메뉴 건너뛰기




Volumn 23, Issue 13, 2007, Pages

From protein microarrays to diagnostic antigen discovery: A study of the pathogen Francisella tularensis

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ANTIGEN;

EID: 34547852232     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm207     Document Type: Conference Paper
Times cited : (77)

References (47)
  • 1
    • 3242883431 scopus 로고    scopus 로고
    • PRED-TMBB: A web server for predicting the topology of beta-barrel outer membrane proteins
    • Bagos, P.G. et al. (2004) PRED-TMBB: A web server for predicting the topology of beta-barrel outer membrane proteins. Nucleic Acids Res., 32, W400-W404.
    • (2004) Nucleic Acids Res , vol.32
    • Bagos, P.G.1
  • 2
    • 0034948896 scopus 로고    scopus 로고
    • A Bayesian framework for the analysis of microarray expression data: Regularized t-test and statistical inferences of gene changes
    • Baldi, P. and Long, A.D. (2001) A Bayesian framework for the analysis of microarray expression data: Regularized t-test and statistical inferences of gene changes. Bioinformatics, 17, 509-519.
    • (2001) Bioinformatics , vol.17 , pp. 509-519
    • Baldi, P.1    Long, A.D.2
  • 4
    • 33748748033 scopus 로고    scopus 로고
    • Analysis of human leukaemias and lymphomas using extensive immunopbenotypes from an antibody microarray
    • Belov et al. (2006) Analysis of human leukaemias and lymphomas using extensive immunopbenotypes from an antibody microarray. Br. J. Haematol., 135, 184-197.
    • (2006) Br. J. Haematol , vol.135 , pp. 184-197
    • Belov1
  • 5
    • 3042521098 scopus 로고    scopus 로고
    • Improved prediction of signal peptides: SignalP 3.0
    • Bendtsen, J.D. et al. (2004) Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol., 340, 783-795.
    • (2004) J. Mol. Biol , vol.340 , pp. 783-795
    • Bendtsen, J.D.1
  • 6
    • 29644437923 scopus 로고    scopus 로고
    • GroEL of Lactobacillus johnsonii La1 (NCC 533) is cell surface associated: Potential role in interactions with the host and the gastric pathogen Helicobacter pylori
    • Bergonzelli, G.E. et al. (2006) GroEL of Lactobacillus johnsonii La1 (NCC 533) is cell surface associated: Potential role in interactions with the host and the gastric pathogen Helicobacter pylori. Infect. Immun, 74, 425-434.
    • (2006) Infect. Immun , vol.74 , pp. 425-434
    • Bergonzelli, G.E.1
  • 7
    • 33646856024 scopus 로고    scopus 로고
    • Avoiding model selection bias in small-sample genomic datasets
    • Berrar, D. et al. (2006) Avoiding model selection bias in small-sample genomic datasets. Bioinformatics, 22, 1245-1250.
    • (2006) Bioinformatics , vol.22 , pp. 1245-1250
    • Berrar, D.1
  • 8
    • 3042678854 scopus 로고    scopus 로고
    • Predicting transmembrane beta-barrels in proteomes
    • Bigelow, H.R. et al. (2004) Predicting transmembrane beta-barrels in proteomes. Nucleic Acids Res., 32, 2566-2577.
    • (2004) Nucleic Acids Res , vol.32 , pp. 2566-2577
    • Bigelow, H.R.1
  • 9
    • 33646377150 scopus 로고    scopus 로고
    • Protein arrays and pattern recognition: New tools to assist in the identification and management of autoimmune disease
    • Bindcr, S.R. et al. (2006) Protein arrays and pattern recognition: new tools to assist in the identification and management of autoimmune disease. Autoimmun. Rev., 5, 234-241.
    • (2006) Autoimmun. Rev , vol.5 , pp. 234-241
    • Bindcr, S.R.1
  • 10
    • 5644277479 scopus 로고    scopus 로고
    • Rapid screening of highly efficient vaccine candidates by immunoproteomics
    • Chen, Z. et al. (2004) Rapid screening of highly efficient vaccine candidates by immunoproteomics. Proteomics, 4, 3203-3213.
    • (2004) Proteomics , vol.4 , pp. 3203-3213
    • Chen, Z.1
  • 11
    • 22144461265 scopus 로고    scopus 로고
    • Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset
    • Choe, S.E. et al. (2005) Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol. 6, R16.
    • (2005) Genome Biol , vol.6
    • Choe, S.E.1
  • 12
    • 17644397901 scopus 로고    scopus 로고
    • Surface analyses and immune reactivities of major cell wall-associated proteins of group A Streptococcus
    • Cole, J.N. et al. (2005) Surface analyses and immune reactivities of major cell wall-associated proteins of group A Streptococcus. Infect Immun., 73, 3137-3146.
    • (2005) Infect Immun , vol.73 , pp. 3137-3146
    • Cole, J.N.1
  • 13
    • 0242495755 scopus 로고    scopus 로고
    • Cutting edge: Long-term B cell memory in humans after smallpox vaccination
    • Crotty, S. et al. (2003) Cutting edge: Long-term B cell memory in humans after smallpox vaccination. J. Immunol., 171, 4969-4973.
    • (2003) J. Immunol , vol.171 , pp. 4969-4973
    • Crotty, S.1
  • 14
    • 20044369888 scopus 로고    scopus 로고
    • Profiling the humoral immune response to infection, by using proteome microarrays: High-throughput vaccine and diagnostic antigen discovery
    • Davies, D.H. et al. (2005a) Profiling the humoral immune response to infection, by using proteome microarrays: High-throughput vaccine and diagnostic antigen discovery. Proc. Natl Acad. Sci. USA, 102 547-552.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 547-552
    • Davies, D.H.1
  • 15
    • 24644490503 scopus 로고    scopus 로고
    • Vaccinia virus H3L envelope protein is a major target of neutralizing antibodies in humans and elicits protection against lethal challenge in mice
    • Davies, D.H. et al. (2005b) Vaccinia virus H3L envelope protein is a major target of neutralizing antibodies in humans and elicits protection against lethal challenge in mice. J. Virol., 79, 11724-11733.
    • (2005) J. Virol , vol.79 , pp. 11724-11733
    • Davies, D.H.1
  • 16
    • 0035816032 scopus 로고    scopus 로고
    • Tularemia as a biological weapon: Medical and public health management
    • Dennis, D.T. et al. (2001) Tularemia as a biological weapon: medical and public health management. Jama, 285, 2763-2773.
    • (2001) Jama , vol.285 , pp. 2763-2773
    • Dennis, D.T.1
  • 17
    • 17644384367 scopus 로고    scopus 로고
    • Minimum redundancy feature selection from microarray gene expression data
    • Ding, C. and Peng, H. (2005) Minimum redundancy feature selection from microarray gene expression data. J. Bioinform. Comput. Biol., 3 185-205.
    • (2005) J. Bioinform. Comput. Biol , vol.3 , pp. 185-205
    • Ding, C.1    Peng, H.2
  • 18
    • 10744220951 scopus 로고    scopus 로고
    • Utilization of genomic sequence information to develop malaria vaccines
    • Doolan, D.L. et al. (2003) Utilization of genomic sequence information to develop malaria vaccines. J. Exp. Biol., 206, 3789-3802.
    • (2003) J. Exp. Biol , vol.206 , pp. 3789-3802
    • Doolan, D.L.1
  • 19
    • 0012572299 scopus 로고    scopus 로고
    • A variance-stabilizing transformation for gene-expression microarray data
    • Durbin, B. et al. (2002) A variance-stabilizing transformation for gene-expression microarray data. Bioinformatics, 18, S105-S110.
    • (2002) Bioinformatics , vol.18
    • Durbin, B.1
  • 20
    • 0036489046 scopus 로고    scopus 로고
    • Comparison of discrimination methods for the classification of tumors using gene expression data
    • Dudoit, S. et al. (2002) Comparison of discrimination methods for the classification of tumors using gene expression data. J. Am. Stat. Assoc., 97, 77-87.
    • (2002) J. Am. Stat. Assoc , vol.97 , pp. 77-87
    • Dudoit, S.1
  • 21
    • 0036780908 scopus 로고    scopus 로고
    • Tularemia
    • Ellis, J. et al. (2002) Tularemia. Clin. Microbiol. Rev., 15, 631-646.
    • (2002) Clin. Microbiol. Rev , vol.15 , pp. 631-646
    • Ellis, J.1
  • 22
    • 33645462222 scopus 로고    scopus 로고
    • Direct repeat mediated deletion of a Type IV pilin gene results in major virulence attenuation of Francisella tularensis
    • Forslund, A.-L. et al. (2006) Direct repeat mediated deletion of a Type IV pilin gene results in major virulence attenuation of Francisella tularensis. Mol. Microbiol., 59, 1818-1830.
    • (2006) Mol. Microbiol , vol.59 , pp. 1818-1830
    • Forslund, A.-L.1
  • 23
    • 0031692318 scopus 로고    scopus 로고
    • Surface-associated hsp60 chaperonin of Legionella pneumophila mediates invasion in a HeLa cell model
    • Garduno, R.A. et al. (1998) Surface-associated hsp60 chaperonin of Legionella pneumophila mediates invasion in a HeLa cell model. Infect. Immun., 66, 4602-4610.
    • (1998) Infect. Immun , vol.66 , pp. 4602-4610
    • Garduno, R.A.1
  • 24
    • 15844431346 scopus 로고    scopus 로고
    • PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis
    • Gardy, J.L. et al. (2005) PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics, 21, 617-623.
    • (2005) Bioinformatics , vol.21 , pp. 617-623
    • Gardy, J.L.1
  • 25
    • 23144440152 scopus 로고    scopus 로고
    • TMB-Hunt: A web server to screen sequence sets for transmembrane beta-barrel proteins
    • Garrow, A.G. et al. (2005) TMB-Hunt: A web server to screen sequence sets for transmembrane beta-barrel proteins. Nucleic Acids Res., 33, W188-W192.
    • (2005) Nucleic Acids Res , vol.33
    • Garrow, A.G.1
  • 26
    • 33750464521 scopus 로고    scopus 로고
    • Use of protein microarrays to define the humoral immune response in leprosy patients and identification of disease-state-specific antigenic profiles
    • Groathouse et al. (2006) Use of protein microarrays to define the humoral immune response in leprosy patients and identification of disease-state-specific antigenic profiles. Infect. Immun., 74 6458-6466.
    • (2006) Infect. Immun , vol.74 , pp. 6458-6466
    • Groathouse1
  • 27
    • 0033569406 scopus 로고    scopus 로고
    • Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring
    • Gohib, T.R. et al. (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science, 286, 531-537.
    • (1999) Science , vol.286 , pp. 531-537
    • Gohib, T.R.1
  • 28
    • 0037323928 scopus 로고    scopus 로고
    • Differential analysis of DNA microarray gene expression data
    • Hatfield, G.W. et al. (2002) Differential analysis of DNA microarray gene expression data. Mol. Microb., 47, 871-877.
    • (2002) Mol. Microb , vol.47 , pp. 871-877
    • Hatfield, G.W.1
  • 29
    • 11244346557 scopus 로고    scopus 로고
    • Variance stabilization applied to microarray data calibration and to the quantification of differential expression, Suppl, S96-S104ISMB
    • Huber, W. et al. (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics, 18 (Suppl.), S96-S104(ISMB 2002).
    • (2002) Bioinformatics , vol.18
    • Huber, W.1
  • 30
    • 0037174983 scopus 로고    scopus 로고
    • Global gene expression profiling in Escherichia coli K12: The effects of leucine-responsive regulatory protein
    • Hung, S.-P. et al. (2002) Global gene expression profiling in Escherichia coli K12: The effects of leucine-responsive regulatory protein. J. Biol. Chem., 277, 40309-40323.
    • (2002) J. Biol. Chem , vol.277 , pp. 40309-40323
    • Hung, S.-P.1
  • 31
    • 20444366966 scopus 로고    scopus 로고
    • Vaccination strategies for Francisella tularensis
    • Isherwood, K.E. et al. (2005) Vaccination strategies for Francisella tularensis. Adv. Drug Deriv. Rev., 57, 1403-1414.
    • (2005) Adv. Drug Deriv. Rev , vol.57 , pp. 1403-1414
    • Isherwood, K.E.1
  • 32
    • 0033626293 scopus 로고    scopus 로고
    • Sequencing of the Francisella tularensis strain Schu 4 genome reveals the shikimate and purine metabolic pathways, targets for the construction of a rationally attenuated auxotrophic vaccine
    • Karlsson, J. et al. (2000) Sequencing of the Francisella tularensis strain Schu 4 genome reveals the shikimate and purine metabolic pathways, targets for the construction of a rationally attenuated auxotrophic vaccine. Microb. Comp. Genomics, 5, 25-39.
    • (2000) Microb. Comp. Genomics , vol.5 , pp. 25-39
    • Karlsson, J.1
  • 33
    • 0035910270 scopus 로고    scopus 로고
    • Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes
    • Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E.L.L. (2001), Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes, J. Mol. Biol., 305, 567-580.
    • (2001) J. Mol. Biol , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    von Heijne, G.3    Sonnhammer, E.L.L.4
  • 34
    • 13944273799 scopus 로고    scopus 로고
    • The complete genome sequence of Francisella tularensis, the causative agent of tularemia
    • Larsson, P. et al. (2005) The complete genome sequence of Francisella tularensis, the causative agent of tularemia. Nat. Genet., 37, 153-159.
    • (2005) Nat. Genet , vol.37 , pp. 153-159
    • Larsson, P.1
  • 35
    • 0038729565 scopus 로고    scopus 로고
    • Classification of multiple cancer types by multicategory support vector machines using gene expression data
    • Lee, Y. and Lee, C.K. (2003) Classification of multiple cancer types by multicategory support vector machines using gene expression data. Bioinformatics, 19, 1132-1139.
    • (2003) Bioinformatics , vol.19 , pp. 1132-1139
    • Lee, Y.1    Lee, C.K.2
  • 36
    • 0035827588 scopus 로고    scopus 로고
    • Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12
    • Long, A.D. et al. (2001) Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J. Biol. Chem., 276, 19937-19944.
    • (2001) J. Biol. Chem , vol.276 , pp. 19937-19944
    • Long, A.D.1
  • 38
    • 0042847140 scopus 로고    scopus 로고
    • Inference for generalization error
    • Nadeau, C. and Bengio, Y. (2003) Inference for generalization error. Mach. Learn., 52, 239-281.
    • (2003) Mach. Learn , vol.52 , pp. 239-281
    • Nadeau, C.1    Bengio, Y.2
  • 39
    • 0036740519 scopus 로고    scopus 로고
    • Multi-class cancer classification via partial least squares with gene expression profiles
    • Nguyen, D.V. and Rocke, D.M. (2002) Multi-class cancer classification via partial least squares with gene expression profiles. Bioinformalics, 18, 1216-1226.
    • (2002) Bioinformalics , vol.18 , pp. 1216-1226
    • Nguyen, D.V.1    Rocke, D.M.2
  • 40
    • 33749347870 scopus 로고    scopus 로고
    • Chromosome rearrangement and diversification of Francisella tularensis revealed by the type B (OSU18) genome sequence
    • Petrosino, J.F. et al. (2006) Chromosome rearrangement and diversification of Francisella tularensis revealed by the type B (OSU18) genome sequence. J. Bacteriol., 188, 6977-6985.
    • (2006) J. Bacteriol , vol.188 , pp. 6977-6985
    • Petrosino, J.F.1
  • 41
    • 0034785966 scopus 로고    scopus 로고
    • Preliminary analysis and annotation of the partial genome sequence of Francisella tularensis strain Schu 4
    • Prior, R.G. et al. (2001) Preliminary analysis and annotation of the partial genome sequence of Francisella tularensis strain Schu 4. J. Appl. Microbiol., 91, 1-7.
    • (2001) J. Appl. Microbiol , vol.91 , pp. 1-7
    • Prior, R.G.1
  • 42
    • 0035684378 scopus 로고    scopus 로고
    • A model for measurement errors for gene expression arrays
    • Rocke, D.M. and Durbin, B. (2001) A model for measurement errors for gene expression arrays. J. Comput. Biol., 8, 557-569.
    • (2001) J. Comput. Biol , vol.8 , pp. 557-569
    • Rocke, D.M.1    Durbin, B.2
  • 43
    • 33747886203 scopus 로고    scopus 로고
    • Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques
    • Sundaresh, S. et al. (2006) Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques. Bioinformatics, 22, 1760-1766.
    • (2006) Bioinformatics , vol.22 , pp. 1760-1766
    • Sundaresh, S.1
  • 44
    • 0037076272 scopus 로고    scopus 로고
    • Diagnosis of multiple cancer types by shrunken centroids of gene expression
    • Tibshirani, R. et al. (2002) Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc. Natl Acad. Sci. USA, 99, 6567-6572.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 6567-6572
    • Tibshirani, R.1
  • 45
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • Tusher, V.G. et al. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci, 98, 5116-5121.
    • (2001) Proc. Natl Acad. Sci , vol.98 , pp. 5116-5121
    • Tusher, V.G.1
  • 47
    • 25444491937 scopus 로고    scopus 로고
    • Protein subcellular localization prediction for Gram-negative bacteria using amino acid subalphabets and a combination of multiple support vector machines
    • Wang, J. et al. (2005) Protein subcellular localization prediction for Gram-negative bacteria using amino acid subalphabets and a combination of multiple support vector machines. BMC Bioinform., 6, 174.
    • (2005) BMC Bioinform , vol.6 , pp. 174
    • Wang, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.