (2009) Expert Rev. Vaccines , vol.8 , pp. 1083-1097
    • Yuki, Y.1    Kiyono, H.2
  • 80
    • 25144503019 scopus 로고    scopus 로고
    • Keynote review: Intestinal peyers patch M cells and oral vaccine targeting
    • Brayden DJ, Jepson MA, Baird AW. Keynote review: intestinal Peyers patch M cells and oral vaccine targeting. Drug Discov Today 2005; 10: 1145-1157.
    • (2005) Drug. Discov. Today , vol.10 , pp. 1145-1157
    • Brayden, D.J.1    Jepson, M.A.2    Baird, A.W.3
  • 81
  • 82
    • 27744548806 scopus 로고    scopus 로고
    • Enhanced mucosal and systemic immune response with intranasal immunization of mice with HIV peptides entrapped in PLG microparticles in combination with ulex Europaeus-I lectin as M cell target
    • Manocha M, Pal PC, Chitralekha KT, Thomas BE, Tripathi V, Gupta SD et al. Enhanced mucosal and systemic immune response with intranasal immunization of mice with HIV peptides entrapped in PLG microparticles in combination with Ulex Europaeus-I lectin as M cell target. Vaccine 2005; 23: 5599-5617.
    • (2005) Vaccine , vol.23 , pp. 5599-5617
    • Manocha, M.1    Pal, P.C.2    Chitralekha, K.T.3    Thomas, B.E.4    Tripathi, V.5    Gupta, S.D.6
  • 84
    • 50949083497 scopus 로고    scopus 로고
    • Comprehensive gene expression profiling of peyers patch M cells villous M-like cells and intestinal epithelial cells
    • Terahara K, Yoshida M, Igarashi O, Nochi T, Pontes GS, Hase K et al. Comprehensive gene expression profiling of Peyers patch M cells, villous M-like cells, and intestinal epithelial cells. J Immunol 2008; 180: 7840-7846.
    • (2008) J. Immunol. , vol.180 , pp. 7840-7846
    • Terahara, K.1    Yoshida, M.2    Igarashi, O.3    Nochi, T.4    Pontes, G.S.5    Hase, K.6
  • 85
    • 70449653428 scopus 로고    scopus 로고
    • Uptake through glycoprotein 2 of FimH + bacteria by M cells initiates mucosal immune response
    • Hase K, Kawano K, Nochi T, Pontes GS, Fukuda S, Ebisawa M et al. Uptake through glycoprotein 2 of FimH(+) bacteria by M cells initiates mucosal immune response. Nature 2009; 462: 226-230.
    • (2009) Nature , vol.462 , pp. 226-230
    • Hase, K.1    Kawano, K.2    Nochi, T.3    Pontes, G.S.4    Fukuda, S.5    Ebisawa, M.6
  • 86
    • 0035697665 scopus 로고    scopus 로고
    • The development of multi-epitope vaccines: Epitope identification vaccine design and clinical evaluation
    • Sette A, Livingston B, McKinney D, Appella E, Fikes J, Sidney J et al. The development of multi-epitope vaccines: epitope identification, vaccine design and clinical evaluation. Biologicals 2001; 29: 271-276.
    • (2001) Biologicals , vol.29 , pp. 271-276
    • Sette, A.1    Livingston, B.2    McKinney, D.3    Appella, E.4    Fikes, J.5    Sidney, J.6
  • 87
    • 2942524864 scopus 로고
    • Prediction of major histocompatibility complex binding regions of protein antigens by sequence pattern analysis
    • USA
    • Sette A, Buus S, Appella E, Smith JA, Chesnut R, Miles C et al. Prediction of major histocompatibility complex binding regions of protein antigens by sequence pattern analysis. Proc Natl Acad Sci USA 1989; 86: 3296-3300.
    • (1989) Proc. Natl. Acad. Sci. , vol.86 , pp. 3296-3300
    • Sette, A.1    Buus, S.2    Appella, E.3    Smith, J.A.4    Chesnut, R.5    Miles, C.6
  • 88
    • 2942528885 scopus 로고    scopus 로고
    • Development of experimental carbohydrate-conjugate vaccines composed of Streptococcus pneumoniae capsular polysaccharides and the universal helper T-lymphocyte epitope padre
    • Alexander J, del Guercio MF, Frame B, Maewal A, Sette A, Nahm MH et al. Development of experimental carbohydrate-conjugate vaccines composed of Streptococcus pneumoniae capsular polysaccharides and the universal helper T-lymphocyte epitope (PADRE). Vaccine 2004; 22: 2362-2367.
    • (2004) Vaccine , vol.22 , pp. 2362-2367
    • Alexander, J.1    Del Guercio, M.F.2    Frame, B.3    Maewal, A.4    Sette, A.5    Nahm, M.H.6
  • 89
    • 0036604410 scopus 로고    scopus 로고
    • A rational strategy to design multiepitope immunogens based on multiple Th lymphocyte epitopes
    • Livingston B, Crimi C, Newman M, Higashimoto Y, Appella E, Sidney J et al. A rational strategy to design multiepitope immunogens based on multiple Th lymphocyte epitopes. J Immunol 2002; 168: 5499-5506.
    • (2002) J. Immunol. , vol.168 , pp. 5499-5506
    • Livingston, B.1    Crimi, C.2    Newman, M.3    Higashimoto, Y.4    Appella, E.5    Sidney, J.6
  • 91
    • 7944235123 scopus 로고    scopus 로고
    • Engineering immunogenic consensus T helper epitopes for a cross-clade HIV vaccine
    • De Groot AS, Bishop EA, Khan B, Lally M, Marcon L, Franco J et al. Engineering immunogenic consensus T helper epitopes for a cross-clade HIV vaccine. Methods 2004; 34: 476-487.
    • (2004) Methods , vol.34 , pp. 476-487
    • De Groot, A.S.1    Bishop, E.A.2    Khan, B.3    Lally, M.4    Marcon, L.5    Franco, J.6
  • 92
    • 0029877833 scopus 로고    scopus 로고
    • Strong cytotoxic T cell and weak neutralizing antibody responses in a subset of persons with stable nonprogressing HIV type 1 infection
    • Harrer T, Harrer E, Kalams SA, Elbeik T, Staprans SI, Feinberg MB et al. Strong cytotoxic T cell and weak neutralizing antibody responses in a subset of persons with stable nonprogressing HIV type 1 infection. AIDS Res Hum Retroviruses 1996; 12: 585-592.
    • (1996) AIDS Res. Hum. Retroviruses , vol.12 , pp. 585-592
    • Harrer, T.1    Harrer, E.2    Kalams, S.A.3    Elbeik, T.4    Staprans, S.I.5    Feinberg, M.B.6
  • 93
    • 0029880783 scopus 로고    scopus 로고
    • Cytotoxic T lymphocytes in asymptomatic long-term nonprogressing HIV-1 infection. Breadth and specificity of the response and relation to in vivo viral quasispecies in a person with prolonged infection and low viral load
    • Harrer T, Harrer E, Kalams SA, Barbosa P, Trocha A, Johnson RP et al. Cytotoxic T lymphocytes in asymptomatic long-term nonprogressing HIV-1 infection. Breadth and specificity of the response and relation to in vivo viral quasispecies in a person with prolonged infection and low viral load. J Immunol 1996; 156: 2616-2623.
    • (1996) J. Immunol. , vol.156 , pp. 2616-2623
    • Harrer, T.1    Harrer, E.2    Kalams, S.A.3    Barbosa, P.4    Trocha, A.5    Johnson, R.P.6
  • 94
    • 0028950823 scopus 로고
    • Kinetics of Gag-specific cytotoxic T lymphocyte responses during the clinical course of HIV-1 infection: A longitudinal analysis of rapid progressors and long-term asymptomatics
    • Klein MR, van Baalen CA, Holwerda AM, Kerkhof Garde SR, Bende RJ, Keet IP et al. Kinetics of Gag-specific cytotoxic T lymphocyte responses during the clinical course of HIV-1 infection: a longitudinal analysis of rapid progressors and long-term asymptomatics. J Exp Med 1995; 181: 1365-1372.
    • (1995) J. Exp. Med. , vol.181 , pp. 1365-1372
    • Klein, M.R.1    Van Baalen, C.A.2    Holwerda, A.M.3    Kerkhof Garde, S.R.4    Bende, R.J.5    Keet, I.P.6
  • 95
    • 33748763304 scopus 로고    scopus 로고
    • Virus-epitope vaccine design: Informatic matching the HLA-I polymorphism to the virus genome
    • Vider-Shalit T, Raffaeli S, Louzoun Y. Virus-epitope vaccine design: informatic matching the HLA-I polymorphism to the virus genome. Mol Immunol 2007; 44: 1253-1261.
    • (2007) Mol. Immunol. , vol.44 , pp. 1253-1261
    • Vider-Shalit, T.1    Raffaeli, S.2    Louzoun, Y.3
  • 96
    • 38849161512 scopus 로고    scopus 로고
    • An integrative bioinformatic approach for studying escape mutations in human immunodeficiency virus type 1 gag in the pumwani sex worker cohort
    • Peters HO, Mendoza MG, Capina RE, Luo M, Mao X, Gubbins M et al. An integrative bioinformatic approach for studying escape mutations in human immunodeficiency virus type 1 gag in the Pumwani Sex Worker Cohort. J Virol 2008; 82: 1980-1992.
    • (2008) J. Virol. , vol.82 , pp. 1980-1992
    • Peters, H.O.1    Mendoza, M.G.2    Capina, R.E.3    Luo, M.4    Mao, X.5    Gubbins, M.6
  • 97
    • 0041589474 scopus 로고    scopus 로고
    • Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors
    • Peters B, Bulik S, Tampe R, Van Endert PM, Holzhutter HG. Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors. J Immunol 2003; 171: 1741-1749.
    • (2003) J. Immunol. , vol.171 , pp. 1741-1749
    • Peters, B.1    Bulik, S.2    Tampe, R.3    Van Endert, P.M.4    Holzhutter, H.G.5
  • 98
    • 33748896583 scopus 로고    scopus 로고
    • Antibodies to conserved epitopes of the HIV-1 envelope in sera from long-term non-progressors: Prevalence and association with neutralizing activity
    • Braibant M, Brunet S, Costagliola D, Rouzioux C, Agut H, Katinger H et al. Antibodies to conserved epitopes of the HIV-1 envelope in sera from long-term non-progressors: prevalence and association with neutralizing activity. AIDS 2006; 20: 1923-1930.
    • (2006) AIDS , vol.20 , pp. 1923-1930
    • Braibant, M.1    Brunet, S.2    Costagliola, D.3    Rouzioux, C.4    Agut, H.5    Katinger, H.6
  • 100
    • 0033942757 scopus 로고    scopus 로고
    • Conserved and exposed epitopes on intact native primary human immunodeficiency virus type 1 virions of group M
    • Nyambi PN, Mbah HA, Burda S, Williams C, Gorny MK, Nádas A et al. Conserved and exposed epitopes on intact, native, primary human immunodeficiency virus type 1 virions of group M. J Virol 2000; 74: 7096-7107.
    • (2000) J. Virol. , vol.74 , pp. 7096-7107
    • Nyambi, P.N.1    Mbah, H.A.2    Burda, S.3    Williams, C.4    Gorny, M.K.5    Nádas, A.6
  • 101
    • 38449086859 scopus 로고    scopus 로고
    • Increased sequence diversity coverage improves detection of HIV-specific T cell responses
    • Frahm N, Kaufmann DE, Yusim K, Muldoon M, Kesmir C, Linde CH et al. Increased sequence diversity coverage improves detection of HIV-specific T cell responses. J Immunol 2007; 179: 6638-6650.
    • (2007) J. Immunol. , vol.179 , pp. 6638-6650
    • Frahm, N.1    Kaufmann, D.E.2    Yusim, K.3    Muldoon, M.4    Kesmir, C.5    Linde, C.H.6
  • 102
    • 0032503576 scopus 로고    scopus 로고
    • Hypervariable epitope constructs representing variability in envelope glycoprotein of SIV induce a broad humoral immune response in rabbits and rhesus macaques
    • Meyer D, Anderson DE, Gardner MB, Torres JV. Hypervariable epitope constructs representing variability in envelope glycoprotein of SIV induce a broad humoral immune response in rabbits and rhesus macaques. AIDS Res Hum Retroviruses 1998; 14: 751-760.
    • (1998) AIDS Res. Hum. Retroviruses , vol.14 , pp. 751-760
    • Meyer, D.1    Anderson, D.E.2    Gardner, M.B.3    Torres, J.V.4
  • 103
    • 42149088946 scopus 로고    scopus 로고
    • Induction of broad cross-subtype-specific HIV-1 immune responses by a novel multivalent HIV-1 peptide vaccine in cynomolgus macaques
    • Azizi A, Anderson DE, Torres JV, Ogrel A, Ghorbani M, Soare C et al. Induction of broad cross-subtype-specific HIV-1 immune responses by a novel multivalent HIV-1 peptide vaccine in cynomolgus macaques. J Immunol 2008; 180: 2174-2186.
    • (2008) J. Immunol. , vol.180 , pp. 2174-2186
    • Azizi, A.1    Anderson, D.E.2    Torres, J.V.3    Ogrel, A.4    Ghorbani, M.5    Soare, C.6
  • 104
    • 57149107971 scopus 로고    scopus 로고
    • Safety and immunogenicity of a CTL multiepitope peptide vaccine for HIV with or without GMCSF in a phase I trial
    • Spearman P, Kalams S, Elizaga M, Metch B, Chiu YL, Allen M et al. Safety and immunogenicity of a CTL multiepitope peptide vaccine for HIV with or without GMCSF in a phase I trial. Vaccine 2009; 27: 243-249.
    • (2009) Vaccine , vol.27 , pp. 243-249
    • Spearman, P.1    Kalams, S.2    Elizaga, M.3    Metch, B.4    Chiu, Y.L.5    Allen, M.6
  • 105
    • 0035972026 scopus 로고    scopus 로고
    • A phase I safety and immunogenicity trial of UBI microparticulate monovalent HIV-1 MN oral peptide immunogen with parenteral boost in HIV-1 seronegative human subjects
    • Lambert JS, Keefer M, Mulligan MJ, Schwartz D, Mestecky J, Weinhold K et al. A phase I safety and immunogenicity trial of UBI microparticulate monovalent HIV-1 MN oral peptide immunogen with parenteral boost in HIV-1 seronegative human subjects. Vaccine 2001; 19: 3033-3042.
    • (2001) Vaccine , vol.19 , pp. 3033-3042
    • Lambert, J.S.1    Keefer, M.2    Mulligan, M.J.3    Schwartz, D.4    Mestecky, J.5    Weinhold, K.6
  • 106
    • 70349596123 scopus 로고    scopus 로고
    • Phase I clinical study of a peptide vaccination for hepatitis C virus-infected patients with different human leukocyte antigen-class I-A alleles
    • Yutani S, Komatsu N, Shichijo S, Yoshida K, Takedatsu H, Itou M et al. Phase I clinical study of a peptide vaccination for hepatitis C virus-infected patients with different human leukocyte antigen-class I-A alleles. Cancer Sci 2009; 100: 1935-1942.
    • (2009) Cancer Sci. , vol.100 , pp. 1935-1942
    • Yutani, S.1    Komatsu, N.2    Shichijo, S.3    Yoshida, K.4    Takedatsu, H.5    Itou, M.6


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