메뉴 건너뛰기




Volumn 4, Issue 2, 2012, Pages 193-205

Systems vaccinology: Learning to compute the behavior of vaccine induced immunity

Author keywords

[No Author keywords available]

Indexed keywords

INFLUENZA VACCINE; VACCINE; YELLOW FEVER VACCINE;

EID: 84863129486     PISSN: 19395094     EISSN: 1939005X     Source Type: Journal    
DOI: 10.1002/wsbm.163     Document Type: Article
Times cited : (76)

References (75)
  • 1
    • 73449088379 scopus 로고    scopus 로고
    • Vaccines: the fourth century.
    • Plotkin SA. Vaccines: the fourth century. Clin Vaccine Immunol 2009, 16:1709-1719.
    • (2009) Clin Vaccine Immunol , vol.16 , pp. 1709-1719
    • Plotkin, S.A.1
  • 2
    • 32944478316 scopus 로고    scopus 로고
    • Translating innate immunity into immunological memory: implications for vaccine development.
    • Pulendran B, Ahmed R. Translating innate immunity into immunological memory: implications for vaccine development. Cell 2006, 124:849-863.
    • (2006) Cell , vol.124 , pp. 849-863
    • Pulendran, B.1    Ahmed, R.2
  • 4
    • 0037079054 scopus 로고    scopus 로고
    • Computational systems biology.
    • Kitano H. Computational systems biology. Nature 2002, 420:206-210.
    • (2002) Nature , vol.420 , pp. 206-210
    • Kitano, H.1
  • 8
    • 75749118260 scopus 로고    scopus 로고
    • Expression of genes associated with immunoproteasome processing of major histocompatibility complex peptides is indicative of protection with adjuvanted RTS,S malaria vaccine.
    • Vahey MT, Wang Z, Kester KE, Cummings J, Heppner DG Jr., Nau ME, Ofori-Anyinam O, Cohen J, Coche T, Ballou WR, et al. Expression of genes associated with immunoproteasome processing of major histocompatibility complex peptides is indicative of protection with adjuvanted RTS, S malaria vaccine. J Infect Dis 2010, 201:580-589.
    • (2010) J Infect Dis , vol.201 , pp. 580-589
    • Vahey, M.T.1    Wang, Z.2    Kester, K.E.3    Cummings, J.4    Heppner, D.G.5    Nau, M.E.6    Ofori-Anyinam, O.7    Cohen, J.8    Coche, T.9    Ballou, W.R.10
  • 10
    • 33748642155 scopus 로고    scopus 로고
    • Differences and similarities in viral life cycle progression and host cell physiology after infection of human dendritic cells with modified vaccinia virus Ankara and vaccinia virus.
    • Chahroudi A, Garber DA, Reeves P, Liu L, Kalman D, Feinberg MB. Differences and similarities in viral life cycle progression and host cell physiology after infection of human dendritic cells with modified vaccinia virus Ankara and vaccinia virus. J Virol 2006, 80:8469-8481.
    • (2006) J Virol , vol.80 , pp. 8469-8481
    • Chahroudi, A.1    Garber, D.A.2    Reeves, P.3    Liu, L.4    Kalman, D.5    Feinberg, M.B.6
  • 11
    • 70350451448 scopus 로고    scopus 로고
    • Immunoproteomic analysis of the development of natural immunity in subjects colonized by Neisseria meningitidis reveals potential vaccine candidates.
    • Williams JN, Skipp PJ, O'Connor CD, Christodoulides M, Heckels JE. Immunoproteomic analysis of the development of natural immunity in subjects colonized by Neisseria meningitidis reveals potential vaccine candidates. Infect Immun 2009, 77:5080-5089.
    • (2009) Infect Immun , vol.77 , pp. 5080-5089
    • Williams, J.N.1    Skipp, P.J.2    O'Connor, C.D.3    Christodoulides, M.4    Heckels, J.E.5
  • 12
    • 0036249166 scopus 로고    scopus 로고
    • Identification of vaccine candidate antigens of Staphylococcus aureus by serological proteome analysis.
    • Vytvytska O, Nagy E, Bluggel M, Meyer HE, Kurzbauer R, Huber LA, Klade CS. Identification of vaccine candidate antigens of Staphylococcus aureus by serological proteome analysis. Proteomics 2002, 2:580-590.
    • (2002) Proteomics , vol.2 , pp. 580-590
    • Vytvytska, O.1    Nagy, E.2    Bluggel, M.3    Meyer, H.E.4    Kurzbauer, R.5    Huber, L.A.6    Klade, C.S.7
  • 13
    • 61849131114 scopus 로고    scopus 로고
    • Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination.
    • Reif DM, Motsinger-Reif AA, McKinney BA, Rock MT, Crowe JE Jr., Moore JH. Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination. Genes Immun 2009, 10:112-119.
    • (2009) Genes Immun , vol.10 , pp. 112-119
    • Reif, D.M.1    Motsinger-Reif, A.A.2    McKinney, B.A.3    Rock, M.T.4    Crowe, J.E.5    Moore, J.H.6
  • 16
    • 70349451542 scopus 로고    scopus 로고
    • Learning immunology from the yellow fever vaccine: innate immunity to systems vaccinology.
    • Pulendran B. Learning immunology from the yellow fever vaccine: innate immunity to systems vaccinology. Nat Rev Immunol 2009, 9:741-747.
    • (2009) Nat Rev Immunol , vol.9 , pp. 741-747
    • Pulendran, B.1
  • 17
    • 0031655831 scopus 로고    scopus 로고
    • Development of viremia and humoral and cellular parameters of immune activation after vaccination with yellow fever virus strain 17D: a model of human flavivirus infection.
    • Reinhardt B, Jaspert R, Niedrig M, Kostner C, L'Age-Stehr J. Development of viremia and humoral and cellular parameters of immune activation after vaccination with yellow fever virus strain 17D: a model of human flavivirus infection. J Med Virol 1998, 56:159-167.
    • (1998) J Med Virol , vol.56 , pp. 159-167
    • Reinhardt, B.1    Jaspert, R.2    Niedrig, M.3    Kostner, C.4    L'Age-Stehr, J.5
  • 19
    • 32944455665 scopus 로고    scopus 로고
    • Yellow fever vaccine YF-17D activates multiple dendritic cell subsets via TLR2, 7, 8, and 9 to stimulate polyvalent immunity.
    • Querec T, Bennouna S, Alkan S, Laouar Y, Gorden K, Flavell R, Akira S, Ahmed R, Pulendran B. Yellow fever vaccine YF-17D activates multiple dendritic cell subsets via TLR2, 7, 8, and 9 to stimulate polyvalent immunity. J Exp Med 2006, 203:413-424.
    • (2006) J Exp Med , vol.203 , pp. 413-424
    • Querec, T.1    Bennouna, S.2    Alkan, S.3    Laouar, Y.4    Gorden, K.5    Flavell, R.6    Akira, S.7    Ahmed, R.8    Pulendran, B.9
  • 20
    • 27944493276 scopus 로고    scopus 로고
    • Classification of microarrays to nearest centroids.
    • Dabney AR. Classification of microarrays to nearest centroids. Bioinformatics 2005, 21:4148-4154.
    • (2005) Bioinformatics , vol.21 , pp. 4148-4154
    • Dabney, A.R.1
  • 21
    • 34249741468 scopus 로고    scopus 로고
    • Large-scale optimization-based classification models in medicine and biology.
    • Lee EK. Large-scale optimization-based classification models in medicine and biology. Ann Biomed Eng 2007, 35:1095-1109.
    • (2007) Ann Biomed Eng , vol.35 , pp. 1095-1109
    • Lee, E.K.1
  • 22
    • 13444259647 scopus 로고    scopus 로고
    • Regulation of cap-dependent translation by eIF4E inhibitory proteins.
    • Richter JD, Sonenberg N. Regulation of cap-dependent translation by eIF4E inhibitory proteins. Nature 2005, 433:477-480.
    • (2005) Nature , vol.433 , pp. 477-480
    • Richter, J.D.1    Sonenberg, N.2
  • 23
    • 38449123517 scopus 로고    scopus 로고
    • Mammalian stress granules and processing bodies.
    • Kedersha N, Anderson P. Mammalian stress granules and processing bodies. Methods Enzymol 2007, 431:61-81.
    • (2007) Methods Enzymol , vol.431 , pp. 61-81
    • Kedersha, N.1    Anderson, P.2
  • 24
    • 34250899722 scopus 로고    scopus 로고
    • Signal integration in the endoplasmic reticulum unfolded protein response.
    • Ron D, Walter P. Signal integration in the endoplasmic reticulum unfolded protein response. Nat Rev Mol Cell Biol 2007, 8:519-529.
    • (2007) Nat Rev Mol Cell Biol , vol.8 , pp. 519-529
    • Ron, D.1    Walter, P.2
  • 27
    • 68049144603 scopus 로고    scopus 로고
    • Next-generation sequencing: a transformative tool for vaccinology.
    • Dhiman N, Smith DI, Poland GA. Next-generation sequencing: a transformative tool for vaccinology. Expert Rev Vaccines 2009, 8:963-967.
    • (2009) Expert Rev Vaccines , vol.8 , pp. 963-967
    • Dhiman, N.1    Smith, D.I.2    Poland, G.A.3
  • 28
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: a revolutionary tool for transcriptomics.
    • Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10:57-63.
    • (2009) Nat Rev Genet , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 29
    • 76949094687 scopus 로고    scopus 로고
    • Integrating genomic signatures for immunologic discovery.
    • Haining WN, Wherry EJ. Integrating genomic signatures for immunologic discovery. Immunity 2010, 32:152-161.
    • (2010) Immunity , vol.32 , pp. 152-161
    • Haining, W.N.1    Wherry, E.J.2
  • 30
    • 38849146505 scopus 로고    scopus 로고
    • Understanding biological functions through molecular networks.
    • Han JDJ. Understanding biological functions through molecular networks. Cell Res 2008, 18:224-237.
    • (2008) Cell Res , vol.18 , pp. 224-237
    • Han, J.D.J.1
  • 31
    • 54249155522 scopus 로고    scopus 로고
    • Network pharmacology: the next paradigm in drug discovery.
    • Hopkins AL. Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol 2008, 4: 682-690.
    • (2008) Nat Chem Biol , vol.4 , pp. 682-690
    • Hopkins, A.L.1
  • 32
    • 77949773550 scopus 로고    scopus 로고
    • Towards genome-scale signalling-network reconstructions.
    • Hyduke DR, Palsson BO. Towards genome-scale signalling-network reconstructions. Nat Rev Genet 2010, 11:297-307.
    • (2010) Nat Rev Genet , vol.11 , pp. 297-307
    • Hyduke, D.R.1    Palsson, B.O.2
  • 33
    • 54249117223 scopus 로고    scopus 로고
    • Targeting and tinkering with interaction networks.
    • Russell RB, Aloy P. Targeting and tinkering with interaction networks. Nat Chem Biol 2008, 4:666-673.
    • (2008) Nat Chem Biol , vol.4 , pp. 666-673
    • Russell, R.B.1    Aloy, P.2
  • 34
    • 70249134919 scopus 로고    scopus 로고
    • Molecular networks as sensors and drivers of common human diseases.
    • Schadt EE. Molecular networks as sensors and drivers of common human diseases. Nature 2009, 461: 218-223.
    • (2009) Nature , vol.461 , pp. 218-223
    • Schadt, E.E.1
  • 35
    • 0001677717 scopus 로고
    • Controlling the false discovery rate-a practical and powerful approach to multiple testing.
    • Benjamini Y, Hochberg Y. Controlling the false discovery rate-a practical and powerful approach to multiple testing. J R Stat Soc Ser B 1995, 57:289-300.
    • (1995) J R Stat Soc Ser B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 36
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genomewide studies.
    • Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 2003, 100:9440-9445.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 9440-9445
    • Storey, J.D.1    Tibshirani, R.2
  • 38
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response.
    • Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 2001, 98: 5116-5121.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 39
    • 29244448340 scopus 로고    scopus 로고
    • Microarray data analysis: from disarray to consolidation and consensus.
    • Allison DB, Cui X, Page GP, Sabripour M. Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet 2006, 7:55-65.
    • (2006) Nat Rev Genet , vol.7 , pp. 55-65
    • Allison, D.B.1    Cui, X.2    Page, G.P.3    Sabripour, M.4
  • 43
    • 75549090213 scopus 로고    scopus 로고
    • KEGG for representation and analysis of molecular networks involving diseases and drugs.
    • Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 2010, 38:D355-D360.
    • (2010) Nucleic Acids Res , vol.38
    • Kanehisa, M.1    Goto, S.2    Furumichi, M.3    Tanabe, M.4    Hirakawa, M.5
  • 46
    • 15944395145 scopus 로고    scopus 로고
    • Insights into host responses against pathogens from transcriptional profiling.
    • Jenner RG, Young RA. Insights into host responses against pathogens from transcriptional profiling. Nat Rev Microbiol 2005, 3:281-294.
    • (2005) Nat Rev Microbiol , vol.3 , pp. 281-294
    • Jenner, R.G.1    Young, R.A.2
  • 48
    • 34547667125 scopus 로고    scopus 로고
    • Distinct gene expression profiles in peripheral blood mononuclear cells from patients infected with vaccinia virus, yellow fever 17D virus, or upper respiratory infections.
    • Scherer CA, Magness CL, Steiger KV, Poitinger ND, Caputo CM, Miner DG, Winokur PL, Klinzman D, McKee J, Pilar C, et al. Distinct gene expression profiles in peripheral blood mononuclear cells from patients infected with vaccinia virus, yellow fever 17D virus, or upper respiratory infections. Vaccine 2007, 25: 6458-6473.
    • (2007) Vaccine , vol.25 , pp. 6458-6473
    • Scherer, C.A.1    Magness, C.L.2    Steiger, K.V.3    Poitinger, N.D.4    Caputo, C.M.5    Miner, D.G.6    Winokur, P.L.7    Klinzman, D.8    McKee, J.9    Pilar, C.10
  • 49
    • 78650735473 scopus 로고    scopus 로고
    • The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.
    • Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol 2010, 28:827-838.
    • (2010) Nat Biotechnol , vol.28 , pp. 827-838
    • Shi, L.1    Campbell, G.2    Jones, W.D.3    Campagne, F.4    Wen, Z.5    Walker, S.J.6    Su, Z.7    Chu, T.M.8    Goodsaid, F.M.9    Pusztai, L.10
  • 51
    • 0037076272 scopus 로고    scopus 로고
    • Diagnosis of multiple cancer types by shrunken centroids of gene expression.
    • Tibshirani R, Hastie T, Narasimhan B, Chu G. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci U S A 2002, 99:6567-6572.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 6567-6572
    • Tibshirani, R.1    Hastie, T.2    Narasimhan, B.3    Chu, G.4
  • 52
    • 10444280144 scopus 로고    scopus 로고
    • An extensive comparison of recent classification tools applied to microarray data.
    • Lee JW, Lee JB, Park M, Song SH. An extensive comparison of recent classification tools applied to microarray data. Comp Stat Data Anal 2005, 48:869-885.
    • (2005) Comp Stat Data Anal , vol.48 , pp. 869-885
    • Lee, J.W.1    Lee, J.B.2    Park, M.3    Song, S.H.4
  • 54
    • 30644464444 scopus 로고    scopus 로고
    • Gene selection and classification of microarray data using random forest.
    • Diaz-Uriarte R, de Andres SA. Gene selection and classification of microarray data using random forest. BMC Bioinform 2006, 7:3.
    • (2006) BMC Bioinform , vol.7 , pp. 3
    • Diaz-Uriarte, R.1    de Andres, S.A.2
  • 55
    • 67749113808 scopus 로고    scopus 로고
    • Transcriptional regulatory circuits: predicting numbers from alphabets.
    • Kim HD, Shay T, O'Shea EK, Regev A. Transcriptional regulatory circuits: predicting numbers from alphabets. Science 2009, 325:429-432.
    • (2009) Science , vol.325 , pp. 429-432
    • Kim, H.D.1    Shay, T.2    O'Shea, E.K.3    Regev, A.4
  • 58
    • 69949083414 scopus 로고    scopus 로고
    • Modulation of adaptive immunity with Toll-like receptors.
    • Manicassamy S, Pulendran B. Modulation of adaptive immunity with Toll-like receptors. Semin Immunol 2009, 21:185-193.
    • (2009) Semin Immunol , vol.21 , pp. 185-193
    • Manicassamy, S.1    Pulendran, B.2
  • 63
    • 1042275615 scopus 로고    scopus 로고
    • Modification-specific proteomics: characterization of post-translational modifications by mass spectrometry.
    • Jensen ON. Modification-specific proteomics: characterization of post-translational modifications by mass spectrometry. Curr Opin Chem Biol 2004, 8:33-41.
    • (2004) Curr Opin Chem Biol , vol.8 , pp. 33-41
    • Jensen, O.N.1
  • 64
    • 79956079190 scopus 로고    scopus 로고
    • Immunological mechanisms of vaccination.
    • Pulendran B, Ahmed R. Immunological mechanisms of vaccination. Nat Immunol 2011, 12:509-517.
    • (2011) Nat Immunol , vol.12 , pp. 509-517
    • Pulendran, B.1    Ahmed, R.2
  • 65
    • 76449115656 scopus 로고    scopus 로고
    • Integrating multiple 'omics' analysis for microbial biology: application and methodologies.
    • Zhang W, Li F, Nie L. Integrating multiple 'omics' analysis for microbial biology: application and methodologies. Microbiology 2010, 156:287-301.
    • (2010) Microbiology , vol.156 , pp. 287-301
    • Zhang, W.1    Li, F.2    Nie, L.3
  • 66
    • 77954384233 scopus 로고    scopus 로고
    • Assessing the human immune system through blood transcriptomics.
    • Chaussabel D, Pascual V, Banchereau J. Assessing the human immune system through blood transcriptomics. BMC Biol 2010, 8:84.
    • (2010) BMC Biol , vol.8 , pp. 84
    • Chaussabel, D.1    Pascual, V.2    Banchereau, J.3
  • 67
    • 67749112023 scopus 로고    scopus 로고
    • Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus.
    • Abbas AR, Wolslegel K, Seshasayee D, Modrusan Z, Clark HF. Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus. PLoS One 2009, 4:e6098.
    • (2009) PLoS One , vol.4
    • Abbas, A.R.1    Wolslegel, K.2    Seshasayee, D.3    Modrusan, Z.4    Clark, H.F.5
  • 71
    • 47549116006 scopus 로고    scopus 로고
    • Vaccines: correlates of vaccine-induced immunity.
    • Plotkin SA. Vaccines: correlates of vaccine-induced immunity. Clin Infect Dis 2008, 47:401-409.
    • (2008) Clin Infect Dis , vol.47 , pp. 401-409
    • Plotkin, S.A.1
  • 73
    • 33645825183 scopus 로고    scopus 로고
    • Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer.
    • Ein-Dor L, Zuk O, Domany E. Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc Natl Acad Sci U S A 2006, 103:5923-5928.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 5923-5928
    • Ein-Dor, L.1    Zuk, O.2    Domany, E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.