-
1
-
-
10544256600
-
Expression monitoring by hybridization to high-density oligonucleotide arrays
-
Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H et al.: Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 1996, 14:1675-1680.
-
(1996)
Nat Biotechnol
, vol.14
, pp. 1675-1680
-
-
Lockhart, D.J.1
Dong, H.2
Byrne, M.C.3
Follettie, M.T.4
Gallo, M.V.5
Chee, M.S.6
Mittmann, M.7
Wang, C.8
Kobayashi, M.9
Horton, H.10
-
2
-
-
0030669030
-
Exploring the metabolic and genetic control of gene expression on a genomic scale
-
DeRisi JL, Iyer VR, Brown PO: Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 1997, 278:680-686.
-
(1997)
Science
, vol.278
, pp. 680-686
-
-
DeRisi, J.L.1
Iyer, V.R.2
Brown, P.O.3
-
3
-
-
0029748326
-
Parallel human genome analysis: Microarray-based expression monitoring of 1000 genes
-
Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW: Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci USA 1996, 93:10614-10619.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 10614-10619
-
-
Schena, M.1
Shalon, D.2
Heller, R.3
Chai, A.4
Brown, P.O.5
Davis, R.W.6
-
4
-
-
0033214149
-
Genome-wide expression profiling in Escherichia coli K-12
-
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.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 3821-3835
-
-
Richmond, C.S.1
Glasner, J.D.2
Mau, R.3
Jin, H.4
Blattner, F.R.5
-
5
-
-
0033891425
-
Global gene expression profiles of Bacillus subtilis grown under anaerobic conditions
-
Ye RW, Tao W, Beddzyk L, Young T, Chen M, Li L: Global gene expression profiles of Bacillus subtilis grown under anaerobic conditions. J Bacteriol 2000, 182:4458-4465.
-
(2000)
J Bacteriol
, vol.182
, pp. 4458-4465
-
-
Ye, R.W.1
Tao, W.2
Beddzyk, L.3
Young, T.4
Chen, M.5
Li, L.6
-
6
-
-
0036156696
-
Transcriptional and proteomic analysis of a ferric uptake regulator (Fur) mutant of Shewanella oneidensis: Possible involvement of Fur in energy metabolism, transcriptional regulation, and oxidative stress
-
Thompson DK, Beliaev AS, Giometti CS, Tollaksen SL, Khare T, Lies DP, Nealson KH, Lim H, Yates J III, Brandt CC et al.: Transcriptional and proteomic analysis of a ferric uptake regulator (Fur) mutant of Shewanella oneidensis: possible involvement of Fur in energy metabolism, transcriptional regulation, and oxidative stress. Appl Environ Microbiol 2002, 68:881-892.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 881-892
-
-
Thompson, D.K.1
Beliaev, A.S.2
Giometti, C.S.3
Tollaksen, S.L.4
Khare, T.5
Lies, D.P.6
Nealson, K.H.7
Lim, H.8
Yates J. III9
Brandt, C.C.10
-
7
-
-
0037388447
-
Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation
-
Liu Y, Zhou J, Omelchenko M, Beliaev A, Venkateswaran A, Stair J, Wu L, Thompson DK, Xu D, Rogozin IB et al.: Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. Proc Natl Acad Sci USA 2003, 100:4191-4196.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 4191-4196
-
-
Liu, Y.1
Zhou, J.2
Omelchenko, M.3
Beliaev, A.4
Venkateswaran, A.5
Stair, J.6
Wu, L.7
Thompson, D.K.8
Xu, D.9
Rogozin, I.B.10
-
8
-
-
0031453850
-
Genome-wide expression monitoring in Saccharomyces cerevisiae
-
Wodicka L, Dong H, Mittmann M, Ho MH, Lockhart DJ: Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat Biotechnol 1997, 15:1359-1367.
-
(1997)
Nat Biotechnol
, vol.15
, pp. 1359-1367
-
-
Wodicka, L.1
Dong, H.2
Mittmann, M.3
Ho, M.H.4
Lockhart, D.J.5
-
9
-
-
0036624982
-
Challenges in applying microarrays to environmental studies
-
Zhou J, Thompson DK: Challenges in applying microarrays to environmental studies. Curr Opin Biotechnol 2002, 13:204-207. This commentary overviewed the application of microarray-based genomic technology for environmental studies, with an emphasis on the key microarray hybridization issues related to specificity, sensitivity and quantitation. This review also highlighted the challenges and future research directions of microarray technology for environmental applications.
-
(2002)
Curr Opin Biotechnol
, vol.13
, pp. 204-207
-
-
Zhou, J.1
Thompson, D.K.2
-
10
-
-
0035656126
-
Development and evaluation of functional gene arrays for detection of selected genes in the environment
-
Wu L, Thompson D, Li G, Hurt RA, Tiedje JM, Zhou J: Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl Environ Microbiol 2001, 67:5780-5790. This is the first report that systematically evaluated the performance of functional gene arrays for environmental applications in terms of specificity, sensitivity and quantitation.
-
(2001)
Appl Environ Microbiol
, vol.67
, pp. 5780-5790
-
-
Wu, L.1
Thompson, D.2
Li, G.3
Hurt, R.A.4
Tiedje, J.M.5
Zhou, J.6
-
11
-
-
17344371740
-
High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays
-
Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y et al.: High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 1998, 20:207-211.
-
(1998)
Nat Genet
, vol.20
, pp. 207-211
-
-
Pinkel, D.1
Segraves, R.2
Sudar, D.3
Clark, S.4
Poole, I.5
Kowbel, D.6
Collins, C.7
Kuo, W.L.8
Chen, C.9
Zhai, Y.10
-
12
-
-
0032823523
-
Genome-wide analysis of DNA copy-number changes using cDNA microarrays
-
Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO: Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 1999, 23:41-46.
-
(1999)
Nat Genet
, vol.23
, pp. 41-46
-
-
Pollack, J.R.1
Perou, C.M.2
Alizadeh, A.A.3
Eisen, M.B.4
Pergamenschikov, A.5
Williams, C.F.6
Jeffrey, S.S.7
Botstein, D.8
Brown, P.O.9
-
13
-
-
0036193078
-
Quantitative detection of microbial genes by using DNA microarrays
-
Cho JC, Tiedje TM: Quantitative detection of microbial genes by using DNA microarrays. Appl Environ Microbiol 2002, 68:1425-1430.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 1425-1430
-
-
Cho, J.C.1
Tiedje, T.M.2
-
15
-
-
0035487188
-
Simultaneous extraction of RNA and DNA from environmental samples
-
Hurt RA, Qiu X, Wu L, Roh Y, Palumbo AV, Teidje JM, Zhou J: Simultaneous extraction of RNA and DNA from environmental samples. Appl Environ Microbiol 2001, 67:4495-4503.
-
(2001)
Appl Environ Microbiol
, vol.67
, pp. 4495-4503
-
-
Hurt, R.A.1
Qiu, X.2
Wu, L.3
Roh, Y.4
Palumbo, A.V.5
Teidje, J.M.6
Zhou, J.7
-
16
-
-
0000254417
-
Reverse sample genome probing of microbial community dynamics
-
Voordouw G: Reverse sample genome probing of microbial community dynamics. ASM News 1998, 64:627-633.
-
(1998)
ASM News
, vol.64
, pp. 627-633
-
-
Voordouw, G.1
-
17
-
-
0030984907
-
Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology
-
Guschin DY, Mobarry BK, Proudnikov D, Stahl DA, Rittmann BE, Mirzabekov AD: Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl Environ Microbiol 1997, 63:2397-2402.
-
(1997)
Appl Environ Microbiol
, vol.63
, pp. 2397-2402
-
-
Guschin, D.Y.1
Mobarry, B.K.2
Proudnikov, D.3
Stahl, D.A.4
Rittmann, B.E.5
Mirzabekov, A.D.6
-
18
-
-
0031213779
-
Manual manufacturing of oligonucleotide, DNA and protein microchips
-
Guschin DG, Yershov A, Zaslavsky A, Gemmell V, Shick D, Proudnikov D, Arenkov P, Mirzabekov A: Manual manufacturing of oligonucleotide, DNA and protein microchips. Anal Biochem 1997, 250:203-211.
-
(1997)
Anal Biochem
, vol.250
, pp. 203-211
-
-
Guschin, D.G.1
Yershov, A.2
Zaslavsky, A.3
Gemmell, V.4
Shick, D.5
Proudnikov, D.6
Arenkov, P.7
Mirzabekov, A.8
-
19
-
-
0035144157
-
Portable system for microbial sample preparation and oligonucleotide microarray analysis
-
Bavykin SG, Akowski JP, Zakhariev VM, Barsky VE, Perov AN, Mirzabekov AD: Portable system for microbial sample preparation and oligonucleotide microarray analysis. Appl Environ Microbiol 2001, 67:922-928.
-
(2001)
Appl Environ Microbiol
, vol.67
, pp. 922-928
-
-
Bavykin, S.G.1
Akowski, J.P.2
Zakhariev, V.M.3
Barsky, V.E.4
Perov, A.N.5
Mirzabekov, A.D.6
-
20
-
-
0036304417
-
Parallel characterization of anaerobic toluene- and ethylbenzene-degrading microbial consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization and DNA microarray technology
-
Koizumi Y, Kelly JJ, Nakagawa T, Urakawa H, El-Fantroussi S, Al-Muzaini S, Fukui M, Urushigawa Y, Stahl DA: Parallel characterization of anaerobic toluene- and ethylbenzene-degrading microbial consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization and DNA microarray technology. Appl Environ Microbiol 2002, 68:3215-3225.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 3215-3225
-
-
Koizumi, Y.1
Kelly, J.J.2
Nakagawa, T.3
Urakawa, H.4
El-Fantroussi, S.5
Al-Muzaini, S.6
Fukui, M.7
Urushigawa, Y.8
Stahl, D.A.9
-
21
-
-
0035486807
-
Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays
-
Small J, Call DR, Brockman FJ, Straub TM, Chandler DP: Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Appl Environ Microbiol 2001, 67:4708-4716.
-
(2001)
Appl Environ Microbiol
, vol.67
, pp. 4708-4716
-
-
Small, J.1
Call, D.R.2
Brockman, F.J.3
Straub, T.M.4
Chandler, D.P.5
-
22
-
-
0033823572
-
Application of sequence-specific labeled 16S rRNA gene oligonucleotide probes for genetic profiling of cyanobacterial abundance and diversity by array hybridization
-
Rudi K, Skulberg OM, Skulberg R, Jakobsen KS: Application of sequence-specific labeled 16S rRNA gene oligonucleotide probes for genetic profiling of cyanobacterial abundance and diversity by array hybridization. Appl Environ Microbiol 2000, 66:4004-4011.
-
(2000)
Appl Environ Microbiol
, vol.66
, pp. 4004-4011
-
-
Rudi, K.1
Skulberg, O.M.2
Skulberg, R.3
Jakobsen, K.S.4
-
23
-
-
0036135264
-
Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses
-
Urakawa H, Noble PA, El Fantroussi S, Kelly JJ, Stahl DA: Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses. Appl Environ Microbiol 2002, 68:235-244. This study evaluated the effects of the single-base-pair near-terminal and terminal mismatches on the melting temperature and microarray hybridization signal intensity using gel-pad oligonucleotide microarrays.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 235-244
-
-
Urakawa, H.1
Noble, P.A.2
El Fantroussi, S.3
Kelly, J.J.4
Stahl, D.A.5
-
24
-
-
0036795787
-
Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment
-
Loy A, Lahner A, Lee N, Adamczyk J, Meier H, Ernst J, Schleifer KH, Wagner M: Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl Environ Microbiol 2002, 68:5064-5081. A glass-based microarray containing 132 SSU rRNA-targeted oligonucleotide probes, which represents all recognized groups of sulfate-reducing prokaryotes was developed and used to determine the diversity of sulfate-reducing prokaryotes in periodontal tooth pockets and a hypersaline cyanobacterial mat.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 5064-5081
-
-
Loy, A.1
Lahner, A.2
Lee, N.3
Adamczyk, J.4
Meier, H.5
Ernst, J.6
Schleifer, K.H.7
Wagner, M.8
-
25
-
-
0036208498
-
Genotyping Cryptosporidium parvum with an hsp70 single-nucleotide polymorphism microarray
-
Straub TM, Daly DS, Wunshel S, Rochelle PA, DeLeon R, Chandler DP: Genotyping Cryptosporidium parvum with an hsp70 single-nucleotide polymorphism microarray. Appl Environ Microbiol 2002, 68:1817-1826.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 1817-1826
-
-
Straub, T.M.1
Daly, D.S.2
Wunshel, S.3
Rochelle, P.A.4
DeLeon, R.5
Chandler, D.P.6
-
26
-
-
0036245011
-
High-density microarray of small-subunit ribosomal DNA probes
-
Wilson KH, Wilson WJ, Radosevich JL, DeSantis TZ, Viswanathan VS, Kuczmarski TA, Andersen GL: High-density microarray of small-subunit ribosomal DNA probes. Appl Environ Microbiol 2002, 68:2535-2541. This paper evaluated a microarray containing 31,179 20-mer oligonucleotide probes specific for SSU rRNA genes for bacterial detection in environmental samples. These are the most comprehensive phylogenetic oligonucleotide arrays that have been designed and evaluated to date.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 2535-2541
-
-
Wilson, K.H.1
Wilson, W.J.2
Radosevich, J.L.3
DeSantis, T.Z.4
Viswanathan, V.S.5
Kuczmarski, T.A.6
Andersen, G.L.7
-
27
-
-
0035859896
-
DNA-DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes
-
Murray AE, Lies D, Li G, Nealson K, Zhou J, Tiedje JM: DNA-DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes. Proc Natl Acad Sci USA 2001, 98:9853-9858. This paper used whole-genome open reading frame (ORF) arrays to evaluate genome diversity and relatedness of several related metal-reducing bacteria within the Shewanella genus. The results also showed that this approach can be used to identify genes or operons that were horizontally transferred.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 9853-9858
-
-
Murray, A.E.1
Lies, D.2
Li, G.3
Nealson, K.4
Zhou, J.5
Tiedje, J.M.6
-
28
-
-
0035318378
-
Genomic interspecies microarray hybridization: Rapid discovery of three thousand genes in the maize endophyte, Klebsiella pneumoniae 342, by microarray hybridization with Escherichia coli K-12 open reading frames
-
Dong Y, Glasner JD, Blattner FR, Triplett EW: Genomic interspecies microarray hybridization: rapid discovery of three thousand genes in the maize endophyte, Klebsiella pneumoniae 342, by microarray hybridization with Escherichia coli K-12 open reading frames. Appl Environ Microbiol 2001, 67:1911-1921. Open reading frame (ORF) arrays for Escherichia coli K-12 were used to identify genes in the closely related bacterium Klebsiella pneumoniae strain 342. About 70% of E. coli genes were found in K. pneumoniae strain 342 with greater than 55% identity and 24% of the E. coli genes were absent in this strain. The study demonstrated that the ORF array is useful for understanding genome diversity of closely related bacteria.
-
(2001)
Appl Environ Microbiol
, vol.67
, pp. 1911-1921
-
-
Dong, Y.1
Glasner, J.D.2
Blattner, F.R.3
Triplett, E.W.4
-
29
-
-
0034687702
-
A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains
-
Salama N, Guillemin K, McDaniel TK, Sherlock G, Tompkins L, Falkow S: A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc Natl Acad Sci USA 2000, 97:14668-14673.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 14668-14673
-
-
Salama, N.1
Guillemin, K.2
McDaniel, T.K.3
Sherlock, G.4
Tompkins, L.5
Falkow, S.6
-
30
-
-
0033612136
-
Comparative genomics of BCG vaccines by whole-genome DNA microarray
-
Behr MA, Wilson MA, Gill WP, Salamon H, Schoolnik GK, Rane S, Small PM: Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science 1999, 284:1520-1523.
-
(1999)
Science
, vol.284
, pp. 1520-1523
-
-
Behr, M.A.1
Wilson, M.A.2
Gill, W.P.3
Salamon, H.4
Schoolnik, G.K.5
Rane, S.6
Small, P.M.7
-
31
-
-
0035433897
-
Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays
-
Cho JC, Tiedje JM: Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays. Appl Environ Microbiol 2001, 67:3677-3682. A microarray containing randomly selected DNA fragments was evaluated for assessing bacterial species relatedness.
-
(2001)
Appl Environ Microbiol
, vol.67
, pp. 3677-3682
-
-
Cho, J.C.1
Tiedje, J.M.2
-
32
-
-
0036956423
-
Fingerprinting closely related Xanthomonas pathovars with random nanomer oligonucleotide microarrays
-
Kingsley MT, Straub TM, Call DR, Daly DS, Wunschel SC, Chandler DP: Fingerprinting closely related Xanthomonas pathovars with random nanomer oligonucleotide microarrays. Appl Environ Microbiol 2002, 68:6361-6370. This paper evaluated glass-based microarrays containing randomly selected nanomer oligonucleotides for fingerprinting closely related bacterial strains.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 6361-6370
-
-
Kingsley, M.T.1
Straub, T.M.2
Call, D.R.3
Daly, D.S.4
Wunschel, S.C.5
Chandler, D.P.6
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