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1
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The transcriptional profile of early to middle sporulation in Bacillus subtilis
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Global gene expression profiling in Escherichia coli K-12. The effects of leucine-responsive regulatory protein
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6
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Whole-genome analysis of genes regulated by the Bacillus subtilis competence transcription factor ComK
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Ogura M, Yamaguchi H, Kobayashi K, Ogasawara N, Fujita Y, Tanaka T: Whole-genome analysis of genes regulated by the Bacillus subtilis competence transcription factor ComK. J Bacteriol 2002, 184:2344-2351.
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Escherichia coli gene expression responsive to levels of the response regulator EvgA
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Masuda N, Church GM: Escherichia coli gene expression responsive to levels of the response regulator EvgA. J Bacteriol 2002, 184:6225-6234.
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0036068774
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Lehnen D, Blumer C, Polen T, Wackwitz B, Wendisch VF, Unden G: LrhA as a new transcriptional key regulator of flagella, motility and chemotaxis genes in Escherichia coli. Mol Microbiol 2002, 45:521-532.
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9
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Microarray transcription profiling of a Shewanella oneidensis etrA mutant
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Beliaev AS, Thompson DK, Fields MW, Wu L, Lies DP, Nealson KH, Zhou J: Microarray transcription profiling of a Shewanella oneidensis etrA mutant. J Bacteriol 2002, 184:4612-4616.
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Microarray analysis of the Bacillus subtilis K-state: Genome-wide expression changes dependent on ComK
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Berka RM, Hahn J, Albano M, Draskovic I, Persuh M, Cui X, Sloma A, Widner W, Dubnau D: Microarray analysis of the Bacillus subtilis K-state: genome-wide expression changes dependent on ComK. Mol Microbiol 2002, 43:1331-1345.
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11
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Oshima T, Aiba H, Masuda Y, Kanaya S, Sugiura M, Wanner BL, Mori H, Mizuno T: Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12. Mol Microbiol 2002, 46:281-291. The authors analysed 36 two-component regulators in Escherichia coli by comparing deletion mutant strains with wild type to provide an 'array' of array data. On the basis of genome-wide expression data the two-component regulators were divided into three groups: those with little or no change; those with significant changes; and those with drastic changes. This approach for studying uncharacterized two-component regulators provides valuable preliminary information on the roles of some of these regulators under standard conditions; however, known regulon members of some of the other two-component systems were not identified. This illustrates the need to explore different physiological conditions when performing these comparisons to ensure that the regulators are in the active 'induced' state in the wild-type strain.
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Mol Microbiol
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Oshima, T.1
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12
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0034703060
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Global gene expression profiling in Escherichia coli K-12. The effects of integration host factor
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Arfin SM, Long AD, Ito ET, Tolleri L, Riehle MM, Paegle ES, Hatfield GW: Global gene expression profiling in Escherichia coli K-12. The effects of integration host factor. J Biol Chem 2000, 275:29672-29684.
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Arfin, S.M.1
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Paegle, E.S.6
Hatfield, G.W.7
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13
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0034710992
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DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli
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Khodursky AB, Peter BJ, Cozzarelli NR, Botstein D, Brown PO, Yanofsky C: 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 2000, 97:12170-12175.
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Khodursky, A.B.1
Peter, B.J.2
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15
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0036307635
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Defining the Bacillus subtilis sigma(W) regulon: A comparative analysis of promoter consensus search, run-off transcription/macroarray analysis (ROMA), and transcriptional profiling approaches
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Cao M, Kobel PA, Morshedi MM, Wu MF, Paddon C, Helmann JD: Defining the Bacillus subtilis sigma(W) regulon: a comparative analysis of promoter consensus search, run-off transcription/macroarray analysis (ROMA), and transcriptional profiling approaches. J Mol Biol 2002, 316:443-457. The authors compared three approaches to identify regulon members. They concluded that no single technique identifies all members, suggesting therefore that a combination of complementary approaches should be used to achieve maximal coverage when defining bacterial regulons.
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Cao, M.1
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Helmann, J.D.6
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16
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0035087098
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Global impact of sdiA amplification revealed by comprehensive gene expression profiling of Escherichia coli
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Wei Y, Lee JM, Smulski DR, LaRossa RA: Global impact of sdiA amplification revealed by comprehensive gene expression profiling of Escherichia coli. J Bacteriol 2001, 183:2265-2272.
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Wei, Y.1
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17
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Comprehensive DNA microarray analysis of Bacillus subtilis two-component regulatory systems
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Kobayashi K, Ogura M, Yamaguchi H, Yoshida K, Ogasawara N, Tanaka T, Fujita Y: Comprehensive DNA microarray analysis of Bacillus subtilis two-component regulatory systems. J Bacteriol 2001, 183:7365-7370.
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Kobayashi, K.1
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Fujita, Y.7
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18
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0035883922
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DNA microarray analysis of Bacillus subtilis DegU, ComA and PhoP regulons: An approach to comprehensive analysis of B. subtilis two-component regulatory systems
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Ogura M, Yamaguchi H, Yoshida K, Fujita Y, Tanaka T: DNA microarray analysis of Bacillus subtilis DegU, ComA and PhoP regulons: an approach to comprehensive analysis of B. subtilis two-component regulatory systems. Nucleic Acids Res 2001, 29:3804-3813.
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19
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0034687819
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Nitrogen regulatory protein C-controlled genes of Escherichia coli: Scavenging as a defense against nitrogen limitation
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Zimmer DP, Soupene E, Lee HL, Wendisch VF, Khodursky AB, Peter BJ, Bender RA, Kustu S: Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation. Proc Natl Acad Sci USA 2000, 97:14674-14679.
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Khodursky, A.B.5
Peter, B.J.6
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Kustu, S.8
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20
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0035023305
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Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli
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Courcelle J, Khodursky A, Peter B, Brown PO, Hanawalt PC: Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli. Genetics 2001, 158:41-64.
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Genetics
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0034977251
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Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate
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Pomposiello PJ, Bennik MH, Demple B: Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate. J Bacteriol 2001, 183:3890-3902.
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Pomposiello, P.J.1
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22
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0036773739
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Dissection of the heat-shock response in Mycobacterium tuberculosis using mutants and microarrays
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Stewart GR, Wernisch L, Stabler R, Mangan JA, Hinds J, Laing KG, Young DB, Butcher PD: Dissection of the heat-shock response in Mycobacterium tuberculosis using mutants and microarrays. Microbiology 2002, 148:3129-3138. This paper illustrates the use of microarrays for bacteria other than Escherichia coli and Bacillus subtilis. The authors obtained an overview of the heat-shock response in wild-type cells by comparing expression profiles of cells grown at 37°C with those shifted to 45°C. The heat-shock response was then dissected by repeating the experiments in strains deleted for the mediating transcription factors, HspR and HrcA. Finally, the authors identified genes from the expression data that are likely to be directly regulated by HspR or HrcA, by searching for binding sites.
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Microbiology
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Global transcriptional response of Bacillus subtilis to heat shock
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Helmann JD, Wu MF, Kobel PA, Gamo FJ, Wilson M, Morshedi MM, Navre M, Paddon C: Global transcriptional response of Bacillus subtilis to heat shock. J Bacteriol 2001, 183:7318-7328. The authors identified the heat-shock stimulon by comparing the expression profiles at multiple-time points of cells grown at 37°C with those after shifting to 48°C. The time-course analysis enabled the authors to identify cascades of gene expression mediated by different transcription factors after heat-shock.
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J Bacteriol
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Helmann, J.D.1
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Genome-wide expression profiling in Escherichia coli K-12
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Richmond CS, Glasner JD, Mau R, Jin H, Blattner FR: Genome-wide expression profiling in Escherichia coli K-12. Nucleic Acids Res 1999, 27:3821-3835.
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Richmond, C.S.1
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25
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0035964413
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Global differential gene expression in response to growth temperature alteration in group A Streptococcus
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Smoot LM, Smoot JC, Graham MR, Somerville GA, Sturdevant DE, Migliaccio CA, Sylva GL, Musser JM: Global differential gene expression in response to growth temperature alteration in group A Streptococcus. Proc Natl Acad Sci USA 2001, 98:10416-10421.
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Global gene expression profiles of Bacillus subtilis grown under anaerobic conditions
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Ye RW, Tao W, Bedzyk L, Young T, Chen M, Li L: Global gene expression profiles of Bacillus subtilis grown under anaerobic conditions. J Bacteriol 2000, 182:4458-4465.
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Ye, R.W.1
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Functional genomics: Expression analysis of Escherichia coli growing on minimal and rich media
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Tao H, Bausch C, Richmond C, Blattner FR, Conway T: Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media. J Bacteriol 1999, 181:6425-6440.
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High-density microarray-mediated gene expression profiling of Escherichia coli
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Wei Y, Lee JM, Richmond C, Blattner FR, Rafalski JA, LaRossa RA: High-density microarray-mediated gene expression profiling of Escherichia coli. J Bacteriol 2001, 183:545-556.
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J Bacteriol
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Wei, Y.1
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29
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0035039607
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Combined, functional genomic-biochemical approach to intermediary metabolism: Interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12
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Smulski DR, Huang LL, McCluskey MP, Reeve MJ, Vollmer AC, Van Dyk TK, LaRossa RA: Combined, functional genomic-biochemical approach to intermediary metabolism: interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12. J Bacteriol 2001, 183:3353-3364.
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J Bacteriol
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Smulski, D.R.1
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30
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Genome-wide dynamic transcriptional profiling of the light-to-dark transition in Synechocystis sp. strain PCC6803
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Gill RT, Katsoulakis E, Schmitt W, Taroncher-Oldenburg G, Misra J, Stephanopoulos G: Genome-wide dynamic transcriptional profiling of the light-to-dark transition in Synechocystis sp. strain PCC6803. J Bacteriol 2002, 184:3671-3681.
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J Bacteriol
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Gill, R.T.1
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31
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0036065206
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Role of the extracytoplasmic-function sigma factor sigma(H) in Mycobacterium tuberculosis global gene expression
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Manganelli R, Voskuil MI, Schoolnik GK, Dubnau E, Gomez M, Smith I: Role of the extracytoplasmic-function sigma factor sigma(H) in Mycobacterium tuberculosis global gene expression. Mol Microbiol 2002, 45:365-374.
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32
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0034932337
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DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide
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Zheng M, Wang X, Templeton LJ, Smulski DR, LaRossa RA, Storz G: DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide. J Bacteriol 2001, 183:4562-4570. The authors analysed the response of Escherichia coli to hydrogen peroxide, mediated by OxyR, by comparing hydrogen peroxide treated and untreated wild-type cells to identify genes sensitive to peroxide stress and also oxyR deleted strains to identify OxyR-dependent peroxide stress genes. Using this approach, the authors identified members of the peroxide-dependent OxyR regulon and also OxyR-independent hydrogen peroxide regulated genes that might be regulated by other peroxide regulators such as the SoxRS system and an unknown regulator of the isc operon involved in Fe-S cluster formation. The genome-wide expression analysis of the OxyR regulon was combined with computer-directed searches for OxyR binding sites in [33].
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J Bacteriol
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Zheng, M.1
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Computation-directed identification of OxyR DNA binding sites in Escherichia coli
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Zheng M, Wang X, Doan B, Lewis KA, Schneider TD, Storz G: Computation-directed identification of OxyR DNA binding sites in Escherichia coli. J Bacteriol 2001, 183:4571-4579.
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J Bacteriol
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Zheng, M.1
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0037007079
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Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle
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Laub MT, Chen SL, Shapiro L, McAdams HH: Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle. Proc Natl Acad Sci USA 2002, 99:4632-4637. The spread of microarray technology to other bacteria is again illustrated here. Perhaps, more importantly, the authors identify functional binding sites of specific transcription factors in vivo by chromatin immunoprecipitation followed by hybridization of the precipitated DNA to arrays containing PCR products of both ORFs and intergenic regions. It is possible that similar results might be achieved for bacteria with short intergenic regions with arrays only containing PCR products of ORFs.
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Proc Natl Acad Sci USA
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Laub, M.T.1
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McAdams, H.H.4
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Co-expression pattern from DNA microarray experiments as a tool for operon prediction
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Sabatti C, Rohlin L, Oh MK, Liao JC: Co-expression pattern from DNA microarray experiments as a tool for operon prediction. Nucleic Acids Res 2002, 30:2886-2893.
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Nucleic Acids Res
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Sabatti, C.1
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Liao, J.C.4
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0033664358
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RNA expression analysis using a 30 base pair resolution Escherichia coli genome array
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Selinger DW, Cheung KJ, Mei R, Johansson EM, Richmond CS, Blattner FR, Lockhart DJ, Church GM: RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat Biotechnol 2000, 18:1262-1268.
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Nat Biotechnol
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Selinger, D.W.1
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Mei, R.3
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Church, G.M.8
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37
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0038199116
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Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis
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Tjaden B, Haynor DR, Stolyar S, Rosenow C, Kolker E: Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis. Bioinformatics 2002, 18:S337-S344.
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Bioinformatics
, vol.18
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Tjaden, B.1
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Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays
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Tjaden B, Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C: Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays. Nucleic Acids Res 2002, 30:3732-3738. The authors use high-density oligonucleotide arrays for identifying the transcripts that make up the transcriptome. Tjaden et al. (2002) [37] published a related paper in which they use hidden Markov models to estimate the boundaries of mRNAs of transcribed genes to define operons and untranslated regions.
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Nucleic Acids Res
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Tjaden, B.1
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Rosenow, C.6
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39
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Identification of novel small RNAs using comparative genomics and microarrays
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Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S: Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev 2001, 15:1637-1651.
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40
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0037162469
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Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays
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Bernstein JA, Khodursky AB, Lin PH, Lin-Chao S, Cohen SN: 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 2002, 99:9697-9702.
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Proc Natl Acad Sci USA
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41
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0038335217
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Genomic DNA standards for gene expression profiling in Mycobacterium tuberculosis
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Talaat AM, Howard ST, Hale W, Lyons R, Garner H, Johnston SA: Genomic DNA standards for gene expression profiling in Mycobacterium tuberculosis. Nucleic Acids Res 2002, 30:e104.
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Nucleic Acids Res
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