-
1
-
-
0032077377
-
From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli
-
Thieffry D., Huerta A.M., Perez-Rueda E., and Collado-Vides J. From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. Bioessays 20 (1998) 433-440
-
(1998)
Bioessays
, vol.20
, pp. 433-440
-
-
Thieffry, D.1
Huerta, A.M.2
Perez-Rueda, E.3
Collado-Vides, J.4
-
2
-
-
0033230874
-
From global expression data to gene networks
-
Thieffry D. From global expression data to gene networks. Bioessays 21 (1999) 895-899
-
(1999)
Bioessays
, vol.21
, pp. 895-899
-
-
Thieffry, D.1
-
3
-
-
0033711710
-
Microarrays and cell cycle transcription in yeast
-
Futcher B. Microarrays and cell cycle transcription in yeast. Curr. Opin. Cell Biol. 12 (2000) 710-715
-
(2000)
Curr. Opin. Cell Biol.
, vol.12
, pp. 710-715
-
-
Futcher, B.1
-
4
-
-
0642281348
-
Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes
-
Caselle M., Di Cunto F., and Provero P. Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes. BMC Bioinformatics 3 (2002) 7
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 7
-
-
Caselle, M.1
Di Cunto, F.2
Provero, P.3
-
5
-
-
0037453009
-
Integrating regulatory motif discovery and genome-wide expression analysis
-
Conlon E.M., Liu X.S., Lieb J.D., and Liu J.S. Integrating regulatory motif discovery and genome-wide expression analysis. Proc. Natl. Acad. Sci. USA 100 (2003) 3339-3344
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 3339-3344
-
-
Conlon, E.M.1
Liu, X.S.2
Lieb, J.D.3
Liu, J.S.4
-
6
-
-
2942582468
-
Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data
-
Gao F., Foat B.C., and Bussemaker H.J. Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. BMC Bioinformatics 5 (2004) 31
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 31
-
-
Gao, F.1
Foat, B.C.2
Bussemaker, H.J.3
-
7
-
-
0031787969
-
Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation
-
Roth F.P., Hughes J.D., Estep P.W., and Church G.M. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat. Biotechnol. 16 (1998) 939-945
-
(1998)
Nat. Biotechnol.
, vol.16
, pp. 939-945
-
-
Roth, F.P.1
Hughes, J.D.2
Estep, P.W.3
Church, G.M.4
-
8
-
-
1942453302
-
Predicting gene expression from sequence
-
Beer M.A., and Tavazoie S. Predicting gene expression from sequence. Cell 117 (2004) 185-198
-
(2004)
Cell
, vol.117
, pp. 185-198
-
-
Beer, M.A.1
Tavazoie, S.2
-
9
-
-
0034666040
-
Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae
-
Coghlan A., and Wolfe K.H. Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast 16 (2000) 1131-1145
-
(2000)
Yeast
, vol.16
, pp. 1131-1145
-
-
Coghlan, A.1
Wolfe, K.H.2
-
10
-
-
0041817645
-
Translational selection and yeast proteome evolution
-
Akashi H. Translational selection and yeast proteome evolution. Genetics 164 (2003) 1291-1303
-
(2003)
Genetics
, vol.164
, pp. 1291-1303
-
-
Akashi, H.1
-
11
-
-
0344237338
-
Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome
-
dos Reis M., Wernisch L., and Savva R. Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome. Nucleic Acids Res. 31 (2003) 6976-6985
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 6976-6985
-
-
dos Reis, M.1
Wernisch, L.2
Savva, R.3
-
12
-
-
0038476173
-
Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models
-
Jansen R., Bussemaker H.J., and Gerstein M. Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models. Nucleic Acids Res. 31 (2003) 2242-2251
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 2242-2251
-
-
Jansen, R.1
Bussemaker, H.J.2
Gerstein, M.3
-
13
-
-
11144241326
-
Correlation of codon bias measures with mRNA levels: analysis of transcriptome data from Escherichia coli
-
Goetz R.M., and Fuglsang A. Correlation of codon bias measures with mRNA levels: analysis of transcriptome data from Escherichia coli. Biochem. Biophys. Res. Commun. 327 (2005) 4-7
-
(2005)
Biochem. Biophys. Res. Commun.
, vol.327
, pp. 4-7
-
-
Goetz, R.M.1
Fuglsang, A.2
-
14
-
-
0023650543
-
The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications
-
Sharp P.M., and Li W.H. The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15 (1987) 1281-1295
-
(1987)
Nucleic Acids Res.
, vol.15
, pp. 1281-1295
-
-
Sharp, P.M.1
Li, W.H.2
-
15
-
-
0032955585
-
Relationships between transcriptional and translational control of gene expression in Saccharomyces cerevisiae: a multiple regression analysis
-
Pavesi A. Relationships between transcriptional and translational control of gene expression in Saccharomyces cerevisiae: a multiple regression analysis. J. Mol. Evol. 48 (1999) 133-141
-
(1999)
J. Mol. Evol.
, vol.48
, pp. 133-141
-
-
Pavesi, A.1
-
16
-
-
0029081824
-
The genus Desulfovibrio: the centennial
-
Voordouw G. The genus Desulfovibrio: the centennial. Appl. Environ. Microbiol. 61 (1995) 2813-2819
-
(1995)
Appl. Environ. Microbiol.
, vol.61
, pp. 2813-2819
-
-
Voordouw, G.1
-
17
-
-
1842732196
-
Genomic insights into gene regulation of Desulfovibrio vulgaris Hildenborough
-
Hemme C.L., and Wall J.D. Genomic insights into gene regulation of Desulfovibrio vulgaris Hildenborough. OMICS 8 (2004) 43-55
-
(2004)
OMICS
, vol.8
, pp. 43-55
-
-
Hemme, C.L.1
Wall, J.D.2
-
18
-
-
0034121140
-
Sulfate-reducing bacteria methylate mercury at variable rates in pure culture and in marine sediments
-
King J.K., Kostka J.E., Frischer M.E., and Saunders F.M. Sulfate-reducing bacteria methylate mercury at variable rates in pure culture and in marine sediments. Appl. Environ. Microbiol. 66 (2000) 2430-2437
-
(2000)
Appl. Environ. Microbiol.
, vol.66
, pp. 2430-2437
-
-
King, J.K.1
Kostka, J.E.2
Frischer, M.E.3
Saunders, F.M.4
-
19
-
-
0033827508
-
Modeling reduction of uranium U(VI) under variable sulfate concentrations by sulfate-reducing bacteria
-
Spear J.R., Figueroa L.A., and Honeyman B.D. Modeling reduction of uranium U(VI) under variable sulfate concentrations by sulfate-reducing bacteria. Appl. Environ. Microbiol. 66 (2000) 3711-3721
-
(2000)
Appl. Environ. Microbiol.
, vol.66
, pp. 3711-3721
-
-
Spear, J.R.1
Figueroa, L.A.2
Honeyman, B.D.3
-
20
-
-
2342475768
-
The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough
-
Heidelberg J.F., Seshadri R., Haveman S.A., Hemme C.L., Paulsen I.T., Kolonay J.F., Eisen J.A., Ward N., Methe B., Brinkac L.M., et al. The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nat. Biotechnol. 22 (2004) 554-559
-
(2004)
Nat. Biotechnol.
, vol.22
, pp. 554-559
-
-
Heidelberg, J.F.1
Seshadri, R.2
Haveman, S.A.3
Hemme, C.L.4
Paulsen, I.T.5
Kolonay, J.F.6
Eisen, J.A.7
Ward, N.8
Methe, B.9
Brinkac, L.M.10
-
21
-
-
33646046282
-
-
W. Zhang, D.E. Culley, J.C.M. Scholten, M. Hogan, L. Vitiritti, F.J. Brockman, Global transcriptomic analysis of Desulfovibrio vulgaris on different electron donors, Antonie van Leeuwenhoek (In press).
-
-
-
-
22
-
-
33646020476
-
-
W. Zhang, D.E. Culley, M. Hogan, L. Vitiritti, F.J. Brockman, Oxidative stress and heat-shock responses in Desulfovibrio vulgaris by genome-wide transcriptomic analysis, Antonie van Leeuwenhoek (In press).
-
-
-
-
23
-
-
0036852098
-
Gene expression analysis using oligonucleotide arrays produced by maskless photolithography
-
Nuwaysir E.F., Huang W., Albert T.J., Singh J., Nuwaysir K., Pitas A., Richmond T., Gorski T., Berg J.P., Ballin J., et al. Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res. 12 (2002) 1749-1755
-
(2002)
Genome Res.
, vol.12
, pp. 1749-1755
-
-
Nuwaysir, E.F.1
Huang, W.2
Albert, T.J.3
Singh, J.4
Nuwaysir, K.5
Pitas, A.6
Richmond, T.7
Gorski, T.8
Berg, J.P.9
Ballin, J.10
-
24
-
-
0034628901
-
Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
-
Hughes J.D., Estep P.W., Tavazoie S., and Church G.M. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol. 296 (2000) 1205-1214
-
(2000)
J. Mol. Biol.
, vol.296
, pp. 1205-1214
-
-
Hughes, J.D.1
Estep, P.W.2
Tavazoie, S.3
Church, G.M.4
-
25
-
-
0028088517
-
Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes
-
Lobry J.R., and Gautier C. Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes. Nucleic Acids Res. 22 (1994) 3174-3180
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 3174-3180
-
-
Lobry, J.R.1
Gautier, C.2
-
26
-
-
0037109119
-
Use and misuse of correspondence analysis in codon usage studies
-
Perriere G., and Thioulouse J. Use and misuse of correspondence analysis in codon usage studies. Nucleic Acids Res. 30 (2002) 4548-4555
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 4548-4555
-
-
Perriere, G.1
Thioulouse, J.2
-
27
-
-
0025318864
-
The 'effective number of codons' used in a gene
-
Wright F. The 'effective number of codons' used in a gene. Gene 87 (1990) 23-29
-
(1990)
Gene
, vol.87
, pp. 23-29
-
-
Wright, F.1
-
28
-
-
0043123153
-
Vienna RNA secondary structure server
-
Hofacker I.L. Vienna RNA secondary structure server. Nucleic Acids Res. 31 (2003) 3429-3431
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3429-3431
-
-
Hofacker, I.L.1
-
29
-
-
28444475607
-
Correlation between mRNA and protein abundance in Desulfovibrio vulgaris: a multiple regression to identify sources of variations
-
Nie L., Wu G., and Zhang W. Correlation between mRNA and protein abundance in Desulfovibrio vulgaris: a multiple regression to identify sources of variations. Biochem. Biophys. Res. Commun. 339 (2006) 603-610
-
(2006)
Biochem. Biophys. Res. Commun.
, vol.339
, pp. 603-610
-
-
Nie, L.1
Wu, G.2
Zhang, W.3
-
30
-
-
0032573426
-
A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome
-
Robison K., McGuire A.M., and Church G.M. A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J. Mol. Biol. 284 (1998) 241-254
-
(1998)
J. Mol. Biol.
, vol.284
, pp. 241-254
-
-
Robison, K.1
McGuire, A.M.2
Church, G.M.3
-
31
-
-
0037133671
-
Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis
-
Akashi H., and Gojobori T. Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc. Natl. Acad. Sci. USA 99 (2002) 3695-3700
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 3695-3700
-
-
Akashi, H.1
Gojobori, T.2
-
32
-
-
0027112993
-
A black box mathematical model to calculate auto-and heterotrophic biomass yields on Gibbs energy dissipation
-
Heijnen J.J., van Loosdrecht M.C.M., and Tijhuis L. A black box mathematical model to calculate auto-and heterotrophic biomass yields on Gibbs energy dissipation. Biotech. Bioeng. 40 (1992) 1139-1154
-
(1992)
Biotech. Bioeng.
, vol.40
, pp. 1139-1154
-
-
Heijnen, J.J.1
van Loosdrecht, M.C.M.2
Tijhuis, L.3
-
33
-
-
0034888743
-
Characterizations of highly expressed genes of four fast-growing bacteria
-
Karlin S., Mrazek J., Campbell A., and Kaiser D. Characterizations of highly expressed genes of four fast-growing bacteria. J. Bacteriol. 183 (2001) 5025-5040
-
(2001)
J. Bacteriol.
, vol.183
, pp. 5025-5040
-
-
Karlin, S.1
Mrazek, J.2
Campbell, A.3
Kaiser, D.4
-
34
-
-
0029931535
-
Synonymous codon bias is related to gene length in Escherichia coli: selection for translational accuracy?
-
Eyre-Walker A. Synonymous codon bias is related to gene length in Escherichia coli: selection for translational accuracy?. Mol. Biol. Evol. 13 (1996) 864-872
-
(1996)
Mol. Biol. Evol.
, vol.13
, pp. 864-872
-
-
Eyre-Walker, A.1
-
35
-
-
0025046732
-
Cleavages in the 5' region of the ompA and bla mRNA control stability: studies with an E. coli mutant altering mRNA stability and a novel endoribonuclease
-
Lundberg U., von Gabain A., and Melefors O. Cleavages in the 5' region of the ompA and bla mRNA control stability: studies with an E. coli mutant altering mRNA stability and a novel endoribonuclease. EMBO J. 9 (1990) 2731-2741
-
(1990)
EMBO J.
, vol.9
, pp. 2731-2741
-
-
Lundberg, U.1
von Gabain, A.2
Melefors, O.3
-
36
-
-
0028945345
-
Identification and characterization of a sequence motif involved in nonsense-mediated mRNA decay
-
Zhang S., Ruiz-Echevarria M.J., Quan Y., and Peltz S.W. Identification and characterization of a sequence motif involved in nonsense-mediated mRNA decay. Mol. Cell Biol. 15 (1995) 2231-2244
-
(1995)
Mol. Cell Biol.
, vol.15
, pp. 2231-2244
-
-
Zhang, S.1
Ruiz-Echevarria, M.J.2
Quan, Y.3
Peltz, S.W.4
-
37
-
-
0035236830
-
Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles
-
Chiang D.Y., Brown P.O., and Eisen M.B. Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles. Bioinformatics 17 (2001) S49-S55
-
(2001)
Bioinformatics
, vol.17
-
-
Chiang, D.Y.1
Brown, P.O.2
Eisen, M.B.3
-
38
-
-
2442446708
-
Genome-wide discovery of transcriptional modules from DNA sequence and gene expression
-
Segal E., Yelensky R., and Koller D. Genome-wide discovery of transcriptional modules from DNA sequence and gene expression. Bioinformatics 19 (2003) i273-i282
-
(2003)
Bioinformatics
, vol.19
-
-
Segal, E.1
Yelensky, R.2
Koller, D.3
-
39
-
-
0035896577
-
The effect of transcription and translation initiation frequencies on the stochastic fluctuations in prokaryotic gene expression
-
Kierzek A.M., Zaim J., and Zielenkiewicz P. The effect of transcription and translation initiation frequencies on the stochastic fluctuations in prokaryotic gene expression. J. Biol. Chem. 276 (2001) 8165-8172
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 8165-8172
-
-
Kierzek, A.M.1
Zaim, J.2
Zielenkiewicz, P.3
-
40
-
-
0025941139
-
The selection-mutation-drift theory of synonymous codon usage
-
Bulmer M. The selection-mutation-drift theory of synonymous codon usage. Genetics 129 (1991) 897-907
-
(1991)
Genetics
, vol.129
, pp. 897-907
-
-
Bulmer, M.1
-
41
-
-
7644223774
-
Why is transcription coupled to translation in bacteria?
-
Gowrishankar J., and Harinarayanan R. Why is transcription coupled to translation in bacteria?. Mol. Microbiol. 54 (2004) 598-603
-
(2004)
Mol. Microbiol.
, vol.54
, pp. 598-603
-
-
Gowrishankar, J.1
Harinarayanan, R.2
-
42
-
-
0032694167
-
A sampling of the yeast proteome
-
Futcher B., Latter G.I., Monardo P., McLaughlin C.S., and Garrels J.I. A sampling of the yeast proteome. Mol. Cell Biol. 19 (1999) 7357-7368
-
(1999)
Mol. Cell Biol.
, vol.19
, pp. 7357-7368
-
-
Futcher, B.1
Latter, G.I.2
Monardo, P.3
McLaughlin, C.S.4
Garrels, J.I.5
-
43
-
-
0033816775
-
Predicted highly expressed genes of diverse prokaryotic genomes
-
Karlin S., and Mrazek J. Predicted highly expressed genes of diverse prokaryotic genomes. J. Bacteriol. 182 (2000) 5238-5250
-
(2000)
J. Bacteriol.
, vol.182
, pp. 5238-5250
-
-
Karlin, S.1
Mrazek, J.2
-
44
-
-
22144453213
-
Predicted highly expressed genes in the genomes of Streptomyces coelicolor and Streptomyces avermitilis and the implications for their metabolism
-
Wu G., Culley D.E., and Zhang W. Predicted highly expressed genes in the genomes of Streptomyces coelicolor and Streptomyces avermitilis and the implications for their metabolism. Microbiology 151 (2005) 2175-2187
-
(2005)
Microbiology
, vol.151
, pp. 2175-2187
-
-
Wu, G.1
Culley, D.E.2
Zhang, W.3
|