메뉴 건너뛰기




Volumn 69, Issue 2, 2005, Pages 197-216

Metabolic engineering in the -omics era: Elucidating and modulating regulatory networks

Author keywords

[No Author keywords available]

Indexed keywords

AEROBIC RESPIRATION CONTROL PROTEIN A; BACTERIAL PROTEIN; CARBON; DNA; ENOLASE; HUR PROTEIN; MESSENGER RNA; OUTER MEMBRANE PROTEIN C; OUTER MEMBRANE PROTEIN F; PHOSPHOGLYCERATE KINASE; POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE; PROTEIN HUB; REGULATOR PROTEIN; RIBONUCLEASE; RIBONUCLEASE II; RNA POLYMERASE; UNCLASSIFIED DRUG;

EID: 20544457864     PISSN: 10922172     EISSN: None     Source Type: Journal    
DOI: 10.1128/MMBR.69.2.197-216.2005     Document Type: Review
Times cited : (109)

References (250)
  • 1
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold, R., and M. Mann. 2003. Mass spectrometry-based proteomics. Nature 422:198-207.
    • (2003) Nature , vol.422 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 2
    • 0042818290 scopus 로고    scopus 로고
    • Genome-wide expression profiling of the response to polyene, pyrimidine, azole, and echinocandin antifungal agents in Saccharomyces cerevisiae
    • Agarwal, A. K., P. D. Rogers, S. R. Baerson, M. R. Jacob, K. S. Barker, J. D. Cleary, L. A. Walker, D. G. Nagle, and A. M. Clark. 2003. Genome-wide expression profiling of the response to polyene, pyrimidine, azole, and echinocandin antifungal agents in Saccharomyces cerevisiae. J. Biol. Chem. 278:34998-35015.
    • (2003) J. Biol. Chem. , vol.278 , pp. 34998-35015
    • Agarwal, A.K.1    Rogers, P.D.2    Baerson, S.R.3    Jacob, M.R.4    Barker, K.S.5    Cleary, J.D.6    Walker, L.A.7    Nagle, D.G.8    Clark, A.M.9
  • 3
    • 0030895921 scopus 로고    scopus 로고
    • A comparison of selected mRNA and protein abundances in human liver
    • Anderson, L., and J. Seilhamer. 1997. A comparison of selected mRNA and protein abundances in human liver. Electrophoresis 18:533-537.
    • (1997) Electrophoresis , vol.18 , pp. 533-537
    • Anderson, L.1    Seilhamer, J.2
  • 5
    • 0034703060 scopus 로고    scopus 로고
    • Global gene expression profiling in Escherichia coli K12. The effects of integration host factor
    • Arfin, S. M., A. D. Long, E. T. Ito, L. Tolleri, M. M. Riehle, E. S. Paegle, and G. W. Hatfield. 2000. Global gene expression profiling in Escherichia coli K12. The effects of integration host factor. J. Biol. Chem. 275:29672-29684.
    • (2000) J. Biol. Chem. , vol.275 , pp. 29672-29684
    • Arfin, S.M.1    Long, A.D.2    Ito, E.T.3    Tolleri, L.4    Riehle, M.M.5    Paegle, E.S.6    Hatfield, G.W.7
  • 6
    • 0030603150 scopus 로고    scopus 로고
    • Positive and negative regulation of a sterol biosynthetic gene (ERG3) in the postsqualene portion of the yeast ergosterol pathway
    • Arthington-Skaggs, B. A., D. N. Crowell, H. Yang, S. L. Sturley, and M. Bard. 1996. Positive and negative regulation of a sterol biosynthetic gene (ERG3) in the postsqualene portion of the yeast ergosterol pathway. FEBS Lett. 392:161-165.
    • (1996) FEBS Lett. , vol.392 , pp. 161-165
    • Arthington-Skaggs, B.A.1    Crowell, D.N.2    Yang, H.3    Sturley, S.L.4    Bard, M.5
  • 8
    • 0025895183 scopus 로고
    • Toward a science of metabolic engineering
    • Bailey, J. E. 1991. Toward a science of metabolic engineering. Science 252:1668-1675.
    • (1991) Science , vol.252 , pp. 1668-1675
    • Bailey, J.E.1
  • 9
    • 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 A. D. Long. 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
  • 10
    • 0034101979 scopus 로고    scopus 로고
    • Genome-wide expression patterns in Saccharomyces cerevisiae: Comparison of drug treatments and genetic alterations affecting biosynthesis of ergosterol
    • Bammert, G. F., and J. M. Fostel. 2000. Genome-wide expression patterns in Saccharomyces cerevisiae: comparison of drug treatments and genetic alterations affecting biosynthesis of ergosterol. Antimicrob. Agents Chemother. 44:1255-1265.
    • (2000) Antimicrob. Agents Chemother. , vol.44 , pp. 1255-1265
    • Bammert, G.F.1    Fostel, J.M.2
  • 13
    • 0038101670 scopus 로고    scopus 로고
    • Identification of genes differentially expressed in association with reduced azole susceptibility in Saccharomyces cerevisiae
    • Barker, K. S., M. M. Pearson, and P. D. Rogers. 2003. Identification of genes differentially expressed in association with reduced azole susceptibility in Saccharomyces cerevisiae. J. Antimicrob. Chemother. 51:1131-1140.
    • (2003) J. Antimicrob. Chemother. , vol.51 , pp. 1131-1140
    • Barker, K.S.1    Pearson, M.M.2    Rogers, P.D.3
  • 15
    • 0037162469 scopus 로고    scopus 로고
    • Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays
    • Bernstein, J. A., A. B. Khodursky, P. H. Lin, S. Lin-Chao, and S. N. Cohen. 2002. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc. Natl. Acad. Sci. USA 99:9697-9702.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 9697-9702
    • Bernstein, J.A.1    Khodursky, A.B.2    Lin, P.H.3    Lin-Chao, S.4    Cohen, S.N.5
  • 16
    • 1542267833 scopus 로고    scopus 로고
    • Global analysis of Escherichia coli RNA degradosome function using DNA microarrays
    • Bernstein, J. A., P. H. Lin, S. N. Cohen, and S. Lin-Chao. 2004. Global analysis of Escherichia coli RNA degradosome function using DNA microarrays. Proc. Natl. Acad. Sci. USA 101:2758-2763.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 2758-2763
    • Bernstein, J.A.1    Lin, P.H.2    Cohen, S.N.3    Lin-Chao, S.4
  • 17
    • 0037337310 scopus 로고    scopus 로고
    • A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling
    • Blagoev, B., I. Kratchmarova, S. E. Ong, M. Nielsen, L. J. Foster, and M. Mann. 2003. A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat. Biotechnol. 21:315-318.
    • (2003) Nat. Biotechnol. , vol.21 , pp. 315-318
    • Blagoev, B.1    Kratchmarova, I.2    Ong, S.E.3    Nielsen, M.4    Foster, L.J.5    Mann, M.6
  • 18
    • 0007658020 scopus 로고    scopus 로고
    • Sequence to array: Probing the genome's secrets
    • Blanchard, A. P., and L. Hood. 1996. Sequence to array: probing the genome's secrets. Nat. Biotechnol. 14:1649.
    • (1996) Nat. Biotechnol. , vol.14 , pp. 1649
    • Blanchard, A.P.1    Hood, L.2
  • 20
    • 0347419457 scopus 로고    scopus 로고
    • The proteomics bottleneck: Strategies for preliminary validation of potential biomarkers and drug targets
    • Bodovitz, S., and T. Joos. 2004. The proteomics bottleneck: strategies for preliminary validation of potential biomarkers and drug targets. Trends Biotechnol. 22:4-7.
    • (2004) Trends Biotechnol. , vol.22 , pp. 4-7
    • Bodovitz, S.1    Joos, T.2
  • 22
    • 0036843965 scopus 로고    scopus 로고
    • Gene networks: How to put the function in genomics
    • Brazhnik, P., A. de la Fuente, and P. Mendes. 2002. Gene networks: how to put the function in genomics. Trends Biotechnol. 20:467-472.
    • (2002) Trends Biotechnol. , vol.20 , pp. 467-472
    • Brazhnik, P.1    De La Fuente, A.2    Mendes, P.3
  • 23
    • 0042357079 scopus 로고    scopus 로고
    • Transcriptional, proteomic, and metabolic responses to lithium in galactose-grown yeast cells
    • Bro, C., B. Regenberg, G. Lagniel, J. Labarre, M. Montero-Lomeli, and J. Nielsen. 2003. Transcriptional, proteomic, and metabolic responses to lithium in galactose-grown yeast cells. J. Biol. Chem. 278:32141-32149.
    • (2003) J. Biol. Chem. , vol.278 , pp. 32141-32149
    • Bro, C.1    Regenberg, B.2    Lagniel, G.3    Labarre, J.4    Montero-Lomeli, M.5    Nielsen, J.6
  • 26
    • 1842525835 scopus 로고    scopus 로고
    • Fundamental Escherichia coli biochemical pathways for biomass and energy production: Creation of overall flux states
    • Carlson, R., and F. Srienc. 2004. Fundamental Escherichia coli biochemical pathways for biomass and energy production: creation of overall flux states. Biotechnol. Bioeng. 86:149-162.
    • (2004) Biotechnol. Bioeng. , vol.86 , pp. 149-162
    • Carlson, R.1    Srienc, F.2
  • 27
    • 0347761259 scopus 로고    scopus 로고
    • Fundamental Escherichia coli biochemical pathways for biomass and energy production: Identification of reactions
    • Carlson, R., and F. Srienc. 2004. Fundamental Escherichia coli biochemical pathways for biomass and energy production: identification of reactions. Biotechnol. Bioeng. 85:1-19.
    • (2004) Biotechnol. Bioeng. , vol.85 , pp. 1-19
    • Carlson, R.1    Srienc, F.2
  • 29
    • 4444282070 scopus 로고    scopus 로고
    • Studying the interactome with the yeast two-hybrid system and mass spectrometry
    • Causier, B. 2004. Studying the interactome with the yeast two-hybrid system and mass spectrometry. Mass Spectrom. Rev. 23:350-367.
    • (2004) Mass Spectrom. Rev. , vol.23 , pp. 350-367
    • Causier, B.1
  • 30
    • 0027925642 scopus 로고
    • Hierarchical functional organization of formal biological systems: A dynamical approach. I. The increase of complexity by self-association increases the domain of stability of a biological system
    • Chauvet, G. A. 1993. Hierarchical functional organization of formal biological systems: a dynamical approach. I. The increase of complexity by self-association increases the domain of stability of a biological system. Phil. Trans. R. Soc. Lond. B Biol. Sci. 339:425-444.
    • (1993) Phil. Trans. R. Soc. Lond. B Biol. Sci. , vol.339 , pp. 425-444
    • Chauvet, G.A.1
  • 32
    • 8444220472 scopus 로고    scopus 로고
    • Gene expression microarray technologies in the development of new therapeutic agents
    • Clarke, P. A., R. T. Poele, and P. Workman. 2004. Gene expression microarray technologies in the development of new therapeutic agents. Eur. J. Cancer. 40:2560-2591.
    • (2004) Eur. J. Cancer. , vol.40 , pp. 2560-2591
    • Clarke, P.A.1    Poele, R.T.2    Workman, P.3
  • 33
    • 0142009811 scopus 로고    scopus 로고
    • Molecular classification of cancer: Unsupervised self-organizing map analysis of gene expression microarray data
    • Covell, D. G., A. Wallqvist, A. A. Rabow, and N. Thanki. 2003. Molecular classification of cancer: unsupervised self-organizing map analysis of gene expression microarray data. Mol. Cancer Ther. 2:317-332.
    • (2003) Mol. Cancer Ther. , vol.2 , pp. 317-332
    • Covell, D.G.1    Wallqvist, A.2    Rabow, A.A.3    Thanki, N.4
  • 34
    • 2342648924 scopus 로고    scopus 로고
    • Integrating high-throughput and computational data elucidates bacterial networks
    • Covert, M. W., E. M. Knight, J. L. Reed, M. J. Herrgard, and B. O. Palsson. 2004. Integrating high-throughput and computational data elucidates bacterial networks. Nature 429:92-96.
    • (2004) Nature , vol.429 , pp. 92-96
    • Covert, M.W.1    Knight, E.M.2    Reed, J.L.3    Herrgard, M.J.4    Palsson, B.O.5
  • 35
    • 0035824029 scopus 로고    scopus 로고
    • Regulation of gene expression in flux balance models of metabolism
    • Covert, M. W, C. H. Schilling, and B. Palsson. 2001. Regulation of gene expression in flux balance models of metabolism. J. Theor. Biol. 213:73-88.
    • (2001) J. Theor. Biol. , vol.213 , pp. 73-88
    • Covert, M.W.1    Schilling, C.H.2    Palsson, B.3
  • 36
    • 0021710080 scopus 로고
    • E. coli integration host factor binds to specific sites in DNA
    • Craig, N. L., and H. A. Nash. 1984. E. coli integration host factor binds to specific sites in DNA. Cell 39:707-716.
    • (1984) Cell , vol.39 , pp. 707-716
    • Craig, N.L.1    Nash, H.A.2
  • 37
    • 1542350073 scopus 로고    scopus 로고
    • Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. A chemostat culture study
    • Daran-Lapujade, P., M. L. Jansen, J. M. Daran, G. W. van, J. H. de Winde, and J. T. Pronk. 2004. Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. A chemostat culture study. J. Biol. Chem. 279:9125-9138.
    • (2004) J. Biol. Chem. , vol.279 , pp. 9125-9138
    • Daran-Lapujade, P.1    Jansen, M.L.2    Daran, J.M.3    Van, G.W.4    De Winde, J.H.5    Pronk, J.T.6
  • 38
    • 1042264072 scopus 로고    scopus 로고
    • Protein localization in proteomics
    • Davis, T. N. 2004. Protein localization in proteomics. Curr. Opin. Chem. Biol. 8:49-53.
    • (2004) Curr. Opin. Chem. Biol. , vol.8 , pp. 49-53
    • Davis, T.N.1
  • 39
    • 13244284551 scopus 로고    scopus 로고
    • Dynamic complex formation during the yeast cell cycle
    • de Lichtenberg, U., L. J. Jensen, S. Brunak, and P. Bork. 2005. Dynamic complex formation during the yeast cell cycle. Science 307:724-727.
    • (2005) Science , vol.307 , pp. 724-727
    • De Lichtenberg, U.1    Jensen, L.J.2    Brunak, S.3    Bork, P.4
  • 40
  • 42
    • 0035941209 scopus 로고    scopus 로고
    • NADP-glutamate dehydrogenase isoenzymes of Saccharomyces cerevisiae. Purification, kinetic properties, and physiological roles
    • DeLuna, A., A. Avendano, L. Riego, and A. Gonzalez. 2001. NADP-glutamate dehydrogenase isoenzymes of Saccharomyces cerevisiae. Purification, kinetic properties, and physiological roles. J. Biol. Chem. 276:43775-43783.
    • (2001) J. Biol. Chem. , vol.276 , pp. 43775-43783
    • Deluna, A.1    Avendano, A.2    Riego, L.3    Gonzalez, A.4
  • 43
    • 10344265937 scopus 로고    scopus 로고
    • Control of rRNA synthesis in Escherichia coli: A systems biology approach
    • Dennis, P. P., M. Ehrenberg, and H. Bremer. 2004. Control of rRNA synthesis in Escherichia coli: a systems biology approach. Microbiol. Mol. Biol. Rev. 68:639-668.
    • (2004) Microbiol. Mol. Biol. Rev. , vol.68 , pp. 639-668
    • Dennis, P.P.1    Ehrenberg, M.2    Bremer, H.3
  • 44
    • 0030669030 scopus 로고    scopus 로고
    • Exploring the metabolic and genetic control of gene expression on a genomic scale
    • DeRisi, J. L., V. R. Iyer, and P. O. Brown. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680-686.
    • (1997) Science , vol.278 , pp. 680-686
    • Derisi, J.L.1    Iyer, V.R.2    Brown, P.O.3
  • 45
    • 0028307609 scopus 로고
    • Growth phase variation of integration host factor level in Escherichia coli
    • Ditto, M. D.. D. Roberts, and R. A. Weisberg. 1994. Growth phase variation of integration host factor level in Escherichia coli. J. Bacteriol. 176:3738-3748.
    • (1994) J. Bacteriol. , vol.176 , pp. 3738-3748
    • Ditto, M.D.1    Roberts, D.2    Weisberg, R.A.3
  • 46
    • 0035125986 scopus 로고    scopus 로고
    • In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
    • Edwards, J. S., R. U. Ibarra, and B. O. Palsson. 2001. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat. Biotechnol. 19:125-130.
    • (2001) Nat. Biotechnol. , vol.19 , pp. 125-130
    • Edwards, J.S.1    Ibarra, R.U.2    Palsson, B.O.3
  • 47
    • 0033580813 scopus 로고    scopus 로고
    • Systems properties of the Haemophilus influenzae Rd metabolic genotype
    • Edwards, J. S., and B. O. Palsson. 1999. Systems properties of the Haemophilus influenzae Rd metabolic genotype. J. Biol. Chem. 274:17410-17416.
    • (1999) J. Biol. Chem. , vol.274 , pp. 17410-17416
    • Edwards, J.S.1    Palsson, B.O.2
  • 48
    • 0033570768 scopus 로고    scopus 로고
    • Normalization of array hybridization experiments in differential gene expression analysis
    • Eickhoff, B., B. Korn, M. Schick, A. Poustka, and J. van der Bosch. 1999. Normalization of array hybridization experiments in differential gene expression analysis. Nucleic Acids Res. 27:e33.
    • (1999) Nucleic Acids Res. , vol.27
    • Eickhoff, B.1    Korn, B.2    Schick, M.3    Poustka, A.4    Van Der Bosch, J.5
  • 49
    • 0033031437 scopus 로고    scopus 로고
    • DNA arrays for analysis of gene expression
    • Eisen, M. B., and P. O. Brown. 1999. DNA arrays for analysis of gene expression. Methods Enzymol. 303:179-205.
    • (1999) Methods Enzymol. , vol.303 , pp. 179-205
    • Eisen, M.B.1    Brown, P.O.2
  • 51
    • 0031568786 scopus 로고    scopus 로고
    • A good turn for DNA: The structure of integration host factor bound to DNA
    • Ellenberger, T., and A. Landy. 1997. A good turn for DNA: the structure of integration host factor bound to DNA. Structure 5:153-157.
    • (1997) Structure , vol.5 , pp. 153-157
    • Ellenberger, T.1    Landy, A.2
  • 52
    • 0344824417 scopus 로고    scopus 로고
    • Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network
    • Famili, I., J. Forster, J. Nielsen, and B. O. Palsson. 2003. Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc. Natl. Acad. Sci. USA 100:13134-13139.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 13134-13139
    • Famili, I.1    Forster, J.2    Nielsen, J.3    Palsson, B.O.4
  • 53
    • 0034024497 scopus 로고    scopus 로고
    • Improving lycopene production in Escherichia coli by engineering metabolic control
    • Farmer, W. R., and J. C. Liao. 2000. Improving lycopene production in Escherichia coli by engineering metabolic control. Nat. Biotechnol. 18:533-537.
    • (2000) Nat. Biotechnol. , vol.18 , pp. 533-537
    • Farmer, W.R.1    Liao, J.C.2
  • 55
    • 0037313750 scopus 로고    scopus 로고
    • Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
    • Forster, J., I. Famili, P. Fu, B. O. Palsson, and J. Nielsen. 2003. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 13:244-253.
    • (2003) Genome Res. , vol.13 , pp. 244-253
    • Forster, J.1    Famili, I.2    Fu, P.3    Palsson, B.O.4    Nielsen, J.5
  • 56
    • 0042816453 scopus 로고    scopus 로고
    • Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae
    • Forster, J., I. Famili, B. O. Palsson, and J. Nielsen. 2003. Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae. OMICS 7:193-202.
    • (2003) OMICS , vol.7 , pp. 193-202
    • Forster, J.1    Famili, I.2    Palsson, B.O.3    Nielsen, J.4
  • 57
    • 0037155592 scopus 로고    scopus 로고
    • An mRNA surveillance mechanism that eliminates transcripts lacking termination codons
    • Frischmeyer, P. A., A. van Hoof, K. O'Donnell, A. L. Guerrerio, R. Parker, and H. C. Dietz. 2002. An mRNA surveillance mechanism that eliminates transcripts lacking termination codons. Science 295:2258-2261.
    • (2002) Science , vol.295 , pp. 2258-2261
    • Frischmeyer, P.A.1    Van Hoof, A.2    O'Donnell, K.3    Guerrerio, A.L.4    Parker, R.5    Dietz, H.C.6
  • 59
    • 1542320707 scopus 로고    scopus 로고
    • Hfq, a new chaperoning role: Binding to messenger RNA determines access for small RNA regulator 6
    • Geissmann, T. A., and D. Touati. 2004. Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator 6. EMBO J. 23:396-405.
    • (2004) EMBO J. , vol.23 , pp. 396-405
    • Geissmann, T.A.1    Touati, D.2
  • 60
    • 0035933597 scopus 로고    scopus 로고
    • Quinones as the redox signal for the arc two-component system of bacteria
    • Georgellis, D., O. Kwon, and E. C. Lin. 2001. Quinones as the redox signal for the arc two-component system of bacteria. Science 292:2314-2316.
    • (2001) Science , vol.292 , pp. 2314-2316
    • Georgellis, D.1    Kwon, O.2    Lin, E.C.3
  • 62
    • 0035154372 scopus 로고    scopus 로고
    • Gene expression changes triggered by exposure of Haemophilus influenzae to novobiocin or ciprofloxacin: Combined transcription and translation analysis
    • Grauender, H., K. Kuratli, P. K. Di, C. P. Gray, W. Keck, and S. Evers. 2001. Gene expression changes triggered by exposure of Haemophilus influenzae to novobiocin or ciprofloxacin: combined transcription and translation analysis. Genome Res. 11:28-42.
    • (2001) Genome Res. , vol.11 , pp. 28-42
    • Grauender, H.1    Kuratli, K.2    Di, P.K.3    Gray, C.P.4    Keck, W.5    Evers, S.6
  • 65
    • 0025180835 scopus 로고
    • Searching for and predicting the activity of sites for DNA binding proteins: Compilation and analysis of the binding sites for Escherichia coli integration host factor (IHF)
    • Goodrich, J. A., M. L. Schwartz, and W. R. McClure. 1990. Searching for and predicting the activity of sites for DNA binding proteins: compilation and analysis of the binding sites for Escherichia coli integration host factor (IHF). Nucleic Acids Res. 18:4993-5000.
    • (1990) Nucleic Acids Res. , vol.18 , pp. 4993-5000
    • Goodrich, J.A.1    Schwartz, M.L.2    McClure, W.R.3
  • 66
    • 4344682527 scopus 로고    scopus 로고
    • The small RNA regulators of Escherichia coli: Roles and mechanisms
    • Gottesman, S. 2004. The small RNA regulators of Escherichia coli: roles and mechanisms. Annu. Rev. Microbiol. 58:303-328.
    • (2004) Annu. Rev. Microbiol. , vol.58 , pp. 303-328
    • Gottesman, S.1
  • 68
    • 2942561052 scopus 로고    scopus 로고
    • Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors
    • Grigull, J., S. Mnaimneh, J. Pootoolal, M. D. Robinson, and T. R. Hughes. 2004. Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors. Mol. Cell. Biol. 24:5534-5547.
    • (2004) Mol. Cell. Biol. , vol.24 , pp. 5534-5547
    • Grigull, J.1    Mnaimneh, S.2    Pootoolal, J.3    Robinson, M.D.4    Hughes, T.R.5
  • 69
    • 0037143757 scopus 로고    scopus 로고
    • Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: Rapid decay is associated with a group of touch- and specific clock-controlled genes
    • Gutierrez, R. A., R. M. Ewing, J. M. Cherry, and P. J. Green. 2002. Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: rapid decay is associated with a group of touch- and specific clock-controlled genes. Proc. Natl. Acad. Sci. USA 99:11513-11518.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 11513-11518
    • Gutierrez, R.A.1    Ewing, R.M.2    Cherry, J.M.3    Green, P.J.4
  • 70
    • 0034662907 scopus 로고    scopus 로고
    • Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology
    • Gygi, S. P., G. L. Corthals, Y. Zhang, Y. Rochon, and R. Aebersold. 2000. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl. Acad. Sci. USA 97:9390-9395.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 9390-9395
    • Gygi, S.P.1    Corthals, G.L.2    Zhang, Y.3    Rochon, Y.4    Aebersold, R.5
  • 71
    • 0033016717 scopus 로고    scopus 로고
    • Correlation between protein and mRNA abundance in yeast
    • Gygi, S. P., Y. Rochon, B. R. Franza, and R. Aebersold. 1999. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19:1720-1730.
    • (1999) Mol. Cell. Biol. , vol.19 , pp. 1720-1730
    • Gygi, S.P.1    Rochon, Y.2    Franza, B.R.3    Aebersold, R.4
  • 72
    • 0035221240 scopus 로고    scopus 로고
    • Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions
    • RESEARCH0004
    • Haab, B. B., M. J. Dunham, and P. O. Brown. 2001. Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol. 2:RESEARCH0004.
    • (2001) Genome Biol. , vol.2
    • Haab, B.B.1    Dunham, M.J.2    Brown, P.O.3
  • 73
    • 0347416978 scopus 로고    scopus 로고
    • Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5′ to 3′ mRNA decay pathways in yeast
    • He, F., X. Li, P. Spatrick, R. Casillo, S. Dong, and A. Jacobson. 2003. Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5′ to 3′ mRNA decay pathways in yeast. Mol. Cell 12:1439-1452.
    • (2003) Mol. Cell , vol.12 , pp. 1439-1452
    • He, F.1    Li, X.2    Spatrick, P.3    Casillo, R.4    Dong, S.5    Jacobson, A.6
  • 75
    • 0037313537 scopus 로고    scopus 로고
    • Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery
    • Hieronymus, H., and P. A. Silver. 2003. Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery. Nat. Genet. 33:155-161.
    • (2003) Nat. Genet. , vol.33 , pp. 155-161
    • Hieronymus, H.1    Silver, P.A.2
  • 76
    • 10044282898 scopus 로고    scopus 로고
    • A systems view of mRNP biology
    • Hieronymus, H., and P. A. Silver. 2004. A systems view of mRNP biology. Genes Dev. 18:2845-2860.
    • (2004) Genes Dev. , vol.18 , pp. 2845-2860
    • Hieronymus, H.1    Silver, P.A.2
  • 79
    • 0036766957 scopus 로고    scopus 로고
    • A personal view of molecular technology and how it has changed biology
    • Hood, L. 2002. A personal view of molecular technology and how it has changed biology. J. Proteome Res. 1:399-409.
    • (2002) J. Proteome Res. , vol.1 , pp. 399-409
    • Hood, L.1
  • 80
    • 0037288767 scopus 로고    scopus 로고
    • Systems biology: Integrating technology, biology, and computation
    • Hood, L. 2003. Systems biology: integrating technology, biology, and computation. Mech. Ageing Dev. 124:9-16.
    • (2003) Mech. Ageing Dev. , vol.124 , pp. 9-16
    • Hood, L.1
  • 81
    • 0036241055 scopus 로고    scopus 로고
    • Visualization of interactions among bZIP and Rel family proteins in living cells using bimolecular fluorescence complementation
    • Hu, C. D., Y. Chinenov, and T. K. Kerppola. 2002. Visualization of interactions among bZIP and Rel family proteins in living cells using bimolecular fluorescence complementation. Mol. Cell 9:789-798.
    • (2002) Mol. Cell , vol.9 , pp. 789-798
    • Hu, C.D.1    Chinenov, Y.2    Kerppola, T.K.3
  • 82
    • 0037995710 scopus 로고    scopus 로고
    • Simultaneous visualization of multiple protein interactions in living cells using multicolor fluorescence complementation analysis
    • Hu, C. D., and T. K. Kerppola. 2003. Simultaneous visualization of multiple protein interactions in living cells using multicolor fluorescence complementation analysis. Nat. Biotechnol. 21:539-545.
    • (2003) Nat. Biotechnol. , vol.21 , pp. 539-545
    • Hu, C.D.1    Kerppola, T.K.2
  • 85
    • 0037174983 scopus 로고    scopus 로고
    • Global gene expression profiling in Escherichia coli K12. The effects of leucine-responsive regulatory protein
    • Hung, S. P., P. Baldi, and G. W. Hatfield. 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    Baldi, P.2    Hatfield, G.W.3
  • 86
    • 0017699914 scopus 로고
    • A field and circuit thermodynamics for integrative physiology. I. Introduction to the general notions
    • Iberall, A. S. 1977. A field and circuit thermodynamics for integrative physiology. I. Introduction to the general notions. Am. J. Physiol. 233: R171-R180.
    • (1977) Am. J. Physiol. , vol.233
    • Iberall, A.S.1
  • 89
    • 0346095291 scopus 로고    scopus 로고
    • Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae
    • Ihmels, J., R. Levy, and N. Barkai. 2004. Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae. Nat. Biotechnol. 22:86-92.
    • (2004) Nat. Biotechnol. , vol.22 , pp. 86-92
    • Ihmels, J.1    Levy, R.2    Barkai, N.3
  • 90
    • 0347717583 scopus 로고    scopus 로고
    • Identification of Lhp1p-associated RNAs by microarray analysis in Saccharomyces cerevisiae reveals association with coding and noncoding RNAs
    • Inada, M., and C. Guthrie. 2004. Identification of Lhp1p-associated RNAs by microarray analysis in Saccharomyces cerevisiae reveals association with coding and noncoding RNAs. Proc. Natl. Acad. Sci. USA 101:434-439.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 434-439
    • Inada, M.1    Guthrie, C.2
  • 91
    • 14644414887 scopus 로고    scopus 로고
    • Analysis of hydrostatic pressure effects on transcription in Escherichia coli by DNA microarray procedure
    • Ishii, A., T. Oshima, T. Sato, K. Nakasone, H. Mori, and C. Kato. 2004. Analysis of hydrostatic pressure effects on transcription in Escherichia coli by DNA microarray procedure. Extremophiles 9:65-73,
    • (2004) Extremophiles , vol.9 , pp. 65-73
    • Ishii, A.1    Oshima, T.2    Sato, T.3    Nakasone, K.4    Mori, H.5    Kato, C.6
  • 92
    • 0010656061 scopus 로고    scopus 로고
    • Exploring the protein interactome using comprehensive two-hybrid projects
    • Ito, T., T. Chiba, and M. Yoshida. 2001. Exploring the protein interactome using comprehensive two-hybrid projects. Trends Biotechnol. 19:S23-S27.
    • (2001) Trends Biotechnol. , vol.19
    • Ito, T.1    Chiba, T.2    Yoshida, M.3
  • 93
    • 0024121496 scopus 로고
    • arcA (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways
    • Iuchi, S., and E. C. Lin. 1988. arcA (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways. Proc. Natl. Acad. Sci. USA 85:1888-1892.
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 1888-1892
    • Iuchi, S.1    Lin, E.C.2
  • 94
    • 0035945567 scopus 로고    scopus 로고
    • Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
    • Iyer, V. R., C. E. Horak, C. S. Scafe, D. Botstein, M. Snyder, and P. O. Brown. 2001. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409:533-538.
    • (2001) Nature , vol.409 , pp. 533-538
    • Iyer, V.R.1    Horak, C.E.2    Scafe, C.S.3    Botstein, D.4    Snyder, M.5    Brown, P.O.6
  • 95
    • 0028797303 scopus 로고
    • RNase e autoregulates its synthesis by controlling the degradation rate of its own mRNA in Escherichia coli: Unusual sensitivity of the rne transcript to RNase E activity
    • Jain, C., and J. G. Belasco. 1995. RNase E autoregulates its synthesis by controlling the degradation rate of its own mRNA in Escherichia coli: unusual sensitivity of the rne transcript to RNase E activity. Genes Dev. 9:84-96.
    • (1995) Genes Dev. , vol.9 , pp. 84-96
    • Jain, C.1    Belasco, J.G.2
  • 96
  • 97
    • 1942520229 scopus 로고    scopus 로고
    • A functional protein chip for pathway optimization and in vitro metabolic engineering
    • Jung, G. Y., and G. Stephanopoulos. 2004. A functional protein chip for pathway optimization and in vitro metabolic engineering. Science 304:428-431.
    • (2004) Science , vol.304 , pp. 428-431
    • Jung, G.Y.1    Stephanopoulos, G.2
  • 98
    • 15044353444 scopus 로고    scopus 로고
    • Transcription control reprogramming in genetic backup circuits
    • Kafri, R., A. Bar-Even, and Y. Pilpel. 2005. Transcription control reprogramming in genetic backup circuits. Nat. Genet. 37:295-299.
    • (2005) Nat. Genet. , vol.37 , pp. 295-299
    • Kafri, R.1    Bar-Even, A.2    Pilpel, Y.3
  • 99
    • 1242300132 scopus 로고    scopus 로고
    • Regulatory network connecting two glucose signal transduction pathways in Saccharomyces cerevisiae
    • Kaniak, A., Z. Xue, D. Macool, J. H. Kim, and M. Johnston. 2004. Regulatory network connecting two glucose signal transduction pathways in Saccharomyces cerevisiae. Eukaryot. Cell 3:221-231.
    • (2004) Eukaryot. Cell , vol.3 , pp. 221-231
    • Kaniak, A.1    Xue, Z.2    Macool, D.3    Kim, J.H.4    Johnston, M.5
  • 100
    • 13244281760 scopus 로고    scopus 로고
    • Implication of membrane localization of target mRNA in the action of a small RNA: Mechanism of post-transcriptional regulation of glucose transporter in Escherichia coli
    • Kawamoto, H., T. Morita, A. Shimizu, T. Inada, and H. Aiba. 2005. Implication of membrane localization of target mRNA in the action of a small RNA: mechanism of post-transcriptional regulation of glucose transporter in Escherichia coli. Genes Dev. 19:328-338.
    • (2005) Genes Dev. , vol.19 , pp. 328-338
    • Kawamoto, H.1    Morita, T.2    Shimizu, A.3    Inada, T.4    Aiba, H.5
  • 101
    • 0036289532 scopus 로고    scopus 로고
    • Eukaryotic mRNPs may represent posttranscriptional operons
    • Keene, J. D., and S. A. Tenenbaum. 2002. Eukaryotic mRNPs may represent posttranscriptional operons. Mol. Cell. 9:1161-1167.
    • (2002) Mol. Cell. , vol.9 , pp. 1161-1167
    • Keene, J.D.1    Tenenbaum, S.A.2
  • 102
    • 0036842183 scopus 로고    scopus 로고
    • Genotype-phenotype mapping: Genes as computer programs
    • Kell, D. B. 2002. Genotype-phenotype mapping: genes as computer programs. Trends Genet. 18:555-559.
    • (2002) Trends Genet. , vol.18 , pp. 555-559
    • Kell, D.B.1
  • 103
    • 0033553144 scopus 로고    scopus 로고
    • Transcriptional regulation of the squalene synthase gene (ERG9) in the yeast Saccharomyces cerevisiae
    • Kennedy, M. A., R. Barbuch, and M. Bard. 1999. Transcriptional regulation of the squalene synthase gene (ERG9) in the yeast Saccharomyces cerevisiae. Biochim. Biophys. Acta. 1445:110-122.
    • (1999) Biochim. Biophys. Acta. , vol.1445 , pp. 110-122
    • Kennedy, M.A.1    Barbuch, R.2    Bard, M.3
  • 104
    • 0346021343 scopus 로고    scopus 로고
    • Linear models for microarray data analysis: Hidden similarities and differences
    • Kerr, M. K. 2003. Linear models for microarray data analysis: hidden similarities and differences. J. Comput. Biol. 10:891-901.
    • (2003) J. Comput. Biol. , vol.10 , pp. 891-901
    • Kerr, M.K.1
  • 105
    • 0000884487 scopus 로고    scopus 로고
    • Experimental design for gene expression microarrays
    • Kerr, M. K., and G. A. Churchill. 2001. Experimental design for gene expression microarrays. Biostatistics 2:183-201.
    • (2001) Biostatistics , vol.2 , pp. 183-201
    • Kerr, M.K.1    Churchill, G.A.2
  • 106
    • 0034927555 scopus 로고    scopus 로고
    • Analysis of variance for gene expression microarray data
    • Kerr, M. K., M. Martin, and G. A. Churchill. 2000. Analysis of variance for gene expression microarray data. J. Comput. Biol. 7:819-837.
    • (2000) J. Comput. Biol. , vol.7 , pp. 819-837
    • Kerr, M.K.1    Martin, M.2    Churchill, G.A.3
  • 107
    • 0037370460 scopus 로고    scopus 로고
    • Life after transcription-revisiting the fate of messenger RNA
    • Khodursky, A. B., and J. A. Bernstein. 2003. Life after transcription-revisiting the fate of messenger RNA. Trends Genet. 19:113-115.
    • (2003) Trends Genet. , vol.19 , pp. 113-115
    • Khodursky, A.B.1    Bernstein, J.A.2
  • 108
    • 0034710992 scopus 로고    scopus 로고
    • DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli
    • Khodursky, A. B., B. J. Peter, N. R. Cozzarelli, D. Botstein, P. O. Brown, and C. Yanofsky. 2000. DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli. Proc. Natl. Acad. Sci. USA 97:12170-12175.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 12170-12175
    • Khodursky, A.B.1    Peter, B.J.2    Cozzarelli, N.R.3    Botstein, D.4    Brown, P.O.5    Yanofsky, C.6
  • 109
    • 0037079054 scopus 로고    scopus 로고
    • Computational systems biology
    • Kitano, H. 2002. Computational systems biology. Nature 420:206-210.
    • (2002) Nature , vol.420 , pp. 206-210
    • Kitano, H.1
  • 110
    • 0001140587 scopus 로고
    • The transition between different physiological states during balanced growth of Salmonella typhimurium
    • Kjeldgaard, N. O., O. Maaloe, and M. Schaechter. 1958. The transition between different physiological states during balanced growth of Salmonella typhimurium. J. Gen. Microbiol. 19:607-616.
    • (1958) J. Gen. Microbiol. , vol.19 , pp. 607-616
    • Kjeldgaard, N.O.1    Maaloe, O.2    Schaechter, M.3
  • 113
    • 1542376957 scopus 로고    scopus 로고
    • In-depth profiling of lysine-producing Corynebacterium glutamicum by combined analysis of the transcriptome, metabolome, and fluxome
    • Kromer, J. O., O. Sorgenfrei, K. Klopprogge, E. Heinzle, and C. Wittmann. 2004. In-depth profiling of lysine-producing Corynebacterium glutamicum by combined analysis of the transcriptome, metabolome, and fluxome. J. Bacteriol. 186:1769-1784.
    • (2004) J. Bacteriol. , vol.186 , pp. 1769-1784
    • Kromer, J.O.1    Sorgenfrei, O.2    Klopprogge, K.3    Heinzle, E.4    Wittmann, C.5
  • 117
    • 0036719292 scopus 로고    scopus 로고
    • mRNA decay in Escherichia coli comes of age
    • Kushner, S. R. 2002. mRNA decay in Escherichia coli comes of age. J. Bacteriol. 184:4658-4665.
    • (2002) J. Bacteriol. , vol.184 , pp. 4658-4665
    • Kushner, S.R.1
  • 118
    • 84984932880 scopus 로고    scopus 로고
    • Array of hope
    • Lander, E. S. 1999. Array of hope. Nat. Genet. 21:3-4.
    • (1999) Nat. Genet. , vol.21 , pp. 3-4
    • Lander, E.S.1
  • 119
    • 0031594985 scopus 로고    scopus 로고
    • Drug-induced phenotypes provide a tool for the functional analysis of yeast genes
    • Launhardt, H., A. Hinnen, and T. Munder. 1998. Drug-induced phenotypes provide a tool for the functional analysis of yeast genes. Yeast 14:935-942.
    • (1998) Yeast , vol.14 , pp. 935-942
    • Launhardt, H.1    Hinnen, A.2    Munder, T.3
  • 120
    • 0034730124 scopus 로고    scopus 로고
    • Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations
    • Lee, M. L., F. C. Kuo, G. A. Whitmore, and J. Sklar. 2000. Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc. Natl. Acad. Sci. USA 97:9834-9839.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 9834-9839
    • Lee, M.L.1    Kuo, F.C.2    Whitmore, G.A.3    Sklar, J.4
  • 122
    • 0038729565 scopus 로고    scopus 로고
    • Classification of multiple cancer types by multicategory support vector machines using gene expression data
    • Lee, Y., and C. K. Lee. 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
  • 123
    • 0036068774 scopus 로고    scopus 로고
    • LrhA as a new transcriptional key regulator of flagella, motility and chemotaxis genes in Escherichia coli
    • Lehnen, D., C. Blumer, T. Polen, B. Wackwitz, V. F. Wendisch, and G. Unden. 2002. LrhA as a new transcriptional key regulator of flagella, motility and chemotaxis genes in Escherichia coli. Mol. Microbiol. 45:521-532.
    • (2002) Mol. Microbiol. , vol.45 , pp. 521-532
    • Lehnen, D.1    Blumer, C.2    Polen, T.3    Wackwitz, B.4    Wendisch, V.F.5    Unden, G.6
  • 124
    • 3142564584 scopus 로고    scopus 로고
    • The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae
    • Lenz, D. H., K. C. Mok, B. N. Lilley, R. V. Kulkarni, N. S. Wingreen, and B. L. Bassler. 2004. The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell 118:69-82.
    • (2004) Cell , vol.118 , pp. 69-82
    • Lenz, D.H.1    Mok, K.C.2    Lilley, B.N.3    Kulkarni, R.V.4    Wingreen, N.S.5    Bassler, B.L.6
  • 125
    • 0030014654 scopus 로고    scopus 로고
    • Characterization of yeast methyl sterol oxidase (ERG25) and identification of a human homologue
    • Li, L., and J. Kaplan. 1996. Characterization of yeast methyl sterol oxidase (ERG25) and identification of a human homologue. J. Biol. Chem. 271: 16927-16933.
    • (1996) J. Biol. Chem. , vol.271 , pp. 16927-16933
    • Li, L.1    Kaplan, J.2
  • 127
    • 3042822422 scopus 로고    scopus 로고
    • Custom design of metabolism
    • Liao, J. C. 2004. Custom design of metabolism. Nat. Biotechnol. 22:823-824.
    • (2004) Nat. Biotechnol. , vol.22 , pp. 823-824
    • Liao, J.C.1
  • 129
    • 0034934774 scopus 로고    scopus 로고
    • Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association
    • Lieb, J. D., X. Liu, D. Botstein, and P. O. Brown. 2001. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat. Genet. 28:327-334.
    • (2001) Nat. Genet. , vol.28 , pp. 327-334
    • Lieb, J.D.1    Liu, X.2    Botstein, D.3    Brown, P.O.4
  • 130
    • 0036166753 scopus 로고    scopus 로고
    • Linear modes of gene expression determined by independent component analysis
    • Liebermeister, W. 2002. Linear modes of gene expression determined by independent component analysis. Bioinformatics 18:51-60.
    • (2002) Bioinformatics , vol.18 , pp. 51-60
    • Liebermeister, W.1
  • 132
    • 0036324753 scopus 로고    scopus 로고
    • An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments
    • Liu, X. S., D. L. Brutlag, and J. S. Liu. 2002. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat. Biotechnol. 20:835-839.
    • (2002) Nat. Biotechnol. , vol.20 , pp. 835-839
    • Liu, X.S.1    Brutlag, D.L.2    Liu, J.S.3
  • 134
    • 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., H. J. Mangalam, B. Y. Chan, L. Tolleri, G. W. Hatfield, and P. Baldi. 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    Mangalam, H.J.2    Chan, B.Y.3    Tolleri, L.4    Hatfield, G.W.5    Baldi, P.6
  • 137
    • 4644326931 scopus 로고    scopus 로고
    • Genomic analysis of regulatory network dynamics reveals large topological changes
    • Luscombe, N. M., M. M. Babu, H. Yu, M. Snyder, S. A. Teichmann, and M. Gerstein. 2004. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431:308-312.
    • (2004) Nature , vol.431 , pp. 308-312
    • Luscombe, N.M.1    Babu, M.M.2    Yu, H.3    Snyder, M.4    Teichmann, S.A.5    Gerstein, M.6
  • 138
    • 0036898579 scopus 로고    scopus 로고
    • Protein microarrays and proteomics
    • MacBeath, G. 2002. Protein microarrays and proteomics. Nat. Genet. 32(Suppl.):526-532.
    • (2002) Nat. Genet. , vol.32 , Issue.SUPPL. , pp. 526-532
    • MacBeath, G.1
  • 139
    • 0034622925 scopus 로고    scopus 로고
    • Printing proteins as microarrays for high-throughput function determination
    • MacBeath, G., and S. L. Schreiber. 2000. Printing proteins as microarrays for high-throughput function determination. Science 289:1760-1763.
    • (2000) Science , vol.289 , pp. 1760-1763
    • MacBeath, G.1    Schreiber, S.L.2
  • 140
    • 0037440734 scopus 로고    scopus 로고
    • Evolution of transcription factors and the gene regulatory network in Escherichia coli
    • Madan, B. M., and S. A. Teichmann. 2003. Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res. 31:1234-1244.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 1234-1244
    • Madan, B.M.1    Teichmann, S.A.2
  • 141
    • 0035100582 scopus 로고    scopus 로고
    • Regulation of RpoS by a novel small RNA: The characterization of RprA
    • Majdalani, N., S. Chen, J. Murrow, J. K. St, and S. Gottesman. 2001. Regulation of RpoS by a novel small RNA: the characterization of RprA. Mol. Microbiol. 39:1382-1394.
    • (2001) Mol. Microbiol. , vol.39 , pp. 1382-1394
    • Majdalani, N.1    Chen, S.2    Murrow, J.3    Gottesman, S.4
  • 142
    • 0036437019 scopus 로고    scopus 로고
    • Regulation and mode of action of the second small RNA activator of RpoS translation, RprA
    • Majdalani, N., D. Hernandez, and S. Gottesman. 2002. Regulation and mode of action of the second small RNA activator of RpoS translation, RprA. Mol. Microbiol. 46:813-826.
    • (2002) Mol. Microbiol. , vol.46 , pp. 813-826
    • Majdalani, N.1    Hernandez, D.2    Gottesman, S.3
  • 143
    • 0038391517 scopus 로고    scopus 로고
    • Engineering a mevalonate pathway in Escherichia coli for production of terpenoids
    • Martin, V. J., D. J. Pitera, S. T. Withers, J. D. Newman, and J. D. Keasling. 2003. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotechnol. 21:796-802.
    • (2003) Nat. Biotechnol. , vol.21 , pp. 796-802
    • Martin, V.J.1    Pitera, D.J.2    Withers, S.T.3    Newman, J.D.4    Keasling, J.D.5
  • 144
    • 0242386460 scopus 로고    scopus 로고
    • Identifying global regulators in transcriptional regulatory networks in bacteria
    • Martinez-Antonio, A., and J. Collado-Vides. 2003. Identifying global regulators in transcriptional regulatory networks in bacteria. Curr. Opin. Microbiol. 6:482-489.
    • (2003) Curr. Opin. Microbiol. , vol.6 , pp. 482-489
    • Martinez-Antonio, A.1    Collado-Vides, J.2
  • 145
    • 0036729529 scopus 로고    scopus 로고
    • The transcriptional program of meiosis and sporulation in fission yeast
    • Mata, J., R. Lyne, G. Burns, and J. Bahler. 2002. The transcriptional program of meiosis and sporulation in fission yeast. Nat. Genet. 32:143-147.
    • (2002) Nat. Genet. , vol.32 , pp. 143-147
    • Mata, J.1    Lyne, R.2    Burns, G.3    Bahler, J.4
  • 146
    • 0033855132 scopus 로고    scopus 로고
    • Tuning of the porin expression under anaerobic growth conditions by his-to-Asp cross-phosphorelay through both the EnvZ-osmosensor and ArcB-anaerosensor in Escherichia coli
    • Matsubara, M., S. I. Kitaoka, S. I. Takeda, and T. Mizuno. 2000. Tuning of the porin expression under anaerobic growth conditions by his-to-Asp cross-phosphorelay through both the EnvZ-osmosensor and ArcB-anaerosensor in Escherichia coli. Genes Cells. 5:555-569.
    • (2000) Genes Cells. , vol.5 , pp. 555-569
    • Matsubara, M.1    Kitaoka, S.I.2    Takeda, S.I.3    Mizuno, T.4
  • 148
    • 0031589010 scopus 로고    scopus 로고
    • Compilation of all genes encoding two-component phosphotransfer signal transducers in the genome of Escherichia coli
    • Mizuno, T. 1997. Compilation of all genes encoding two-component phosphotransfer signal transducers in the genome of Escherichia coli. DNA Res. 4:161-168.
    • (1997) DNA Res. , vol.4 , pp. 161-168
    • Mizuno, T.1
  • 149
    • 0142030030 scopus 로고    scopus 로고
    • Genomic analysis in Escherichia coli demonstrates differential roles for polynucleotide phosphorylase and RNase II in mRNA abundance and decay
    • Mohanty, B. K., and S. R. Kushner. 2003. Genomic analysis in Escherichia coli demonstrates differential roles for polynucleotide phosphorylase and RNase II in mRNA abundance and decay. Mol. Microbiol. 50:645-658.
    • (2003) Mol. Microbiol. , vol.50 , pp. 645-658
    • Mohanty, B.K.1    Kushner, S.R.2
  • 150
    • 1242318677 scopus 로고    scopus 로고
    • Transcriptome and proteome analysis of Bacillus subtilis gene expression in response to superoxide and peroxide stress
    • Mostertz, J., C. Scharf, M. Hecker, and G. Homuth. 2004. Transcriptome and proteome analysis of Bacillus subtilis gene expression in response to superoxide and peroxide stress. Microbiology 150:497-512.
    • (2004) Microbiology , vol.150 , pp. 497-512
    • Mostertz, J.1    Scharf, C.2    Hecker, M.3    Homuth, G.4
  • 152
    • 0028577728 scopus 로고
    • Targeting of the polyhydroxybutyrate biosynthetic pathway to the plastids of Arabidopsis thaliana results in high levels of polymer accumulation
    • Nawrath, C., Y. Poirier, and C. Somerville. 1994. Targeting of the polyhydroxybutyrate biosynthetic pathway to the plastids of Arabidopsis thaliana results in high levels of polymer accumulation. Proc. Natl. Acad. Sci. USA 91:12760-12764.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 12760-12764
    • Nawrath, C.1    Poirier, Y.2    Somerville, C.3
  • 154
    • 0037595546 scopus 로고    scopus 로고
    • Comprehensive identification of human bZIP interactions with coiled-coil arrays
    • Newman, J. R., and A. E. Keating. 2003. Comprehensive identification of human bZIP interactions with coiled-coil arrays. Science 300:2097-2101.
    • (2003) Science , vol.300 , pp. 2097-2101
    • Newman, J.R.1    Keating, A.E.2
  • 155
    • 0347506028 scopus 로고    scopus 로고
    • It is all about metabolic fluxes
    • Nielsen, J. 2003. It is all about metabolic fluxes. J. Bacteriol. 185:7031-7035.
    • (2003) J. Bacteriol. , vol.185 , pp. 7031-7035
    • Nielsen, J.1
  • 156
    • 1342346607 scopus 로고    scopus 로고
    • Role of histone-like protein H-NS in multidrug resistance of Escherichia coli
    • Nishino, K., and A. Yamaguchi. 2004. Role of histone-like protein H-NS in multidrug resistance of Escherichia coli. J. Bacteriol. 186:1423-1429.
    • (2004) J. Bacteriol. , vol.186 , pp. 1423-1429
    • Nishino, K.1    Yamaguchi, A.2
  • 157
  • 159
    • 0034161329 scopus 로고    scopus 로고
    • Mapping chromosomal proteins in vivo by formaldehyde-crosslinked- chromatin immunoprecipitation
    • Orlando, V. 2000. Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation. Trends Biochem. Sci. 25:99-104.
    • (2000) Trends Biochem. Sci. , vol.25 , pp. 99-104
    • Orlando, V.1
  • 161
    • 0033664269 scopus 로고    scopus 로고
    • Increasing galactose consumption by Saccharomyces cerevisiae through metabolic engineering of the GAL gene regulatory network
    • Ostergaard, S., L. Olsson, M. Johnston, and J. Nielsen. 2000. Increasing galactose consumption by Saccharomyces cerevisiae through metabolic engineering of the GAL gene regulatory network. Nat. Biotechnol. 18:1283-1286.
    • (2000) Nat. Biotechnol. , vol.18 , pp. 1283-1286
    • Ostergaard, S.1    Olsson, L.2    Johnston, M.3    Nielsen, J.4
  • 162
    • 0036197752 scopus 로고    scopus 로고
    • RNase E levels in Escherichia coli are controlled by a complex regulatory system that involves transcription of the me gene from three promoters
    • Ow, M. C., Q. Liu, B. K. Mohanty, M. E. Andrew, V. F. Maples, and S. R. Kushner. 2002. RNase E levels in Escherichia coli are controlled by a complex regulatory system that involves transcription of the me gene from three promoters. Mol. Microbiol. 43:159-171.
    • (2002) Mol. Microbiol. , vol.43 , pp. 159-171
    • Ow, M.C.1    Liu, Q.2    Mohanty, B.K.3    Andrew, M.E.4    Maples, V.F.5    Kushner, S.R.6
  • 163
    • 4444353693 scopus 로고    scopus 로고
    • Kernel-based self-organized maps trained with supervised bias for gene expression data analysis
    • Papadimitriou, S., and S. D. Likothanassis. 2004. Kernel-based self-organized maps trained with supervised bias for gene expression data analysis. J. Bioinform. Comput. Biol. 1:647-680.
    • (2004) J. Bioinform. Comput. Biol. , vol.1 , pp. 647-680
    • Papadimitriou, S.1    Likothanassis, S.D.2
  • 164
  • 165
    • 14544268137 scopus 로고    scopus 로고
    • Uncovering transcriptional regulation of metabolism by using metabolic network topology
    • Patil, K. R., and J. Nielsen. 2005. Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc. Natl. Acad. Sci. USA 102:2685-2689.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 2685-2689
    • Patil, K.R.1    Nielsen, J.2
  • 166
    • 0037370373 scopus 로고    scopus 로고
    • Proteomics: The first decade and beyond
    • Patterson, S. D., and R. H. Aebersold. 2003. Proteomics: the first decade and beyond. Nat. Genet. 33(Suppl.):311-323.
    • (2003) Nat. Genet. , vol.33 , Issue.SUPPL. , pp. 311-323
    • Patterson, S.D.1    Aebersold, R.H.2
  • 168
    • 2142806748 scopus 로고    scopus 로고
    • Gene expression analysis of messenger RNP complexes
    • Penalva, L. O., S. A. Tenenbaum, and J. D. Keene. 2004. Gene expression analysis of messenger RNP complexes. Methods Mol. Biol. 257:125-134.
    • (2004) Methods Mol. Biol. , vol.257 , pp. 125-134
    • Penalva, L.O.1    Tenenbaum, S.A.2    Keene, J.D.3
  • 169
    • 0346156102 scopus 로고    scopus 로고
    • Detection of functional modules from protein interaction networks
    • Pereira-Leal, J. B., A. J. Enright, and C. A. Ouzounis. 2004. Detection of functional modules from protein interaction networks. Proteins 54:49-57.
    • (2004) Proteins , vol.54 , pp. 49-57
    • Pereira-Leal, J.B.1    Enright, A.J.2    Ouzounis, C.A.3
  • 170
    • 0029922992 scopus 로고    scopus 로고
    • A DEAD-box RNA helicase in the Escherichia coli RNA degradosome
    • Py, B., C. F. Higgins, H. M. Krisch, and A. J. Carpousis. 1996. A DEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature 381: 169-172.
    • (1996) Nature , vol.381 , pp. 169-172
    • Py, B.1    Higgins, C.F.2    Krisch, H.M.3    Carpousis, A.J.4
  • 175
    • 0037199968 scopus 로고    scopus 로고
    • Hierarchical organization of modularity in metabolic networks
    • Ravasz, E., A. L. Somera, D. A. Mongru, Z. N. Oltvai, and A. L. Barabasi. 2002. Hierarchical organization of modularity in metabolic networks. Science 297:1551-1555.
    • (2002) Science , vol.297 , pp. 1551-1555
    • Ravasz, E.1    Somera, A.L.2    Mongru, D.A.3    Oltvai, Z.N.4    Barabasi, A.L.5
  • 176
    • 0037406843 scopus 로고    scopus 로고
    • Thirteen years of building constraint-based in silico models of Escherichia coli
    • Reed, J. L., and B. O. Palsson. 2003. Thirteen years of building constraint-based in silico models of Escherichia coli. J. Bacteriol. 185:2692-2699.
    • (2003) J. Bacteriol. , vol.185 , pp. 2692-2699
    • Reed, J.L.1    Palsson, B.O.2
  • 177
    • 0344328817 scopus 로고    scopus 로고
    • An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
    • Reed, J. L., T. D. Vo, C. H. Schilling, and B. O. Palsson. 2003. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol. 4:R54.
    • (2003) Genome Biol. , vol.4
    • Reed, J.L.1    Vo, T.D.2    Schilling, C.H.3    Palsson, B.O.4
  • 179
    • 1642418867 scopus 로고    scopus 로고
    • Protective role for H-NS protein in IS1 transposition
    • Rouquette, C., M. C. Serre, and D. Lane. 2004. Protective role for H-NS protein in IS1 transposition. J. Bacteriol. 186:2091-2098.
    • (2004) J. Bacteriol. , vol.186 , pp. 2091-2098
    • Rouquette, C.1    Serre, M.C.2    Lane, D.3
  • 180
    • 11144234660 scopus 로고    scopus 로고
    • Global network analysis of phenotypic effects: Protein networks and toxicity modulation in Saccharomyces cerevisiae
    • Said, M. R., T. J. Begley, A. V. Oppenheim, D. A. Lauffenburger, and L. D. Samson. 2004. Global network analysis of phenotypic effects: protein networks and toxicity modulation in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 101:18006-18011.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 18006-18011
    • Said, M.R.1    Begley, T.J.2    Oppenheim, A.V.3    Lauffenburger, D.A.4    Samson, L.D.5
  • 182
    • 17644381300 scopus 로고    scopus 로고
    • Global gene expression profiling in Escherichia coli K12: The effects of oxygen availability and ArcA
    • Salmon, K. A., S. P. Hung, N. R. Steffan, R. Krupp, P. Baldi, G. W. Hatfield, and R. P. Gunsalus. 2005. Global gene expression profiling in Escherichia coli K12: the effects of oxygen availability and ArcA. J. Biol. Chem. 280: 15084-15096.
    • (2005) J. Biol. Chem. , vol.280 , pp. 15084-15096
    • Salmon, K.A.1    Hung, S.P.2    Steffan, N.R.3    Krupp, R.4    Baldi, P.5    Hatfield, G.W.6    Gunsalus, R.P.7
  • 183
    • 1242306261 scopus 로고    scopus 로고
    • High-throughput phenomics: Experimental methods for mapping fluxomes
    • Sauer, U. 2004. High-throughput phenomics: experimental methods for mapping fluxomes. Curr. Opin. Biotechnol. 15:58-63.
    • (2004) Curr. Opin. Biotechnol. , vol.15 , pp. 58-63
    • Sauer, U.1
  • 185
    • 0001140586 scopus 로고
    • Dependency on medium and temperature of cell size and chemical composition during balanced grown of Salmonella typhimurium
    • Schaechter, M., O. Maaloe, and N. O. Kjeldgaard. 1958. Dependency on medium and temperature of cell size and chemical composition during balanced grown of Salmonella typhimurium. J. Gen. Microbiol. 19:592-606.
    • (1958) J. Gen. Microbiol. , vol.19 , pp. 592-606
    • Schaechter, M.1    Maaloe, O.2    Kjeldgaard, N.O.3
  • 186
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • Schena, M., D. Shalon, R. W. Davis, and P. O. Brown. 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470.
    • (1995) Science , vol.270 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 188
    • 0034447725 scopus 로고    scopus 로고
    • Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems
    • Schilling, C. H., J. S. Edwards, D. Letscher, and B. O. Palsson. 2000. Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems. Biotechnol. Bioeng. 71:286-306.
    • (2000) Biotechnol. Bioeng. , vol.71 , pp. 286-306
    • Schilling, C.H.1    Edwards, J.S.2    Letscher, D.3    Palsson, B.O.4
  • 189
    • 0037783314 scopus 로고    scopus 로고
    • Translational repression mechanisms in prokaryotes
    • Schlax, P. J., and D. J. Worhunsky. 2003. Translational repression mechanisms in prokaryotes. Mol. Microbiol. 48:1157-1169.
    • (2003) Mol. Microbiol. , vol.48 , pp. 1157-1169
    • Schlax, P.J.1    Worhunsky, D.J.2
  • 190
    • 0242407063 scopus 로고    scopus 로고
    • Microarrays to characterize protein interactions on a whole-proteome scale
    • Schweitzer, B., P. Predki, and M. Snyder. 2003. Microarrays to characterize protein interactions on a whole-proteome scale. Proteomics 3:2190-2499.
    • (2003) Proteomics , vol.3 , pp. 2190-2499
    • Schweitzer, B.1    Predki, P.2    Snyder, M.3
  • 191
    • 0033669189 scopus 로고    scopus 로고
    • A network of protein-protein interactions in yeast
    • Schwikowski, B., P. Uetz, and S. Fields. 2000. A network of protein-protein interactions in yeast. Nat. Biotechnol. 18:1257-1261.
    • (2000) Nat. Biotechnol. , vol.18 , pp. 1257-1261
    • Schwikowski, B.1    Uetz, P.2    Fields, S.3
  • 192
    • 0030911425 scopus 로고    scopus 로고
    • Mex67p, a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores
    • Segref, A., K. Sharma, V. Doye, A. Hellwig, J. Huber, R. Luhrmann, and E. Hurt. 1997. Mex67p, a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. EMBO J. 16:3256-3271.
    • (1997) EMBO J. , vol.16 , pp. 3256-3271
    • Segref, A.1    Sharma, K.2    Doye, V.3    Hellwig, A.4    Huber, J.5    Luhrmann, R.6    Hurt, E.7
  • 193
    • 0042697666 scopus 로고    scopus 로고
    • Comparison of the changes in global gene expression of Escherichia coli induced by four bactericidal agents
    • Shaw, K. J., N. Miller, X. Liu, D. Lerner, J. Wan, A. Bittner, and B. J. Morrow. 2003. Comparison of the changes in global gene expression of Escherichia coli induced by four bactericidal agents. J. Mol. Microbiol. Biotechnol. 5:105-122.
    • (2003) J. Mol. Microbiol. Biotechnol. , vol.5 , pp. 105-122
    • Shaw, K.J.1    Miller, N.2    Liu, X.3    Lerner, D.4    Wan, J.5    Bittner, A.6    Morrow, B.J.7
  • 196
    • 0037079050 scopus 로고    scopus 로고
    • Metabolic network structure determines key aspects of functionality and regulation
    • Stelling, J., S. Klamt, K. Bettenbrock, S. Schuster, and E. D. Gilles. 2002. Metabolic network structure determines key aspects of functionality and regulation. Nature 420:190-193.
    • (2002) Nature , vol.420 , pp. 190-193
    • Stelling, J.1    Klamt, S.2    Bettenbrock, K.3    Schuster, S.4    Gilles, E.D.5
  • 197
    • 0025866296 scopus 로고
    • Network rigidity and metabolic engineering in metabolite overproduction
    • Stephanopoulos, G., and J. J. Vallino. 1991. Network rigidity and metabolic engineering in metabolite overproduction. Science 252:1675-1681.
    • (1991) Science , vol.252 , pp. 1675-1681
    • Stephanopoulos, G.1    Vallino, J.J.2
  • 199
    • 4444286925 scopus 로고    scopus 로고
    • Normalization of single-channel DNA array data by principal component analysis
    • Stoyanova, R., T. D. Querec, T. R. Brown, and C. Patriotis. 2004. Normalization of single-channel DNA array data by principal component analysis. Bioinformatics 20:1772-1784.
    • (2004) Bioinformatics , vol.20 , pp. 1772-1784
    • Stoyanova, R.1    Querec, T.D.2    Brown, T.R.3    Patriotis, C.4
  • 200
    • 0038697629 scopus 로고    scopus 로고
    • The interplay of nuclear mRNP assembly, mRNA surveillance and export
    • Stutz, F., and E. Izaurralde. 2003. The interplay of nuclear mRNP assembly, mRNA surveillance and export. Trends Cell Biol. 13:319-327.
    • (2003) Trends Cell Biol. , vol.13 , pp. 319-327
    • Stutz, F.1    Izaurralde, E.2
  • 201
    • 0031594984 scopus 로고    scopus 로고
    • 13C-NMR, MS and metabolic flux balancing in biotechnology research
    • Szyperski, T. 1998. 13C-NMR, MS and metabolic flux balancing in biotechnology research. Q. Rev. Biophys. 31:41-106.
    • (1998) Q. Rev. Biophys. , vol.31 , pp. 41-106
    • Szyperski, T.1
  • 202
    • 0029146299 scopus 로고
    • Biosynthetically directed fractional 13C-labeling of proteinogenic amino acids. An efficient analytical tool to investigate intermediary metabolism
    • Szyperski, T. 1995. Biosynthetically directed fractional 13C-labeling of proteinogenic amino acids. An efficient analytical tool to investigate intermediary metabolism. Eur. J. Biochem. 232:433-448.
    • (1995) Eur. J. Biochem. , vol.232 , pp. 433-448
    • Szyperski, T.1
  • 203
    • 0034644626 scopus 로고    scopus 로고
    • Plasma membrane compartmentalization in yeast by messenger RNA transport and a septin diffusion barrier
    • Takizawa, P. A., J. L. DeRisi, J. E. Wilhelm, and R. D. Vale. 2000. Plasma membrane compartmentalization in yeast by messenger RNA transport and a septin diffusion barrier. Science 290:341-344.
    • (2000) Science , vol.290 , pp. 341-344
    • Takizawa, P.A.1    Derisi, J.L.2    Wilhelm, J.E.3    Vale, R.D.4
  • 204
    • 14644388890 scopus 로고    scopus 로고
    • Making connections between novel transcription factors and their DNA motifs
    • Tan, K., L. A. McCue, and G. D. Stormo. 2005. Making connections between novel transcription factors and their DNA motifs. Genome Res. 15:312-320.
    • (2005) Genome Res. , vol.15 , pp. 312-320
    • Tan, K.1    McCue, L.A.2    Stormo, G.D.3
  • 206
    • 0034967661 scopus 로고    scopus 로고
    • Disruption of a global regulatory gene to enhance central carbon flux into phenylalanine biosynthesis in Escherichia coli
    • Tatarko, M., and T. Romeo. 2001. Disruption of a global regulatory gene to enhance central carbon flux into phenylalanine biosynthesis in Escherichia coli. Curr. Microbiol. 43:26-32.
    • (2001) Curr. Microbiol. , vol.43 , pp. 26-32
    • Tatarko, M.1    Romeo, T.2
  • 211
    • 0034687794 scopus 로고    scopus 로고
    • Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays
    • Tenenbaum, S. A., C. C. Carson, P. J. Lager, and J. D. Keene. 2000. Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc. Natl. Acad. Sci. USA 97:14085-14090.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 14085-14090
    • Tenenbaum, S.A.1    Carson, C.C.2    Lager, P.J.3    Keene, J.D.4
  • 212
    • 0036351379 scopus 로고    scopus 로고
    • Ribonomics: Identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays
    • Tenenbaum, S. A., P. J. Lager, C. C. Carson, and J. D. Keene. 2002. Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays. Methods 26:191-198.
    • (2002) Methods , vol.26 , pp. 191-198
    • Tenenbaum, S.A.1    Lager, P.J.2    Carson, C.C.3    Keene, J.D.4
  • 213
    • 0042863923 scopus 로고    scopus 로고
    • Analysis of gene expression data using self-organizing maps
    • Toronen, P., M. Kolehmainen, G. Wong, and E. Castren. 1999. Analysis of gene expression data using self-organizing maps. FEBS Lett. 451:142-146.
    • (1999) FEBS Lett. , vol.451 , pp. 142-146
    • Toronen, P.1    Kolehmainen, M.2    Wong, G.3    Castren, E.4
  • 214
    • 0035313629 scopus 로고    scopus 로고
    • Gene discovery via metabolic profiling
    • Trethewey, R. N. 2001. Gene discovery via metabolic profiling. Curr. Opin. Biotechnol. 12:135-138.
    • (2001) Curr. Opin. Biotechnol. , vol.12 , pp. 135-138
    • Trethewey, R.N.1
  • 216
    • 0028281964 scopus 로고
    • Cloning and characterization of a yeast cytochrome b5-encoding gene which suppresses ketoconazole hypersensitivity in a NADPH-P-450 reductase-deficient strain
    • Truan, G., J. C. Epinat, C. Rougeulle, C. Cullin, and D. Pompon. 1994. Cloning and characterization of a yeast cytochrome b5-encoding gene which suppresses ketoconazole hypersensitivity in a NADPH-P-450 reductase-deficient strain. Gene 142:123-127.
    • (1994) Gene , vol.142 , pp. 123-127
    • Truan, G.1    Epinat, J.C.2    Rougeulle, C.3    Cullin, C.4    Pompon, D.5
  • 217
    • 0037195138 scopus 로고    scopus 로고
    • Quantitative noise analysis for gene expression microarray experiments
    • Tu, Y., G. Stolovitzky, and U. Klein. 2002. Quantitative noise analysis for gene expression microarray experiments. Proc. Natl. Acad. Sci. USA 99: 14031-14036.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 14031-14036
    • Tu, Y.1    Stolovitzky, G.2    Klein, U.3
  • 218
    • 11144351004 scopus 로고    scopus 로고
    • GenSo-FDSS: A neural-fuzzy decision support system for pediatric ALL cancer subtype identification using gene expression data
    • Tung, W. L., and C. Quek. 2005. GenSo-FDSS: a neural-fuzzy decision support system for pediatric ALL cancer subtype identification using gene expression data. Artif. Intell. Med. 33:61-88.
    • (2005) Artif. Intell. Med. , vol.33 , pp. 61-88
    • Tung, W.L.1    Quek, C.2
  • 220
    • 0032884023 scopus 로고    scopus 로고
    • Difference gel electrophoresis
    • Unlu, M. 1999. Difference gel electrophoresis. Biochem. Soc. Trans. 27: 547-549.
    • (1999) Biochem. Soc. Trans. , vol.27 , pp. 547-549
    • Unlu, M.1
  • 221
    • 0036851381 scopus 로고    scopus 로고
    • Gene expression data analysis of human lymphoma using support vector machines and output coding ensembles
    • Valentini, G. 2002. Gene expression data analysis of human lymphoma using support vector machines and output coding ensembles. Artif. Intell. Med. 26:281-304.
    • (2002) Artif. Intell. Med. , vol.26 , pp. 281-304
    • Valentini, G.1
  • 222
    • 8544271637 scopus 로고    scopus 로고
    • Involvement of a novel transcriptional activator and small RNA in post-transcriptional regulation of the glucose phosphoenolpyruvate phosphotransferase system
    • Vanderpool, C. K., and S. Gottesman. 2004. Involvement of a novel transcriptional activator and small RNA in post-transcriptional regulation of the glucose phosphoenolpyruvate phosphotransferase system. Mol. Microbiol. 54:1076-1089.
    • (2004) Mol. Microbiol. , vol.54 , pp. 1076-1089
    • Vanderpool, C.K.1    Gottesman, S.2
  • 223
    • 0037155584 scopus 로고    scopus 로고
    • Exosome-mediated recognition and degradation of mRNAs lacking a termination codon
    • van Hoof, A., P. A. Frischmeyer, H. C. Dietz, and R. Parker. 2002. Exosome-mediated recognition and degradation of mRNAs lacking a termination codon. Science 295:2262-2264.
    • (2002) Science , vol.295 , pp. 2262-2264
    • Van Hoof, A.1    Frischmeyer, P.A.2    Dietz, H.C.3    Parker, R.4
  • 224
    • 0141534473 scopus 로고    scopus 로고
    • Simultaneous analysis of amino and nonamino organic acids as methyl chloroformate derivatives using gas chromatography-mass spectrometry
    • Villas-Boas, S. G., D. G. Delicado, M. Akesson, and J. Nielsen. 2003. Simultaneous analysis of amino and nonamino organic acids as methyl chloroformate derivatives using gas chromatography-mass spectrometry. Anal. Biochem. 322:134-138.
    • (2003) Anal. Biochem. , vol.322 , pp. 134-138
    • Villas-Boas, S.G.1    Delicado, D.G.2    Akesson, M.3    Nielsen, J.4
  • 226
    • 0141446194 scopus 로고    scopus 로고
    • Identification of mRNAs associated with alphaCP2-containing RNP complexes
    • Waggoner, S. A., and S. A. Liebhaber. 2003. Identification of mRNAs associated with alphaCP2-containing RNP complexes. Mol. Cell. Biol. 23: 7055-7067.
    • (2003) Mol. Cell. Biol. , vol.23 , pp. 7055-7067
    • Waggoner, S.A.1    Liebhaber, S.A.2
  • 227
    • 2942756043 scopus 로고    scopus 로고
    • Serial 13C-based flux analysis of an L-phenylalanine-producing E. coli strain using the sensor reactor
    • Wahl, A., M. El Massaoudi, D. Schipper, W. Wiechert, and R. Takors. 2004. Serial 13C-based flux analysis of an L-phenylalanine-producing E. coli strain using the sensor reactor. Biotechnol. Prog. 20:706-714.
    • (2004) Biotechnol. Prog. , vol.20 , pp. 706-714
    • Wahl, A.1    El Massaoudi, M.2    Schipper, D.3    Wiechert, W.4    Takors, R.5
  • 230
    • 9344257332 scopus 로고    scopus 로고
    • Normalization of cDNA microarray data using wavelet regressions
    • Wang, J., J. Z. Ma, and M. D. Li. 2004. Normalization of cDNA microarray data using wavelet regressions. Comb. Chem. High Throughput Screen. 7:783-791.
    • (2004) Comb. Chem. High Throughput Screen. , vol.7 , pp. 783-791
    • Wang, J.1    Ma, J.Z.2    Li, M.D.3
  • 232
    • 0035106351 scopus 로고    scopus 로고
    • Large-scale analysis of the yeast proteome by multidimensional protein identification technology
    • Washburn, M. P., D. Wolters, and J. R. Yates III. 2001. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19:242-247.
    • (2001) Nat. Biotechnol. , vol.19 , pp. 242-247
    • Washburn, M.P.1    Wolters, D.2    Yates III, J.R.3
  • 233
    • 0142040405 scopus 로고    scopus 로고
    • Metabolomics in systems biology
    • Weckwerth, W. 2003. Metabolomics in systems biology. Annu. Rev. Plant Biol. 54:669-689.
    • (2003) Annu. Rev. Plant Biol. , vol.54 , pp. 669-689
    • Weckwerth, W.1
  • 234
    • 3142783423 scopus 로고    scopus 로고
    • Protein arrays from cDNA expression libraries
    • Weiner, H., T. Faupel, and K. Bussow. 2004. Protein arrays from cDNA expression libraries. Methods Mol. Biol. 264:1-13.
    • (2004) Methods Mol. Biol. , vol.264 , pp. 1-13
    • Weiner, H.1    Faupel, T.2    Bussow, K.3
  • 235
    • 0035369115 scopus 로고    scopus 로고
    • Histidine kinases and response regulator proteins in two-component signaling systems
    • West, A. H., and A. M. Stock. 2001. Histidine kinases and response regulator proteins in two-component signaling systems. Trends Biochem. Sci. 26:369-376.
    • (2001) Trends Biochem. Sci. , vol.26 , pp. 369-376
    • West, A.H.1    Stock, A.M.2
  • 238
    • 0034807713 scopus 로고    scopus 로고
    • Analysing gene expression data from DNA microarrays to identify candidate genes
    • Wu, T. D. 2001. Analysing gene expression data from DNA microarrays to identify candidate genes. J. Pathol. 195:53-65.
    • (2001) J. Pathol. , vol.195 , pp. 53-65
    • Wu, T.D.1
  • 239
    • 0034847379 scopus 로고    scopus 로고
    • Two closely related human nuclear export factors utilize entirely distinct export pathways
    • Yang, J., H. P. Bogerd, P. J. Wang, D. C. Page, and B. R. Cullen. 2001. Two closely related human nuclear export factors utilize entirely distinct export pathways. Mol. Cell. 8:397-406.
    • (2001) Mol. Cell. , vol.8 , pp. 397-406
    • Yang, J.1    Bogerd, H.P.2    Wang, P.J.3    Page, D.C.4    Cullen, B.R.5
  • 240
    • 0018472524 scopus 로고
    • Integrative physiology as physical biology
    • Yates, F. E. 1979. Integrative physiology as physical biology. Am. J. Physiol. 236:R239-R240.
    • (1979) Am. J. Physiol. , vol.236
    • Yates, F.E.1
  • 243
    • 13244252322 scopus 로고    scopus 로고
    • Two-stage normalization using background intensities in cDNA microarray data
    • Yoon, D., S. G. Yi, J. H. Kim, and T. Park. 2004. Two-stage normalization using background intensities in cDNA microarray data. BMC Bioinformatics 5:97.
    • (2004) BMC Bioinformatics , vol.5 , pp. 97
    • Yoon, D.1    Yi, S.G.2    Kim, J.H.3    Park, T.4
  • 244
    • 0037473189 scopus 로고    scopus 로고
    • Combined transcriptome and proteome analysis of Escherichia coli during high cell density culture
    • Yoon, S. H., M. J. Han, S. Y. Lee, K. J. Jeong, and J. S. Yoo. 2003. Combined transcriptome and proteome analysis of Escherichia coli during high cell density culture. Biotechnol. Bioeng. 81:753-767.
    • (2003) Biotechnol. Bioeng. , vol.81 , pp. 753-767
    • Yoon, S.H.1    Han, M.J.2    Lee, S.Y.3    Jeong, K.J.4    Yoo, J.S.5
  • 245
    • 0023134858 scopus 로고
    • Interaction of azole antifungal agents with cytochrome P-45014DM purified from Saccharomyces cerevisiae microsomes
    • Yoshida, Y., and Y. Aoyama. 1987. Interaction of azole antifungal agents with cytochrome P-45014DM purified from Saccharomyces cerevisiae microsomes. Biochem. Pharmacol. 36:229-235.
    • (1987) Biochem. Pharmacol. , vol.36 , pp. 229-235
    • Yoshida, Y.1    Aoyama, Y.2
  • 246
    • 0035992124 scopus 로고    scopus 로고
    • Response of gene expression in Saccharomyces cerevisiae to amphotericin B and nystatin measured by microarrays
    • Zhang, L., Y. Zhang, Y. Zhou, S. An, Y. Zhou, and J. Cheng. 2002. Response of gene expression in Saccharomyces cerevisiae to amphotericin B and nystatin measured by microarrays. J. Antimicrob. Chemother. 49:905-915.
    • (2002) J. Antimicrob. Chemother. , vol.49 , pp. 905-915
    • Zhang, L.1    Zhang, Y.2    Zhou, Y.3    An, S.4    Zhou, Y.5    Cheng, J.6
  • 247
    • 0029019484 scopus 로고
    • Control of the Escherichia coli rrnB P1 promoter strength by ppGpp
    • Zhang, X., and H. Bremer. 1995. Control of the Escherichia coli rrnB P1 promoter strength by ppGpp. J. Biol. Chem. 270:11181-11189.
    • (1995) J. Biol. Chem. , vol.270 , pp. 11181-11189
    • Zhang, X.1    Bremer, H.2
  • 248
    • 0036818941 scopus 로고    scopus 로고
    • Kinetic properties of rrn promoters in Escherichia coli
    • Zhang, X., P. Dennis, M. Ehrenberg, and H. Bremer. 2002. Kinetic properties of rrn promoters in Escherichia coli. Biochimie 84:981-996.
    • (2002) Biochimie , vol.84 , pp. 981-996
    • Zhang, X.1    Dennis, P.2    Ehrenberg, M.3    Bremer, H.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.