-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S., T. Madden, A. Schäffer, J. Zhang, W. Miller, and D. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.1
Madden, T.2
Schäffer, A.3
Zhang, J.4
Miller, W.5
Lipman, D.6
-
2
-
-
1342303735
-
Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray
-
Bozdech, Z., J. Zhu, M. P. Joachimiak, F. E. Cohen, B. Pulliam, and J. U DeRisi. 2003. Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biol. 4:R9.
-
(2003)
Genome Biol.
, vol.4
-
-
Bozdech, Z.1
Zhu, J.2
Joachimiak, M.P.3
Cohen, F.E.4
Pulliam, B.5
DeRisi, J.U.6
-
3
-
-
25144448354
-
DNA microarrays in drug discovery and development: Progress and potential
-
Debouck, C., and P. N. Goodfellow. 1999. DNA microarrays in drug discovery and development: progress and potential. Biochem. Pharmacol. 62:1311-1336.
-
(1999)
Biochem. Pharmacol.
, vol.62
, pp. 1311-1336
-
-
Debouck, C.1
Goodfellow, P.N.2
-
4
-
-
0030669030
-
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
-
5
-
-
7744230895
-
Global transcriptome analysis of the heat shock response of Shewanella oneidensis
-
Gao, H., Y. Wang, X. Liu, T. Van, L. Wu, E. Aim, A. Arkin, D. K. Thompson, and J. Zhou. 2004. Global transcriptome analysis of the heat shock response of Shewanella oneidensis. J. Bacteriol. 186:7796-7803.
-
(2004)
J. Bacteriol.
, vol.186
, pp. 7796-7803
-
-
Gao, H.1
Wang, Y.2
Liu, X.3
Van, T.4
Wu, L.5
Aim, E.6
Arkin, A.7
Thompson, D.K.8
Zhou, J.9
-
6
-
-
0033569406
-
Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring
-
Golub, T. R., D. K. Slonim, P. Tamayo, C. Huard, M. Gaasenbeek, J. P. Mesirov, H. Coller, M. L. Loh, J. R. Downing, M. A. Caligiuri, C. D. Bloomfield, and E. S. Lander. 1999. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286:531-537.
-
(1999)
Science
, vol.286
, pp. 531-537
-
-
Golub, T.R.1
Slonim, D.K.2
Tamayo, P.3
Huard, C.4
Gaasenbeek, M.5
Mesirov, J.P.6
Coller, H.7
Loh, M.L.8
Downing, J.R.9
Caligiuri, M.A.10
Bloomfield, C.D.11
Lander, E.S.12
-
7
-
-
22144441403
-
Empirical establishment of oligonucleotide probe design criteria
-
He, Z., L. Wu, X. Li, M. W. Fields, and J. Zhou. 2005. Empirical establishment of oligonucleotide probe design criteria. Appl. Environ. Microbiol. 71:3753-3760.
-
(2005)
Appl. Environ. Microbiol.
, vol.71
, pp. 3753-3760
-
-
He, Z.1
Wu, L.2
Li, X.3
Fields, M.W.4
Zhou, J.5
-
8
-
-
0034616930
-
Functional discovery via a compendium of expression profiles
-
Hughes, T. R., M. J. Marion, A. R. Jones, C. J. Roberts, R. Stoughton, C. D. Armour, H. A. Bennett, E. Coffey, H. Dai, Y. D. He, M. J. Kidd, A. M. King, M. R. Meyer, D. Slade, P. Y. Lum, S. B. Stepaniants, D. D. Shoemaker, D. Gachotte, K. Chakraburtty, J. Simon, M. Bard, and S. H. Friend. 2000. Functional discovery via a compendium of expression profiles. Cell 102:109-126.
-
(2000)
Cell
, vol.102
, pp. 109-126
-
-
Hughes, T.R.1
Marion, M.J.2
Jones, A.R.3
Roberts, C.J.4
Stoughton, R.5
Armour, C.D.6
Bennett, H.A.7
Coffey, E.8
Dai, H.9
He, Y.D.10
Kidd, M.J.11
King, A.M.12
Meyer, M.R.13
Slade, D.14
Lum, P.Y.15
Stepaniants, S.B.16
Shoemaker, D.D.17
Gachotte, D.18
Chakraburtty, K.19
Simon, J.20
Bard, M.21
Friend, S.H.22
more..
-
9
-
-
0035072249
-
Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer
-
Hughes, T. R., M. Mao, A. R. Jones, J. Burchard, M. J. Marton, K. W. Shannon, S. M. Lefkowitz, M. Ziman, J. M. Schelter, M. R. Meyer, S. Kobayashi, C. Davis, H. Dai, Y. D. He, S. B. Stephaniants, G. Cavet, W. L. Walker, A. West, E. Coffey, D. D. Showmarker, R. Stoughton, A. P. Blanchard, S. H. Friend, and P. S. Linsley. 2001. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol. 19:342-347.
-
(2001)
Nat. Biotechnol.
, vol.19
, pp. 342-347
-
-
Hughes, T.R.1
Mao, M.2
Jones, A.R.3
Burchard, J.4
Marton, M.J.5
Shannon, K.W.6
Lefkowitz, S.M.7
Ziman, M.8
Schelter, J.M.9
Meyer, M.R.10
Kobayashi, S.11
Davis, C.12
Dai, H.13
He, Y.D.14
Stephaniants, S.B.15
Cavet, G.16
Walker, W.L.17
West, A.18
Coffey, E.19
Showmarker, D.D.20
Stoughton, R.21
Blanchard, A.P.22
Friend, S.H.23
Linsley, P.S.24
more..
-
10
-
-
0034189614
-
DNA microarray technology and antimicrobial drug discovery
-
Ivanov, I., C. Schaab, S. Planitzer, U. Teichmann, A. Machl, S. Theml, S. Meier-Ewert, B. Seizinger, and H. Loferer. 2000. DNA microarray technology and antimicrobial drug discovery. Pharmacogenomics 1:169-178.
-
(2000)
Pharmacogenomics
, vol.1
, pp. 169-178
-
-
Ivanov, I.1
Schaab, C.2
Planitzer, S.3
Teichmann, U.4
Machl, A.5
Theml, S.6
Meier-Ewert, S.7
Seizinger, B.8
Loferer, H.9
-
11
-
-
0034669668
-
Assessment of the specificity and sensitivity of oligonucleotide (50mer) microarrays
-
Kane, M. D., T. A. Jatkoe, C. R. Stumpf, J. Lu, J. D. Thomas, and J. M. Madore. 2000. Assessment of the specificity and sensitivity of oligonucleotide (50mer) microarrays. Nucleic Acids Res. 28:4552-1557.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 4552-11557
-
-
Kane, M.D.1
Jatkoe, T.A.2
Stumpf, C.R.3
Lu, J.4
Thomas, J.D.5
Madore, J.M.6
-
12
-
-
0033621553
-
70 is the principal sigma factor responsible for transcription of acs, which encodes acetyl coenzyme A synthetase in Escherichia coli
-
70 is the principal sigma factor responsible for transcription of acs, which encodes acetyl coenzyme A synthetase in Escherichia coli. J. Bacteriol. 182:551-554.
-
(2000)
J. Bacteriol.
, vol.182
, pp. 551-554
-
-
Kumari, S.1
Simel, E.J.2
Wolfe, A.J.3
-
13
-
-
0032401519
-
Expression of genes encoding the E2 and E3 components of the Bacillus stearothermophilus pyruvate dehydrogenase complex and the stoichiometry of subunit interaction in assembly in vitro
-
Lessard, I. A. D., G. J. Domingo, A. Borges, and R. N. Perham. 1998. Expression of genes encoding the E2 and E3 components of the Bacillus stearothermophilus pyruvate dehydrogenase complex and the stoichiometry of subunit interaction in assembly in vitro. Eur. J. Biochem. 258:491-501.
-
(1998)
Eur. J. Biochem.
, vol.258
, pp. 491-501
-
-
Lessard, I.A.D.1
Domingo, G.J.2
Borges, A.3
Perham, R.N.4
-
14
-
-
0034303643
-
Molecular profiling of human cancer
-
Liotta, L., and E. Petricoin. 2000. Molecular profiling of human cancer. Nat. Rev. Genet. 1:48-56.
-
(2000)
Nat. Rev. Genet.
, vol.1
, pp. 48-56
-
-
Liotta, L.1
Petricoin, E.2
-
15
-
-
0037388447
-
Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation
-
Liu, Y., J. Zhou, M. Omelchenko, A. Beliaev, A. Venkateswaran, J. Stair, L. Wu, D. K. Thompson D. Xu, I. B. Rogozin, E. K. Gaidamakova, M. Zhai, K. S. Makarova, E. V. Koonin, and M. J. Daly. 2003. Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. Proc. Natl. Acad. Sci. USA 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
Gaidamakova, E.K.11
Zhai, M.12
Makarova, K.S.13
Koonin, E.V.14
Daly, M.J.15
-
16
-
-
10544256600
-
Expression monitoring by hybridization to high-density oligonucleotide arrays
-
Lockhart, D. J., H. Dong, M. C. Byrne, M. T. Follettie, M. V. Gallo, M. S. Chee, M. Mittmann, C. Wang, M. Kobayashi, H. Horton, and E. L. Brown. 1996. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 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
Brown, E.L.11
-
17
-
-
0035029243
-
Microarray application in neuroscience
-
Luo, Z., and D. H. Geschwind. 2001. Microarray application in neuroscience. Neurobiol. Dis. 8:183-193.
-
(2001)
Neurobiol. Dis.
, vol.8
, pp. 183-193
-
-
Luo, Z.1
Geschwind, D.H.2
-
18
-
-
0037336455
-
Microarray in cancer: Research and application
-
Ochs, M. F., and A. K. Godwin. 2003. Microarray in cancer: research and application. BioTechniques 34:S4-S15.
-
(2003)
BioTechniques
, vol.34
-
-
Ochs, M.F.1
Godwin, A.K.2
-
19
-
-
0036900945
-
Medical application of microarray technologies: A regulatory science perspective
-
Petricoin, E. F., J. L. Hackett, L. J. Lesko, R. K. Puri, S. I. Gutman, K. Chumakov, J. Woodcock, D. W. Feigal, Jr., K. C. Zoon, and F. D. Sistare. 2002. Medical application of microarray technologies: a regulatory science perspective. Nat. Genet. 32:474-479.
-
(2002)
Nat. Genet.
, vol.32
, pp. 474-479
-
-
Petricoin, E.F.1
Hackett, J.L.2
Lesko, L.J.3
Puri, R.K.4
Gutman, S.I.5
Chumakov, K.6
Woodcock, J.7
Feigal Jr., D.W.8
Zoon, K.C.9
Sistare, F.D.10
-
20
-
-
0036615598
-
Optimization of oligonucleotide-based DNA microarrays
-
Relogio, A., C. Schwager, A. Richter, W. Ansorge, and A. Valcarcel. 2002. Optimization of oligonucleotide-based DNA microarrays. Nucleic Acids Res. 30:e51.
-
(2002)
Nucleic Acids Res.
, vol.30
-
-
Relogio, A.1
Schwager, C.2
Richter, A.3
Ansorge, W.4
Valcarcel, A.5
-
21
-
-
3242773890
-
Detection of biodegradation and biotransformation genes in microbial communities using 50-mer oligonucleotide microarrays
-
Rhee, S. K., X. Liu, L. Wu, S. C. Chong, X. Wan, and J. Zhou. 2004. Detection of biodegradation and biotransformation genes in microbial communities using 50-mer oligonucleotide microarrays. Appl. Environ. Microbiol. 70:4303-41317.
-
(2004)
Appl. Environ. Microbiol.
, vol.70
, pp. 4303-41317
-
-
Rhee, S.K.1
Liu, X.2
Wu, L.3
Chong, S.C.4
Wan, X.5
Zhou, J.6
-
22
-
-
0033214149
-
Genome-wide expression profiling in Escherichia coli K-12
-
Richmond, C. S., J. D. Glasner, R. Mau, H. Jin, and F. R. Blattner. 1999. Genome-wide expression profiling in Escherichia coli K-12. Nucleic Acids Res. 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
-
23
-
-
0030862620
-
Steric factors influencing hybridization of nucleic acids to oligonucleotide arrays
-
Shchepinov, M. S., S. C. Case-Green, and E. M. Southern. 1997. Steric factors influencing hybridization of nucleic acids to oligonucleotide arrays. Nucleic Acids Res. 25:1155-1161.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 1155-1161
-
-
Shchepinov, M.S.1
Case-Green, S.C.2
Southern, E.M.3
-
24
-
-
0035865260
-
Experimental annotation of the human genome using microarray technology
-
Shoemaker, D. D., E. E. Schadt, C. D. Armour, Y. D. He, P. Garrett-Engele, P. D. McDonagh, P. M. Loerch, A. Leonardson, P. Y. Lum, G. Cavet, L. F. Wu, S. J. Altschuler, S. Edwards, J. King, J. S. Tsang, G. Schimmack, J. M. Scheliter, J. Koch, M. Ziman, M. J. Marton, B. Li, P. Cundiff, T. Ward, J. Castle, M. Krolewski, M. R. Meyer, M. Mao, J. Burchard, M. J. Kidd, H. Dai, J. W. Phillips, P. S. Linsley, R. Stoughton, S. Scherler, and M. S. Boguski. 2001. Experimental annotation of the human genome using microarray technology. Nature 409:922-927.
-
(2001)
Nature
, vol.409
, pp. 922-927
-
-
Shoemaker, D.D.1
Schadt, E.E.2
Armour, C.D.3
He, Y.D.4
Garrett-Engele, P.5
McDonagh, P.D.6
Loerch, P.M.7
Leonardson, A.8
Lum, P.Y.9
Cavet, G.10
Wu, L.F.11
Altschuler, S.J.12
Edwards, S.13
King, J.14
Tsang, J.S.15
Schimmack, G.16
Scheliter, J.M.17
Koch, J.18
Ziman, M.19
Marton, M.J.20
Li, B.21
Cundiff, P.22
Ward, T.23
Castle, J.24
Krolewski, M.25
Meyer, M.R.26
Mao, M.27
Burchard, J.28
Kidd, M.J.29
Dai, H.30
Phillips, J.W.31
Linsley, P.S.32
Stoughton, R.33
Scherler, S.34
Boguski, M.S.35
more..
-
26
-
-
0035486807
-
Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays
-
Small, J., D. R. Call, F. J. Brockman, T. M. Straub, and D. P. Chandler. 2001. Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Appl. Environ. Microbiol. 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
-
27
-
-
0036062240
-
pH-dependent expression of periplasmic proteins and amino acid catabolism in Escherichia coli
-
Stancik, L. M., D. M. Stancik, B. Schmidt, D. M. Barnhart, Y. N. Yoncheva, and J. L. Slonczewski. 2002. pH-dependent expression of periplasmic proteins and amino acid catabolism in Escherichia coli. J. Bacteriol. 184:4246-4258.
-
(2002)
J. Bacteriol.
, vol.184
, pp. 4246-4258
-
-
Stancik, L.M.1
Stancik, D.M.2
Schmidt, B.3
Barnhart, D.M.4
Yoncheva, Y.N.5
Slonczewski, J.L.6
-
28
-
-
0037316061
-
Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment
-
Taroncher-Oldedburg, G., E. M. Griner, C. A. Francis, and B. B. Ward. 2003. Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl. Environ. Microbiol. 69:1159-1171.
-
(2003)
Appl. Environ. Microbiol.
, vol.69
, pp. 1159-1171
-
-
Taroncher-Oldedburg, G.1
Griner, E.M.2
Francis, C.A.3
Ward, B.B.4
-
29
-
-
1842579620
-
Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples
-
Tiquia, S. M., L. Wu, S. C. Chong, S. Passovets, D. Xu, Y. Xu, and J. Zhou. 2004. Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. BioTechniques 36:664-675.
-
(2004)
BioTechniques
, vol.36
, pp. 664-675
-
-
Tiquia, S.M.1
Wu, L.2
Chong, S.C.3
Passovets, S.4
Xu, D.5
Xu, Y.6
Zhou, J.7
-
30
-
-
0033010261
-
+ uptake system in Escherichia coli upon hyper-osmotic stress at a low pH
-
+ uptake system in Escherichia coli upon hyper-osmotic stress at a low pH. FEBS Lett. 447:144-148.
-
(1999)
FEBS Lett.
, vol.447
, pp. 144-148
-
-
Trchounian, A.1
Kobayashi, H.2
-
31
-
-
1842494853
-
Key considerations for accurate microarray scanning and image analysis
-
G. Kamberova (ed.), DNA Press LLC, Salem, MA
-
Verdick, D., S. Handran, and S. Pickett. 2002. Key considerations for accurate microarray scanning and image analysis, p. 83-98. In G. Kamberova (ed.), DNA image analysis: nuts and bolts, DNA Press LLC, Salem, MA.
-
(2002)
DNA Image Analysis: Nuts and Bolts
, pp. 83-98
-
-
Verdick, D.1
Handran, S.2
Pickett, S.3
-
32
-
-
10044252092
-
Defining the Shewanella oneidensis fur regulon: Integration of genome-wide expression analysis, proteome characterization, and regulatory motif discovery
-
Wan, X., N. C. VerBerkmoes, L. A. McCue, D. Stanek, H. Connelly, L. Wu, X. Liu, T. Yan, A. Leaphart, R. L. Hettich, J. Zhou, and D. K. Thompson. 2004. Defining the Shewanella oneidensis FUR regulon: integration of genome-wide expression analysis, proteome characterization, and regulatory motif discovery. J. Bacteriol. 186:8385-8400.
-
(2004)
J. Bacteriol.
, vol.186
, pp. 8385-8400
-
-
Wan, X.1
Verberkmoes, N.C.2
McCue, L.A.3
Stanek, D.4
Connelly, H.5
Wu, L.6
Liu, X.7
Yan, T.8
Leaphart, A.9
Hettich, R.L.10
Zhou, J.11
Thompson, D.K.12
-
33
-
-
0031453850
-
Genome-wide expression monitoring in Saccharomyces cerevisiae
-
Wodleka, L., H. Dong, M. Mittmann, M. H. Ho, and D. J. Lockhart. 1997. Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat. Biotechnol. 15:1359-1367.
-
(1997)
Nat. Biotechnol.
, vol.15
, pp. 1359-1367
-
-
Wodleka, L.1
Dong, H.2
Mittmann, M.3
Ho, M.H.4
Lockhart, D.J.5
-
34
-
-
0035656126
-
Development and evaluation of functional gene arrays for detection of selected genes in the environment
-
Wu, L., D. K. Thompson, G. Li, R. A. Hurt, J. M. Tiedje, and J. Zhou. 2001. Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl. Environ. Microbiol. 67:5780-5790.
-
(2001)
Appl. Environ. Microbiol.
, vol.67
, pp. 5780-5790
-
-
Wu, L.1
Thompson, D.K.2
Li, G.3
Hurt, R.A.4
Tiedje, J.M.5
Zhou, J.6
-
35
-
-
1842844023
-
PRIMEGENS: Robust and efficient design of gene-specific probes for microarray analysis
-
Xu, D., G. Li, L. Wu, J. Zhou, and Y. Xu. 2002. PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis. Bioinformatics 18:1432-1437.
-
(2002)
Bioinformatics
, vol.18
, pp. 1432-1437
-
-
Xu, D.1
Li, G.2
Wu, L.3
Zhou, J.4
Xu, Y.5
-
36
-
-
0037772204
-
Microarrays for bacterial detection and microbial community analysis
-
Zhou, J. 2003. Microarrays for bacterial detection and microbial community analysis. Curr. Opin. Microbiol. 6:288-294.
-
(2003)
Curr. Opin. Microbiol.
, vol.6
, pp. 288-294
-
-
Zhou, J.1
-
38
-
-
0036624982
-
Challenge in applying microarrays to environmental studies
-
Zhou, J., and D. K. Thompson. 2002. Challenge in applying microarrays to environmental studies. Curr. Opin. Biotechnol. 13:204-207.
-
(2002)
Curr. Opin. Biotechnol.
, vol.13
, pp. 204-207
-
-
Zhou, J.1
Thompson, D.K.2
-
39
-
-
0042121256
-
Mfold web server for nucleic acid folding and hybridization prediction
-
Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31:3406-3415.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3406-3415
-
-
Zuker, M.1
|