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Volumn 300, Issue 2-3, 2010, Pages 88-97

New approaches for functional genomic studies in staphylococci

Author keywords

High throughput sequencing; Microarrays; NanoString nCounterTM assay; RNA seq; RT PCR; SAGE; Staphylococcus aureus; Transcriptomics

Indexed keywords

BACTERIAL VIRULENCE; COMPARATIVE GENOMIC HYBRIDIZATION; FUNCTIONAL GENOMICS; MEDICAL RESEARCH; MICROARRAY ANALYSIS; NONHUMAN; REAL TIME POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; SHORT SURVEY; STAPHYLOCOCCUS; TRANSCRIPTOMICS;

EID: 73649095077     PISSN: 14384221     EISSN: 16180607     Source Type: Journal    
DOI: 10.1016/j.ijmm.2009.11.001     Document Type: Short Survey
Times cited : (10)

References (85)
  • 6
    • 57049134826 scopus 로고    scopus 로고
    • Serial daptomycin selection generates daptomycin-nonsusceptible Staphylococcus aureus strains with a heterogeneous vancomycin-intermediate phenotype
    • Camargo I.L., Neoh H.M., Cui L., and Hiramatsu K. Serial daptomycin selection generates daptomycin-nonsusceptible Staphylococcus aureus strains with a heterogeneous vancomycin-intermediate phenotype. Antimicrob. Agents Chemother. 52 (2008) 4289-4299
    • (2008) Antimicrob. Agents Chemother. , vol.52 , pp. 4289-4299
    • Camargo, I.L.1    Neoh, H.M.2    Cui, L.3    Hiramatsu, K.4
  • 7
    • 58849111811 scopus 로고    scopus 로고
    • Pathogenesis of staphylococcal infection: a manner of expression
    • Chambers H.F. Pathogenesis of staphylococcal infection: a manner of expression. J. Infect. Dis. 199 (2009) 291-293
    • (2009) J. Infect. Dis. , vol.199 , pp. 291-293
    • Chambers, H.F.1
  • 8
    • 25444518699 scopus 로고    scopus 로고
    • A generic approach for the design of whole-genome oligoarrays, validated for genomotyping, deletion mapping and gene expression analysis on Staphylococcus aureus
    • Charbonnier Y., Gettler B.M., Francois P., Bento M., Renzoni A., Vaudaux P., Schlegel W., and Schrenzel J. A generic approach for the design of whole-genome oligoarrays, validated for genomotyping, deletion mapping and gene expression analysis on Staphylococcus aureus. BMC Genomics 6 (2005) 95
    • (2005) BMC Genomics , vol.6 , pp. 95
    • Charbonnier, Y.1    Gettler, B.M.2    Francois, P.3    Bento, M.4    Renzoni, A.5    Vaudaux, P.6    Schlegel, W.7    Schrenzel, J.8
  • 10
    • 10044287197 scopus 로고    scopus 로고
    • Evaluation of a high-density oligonucleotide array for characterization of grlA, grlB, gyrA and gyrB mutations in fluoroquinolone resistant Staphylococcus aureus isolates
    • Couzinet S., Yugueros J., Barras C., Visomblin N., Francois P., Lacroix B., Vernet G., Lew D., Troesch A., Schrenzel J., and Jay C. Evaluation of a high-density oligonucleotide array for characterization of grlA, grlB, gyrA and gyrB mutations in fluoroquinolone resistant Staphylococcus aureus isolates. J. Microbiol. Methods 60 (2005) 275-279
    • (2005) J. Microbiol. Methods , vol.60 , pp. 275-279
    • Couzinet, S.1    Yugueros, J.2    Barras, C.3    Visomblin, N.4    Francois, P.5    Lacroix, B.6    Vernet, G.7    Lew, D.8    Troesch, A.9    Schrenzel, J.10    Jay, C.11
  • 11
    • 23044474892 scopus 로고    scopus 로고
    • DNA microarray-based identification of genes associated with glycopeptide resistance in Staphylococcus aureus
    • Cui L., Lian J.Q., Neoh H.M., Reyes E., and Hiramatsu K. DNA microarray-based identification of genes associated with glycopeptide resistance in Staphylococcus aureus. Antimicrob. Agents Chemother. 49 (2005) 3404-3413
    • (2005) Antimicrob. Agents Chemother. , vol.49 , pp. 3404-3413
    • Cui, L.1    Lian, J.Q.2    Neoh, H.M.3    Reyes, E.4    Hiramatsu, K.5
  • 12
    • 84984934048 scopus 로고    scopus 로고
    • DNA microarrays in drug discovery and development
    • Debouck C., and Goodfellow P.N. DNA microarrays in drug discovery and development. Nat. Genet. 21 (1999) 48-50
    • (1999) Nat. Genet. , vol.21 , pp. 48-50
    • Debouck, C.1    Goodfellow, P.N.2
  • 18
    • 0035520472 scopus 로고    scopus 로고
    • Evolutionary genomics of pathogenic bacteria
    • Fitzgerald J.R., and Musser J.M. Evolutionary genomics of pathogenic bacteria. Trends Microbiol. 9 (2001) 547-553
    • (2001) Trends Microbiol. , vol.9 , pp. 547-553
    • Fitzgerald, J.R.1    Musser, J.M.2
  • 19
    • 0035902534 scopus 로고    scopus 로고
    • Evolutionary genomics of Staphylococcus aureus: insights into the origin of methicillin-resistant strains and the toxic shock syndrome epidemic
    • Fitzgerald J.R., Sturdevant D.E., Mackie S.M., Gill S.R., and Musser J.M. Evolutionary genomics of Staphylococcus aureus: insights into the origin of methicillin-resistant strains and the toxic shock syndrome epidemic. Proc. Natl. Acad. Sci. USA 98 (2001) 8821-8826
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 8821-8826
    • Fitzgerald, J.R.1    Sturdevant, D.E.2    Mackie, S.M.3    Gill, S.R.4    Musser, J.M.5
  • 21
    • 0026108692 scopus 로고
    • Light-directed, spatially addressable parallel chemical synthesis
    • Fodor S.P., Read J.L., Pirrung M.C., Stryer L., Lu A.T., and Solas D. Light-directed, spatially addressable parallel chemical synthesis. Science 251 (1991) 767-773
    • (1991) Science , vol.251 , pp. 767-773
    • Fodor, S.P.1    Read, J.L.2    Pirrung, M.C.3    Stryer, L.4    Lu, A.T.5    Solas, D.6
  • 27
    • 0035108693 scopus 로고    scopus 로고
    • Quantification of bacterial transcripts during infection using competitive reverse transcription-PCR (RT-PCR) and LightCycler RT-PCR
    • Goerke C., Bayer M.G., and Wolz C. Quantification of bacterial transcripts during infection using competitive reverse transcription-PCR (RT-PCR) and LightCycler RT-PCR. Clin. Diagn. Lab. Immunol. 8 (2001) 279-282
    • (2001) Clin. Diagn. Lab. Immunol. , vol.8 , pp. 279-282
    • Goerke, C.1    Bayer, M.G.2    Wolz, C.3
  • 28
    • 18844397838 scopus 로고    scopus 로고
    • Staphylococcus aureus strain designation by agr and cap polymorphism typing and delineation of agr diversification by sequence analysis
    • Goerke C., Esser S., Kummel M., and Wolz C. Staphylococcus aureus strain designation by agr and cap polymorphism typing and delineation of agr diversification by sequence analysis. Int. J. Med. Microbiol. 295 (2005) 67-75
    • (2005) Int. J. Med. Microbiol. , vol.295 , pp. 67-75
    • Goerke, C.1    Esser, S.2    Kummel, M.3    Wolz, C.4
  • 33
    • 43149085041 scopus 로고    scopus 로고
    • De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer
    • Hernandez D., Francois P., Farinelli L., Osteras M., and Schrenzel J. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res. 18 (2008) 802-809
    • (2008) Genome Res. , vol.18 , pp. 802-809
    • Hernandez, D.1    Francois, P.2    Farinelli, L.3    Osteras, M.4    Schrenzel, J.5
  • 34
    • 42549144495 scopus 로고    scopus 로고
    • Molecular correlates of host specialization in Staphylococcus aureus
    • Herron-Olson L., Fitzgerald J.R., Musser J.M., and Kapur V. Molecular correlates of host specialization in Staphylococcus aureus. PLoS One 2 (2007) e1120
    • (2007) PLoS One , vol.2
    • Herron-Olson, L.1    Fitzgerald, J.R.2    Musser, J.M.3    Kapur, V.4
  • 41
    • 40049104732 scopus 로고    scopus 로고
    • SOAP: short oligonucleotide alignment program
    • Li R.Q., Li Y.R., Kristiansen K., and Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 24 (2008) 713-714
    • (2008) Bioinformatics , vol.24 , pp. 713-714
    • Li, R.Q.1    Li, Y.R.2    Kristiansen, K.3    Wang, J.4
  • 42
    • 30744457635 scopus 로고    scopus 로고
    • Microarrays reveal that each of the ten dominant lineages of Staphylococcus aureus has a unique combination of surface-associated and regulatory genes
    • Lindsay J.A., Moore C.E., Day N.P., Peacock S.J., Witney A.A., Stabler R.A., Husain S.E., Butcher P.D., and Hinds J. Microarrays reveal that each of the ten dominant lineages of Staphylococcus aureus has a unique combination of surface-associated and regulatory genes. J. Bacteriol. 188 (2006) 669-676
    • (2006) J. Bacteriol. , vol.188 , pp. 669-676
    • Lindsay, J.A.1    Moore, C.E.2    Day, N.P.3    Peacock, S.J.4    Witney, A.A.5    Stabler, R.A.6    Husain, S.E.7    Butcher, P.D.8    Hinds, J.9
  • 44
    • 64549149245 scopus 로고    scopus 로고
    • Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing
    • Liu J.M., Livny J., Lawrence M.S., Kimball M.D., Waldor M.K., and Camilli A. Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing. Nucleic Acids Res. 37 (2009) e46
    • (2009) Nucleic Acids Res. , vol.37
    • Liu, J.M.1    Livny, J.2    Lawrence, M.S.3    Kimball, M.D.4    Waldor, M.K.5    Camilli, A.6
  • 45
    • 58849131103 scopus 로고    scopus 로고
    • Virulence gene expression in human community-acquired Staphylococcus aureus infection
    • Loughman J.A., Fritz S.A., Storch G.A., and Hunstad D.A. Virulence gene expression in human community-acquired Staphylococcus aureus infection. J. Infect. Dis. 199 (2009) 294-301
    • (2009) J. Infect. Dis. , vol.199 , pp. 294-301
    • Loughman, J.A.1    Fritz, S.A.2    Storch, G.A.3    Hunstad, D.A.4
  • 47
    • 63249121217 scopus 로고    scopus 로고
    • Application of 'next-generation' sequencing technologies to microbial genetics
    • MacLean D., Jones J.D., and Studholme D.J. Application of 'next-generation' sequencing technologies to microbial genetics. Nat. Rev. Microbiol. 7 (2009) 287-296
    • (2009) Nat. Rev. Microbiol. , vol.7 , pp. 287-296
    • MacLean, D.1    Jones, J.D.2    Studholme, D.J.3
  • 48
    • 50649089207 scopus 로고    scopus 로고
    • RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
    • Marioni J.C., Mason C.E., Mane S.M., Stephens M., and Gilad Y. RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 18 (2008) 1509-1517
    • (2008) Genome Res. , vol.18 , pp. 1509-1517
    • Marioni, J.C.1    Mason, C.E.2    Mane, S.M.3    Stephens, M.4    Gilad, Y.5
  • 49
    • 60549092956 scopus 로고    scopus 로고
    • High-resolution mapping of plasmid transcriptomes in different host bacteria
    • Miyakoshi M., Nishida H., Shintani M., Yamane H., and Nojiri H. High-resolution mapping of plasmid transcriptomes in different host bacteria. BMC Genomics 10 (2009) 12
    • (2009) BMC Genomics , vol.10 , pp. 12
    • Miyakoshi, M.1    Nishida, H.2    Shintani, M.3    Yamane, H.4    Nojiri, H.5
  • 50
    • 0034671796 scopus 로고    scopus 로고
    • Evolutionary dynamics of full genome content in Escherichia coli
    • Ochman H., and Jones I.B. Evolutionary dynamics of full genome content in Escherichia coli. EMBO J. 19 (2000) 6637-6643
    • (2000) EMBO J. , vol.19 , pp. 6637-6643
    • Ochman, H.1    Jones, I.B.2
  • 51
    • 33846067980 scopus 로고    scopus 로고
    • SwissRegulon: a database of genome-wide annotations of regulatory sites
    • Pachkov M., Erb I., Molina N., and van Nimwegen E. SwissRegulon: a database of genome-wide annotations of regulatory sites. Nucleic Acids Res. 35 (2007) D127-D131
    • (2007) Nucleic Acids Res. , vol.35
    • Pachkov, M.1    Erb, I.2    Molina, N.3    van Nimwegen, E.4
  • 55
    • 0035375137 scopus 로고    scopus 로고
    • Computational analysis of microarray data
    • Quackenbush J. Computational analysis of microarray data. Nat. Rev. Genet. 2 (2001) 418-427
    • (2001) Nat. Rev. Genet. , vol.2 , pp. 418-427
    • Quackenbush, J.1
  • 59
    • 0036208669 scopus 로고    scopus 로고
    • OligoArray: genome-scale oligonucleotide design for microarrays
    • Rouillard J.M., Herbert C.J., and Zuker M. OligoArray: genome-scale oligonucleotide design for microarrays. Bioinformatics 18 (2002) 486-487
    • (2002) Bioinformatics , vol.18 , pp. 486-487
    • Rouillard, J.M.1    Herbert, C.J.2    Zuker, M.3
  • 60
    • 0038239283 scopus 로고    scopus 로고
    • OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach
    • Rouillard J.M., Zuker M., and Gulari E. OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res. 31 (2003) 3057-3062
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3057-3062
    • Rouillard, J.M.1    Zuker, M.2    Gulari, E.3
  • 61
    • 63849112026 scopus 로고    scopus 로고
    • Cheap third-generation sequencing
    • Rusk N. Cheap third-generation sequencing. Nat. Methods 6 (2009) 244-245
    • (2009) Nat. Methods , vol.6 , pp. 244-245
    • Rusk, N.1
  • 63
    • 0038679712 scopus 로고    scopus 로고
    • Community-acquired methicillin-resistant Staphylococcus aureus: an emerging pathogen
    • Said-Salim B., Mathema B., and Kreiswirth B.N. Community-acquired methicillin-resistant Staphylococcus aureus: an emerging pathogen. Infect. Control Hosp. Epidemiol. 24 (2003) 451-455
    • (2003) Infect. Control Hosp. Epidemiol. , vol.24 , pp. 451-455
    • Said-Salim, B.1    Mathema, B.2    Kreiswirth, B.N.3
  • 65
    • 9144220943 scopus 로고    scopus 로고
    • A virulence-associated gene microarray: a tool for investigation of the evolution and pathogenic potential of Staphylococcus aureus
    • Saunders N.A., Underwood A., Kearns A.M., and Hallas G. A virulence-associated gene microarray: a tool for investigation of the evolution and pathogenic potential of Staphylococcus aureus. Microbiology 150 (2004) 3763-3771
    • (2004) Microbiology , vol.150 , pp. 3763-3771
    • Saunders, N.A.1    Underwood, A.2    Kearns, A.M.3    Hallas, G.4
  • 66
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • Schena M., Shalon D., Davis R.W., and Brown P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270 (1995) 467-470
    • (1995) Science , vol.270 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 69
    • 0030862620 scopus 로고    scopus 로고
    • Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays
    • Shchepinov M.S., Case-Green S.C., and Southern E.M. Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays. Nucleic Acids Res. 25 (1997) 1155-1161
    • (1997) Nucleic Acids Res. , vol.25 , pp. 1155-1161
    • Shchepinov, M.S.1    Case-Green, S.C.2    Southern, E.M.3
  • 72
  • 73
    • 0026484885 scopus 로고
    • Population transcript accumulation of Pseudomonas aeruginosa exotoxin A and elastase in sputa from patients with cystic fibrosis
    • Storey D.G., Ujack E.E., and Rabin H.R. Population transcript accumulation of Pseudomonas aeruginosa exotoxin A and elastase in sputa from patients with cystic fibrosis. Infect. Immun. 60 (1992) 4687-4694
    • (1992) Infect. Immun. , vol.60 , pp. 4687-4694
    • Storey, D.G.1    Ujack, E.E.2    Rabin, H.R.3
  • 74
    • 0036169031 scopus 로고    scopus 로고
    • Genesis: cluster analysis of microarray data
    • Sturn A., Quackenbush J., and Trajanoski Z. Genesis: cluster analysis of microarray data. Bioinformatics 18 (2002) 207-208
    • (2002) Bioinformatics , vol.18 , pp. 207-208
    • Sturn, A.1    Quackenbush, J.2    Trajanoski, Z.3
  • 75
    • 67349171520 scopus 로고    scopus 로고
    • A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo
    • Su Y.H., Li E., Geiss G.K., Longabaugh W.J., Kramer A., and Davidson E.H. A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo. Dev. Biol. 329 (2009) 410-421
    • (2009) Dev. Biol. , vol.329 , pp. 410-421
    • Su, Y.H.1    Li, E.2    Geiss, G.K.3    Longabaugh, W.J.4    Kramer, A.5    Davidson, E.H.6
  • 80
    • 29044443534 scopus 로고    scopus 로고
    • How to find small non-coding RNAs in bacteria
    • Vogel J., and Sharma C.M. How to find small non-coding RNAs in bacteria. Biol. Chem. 386 (2005) 1219-1238
    • (2005) Biol. Chem. , vol.386 , pp. 1219-1238
    • Vogel, J.1    Sharma, C.M.2
  • 83
    • 0036154488 scopus 로고    scopus 로고
    • Repression of the Staphylococcus aureus accessory gene regulator in serum and in vivo
    • Yarwood J.M., McCormick J.K., Paustian M.L., Kapur V., and Schlievert P.M. Repression of the Staphylococcus aureus accessory gene regulator in serum and in vivo. J. Bacteriol. 184 (2002) 1095-1101
    • (2002) J. Bacteriol. , vol.184 , pp. 1095-1101
    • Yarwood, J.M.1    McCormick, J.K.2    Paustian, M.L.3    Kapur, V.4    Schlievert, P.M.5
  • 85
    • 34548396885 scopus 로고    scopus 로고
    • ChIP-chip: data, model, and analysis
    • Zheng M., Barrera L.O., Ren B., and Wu Y.N. ChIP-chip: data, model, and analysis. Biometrics 63 (2007) 787-796
    • (2007) Biometrics , vol.63 , pp. 787-796
    • Zheng, M.1    Barrera, L.O.2    Ren, B.3    Wu, Y.N.4


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