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Volumn 5, Issue 2, 2010, Pages 313-328

Integration of 'omics data: Does it lead to new insights into host-microbe interactions?

Author keywords

Commensal; Data integration; High throughput; Hostmicrobe interaction; Pathogen; Systems biology

Indexed keywords

MESSENGER RNA;

EID: 77951111554     PISSN: 17460913     EISSN: None     Source Type: Journal    
DOI: 10.2217/fmb.10.1     Document Type: Review
Times cited : (29)

References (128)
  • 2
    • 77951118325 scopus 로고    scopus 로고
    • Interactions of the intestinal epithelium with the pathogen and the indigenous microbiota: A three-way crosstalk
    • Srikanth CV, McCormick BA: Interactions of the intestinal epithelium with the pathogen and the indigenous microbiota: a three-way crosstalk. Interdiscip. Perspect. Infect. Dis. 2008, 626827 (2008).
    • (2008) Interdiscip. Perspect. Infect. Dis. 2008 , pp. 626827
    • Srikanth, C.V.1    McCormick, B.A.2
  • 3
    • 70350712113 scopus 로고    scopus 로고
    • Examination of post-transcriptional regulations in prokaryotes by integrative biology
    • Picard F, Dressaire C, Girbal L, Cocaign-Bousquet M: Examination of post-transcriptional regulations in prokaryotes by integrative biology. Comptes. Rendus Biologies 332(11), 958-973 (2009).
    • (2009) Comptes. Rendus Biologies , vol.332 , Issue.11 , pp. 958-973
    • Picard, F.1    Dressaire, C.2    Girbal, L.3    Cocaign-Bousquet, M.4
  • 4
    • 20644462362 scopus 로고    scopus 로고
    • Micros for microbes: Non-coding regulatory RNAs in bacteria
    • Gottesman S: Micros for microbes: non-coding regulatory RNAs in bacteria. Trends Genetics 21(7), 399-404 (2005).
    • (2005) Trends Genetics , vol.21 , Issue.7 , pp. 399-404
    • Gottesman, S.1
  • 5
    • 60149089144 scopus 로고    scopus 로고
    • Regulatory RNAs in bacteria
    • Waters LS, Storz G: Regulatory RNAs in bacteria. Cell 136(4), 615-628 (2009).
    • (2009) Cell , vol.136 , Issue.4 , pp. 615-628
    • Waters, L.S.1    Storz, G.2
  • 6
    • 77951126712 scopus 로고    scopus 로고
    • Host-microbe interaction systems biology: Lifecycle transcriptomics and comparative genomics
    • Sturdevant DE, Virtaneva K, Martens C et al.: Host-microbe interaction systems biology: lifecycle transcriptomics and comparative genomics. Future Microbiol. 5(2) 205-219 (2010).
    • (2010) Future Microbiol , vol.5 , Issue.2 , pp. 205-219
    • Sturdevant, D.E.1    Virtaneva, K.2    Martens, C.3
  • 7
    • 77951140853 scopus 로고    scopus 로고
    • Proteomics as a probe of microbial pathogenesis and its molecular boundaries
    • Bhavsar AP, Auweter SD, Finlay BB: Proteomics as a probe of microbial pathogenesis and its molecular boundaries. Future Microbiol. 5(2) 253-265 (2010).
    • (2010) Future Microbiol , vol.5 , Issue.2 , pp. 253-265
    • Bhavsar, A.P.1    Auweter, S.D.2    Finlay, B.B.3
  • 8
    • 77951098667 scopus 로고    scopus 로고
    • Defining the humoral immune response to infectious agents using high-density protein microarrays
    • Vigil A, Davies DH, Felgner PL: Defining the humoral immune response to infectious agents using high-density protein microarrays. Future Microbiol. 5(2) 241-251 (2010).
    • (2010) Future Microbiol , vol.5 , Issue.2 , pp. 241-251
    • Vigil, A.1    Davies, D.H.2    Felgner, P.L.3
  • 9
    • 77950865479 scopus 로고    scopus 로고
    • Vaccinia virus leads the way: Uncovering the interplay between CD8 CD4 and antibody responses to complex pathogens
    • Moutaftsi M, Tscharke DC, Vaughan K et al.: Vaccinia virus leads the way: uncovering the interplay between CD8, CD4 and antibody responses to complex pathogens. Future Microbiol. 5(2) 221-239 (2010).
    • (2010) Future Microbiol , vol.5 , Issue.2 , pp. 221-239
    • Moutaftsi, M.1    Tscharke, D.C.2    Vaughan, K.3
  • 10
    • 70449722954 scopus 로고    scopus 로고
    • Custom design and analysis of high-density oligonucleotide bacterial tiling microarrays
    • Thomassen GOS, Rowe AD, Lagesen K, Lindvall JM, Rognes T: Custom design and analysis of high-density oligonucleotide bacterial tiling microarrays. PLoS ONE 4(6), E5943 (2009).
    • (2009) PLoS ONE , vol.4 , Issue.6
    • Thomassen, G.O.S.1    Rowe, A.D.2    Lagesen, K.3    Lindvall, J.M.4    Rognes, T.5
  • 11
    • 67649268395 scopus 로고    scopus 로고
    • The Listeria transcriptional landscape from saprophytism to virulence
    • Toledo-Arana A, Dussurget O, Nikitas G et al.: The Listeria transcriptional landscape from saprophytism to virulence. Nature 459, 950-956 (2009).
    • (2009) Nature , vol.459 , pp. 950-956
    • Toledo-Arana, A.1    Dussurget, O.2    Nikitas, G.3
  • 12
    • 70049087126 scopus 로고    scopus 로고
    • Comprehensive identification of Salmonella enterica serovar Typhimurium genes required for infection of BALB/c mice
    • Chaudhuri RR, Peters SE, Pleasance SJ et al.: Comprehensive identification of Salmonella enterica serovar Typhimurium genes required for infection of BALB/c mice. PLoS Pathog. 5(7), e1000529 (2009).
    • (2009) PLoS Pathog , vol.5 , Issue.7
    • Chaudhuri, R.R.1    Peters, S.E.2    Pleasance, S.J.3
  • 13
    • 68849123336 scopus 로고    scopus 로고
    • Comprehensive identification of essential Staphylococcus aureus genes using transposon-mediated differential hybridisation (TMDH)
    • Chaudhuri RR, Allen AG, Owen PJ et al.: Comprehensive identification of essential Staphylococcus aureus genes using transposon-mediated differential hybridisation (TMDH). BMC Genomics 10, 291 (2009).
    • (2009) BMC Genomics , vol.10 , pp. 291
    • Chaudhuri, R.R.1    Allen, A.G.2    Owen, P.J.3
  • 14
    • 69349099557 scopus 로고    scopus 로고
    • Analysis of pools of targeted Salmonella deletion mutants identifies novel genes affecting fitness during competitive infection in mice
    • Santiviago CA, Reynolds MM, Porwollik S et al.: Analysis of pools of targeted Salmonella deletion mutants identifies novel genes affecting fitness during competitive infection in mice. PLoS Pathog. 5(7), E1000477 (2009).
    • (2009) PLoS Pathog , vol.5 , Issue.7
    • Santiviago, C.A.1    Reynolds, M.M.2    Porwollik, S.3
  • 15
    • 33845311869 scopus 로고    scopus 로고
    • Signature-tagged mutagenesis: Barcoding mutants for genome-wide screens
    • Mazurkiewicz P, Tang CM, Boone C, Holden DW: Signature-tagged mutagenesis: barcoding mutants for genome-wide screens. Nat. Rev. Genetics 7, 929-939 (2006).
    • (2006) Nat. Rev. Genetics , vol.7 , pp. 929-939
    • Mazurkiewicz, P.1    Tang, C.M.2    Boone, C.3    Holden, D.W.4
  • 16
    • 61449198592 scopus 로고    scopus 로고
    • Deletion of tolA in Salmonella Typhimurium generates an attenuated strain with vaccine potential
    • Paterson GK, Northen H, Cone DB, Willers C, Peters SE, Maskell DJ: Deletion of tolA in Salmonella Typhimurium generates an attenuated strain with vaccine potential. Microbiology 155, 220-228 (2009).
    • (2009) Microbiology , vol.155 , pp. 220-228
    • Paterson, G.K.1    Northen, H.2    Cone, D.B.3    Willers, C.4    Peters, S.E.5    Maskell, D.J.6
  • 17
    • 10644247621 scopus 로고    scopus 로고
    • Applications of DNA tiling arrays for whole-genome analysis
    • Mockler TC, Ecker JR: Applications of DNA tiling arrays for whole-genome analysis. Genomics 85, 1-15 (2005).
    • (2005) Genomics , vol.85 , pp. 1-15
    • Mockler, T.C.1    Ecker, J.R.2
  • 18
    • 1242316281 scopus 로고    scopus 로고
    • ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments
    • Buck MJ, Lieb JD: ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83(3), 349-360 (2004).
    • (2004) Genomics , vol.83 , Issue.3 , pp. 349-360
    • Buck, M.J.1    Lieb, J.D.2
  • 19
    • 63249132195 scopus 로고    scopus 로고
    • DNA sampling: A method for probing protein binding at specific loci on bacterial chromosomes
    • Butala M, Busby SJW, Lee DJ: DNA sampling: a method for probing protein binding at specific loci on bacterial chromosomes. Nucleic Acids Res. 37(5), e37 (2009).
    • (2009) Nucleic Acids Res , vol.37 , Issue.5
    • Butala, M.1    Busby, S.J.W.2    Lee, D.J.3
  • 20
    • 65549122479 scopus 로고    scopus 로고
    • Dissecting regulatory networks in host-pathogen interaction using ChIP-on-chip technology
    • Sala C, Grainger DC, Cole ST: Dissecting regulatory networks in host-pathogen interaction using ChIP-on-chip technology. Cell Host Microbe. 5(5), 430-437 (2009).
    • (2009) Cell Host Microbe , vol.5 , Issue.5 , pp. 430-437
    • Sala, C.1    Grainger, D.C.2    Cole, S.T.3
  • 21
    • 13844321755 scopus 로고    scopus 로고
    • Extraction of transcription regulatory signals from genome-wide DNA-protein interaction data
    • Garten Y, Kaplan S, Pilpel Y: Extraction of transcription regulatory signals from genome-wide DNA-protein interaction data. Nucleic Acids Res. 33(2), 605-615 (2005).
    • (2005) Nucleic Acids Res , vol.33 , Issue.2 , pp. 605-615
    • Garten, Y.1    Kaplan, S.2    Pilpel, Y.3
  • 22
    • 38549140094 scopus 로고    scopus 로고
    • RegulonDB (version 6.0): Gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation
    • Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M et al.: RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res. 36, D120-D124 (2008).
    • (2008) Nucleic Acids Res , vol.36
    • Gama-Castro, S.1    Jimenez-Jacinto, V.2    Peralta-Gil, M.3
  • 23
    • 0347126296 scopus 로고    scopus 로고
    • DBTBS: Database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics
    • Makita Y, Nakao M, Ogasawara N, Nakai K: DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics. Nucleic Acids Res. 32, D75-D77 (2004).
    • (2004) Nucleic Acids Res , vol.32
    • Makita, Y.1    Nakao, M.2    Ogasawara, N.3    Nakai, K.4
  • 24
    • 19544390556 scopus 로고    scopus 로고
    • MtbRegList, a database dedicated to the analysis of transcriptional regulation in Mycobacterium tuberculosis
    • Jacques PE, Gervais AL, Cantin M et al.: MtbRegList, a database dedicated to the analysis of transcriptional regulation in Mycobacterium tuberculosis. Bioinformatics 21(10), 2563-2565 (2005).
    • (2005) Bioinformatics , vol.21 , Issue.10 , pp. 2563-2565
    • Jacques, P.E.1    Gervais, A.L.2    Cantin, M.3
  • 25
    • 41849115550 scopus 로고    scopus 로고
    • A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli
    • Ernst J, Beg QK, Kay KA, Balazsi G, Oltvai ZN, Bar-Joseph Z: A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli. PLoS Comput. Biol. 4(3), e1000044 (2008).
    • (2008) PLoS Comput. Biol , vol.4 , Issue.3
    • Ernst, J.1    Beg, Q.K.2    Kay, K.A.3    Balazsi, G.4    Oltvai, Z.N.5    Bar-Joseph, Z.6
  • 26
    • 10744226222 scopus 로고    scopus 로고
    • Computational discovery of gene modules and regulatory networks
    • Bar-Joseph Z, Gerber GK, Lee TI et al.: Computational discovery of gene modules and regulatory networks. Nat. Biotechnol. 21(11), 1337-1342 (2003).
    • (2003) Nat. Biotechnol , vol.21 , Issue.11 , pp. 1337-1342
    • Bar-Joseph, Z.1    Gerber, G.K.2    Lee, T.I.3
  • 27
    • 1542357674 scopus 로고    scopus 로고
    • Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data
    • Tanay A, Sharan R, Kupiec M, Shamir R: Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. Proc. Natl Acad. Sci. USA 101(9), 2981-2986 (2004).
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , Issue.9 , pp. 2981-2986
    • Tanay, A.1    Sharan, R.2    Kupiec, M.3    Shamir, R.4
  • 28
    • 33745128746 scopus 로고    scopus 로고
    • Inferring transcriptional modules from ChIP-chip, motif and microarray data
    • Lemmens K, Dhollander T, De Bie T et al.: Inferring transcriptional modules from ChIP-chip, motif and microarray data. Genome Biol. 7(5), R37 (2006).
    • (2006) Genome Biol , vol.7 , Issue.5
    • Lemmens, K.1    Dhollander, T.2    De Bie, T.3
  • 29
    • 63449134229 scopus 로고    scopus 로고
    • DISTILLER: A data integration framework to reveal condition dependency of complex regulons in Escherichia coli
    • Lemmens K, De Bie T, Dhollander T et al.: DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli. Genome Biol. 10(3), R27 (2009).
    • (2009) Genome Biol , vol.10 , Issue.3
    • Lemmens, K.1    De Bie, T.2    Dhollander, T.3
  • 31
    • 33746008173 scopus 로고    scopus 로고
    • Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella
    • Navarre WW, Porwollik S, Wang YP et al.: Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella. Science 313(5784), 236-238 (2006).
    • (2006) Science , vol.313 , Issue.5784 , pp. 236-238
    • Navarre, W.W.1    Porwollik, S.2    Wang, Y.P.3
  • 32
    • 68249102779 scopus 로고    scopus 로고
    • A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella Typhi
    • Perkins TT, Kingsley RA, Fookes MC et al.: A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella Typhi. PLoS Genet. 5(7), E1000569 (2009).
    • (2009) PLoS Genet , vol.5 , Issue.7
    • Perkins, T.T.1    Kingsley, R.A.2    Fookes, M.C.3
  • 33
    • 69949123813 scopus 로고    scopus 로고
    • Identifying genetic determinants needed to establish a human gut symbiont in its habitat
    • Goodman AL, McNulty NP, Zhao Y et al.: Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host Microbe 6, 279-289 (2009).
    • (2009) Cell Host Microbe , vol.6 , pp. 279-289
    • Goodman, A.L.1    McNulty, N.P.2    Zhao, Y.3
  • 34
    • 73249130761 scopus 로고    scopus 로고
    • Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants
    • Langridge GC, Phan M-D, Turner DJ et al.: Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. Genome Res. 19(12), 2308-2316 (2009).
    • (2009) Genome Res , vol.19 , Issue.12 , pp. 2308-2316
    • Langridge, G.C.1    Phan, M.-D.2    Turner, D.J.3
  • 35
    • 70349510646 scopus 로고    scopus 로고
    • Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung
    • Gawronski JD, Wong SMS, Giannoukos G, Ward DV, Akerley BJ: Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung. Proc. Natl Acad. Sci. USA 106(38), 16422-16427 (2009).
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , Issue.38 , pp. 16422-16427
    • Gawronski, J.D.1    Wong, S.M.S.2    Giannoukos, G.3    Ward, D.V.4    Akerley, B.J.5
  • 36
    • 70349611730 scopus 로고    scopus 로고
    • Tn-seq: High-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms
    • van Opijnen T, Bodi KL, Camilli A: Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms. Nat. Methods 6(10), 767-772 (2009).
    • (2009) Nat. Methods , vol.6 , Issue.10 , pp. 767-772
    • Van Opijnen, T.1    Bodi, K.L.2    Camilli, A.3
  • 37
    • 1642565815 scopus 로고    scopus 로고
    • The bacterial Sm-like protein Hfq: A key player in RNA transactions
    • Valentin-Hansen P, Eriksen M, Udesen C: The bacterial Sm-like protein Hfq: a key player in RNA transactions. Mol. Microbiol. 51(6), 1525-1533 (2004).
    • (2004) Mol. Microbiol , vol.51 , Issue.6 , pp. 1525-1533
    • Valentin-Hansen, P.1    Eriksen, M.2    Udesen, C.3
  • 38
    • 55549099601 scopus 로고    scopus 로고
    • Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools
    • Sonnleitner E, Sorger-Domenigg T, Madej MJ et al.: Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools. Microbiology 154, 3175-3187 (2008).
    • (2008) Microbiology , vol.154 , pp. 3175-3187
    • Sonnleitner, E.1    Sorger-Domenigg, T.2    Madej, M.J.3
  • 39
    • 50849105413 scopus 로고    scopus 로고
    • Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator Hfq
    • Sittka A, Lucchini S, Papenfort K et al.: Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet. 4(8), e1000163 (2008).
    • (2008) PLoS Genet , vol.4 , Issue.8
    • Sittka, A.1    Lucchini, S.2    Papenfort, K.3
  • 40
    • 67349278437 scopus 로고    scopus 로고
    • Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes
    • Sittka A, Sharma A, Rolle K, Vogel J: Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes. RNA Biology 6(3), 266-275 (2009).
    • (2009) RNA Biology , vol.6 , Issue.3 , pp. 266-275
    • Sittka, A.1    Sharma, A.2    Rolle, K.3    Vogel, J.4
  • 41
    • 34548679810 scopus 로고    scopus 로고
    • Computational approaches for the discovery of bacterial small RNAs
    • Kulkarni RV, Kulkarni PR: Computational approaches for the discovery of bacterial small RNAs. Methods 43, 131-139 (2007).
    • (2007) Methods , vol.43 , pp. 131-139
    • Kulkarni, R.V.1    Kulkarni, P.R.2
  • 42
    • 57249116905 scopus 로고    scopus 로고
    • Small RNA gene identification and mRNA target predictions in bacteria
    • Pichon C, Felden B: Small RNA gene identification and mRNA target predictions in bacteria. Bioinformatics 24(24), 2807-2813 (2008).
    • (2008) Bioinformatics , vol.24 , Issue.24 , pp. 2807-2813
    • Pichon, C.1    Felden, B.2
  • 43
    • 36148952518 scopus 로고    scopus 로고
    • Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics
    • del Val C, Rivas E, Torres-Quesada O, Toro N, Jimenez-Zurdo JI: Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics. Mol. Microbiol. 66, 1080-1091 (2007).
    • (2007) Mol. Microbiol , vol.66 , pp. 1080-1091
    • Del Val, C.1    Rivas, E.2    Torres-Quesada, O.3    Toro, N.4    Jimenez-Zurdo, J.I.5
  • 44
    • 52449093583 scopus 로고    scopus 로고
    • High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs
    • Livny J, Teonadi H, Livny M, Waldor MK: High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs. PLoS ONE 3(9), E3197 (2008).
    • (2008) PLoS ONE , vol.3 , Issue.9
    • Livny, J.1    Teonadi, H.2    Livny, M.3    Waldor, M.K.4
  • 45
    • 58149177178 scopus 로고    scopus 로고
    • SRNAMAP: Genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes
    • Huang HY, Chang HY, Chou CH et al.: sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes. Nucleic Acids Res. 37, D150-D154 (2009).
    • (2009) Nucleic Acids Res , vol.37
    • Huang, H.Y.1    Chang, H.Y.2    Chou, C.H.3
  • 46
    • 65349177758 scopus 로고    scopus 로고
    • A genetic approach for finding small RNAs regulators of genes of interest identifies RybC as regulating the DpiA/DpiB two-component system
    • Mandin P, Gottesman S: A genetic approach for finding small RNAs regulators of genes of interest identifies RybC as regulating the DpiA/DpiB two-component system. Mol. Microbiol. 72(3), 551-565 (2009).
    • (2009) Mol. Microbiol , vol.72 , Issue.3 , pp. 551-565
    • Mandin, P.1    Gottesman, S.2
  • 47
    • 0031472242 scopus 로고    scopus 로고
    • The E. coli signal recognition particle is required for the insertion of a subset of inner membrane proteins
    • Ulbrandt ND, Newitt JA, Bernstein HD: The E. coli signal recognition particle is required for the insertion of a subset of inner membrane proteins. Cell 88(2), 187-196 (1997).
    • (1997) Cell , vol.88 , Issue.2 , pp. 187-196
    • Ulbrandt, N.D.1    Newitt, J.A.2    Bernstein, H.D.3
  • 48
    • 4644351908 scopus 로고    scopus 로고
    • SOS response induction by b-lactams and bacterial defense against antibiotic lethality
    • Miller C, Thomsen LE, Gaggero C, Mosseri R, Ingmer H, Cohen SN: SOS response induction by b-lactams and bacterial defense against antibiotic lethality. Science 305(5690), 1629-1631 (2004).
    • (2004) Science , vol.305 , Issue.5690 , pp. 1629-1631
    • Miller, C.1    Thomsen, L.E.2    Gaggero, C.3    Mosseri, R.4    Ingmer, H.5    Cohen, S.N.6
  • 49
    • 51149113074 scopus 로고    scopus 로고
    • Phosphoproteomics in bacteria: Towards a systemic understanding of bacterial phosphorylation networks
    • Jers C, Soufi B, Grangeasse C, Deutscher J, Mijakovic I: Phosphoproteomics in bacteria: towards a systemic understanding of bacterial phosphorylation networks. Expert Rev. Proteomics 5(4), 619-627 (2008).
    • (2008) Expert Rev. Proteomics , vol.5 , Issue.4 , pp. 619-627
    • Jers, C.1    Soufi, B.2    Grangeasse, C.3    Deutscher, J.4    Mijakovic, I.5
  • 51
    • 34247325212 scopus 로고    scopus 로고
    • The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis.
    • Macek B, Mijakovic I, Olsen JV et al.: The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6, 697-707 (2007).
    • (2007) Mol. Cell. Proteomics , vol.6 , pp. 697-707
    • MacEk, B.1    Mijakovic, I.2    Olsen, J.V.3
  • 52
    • 39749166860 scopus 로고    scopus 로고
    • Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/ Thr/Tyr phosphorylation
    • Macek B, Gnad F, Soufi B et al.: Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/ Thr/Tyr phosphorylation. Mol. Cell. Proteomics 7, 299-307 (2008).
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 299-307
    • MacEk, B.1    Gnad, F.2    Soufi, B.3
  • 53
    • 52649125713 scopus 로고    scopus 로고
    • The Ser/Thr/Tyr phosphoproteome of Lactococcus lactis IL1403 reveals multiply phosphorylated proteins
    • Soufi B, Gnad F, Jensen PR et al.: The Ser/Thr/Tyr phosphoproteome of Lactococcus lactis IL1403 reveals multiply phosphorylated proteins. Proteomics 8, 3486-3493 (2008).
    • (2008) Proteomics , vol.8 , pp. 3486-3493
    • Soufi, B.1    Gnad, F.2    Jensen, P.R.3
  • 54
    • 2942534300 scopus 로고    scopus 로고
    • Interactome data and databases: Different types of protein interaction
    • Las Rivas J, de Luis A: Interactome data and databases: different types of protein interaction. Comp. Funct. Genomics 5(2), 173-178 (2004).
    • (2004) Comp. Funct. Genomics , vol.5 , Issue.2 , pp. 173-178
    • Las Rivas, J.1    De Luis, A.2
  • 55
    • 65249116382 scopus 로고    scopus 로고
    • A method for investigating protein-protein interactions related to Salmonella Typhimurium pathogenesis
    • Chowdhury SM, Shi L, Yoon H et al.: A method for investigating protein-protein interactions related to Salmonella Typhimurium pathogenesis. J. Proteome Res. 8, 1504-1514 (2009).
    • (2009) J. Proteome Res , vol.8 , pp. 1504-1514
    • Chowdhury, S.M.1    Shi, L.2    Yoon, H.3
  • 57
    • 0035281870 scopus 로고    scopus 로고
    • Metabolic modeling of microbial strains in silico
    • Covert MW, Schilling CH, Famili I et al.: Metabolic modeling of microbial strains in silico. Trends Biochem. Sci. 26(3), 179-186 (2001).
    • (2001) Trends Biochem. Sci , vol.26 , Issue.3 , pp. 179-186
    • Covert, M.W.1    Schilling, C.H.2    Famili, I.3
  • 58
    • 41149163825 scopus 로고    scopus 로고
    • Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1
    • Oberhardt MA, Puchalka J, Fryer KE, dos Santos VAPM, Papin JA: Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1. J. Bacteriol. 190(8), 2790-2803 (2008).
    • (2008) J. Bacteriol , vol.190 , Issue.8 , pp. 2790-2803
    • Oberhardt, M.A.1    Puchalka, J.2    Fryer, K.E.3    Dos Santos, V.A.P.M.4    Papin, J.A.5
  • 59
    • 65649105134 scopus 로고    scopus 로고
    • Constraint-based analysis of metabolic capacity of Salmonella Typhimurium during host-pathogen interaction
    • Raghunathan A, Reed J, Shin S, Palsson B, Daefler S: Constraint-based analysis of metabolic capacity of Salmonella Typhimurium during host-pathogen interaction. BMC Syst. Biol. 3 (2009).
    • (2009) BMC Syst. Biol , vol.3
    • Raghunathan, A.1    Reed, J.2    Shin, S.3    Palsson, B.4    Daefler, S.5
  • 60
    • 62949176320 scopus 로고    scopus 로고
    • Genome-scale reconstruction of the metabolic network in Yersinia pestis, strain 91001
    • Navid A, Almaas E: Genome-scale reconstruction of the metabolic network in Yersinia pestis, strain 91001. Mol. Biosyst. 5(4), 368-375 (2009).
    • (2009) Mol. Biosyst , vol.5 , Issue.4 , pp. 368-375
    • Navid, A.1    Almaas, E.2
  • 61
    • 34548861262 scopus 로고    scopus 로고
    • GSMN-TB: A web-based genome scale network model of Mycobacterium tuberculosis metabolism
    • Beste DJV, Hooper T, Stewart G et al.: GSMN-TB: a web-based genome scale network model of Mycobacterium tuberculosis metabolism. Genome Biol. 8(5), R89 (2007).
    • (2007) Genome Biol , vol.8 , Issue.5
    • Beste, D.J.V.1    Hooper, T.2    Stewart, G.3
  • 62
    • 70349745413 scopus 로고    scopus 로고
    • Novel biological insights through metabolomics and C-13-flux analysis
    • Zamboni N, Sauer U: Novel biological insights through metabolomics and C-13-flux analysis. Curr. Opin. Microbiol. 12(5), 553-558 (2009).
    • (2009) Curr. Opin. Microbiol , vol.12 , Issue.5 , pp. 553-558
    • Zamboni, N.1    Sauer, U.2
  • 63
    • 70349971144 scopus 로고    scopus 로고
    • Mass spectrometry based metabolomics and enzymatic assays for functional genomics
    • Baran R, Reindl W, Northen TR: Mass spectrometry based metabolomics and enzymatic assays for functional genomics. Curr. Opin. Microbiol. 12(5), 547-552 (2009).
    • (2009) Curr. Opin. Microbiol , vol.12 , Issue.5 , pp. 547-552
    • Baran, R.1    Reindl, W.2    Northen, T.R.3
  • 64
    • 57549102595 scopus 로고    scopus 로고
    • Genome-scale models of bacterial metabolism: Reconstruction and applications
    • Durot M, Bourguignon P, Schachter V: Genome-scale models of bacterial metabolism: reconstruction and applications. FEMS Microbiol. Rev. 33, 164-190 (2009).
    • (2009) FEMS Microbiol. Rev , vol.33 , pp. 164-190
    • Durot, M.1    Bourguignon, P.2    Schachter, V.3
  • 65
    • 34247374704 scopus 로고    scopus 로고
    • Prediction of missing enzyme genes in a bacterial metabolic network. Reconstruction of the lysine-degradation pathway of Pseudomonas aeruginosa
    • Yamanishi Y, Mihara H, Osaki M et al.: Prediction of missing enzyme genes in a bacterial metabolic network. Reconstruction of the lysine-degradation pathway of Pseudomonas aeruginosa. FEBS J. 274, 2262-2273 (2007).
    • (2007) FEBS J , vol.274 , pp. 2262-2273
    • Yamanishi, Y.1    Mihara, H.2    Osaki, M.3
  • 66
    • 63049115956 scopus 로고    scopus 로고
    • Metabolic pathway alignment between species using a comprehensive and flexible similarity measure
    • Li Y, de Ridder D, de Groot MJ, Reinders MJ: Metabolic pathway alignment between species using a comprehensive and flexible similarity measure. BMC Syst. Biol. 2, 111 (2008).
    • (2008) BMC Syst. Biol , vol.2 , pp. 111
    • Li, Y.1    De Ridder, D.2    De Groot, M.J.3    Reinders, M.J.4
  • 67
    • 33645030241 scopus 로고    scopus 로고
    • Robust Salmonella metabolism limits possibilities for new antimicrobials
    • Becker D, Sebach M, Rollenhagen C et al.: Robust Salmonella metabolism limits possibilities for new antimicrobials. Nature 440, 303-307 (2006).
    • (2006) Nature , vol.440 , pp. 303-307
    • Becker, D.1    Sebach, M.2    Rollenhagen, C.3
  • 68
    • 70349751621 scopus 로고    scopus 로고
    • System-level analysis of Salmonella metabolism during infection.
    • Bumann D: System-level analysis of Salmonella metabolism during infection. Curr. Opin. Microbiol. 12, 559-567 (2009).
    • (2009) Curr. Opin. Microbiol , vol.12 , pp. 559-567
    • Bumann, D.1
  • 69
    • 41149099000 scopus 로고    scopus 로고
    • Symbiotic gut microbes modulate human metabolic phenotypes
    • Li M, Wang BH, Zhang MH et al.: Symbiotic gut microbes modulate human metabolic phenotypes. Proc. Natl Acad. Sci. USA 105(6), 2117-2122 (2008).
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , Issue.6 , pp. 2117-2122
    • Li, M.1    Wang, B.H.2    Zhang, M.H.3
  • 70
    • 53949089441 scopus 로고    scopus 로고
    • Systemic multicompartmental effects of the gut microbiome on mouse metabolic phenotypes
    • Claus SP, Tsang TM, Wang YL et al.: Systemic multicompartmental effects of the gut microbiome on mouse metabolic phenotypes. Mol. Syst. Biol. 4, 219 (2008).
    • (2008) Mol. Syst. Biol , vol.4 , pp. 219
    • Claus, S.P.1    Tsang, T.M.2    Wang, Y.L.3
  • 71
    • 47349114231 scopus 로고    scopus 로고
    • Top-down systems biology integration of conditional prebiotic modulated transgenomic interactions in a humanized microbiome mouse model
    • Martin FPJ, Wang YL, Sprenger N et al.: Top-down systems biology integration of conditional prebiotic modulated transgenomic interactions in a humanized microbiome mouse model. Mol. Syst. Biol. 4(205) (2008).
    • (2008) Mol. Syst. Biol , vol.4 , pp. 205
    • Martin, F.P.J.1    Wang, Y.L.2    Sprenger, N.3
  • 72
    • 57649123534 scopus 로고    scopus 로고
    • Global phenotypic characterization of bacteria
    • Bochner BR: Global phenotypic characterization of bacteria. FEMS Microbiol. Rev. 33(1), 191-205 (2009).
    • (2009) FEMS Microbiol. Rev , vol.33 , Issue.1 , pp. 191-205
    • Bochner, B.R.1
  • 73
    • 31544450286 scopus 로고    scopus 로고
    • Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: The Keio collection
    • Baba T, Ara T, Hasegawa M et al.: Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2, 2006.0008 (2006).
    • (2006) Mol. Syst. Biol , vol.2 , pp. 2006
    • Baba, T.1    Ara, T.2    Hasegawa, M.3
  • 75
    • 62849101179 scopus 로고    scopus 로고
    • Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella: Implications for virulence and global protein translation
    • Ansong C, Yoon H, Porwollik S et al.: Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella: implications for virulence and global protein translation. PLoS ONE 4, E4809 (2009).
    • (2009) PLoS ONE , vol.4
    • Ansong, C.1    Yoon, H.2    Porwollik, S.3
  • 77
    • 33845508443 scopus 로고    scopus 로고
    • Genomic and metabolic studies of the impact of probiotics on a model gut symbiont and host
    • Sonnenburg JL, Chen CTL, Gordon JI: Genomic and metabolic studies of the impact of probiotics on a model gut symbiont and host. PLoS Biol. 4(12), 2213-2226 (2006).
    • (2006) PLoS Biol , vol.4 , Issue.12 , pp. 2213-2226
    • Sonnenburg, J.L.1    Chen, C.T.L.2    Gordon, J.I.3
  • 78
    • 34547556624 scopus 로고    scopus 로고
    • The protein network of bacterial motility
    • Rajagopala SV, Titz B, Goll J et al.: The protein network of bacterial motility. Mol. Syst. Biol. 3, 128 (2007).
    • (2007) Mol. Syst. Biol , vol.3 , pp. 128
    • Rajagopala, S.V.1    Titz, B.2    Goll, J.3
  • 79
    • 34748871477 scopus 로고    scopus 로고
    • Regulation of gene expression by small non-coding RNAs: A quantitative view
    • Shimoni Y, Friedlander G, Hetzroni G et al.: Regulation of gene expression by small non-coding RNAs: a quantitative view. Mol. Syst. Biol. 3, 138 (2007).
    • (2007) Mol. Syst. Biol , vol.3 , pp. 138
    • Shimoni, Y.1    Friedlander, G.2    Hetzroni, G.3
  • 80
    • 68249156618 scopus 로고    scopus 로고
    • Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation
    • Pfeiffer V, Papenfort K, Lucchini S, Hinton JCD, Vogel J: Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation. Nat. Struct. Mol. Biol. 16, 840-846 (2009).
    • (2009) Nat. Struct. Mol. Biol , vol.16 , pp. 840-846
    • Pfeiffer, V.1    Papenfort, K.2    Lucchini, S.3    Hinton, J.C.D.4    Vogel, J.5
  • 81
    • 69749123311 scopus 로고    scopus 로고
    • Caught at its own game: Regulatory small RNA inactivated by an inducible transcript mimicking its target
    • Figueroa-Bossi N, Valentini M, Malleret L, Bossi L: Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target. Genes Dev. 23(17), 1981-1985 (2009).
    • (2009) Genes Dev , vol.23 , Issue.17 , pp. 1981-1985
    • Figueroa-Bossi, N.1    Valentini, M.2    Malleret, L.3    Bossi, L.4
  • 82
    • 62949231327 scopus 로고    scopus 로고
    • Hydrophobic peptides: Novel regulators within bacterial membrane
    • Alix E, Blanc-Potard AB: Hydrophobic peptides: novel regulators within bacterial membrane. Mol. Microbiol. 72(1), 5-11 (2009).
    • (2009) Mol. Microbiol , vol.72 , Issue.1 , pp. 5-11
    • Alix, E.1    Blanc-Potard, A.B.2
  • 83
    • 33846465923 scopus 로고    scopus 로고
    • H-NS, the genome sentinel
    • Dorman CJ: H-NS, the genome sentinel. Nat. Rev. Microbiol. 5, 157-161 (2007).
    • (2007) Nat. Rev. Microbiol , vol.5 , pp. 157-161
    • Dorman, C.J.1
  • 84
    • 64349112326 scopus 로고    scopus 로고
    • Roles of DNA adenine methylation in host-pathogen interactions: Mismatch repair, transcriptional regulation, and more
    • Marinus MG, Casadesus J: Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more. FEMS Microbiol. Rev. 33(3), 488-503 (2009).
    • (2009) FEMS Microbiol. Rev , vol.33 , Issue.3 , pp. 488-503
    • Marinus, M.G.1    Casadesus, J.2
  • 85
    • 50849098825 scopus 로고    scopus 로고
    • ESGA: E. coli synthetic genetic array analysis
    • Butland G, Babu M, Diaz-Mejia JJ et al.: eSGA: E. coli synthetic genetic array analysis. Nat. Methods 5(9), 789-795 (2008).
    • (2008) Nat. Methods , vol.5 , Issue.9 , pp. 789-795
    • Butland, G.1    Babu, M.2    Diaz-Mejia, J.J.3
  • 86
    • 65249137629 scopus 로고    scopus 로고
    • Global and site-specific quantitative phosphoproteomics: Principles and applications
    • Macek B, Mann M, Olsen JV: Global and site-specific quantitative phosphoproteomics: principles and applications. Ann. Rev. Pharmacol. Toxicol. 49, 199-221 (2009).
    • (2009) Ann. Rev. Pharmacol. Toxicol , vol.49 , pp. 199-221
    • MacEk, B.1    Mann, M.2    Olsen, J.V.3
  • 88
    • 67651204625 scopus 로고    scopus 로고
    • Proteomic investigation of the time course responses of RAW 264.7 macrophages to infection with Salmonella enterica
    • Shi L, Chowdhury SM, Smallwood HS et al.: Proteomic investigation of the time course responses of RAW 264.7 macrophages to infection with Salmonella enterica. Infect. Immun. 77, 3227-3233 (2009).
    • (2009) Infect. Immun , vol.77 , pp. 3227-3233
    • Shi, L.1    Chowdhury, S.M.2    Smallwood, H.S.3
  • 89
    • 34447296622 scopus 로고    scopus 로고
    • Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut
    • Samuel BS, Hansen EE, Manchester JK et al.: Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc. Natl Acad. Sci. USA 104(25), 10643-10648 (2007).
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , Issue.25 , pp. 10643-10648
    • Samuel, B.S.1    Hansen, E.E.2    Manchester, J.K.3
  • 90
    • 4344567816 scopus 로고    scopus 로고
    • Identification of Lactobacillus plantarum genes that are induced in the gastrointestinal tract of mice
    • Bron PA, Grangette C, Mercenier A, de Vos WM, Kleerebezem M: Identification of Lactobacillus plantarum genes that are induced in the gastrointestinal tract of mice. J. Bacteriol. 186(17), 5721-5729 (2004).
    • (2004) J. Bacteriol , vol.186 , Issue.17 , pp. 5721-5729
    • Bron, P.A.1    Grangette, C.2    Mercenier, A.3    De Vos, W.M.4    Kleerebezem, M.5
  • 91
    • 0033613213 scopus 로고    scopus 로고
    • Identification of Mycobacterium tuberculosis RNAs synthesized in response to phagocytosis by human macrophages by selective capture of transcribed sequences (SCOTS)
    • Graham JE, Clark-Curtiss JE: Identification of Mycobacterium tuberculosis RNAs synthesized in response to phagocytosis by human macrophages by selective capture of transcribed sequences (SCOTS). Proc. Natl Acad. Sci. USA 96(20), 11554-11559 (1999).
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , Issue.20 , pp. 11554-11559
    • Graham, J.E.1    Clark-Curtiss, J.E.2
  • 92
    • 2942560683 scopus 로고    scopus 로고
    • Benefits and pitfalls of using microarrays to monitor bacterial gene expression during infection
    • Hinton JCD, Hautefort I, Eriksson S, Thompson A, Rhen M: Benefits and pitfalls of using microarrays to monitor bacterial gene expression during infection. Curr. Opin. Microbiol. 7, 277-282 (2004).
    • (2004) Curr. Opin. Microbiol , vol.7 , pp. 277-282
    • Hinton, J.C.D.1    Hautefort, I.2    Eriksson, S.3    Thompson, A.4    Rhen, M.5
  • 94
    • 60749119754 scopus 로고    scopus 로고
    • Systems biology: Functional analysis of natural microbial consortia using community proteomics
    • VerBerkmoes NC, Denef VJ, Hettich RL, Banfield JF: Systems biology: functional analysis of natural microbial consortia using community proteomics. Nat. Rev. Microbiol. 7(3), 196-205 (2009).
    • (2009) Nat. Rev. Microbiol , vol.7 , Issue.3 , pp. 196-205
    • Verberkmoes, N.C.1    Denef, V.J.2    Hettich, R.L.3    Banfield, J.F.4
  • 95
    • 36549028432 scopus 로고    scopus 로고
    • Gastrointestinal microbiology enters the metagenomics era
    • Frank DN, Pace NR: Gastrointestinal microbiology enters the metagenomics era. Curr. Opin. Gastroenterol. 24(1), 4-10 (2008).
    • (2008) Curr. Opin. Gastroenterol , vol.24 , Issue.1 , pp. 4-10
    • Frank, D.N.1    Pace, N.R.2
  • 96
    • 66149151286 scopus 로고    scopus 로고
    • Viruses manipulate the marine environment
    • Rohwer F, Thurber RV: Viruses manipulate the marine environment. Nature 459(7244), 207-212 (2009).
    • (2009) Nature , vol.459 , Issue.7244 , pp. 207-212
    • Rohwer, F.1    Thurber, R.V.2
  • 97
    • 39149142575 scopus 로고    scopus 로고
    • CRISPR [MDASH] a widespread system that provides acquired resistance against phages in bacteria and archaea
    • Sorek R, Kunin V, Hugenholtz P: CRISPR [MDASH] a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat. Rev. Microbiol. 6(3), 181-186 (2008).
    • (2008) Nat. Rev. Microbiol , vol.6 , Issue.3 , pp. 181-186
    • Sorek, R.1    Kunin, V.2    Hugenholtz, P.3
  • 98
    • 34247612307 scopus 로고    scopus 로고
    • Multiple high-throughput analyses monitor the response of E. coli to perturbations
    • Ishii N, Nakahigashi K, Baba T et al.: Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science 316(5824), 593-597 (2007).
    • (2007) Science , vol.316 , Issue.5824 , pp. 593-597
    • Ishii, N.1    Nakahigashi, K.2    Baba, T.3
  • 100
    • 33846064113 scopus 로고    scopus 로고
    • NCBI GEO: Mining tens of millions of expression Profiles - Database and tools update
    • Barrett T, Troup DB, Wilhite SE et al.: NCBI GEO: mining tens of millions of expression profiles - database and tools update. Nucleic Acids Res. 35, D760-D765 (2007).
    • (2007) Nucleic Acids Res , vol.35
    • Barrett, T.1    Troup, D.B.2    Wilhite, S.E.3
  • 101
    • 33846039701 scopus 로고    scopus 로고
    • Array Express - A public database of microarray experiments and gene expression profiles
    • Parkinson H, Kapushesky M, Shojatalab M et al.: ArrayExpress - a public database of microarray experiments and gene expression profiles. Nucleic Acids Res. 35, D747-D750 (2007).
    • (2007) Nucleic Acids Res , vol.35
    • Parkinson, H.1    Kapushesky, M.2    Shojatalab, M.3
  • 102
    • 33846400424 scopus 로고    scopus 로고
    • Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
    • Faith JJ, Hayete B, Thaden JT et al.: Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol. 5(1), 54-66 (2007).
    • (2007) PLoS Biol , vol.5 , Issue.1 , pp. 54-66
    • Faith, J.J.1    Hayete, B.2    Thaden, J.T.3
  • 103
    • 63849229020 scopus 로고    scopus 로고
    • The condition-dependent transcriptional network in Escherichia coli
    • Lemmens K, De Bie T, Dhollander T et al.: The condition-dependent transcriptional network in Escherichia coli. Ann. NY Acad. Sci. 1158, 29-35 (2009).
    • (2009) Ann. NY Acad. Sci , vol.1158 , pp. 29-35
    • Lemmens, K.1    De Bie, T.2    Dhollander, T.3
  • 105
    • 33747813561 scopus 로고    scopus 로고
    • The Inferelator: An algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
    • Bonneau R, Reiss DJ, Shannon P et al.: The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol. 7(5), R36 (2006).
    • (2006) Genome Biol , vol.7 , Issue.5
    • Bonneau, R.1    Reiss, D.J.2    Shannon, P.3
  • 106
    • 60149110901 scopus 로고    scopus 로고
    • Module networks revisited: Computational assessment and prioritization of model predictions
    • Joshi A, De Smet R, Marchal K, Van de Peer Y, Michoel T: Module networks revisited: computational assessment and prioritization of model predictions. Bioinformatics 25(4), 490-496 (2009).
    • (2009) Bioinformatics , vol.25 , Issue.4 , pp. 490-496
    • Joshi, A.1    De Smet, R.2    Marchal, K.3    Van De Peer, Y.4    Michoel, T.5
  • 107
    • 66449116353 scopus 로고    scopus 로고
    • Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks
    • Michoel T, De Smet R, Joshi A, de Peer YV, Marchal K: Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks. BMC Syst. Biol. 3, 49 (2009).
    • (2009) BMC Syst. Biol , vol.3 , pp. 49
    • Michoel, T.1    De Smet, R.2    Joshi, A.3    De Peer, Y.V.4    Marchal, K.5
  • 108
    • 59649108558 scopus 로고    scopus 로고
    • Bottlenecks and hubs in inferred networks are important for virulence in Salmonella Typhimurium.
    • McDermott JE, Taylor RC, Yoon H, Heffron F: Bottlenecks and hubs in inferred networks are important for virulence in Salmonella Typhimurium. J. Comput. Biol. 16, 169-180 (2009).
    • (2009) J. Comput. Biol , vol.16 , pp. 169-180
    • McDermott, J.E.1    Taylor, R.C.2    Yoon, H.3    Heffron, F.4
  • 109
    • 59649095559 scopus 로고    scopus 로고
    • Coordinated regulation of virulence during systemic infection of Salmonella enterica serovar Typhimurium
    • Yoon H, McDermott JE, Porwollik S, McClelland M, Heffron F: Coordinated regulation of virulence during systemic infection of Salmonella enterica serovar Typhimurium. PLoS Pathog. 5(2), e1000306 (2009).
    • (2009) PLoS Pathog , vol.5 , Issue.2
    • Yoon, H.1    McDermott, J.E.2    Porwollik, S.3    McClelland, M.4    Heffron, F.5
  • 110
    • 33644527950 scopus 로고    scopus 로고
    • The model organism as a system: Integrating 'omics' data sets
    • Joyce AR, Palsson BO: The model organism as a system: integrating 'omics' data sets. Nat. Rev. Mol. Cell Biol. 7(3), 198-210 (2006).
    • (2006) Nat. Rev. Mol. Cell Biol , vol.7 , Issue.3 , pp. 198-210
    • Joyce, A.R.1    Palsson, B.O.2
  • 111
    • 55549111608 scopus 로고    scopus 로고
    • The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest
    • Balazsi G, Heath AP, Shi LB, Gennaro ML: The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 4, 225 (2008).
    • (2008) Mol. Syst. Biol , vol.4 , pp. 225
    • Balazsi, G.1    Heath, A.P.2    Shi, L.B.3    Gennaro, M.L.4
  • 112
    • 61449254451 scopus 로고    scopus 로고
    • Principles of transcriptional regulation and evolution of the metabolic system in E. coli
    • Seshasayee ASN, Fraser GM, Babu MM, Luscombe NM: Principles of transcriptional regulation and evolution of the metabolic system in E. coli. Genome Res. 19(1), 79-91 (2009).
    • (2009) Genome Res , vol.19 , Issue.1 , pp. 79-91
    • Seshasayee, A.S.N.1    Fraser, G.M.2    Babu, M.M.3    Luscombe, N.M.4
  • 113
    • 17844404232 scopus 로고    scopus 로고
    • Gut microorganisms, mammalian metabolism and personalized health care
    • Nicholson JK, Holmes E, Wilson ID: Gut microorganisms, mammalian metabolism and personalized health care. Nat. Rev. Microbiol. 3(5), 431-438 (2005).
    • (2005) Nat. Rev. Microbiol , vol.3 , Issue.5 , pp. 431-438
    • Nicholson, J.K.1    Holmes, E.2    Wilson, I.D.3
  • 114
    • 37349009767 scopus 로고    scopus 로고
    • Synthetic biology: Promises and challenges
    • Serrano L: Synthetic biology: promises and challenges. Mol. Syst. Biol. 3, 158 (2007).
    • (2007) Mol. Syst. Biol , vol.3 , pp. 158
    • Serrano, L.1
  • 115
    • 70349303484 scopus 로고    scopus 로고
    • Engineering the Salmonella type III secretion system to export spider silk monomers
    • Widmaier DM, Tullman-Ercek D, Mirsky EA et al.: Engineering the Salmonella type III secretion system to export spider silk monomers. Mol. Syst. Biol. 5, 309 (2009).
    • (2009) Mol. Syst. Biol , vol.5 , pp. 309
    • Widmaier, D.M.1    Tullman-Ercek, D.2    Mirsky, E.A.3
  • 116
    • 70349311579 scopus 로고    scopus 로고
    • The impact of synthetic biology on drug discovery
    • Weber W, Fussenegger M: The impact of synthetic biology on drug discovery. Drug Discov. Today 14, 956-963 (2009).
    • (2009) Drug Discov. Today , vol.14 , pp. 956-963
    • Weber, W.1    Fussenegger, M.2
  • 117
    • 33745454125 scopus 로고    scopus 로고
    • Synthetic biology: New engineering rules for an emerging discipline
    • Andrianantoandro E, Basu S, Karig DK, Weiss R: Synthetic biology: new engineering rules for an emerging discipline. Mol. Syst. Biol. 2, 2006.0028 (2006).
    • (2006) Mol. Syst. Biol , vol.2 , pp. 2006
    • Andrianantoandro, E.1    Basu, S.2    Karig, D.K.3    Weiss, R.4
  • 118
    • 33846015876 scopus 로고    scopus 로고
    • Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period
    • Bjursell MK, Martens EC, Gordon JI: Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period. J. Biol. Chem. 281(47), 36269-36279 (2006).
    • (2006) J. Biol. Chem , vol.281 , Issue.47 , pp. 36269-36279
    • Bjursell, M.K.1    Martens, E.C.2    Gordon, J.I.3
  • 119
    • 70350455898 scopus 로고    scopus 로고
    • An interactive regulatory network controls stress response in Bifidobacterium breve UCC2003
    • Zomer A, Fernandez M, Kearney B, Fitzgerald GF, Ventura M, van Sinderen D: An interactive regulatory network controls stress response in Bifidobacterium breve UCC2003. J. Bacteriol. 191(22), 7039-7049 (2009).
    • (2009) J. Bacteriol , vol.191 , Issue.22 , pp. 7039-7049
    • Zomer, A.1    Fernandez, M.2    Kearney, B.3    Fitzgerald, G.F.4    Ventura, M.5    Van Sinderen, D.6
  • 120
    • 55549085860 scopus 로고    scopus 로고
    • Synergistic contribution of the Legionella pneumophila lqs genes to pathogen-host interactions
    • Tiaden A, Spirig T, Carranza P et al.: Synergistic contribution of the Legionella pneumophila lqs genes to pathogen-host interactions. J. Bacteriol. 190(22), 7532-7547 (2008).
    • (2008) J. Bacteriol , vol.190 , Issue.22 , pp. 7532-7547
    • Tiaden, A.1    Spirig, T.2    Carranza, P.3
  • 121
    • 46749114435 scopus 로고    scopus 로고
    • Genomic and proteomic analysis of the alkali-tolerance response (AlTR) in Listeria monocytogenes 10403S
    • Giotis ES, Muthaiyan A, Blair IS, Wilkinson BJ, McDowell DA: Genomic and proteomic analysis of the alkali-tolerance response (AlTR) in Listeria monocytogenes 10403S. BMC Microbiol. 8, 102 (2008).
    • (2008) BMC Microbiol , vol.8 , pp. 102
    • Giotis, E.S.1    Muthaiyan, A.2    Blair, I.S.3    Wilkinson, B.J.4    McDowell, D.A.5
  • 122
    • 67649229164 scopus 로고    scopus 로고
    • Insight into the core and variant exoproteomes of Listeria monocytogenes species by comparative subproteomic analysis
    • Dumas E, Desvaux M, Chambon C, Hebraud M: Insight into the core and variant exoproteomes of Listeria monocytogenes species by comparative subproteomic analysis. Proteomics 9(11), 3136-3155 (2009).
    • (2009) Proteomics , vol.9 , Issue.11 , pp. 3136-3155
    • Dumas, E.1    Desvaux, M.2    Chambon, C.3    Hebraud, M.4
  • 123
    • 17844401762 scopus 로고    scopus 로고
    • Comparative proteome analysis of secretory proteins from pathogenic and nonpathogenic Listeria species
    • Trost M, Wehmhöner D, Kärst U, Dieterich G, Wehland J, Jänsch L: Comparative proteome analysis of secretory proteins from pathogenic and nonpathogenic Listeria species. Proteomics 5, 1544-1557 (2005).
    • (2005) Proteomics , vol.5 , pp. 1544-1557
    • Trost, M.1    Wehmhöner, D.2    Kärst, U.3    Dieterich, G.4    Wehland, J.5    Jänsch, L.6
  • 124
    • 67651219385 scopus 로고    scopus 로고
    • The GacS/GacA signal transduction system of Pseudomonas aeruginosa acts exclusively through its control over the transcription of the RsmY and RsmZ regulatory small RNAs
    • Brencic A, McFarland KA, McManus HR et al.: The GacS/GacA signal transduction system of Pseudomonas aeruginosa acts exclusively through its control over the transcription of the RsmY and RsmZ regulatory small RNAs. Mol. Microbiol. 73(3), 434-445 (2009).
    • (2009) Mol. Microbiol , vol.73 , Issue.3 , pp. 434-445
    • Brencic, A.1    McFarland, K.A.2    McManus, H.R.3
  • 125
    • 34347374506 scopus 로고    scopus 로고
    • Delineation of the Salmonella enterica serovar Typhimurium HilA regulon through genome-wide location and transcript analysis
    • Thijs IMV, De Keersmaecker SCJ, Fadda A et al.: Delineation of the Salmonella enterica serovar Typhimurium HilA regulon through genome-wide location and transcript analysis. J. Bacteriol. 189(13), 4587-4596 (2007).
    • (2007) J. Bacteriol , vol.189 , Issue.13 , pp. 4587-4596
    • Thijs, I.M.V.1    De Keersmaecker, S.C.J.2    Fadda, A.3
  • 126
    • 70350176597 scopus 로고    scopus 로고
    • Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA
    • Papenfort K, Said N, Welsink T, Lucchini S, Hinton JCD, Vogel J: Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA. Mol. Microbiol. 74(1), 139-158 (2009).
    • (2009) Mol. Microbiol , vol.74 , Issue.1 , pp. 139-158
    • Papenfort, K.1    Said, N.2    Welsink, T.3    Lucchini, S.4    Hinton, J.C.D.5    Vogel, J.6
  • 127
    • 33748322018 scopus 로고    scopus 로고
    • Analysis of the Salmonella Typhimurium proteome through environmental response toward infectious conditions
    • Adkins JN, Mottaz HM, Norbeck AD et al.: Analysis of the Salmonella Typhimurium proteome through environmental response toward infectious conditions. Mol. Cell. Proteomics 5(8), 1450-1461 (2006).
    • (2006) Mol. Cell. Proteomics , vol.5 , Issue.8 , pp. 1450-1461
    • Adkins, J.N.1    Mottaz, H.M.2    Norbeck, A.D.3
  • 128
    • 33947718811 scopus 로고    scopus 로고
    • From proteomics to systems biology of bacterial pathogens: Approaches, tools, and applications
    • Plikat U, Voshol H, Dangendorf Y et al.: From proteomics to systems biology of bacterial pathogens: approaches, tools, and applications. Proteomics 7(6), 992-1003 (2007).
    • (2007) Proteomics , vol.7 , Issue.6 , pp. 992-1003
    • Plikat, U.1    Voshol, H.2    Dangendorf, Y.3


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