-
1
-
-
0028072561
-
The dipeptide permease of Escherichia coli closely resembles other bacterial transport systems and shows growth-phase-dependent expression
-
Abouhamad, W. N., and M. D. Manson. 1994. The dipeptide permease of Escherichia coli closely resembles other bacterial transport systems and shows growth-phase-dependent expression. Mol. Microbiol. 14:1077-1092.
-
(1994)
Mol. Microbiol
, vol.14
, pp. 1077-1092
-
-
Abouhamad, W.N.1
Manson, M.D.2
-
2
-
-
49649117268
-
Critical dynamics in genetic regulatory networks: Examples from four kingdoms
-
Balleza, E., E. R. Alvarez-Buylla, A. Chaos, S. Kauffman, I. Shmulevich, and M. Aldana. 2008. Critical dynamics in genetic regulatory networks: examples from four kingdoms. PLoS ONE 3:e2456.
-
(2008)
PLoS ONE
, vol.3
-
-
Balleza, E.1
Alvarez-Buylla, E.R.2
Chaos, A.3
Kauffman, S.4
Shmulevich, I.5
Aldana, M.6
-
3
-
-
0036331039
-
Microarray transcription profiling of a Shewanella oneidensis etrA mutant
-
Beliaev, A. S., D. K. Thompson, M. W. Fields, L. Wu, D. P. Lies, K. H. Nealson, and J. Zhou. 2002. Microarray transcription profiling of a Shewanella oneidensis etrA mutant. J. Bacteriol. 184:4612-4616.
-
(2002)
J. Bacteriol
, vol.184
, pp. 4612-4616
-
-
Beliaev, A.S.1
Thompson, D.K.2
Fields, M.W.3
Wu, L.4
Lies, D.P.5
Nealson, K.H.6
Zhou, J.7
-
4
-
-
0029999921
-
Location of the C-terminal domain of the RNA polymerase alpha subunit in different open complexes at the Escherichia coli galactose operon regulatory region
-
Belyaeva, T. A., J. A. Bown, N. Fujita, A. Ishihama, and S. J. Busby. 1996. Location of the C-terminal domain of the RNA polymerase alpha subunit in different open complexes at the Escherichia coli galactose operon regulatory region. Nucleic Acids Res. 24:2242-2251.
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 2242-2251
-
-
Belyaeva, T.A.1
Bown, J.A.2
Fujita, N.3
Ishihama, A.4
Busby, S.J.5
-
5
-
-
0032502838
-
Transcription activation at promoters carrying tandem DNA sites for the Escherichia coli cyclic AMP receptor protein: Organisation of the RNA polymerase alpha subunits
-
Belyaeva, T. A., V. A. Rhodius, C. L. Webster, and S. J. Busby. 1998. Transcription activation at promoters carrying tandem DNA sites for the Escherichia coli cyclic AMP receptor protein: organisation of the RNA polymerase alpha subunits. J. Mol. Biol. 277:789-804.
-
(1998)
J. Mol. Biol
, vol.277
, pp. 789-804
-
-
Belyaeva, T.A.1
Rhodius, V.A.2
Webster, C.L.3
Busby, S.J.4
-
6
-
-
33846913192
-
Operon prediction for sequenced bacterial genomes without experimental information
-
Bergman, N. H., K. D. Passalacqua, P. C. Hanna, and Z. S. Qin. 2007. Operon prediction for sequenced bacterial genomes without experimental information. Appl. Environ. Microbiol. 73:846-854.
-
(2007)
Appl. Environ. Microbiol
, vol.73
, pp. 846-854
-
-
Bergman, N.H.1
Passalacqua, K.D.2
Hanna, P.C.3
Qin, Z.S.4
-
7
-
-
43149105201
-
Rapid changes in gene expression dynamics in response to superoxide reveal SoxRS-dependent and independent transcriptional networks
-
Blanchard, J. L., W. Y. Wholey, E. M. Conlon, and P. J. Pomposiello. 2007. Rapid changes in gene expression dynamics in response to superoxide reveal SoxRS-dependent and independent transcriptional networks. PLoS ONE 2:e1186.
-
(2007)
PLoS ONE
, vol.2
-
-
Blanchard, J.L.1
Wholey, W.Y.2
Conlon, E.M.3
Pomposiello, P.J.4
-
8
-
-
0037480741
-
A Bayesian network approach to operon prediction
-
Bockhorst, J., M. Craven, D. Page, J. Shavlik, and J. Glasner. 2003. A Bayesian network approach to operon prediction. Bioinformatics 19:1227-1235.
-
(2003)
Bioinformatics
, vol.19
, pp. 1227-1235
-
-
Bockhorst, J.1
Craven, M.2
Page, D.3
Shavlik, J.4
Glasner, J.5
-
9
-
-
37349099750
-
A predictive model for transcriptional control of physiology in a free living cell
-
Bonneau, R., M. T. Facciotti, D. J. Reiss, A. K. Schmid, M. Pan, A. Kaur, V. Thorsson, P. Shannon, M. H. Johnson, J. C. Bare, W. Longabaugh, M. Vuthoori, K. Whitehead, A. Madar, L. Suzuki, T. Mori, D. E. Chang, J. Diruggiero, C. H. Johnson, L. Hood, and N. S. Baliga. 2007. A predictive model for transcriptional control of physiology in a free living cell. Cell 131:1354-1365.
-
(2007)
Cell
, vol.131
, pp. 1354-1365
-
-
Bonneau, R.1
Facciotti, M.T.2
Reiss, D.J.3
Schmid, A.K.4
Pan, M.5
Kaur, A.6
Thorsson, V.7
Shannon, P.8
Johnson, M.H.9
Bare, J.C.10
Longabaugh, W.11
Vuthoori, M.12
Whitehead, K.13
Madar, A.14
Suzuki, L.15
Mori, T.16
Chang, D.E.17
Diruggiero, J.18
Johnson, C.H.19
Hood, L.20
Baliga, N.S.21
more..
-
10
-
-
48449094106
-
NeAT: A toolbox for the analysis of biological networks, clusters, classes and pathways
-
Brohee, S., K. Faust, G. Lima-Mendez, O. Sand, R. Janky, G. Vanderstocken, Y. Deville, and J. van Helden. 2008. NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways. Nucleic Acids Res. 36:W444-W451.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Brohee, S.1
Faust, K.2
Lima-Mendez, G.3
Sand, O.4
Janky, R.5
Vanderstocken, G.6
Deville, Y.7
van Helden, J.8
-
11
-
-
15844412591
-
Improving promoter prediction for the NNPP2.2 algorithm: A case study using Escherichia coli DNA sequences
-
Burden, S., Y. X. Lin, and R. Zhang. 2005. Improving promoter prediction for the NNPP2.2 algorithm: a case study using Escherichia coli DNA sequences. Bioinformatics 21:601-607.
-
(2005)
Bioinformatics
, vol.21
, pp. 601-607
-
-
Burden, S.1
Lin, Y.X.2
Zhang, R.3
-
12
-
-
0032698634
-
Transcription activation by catabolite activator protein (CAP)
-
Busby, S., and R. H. Ebright. 1999. Transcription activation by catabolite activator protein (CAP). J. Mol. Biol. 293:199-213.
-
(1999)
J. Mol. Biol
, vol.293
, pp. 199-213
-
-
Busby, S.1
Ebright, R.H.2
-
13
-
-
0028094718
-
Transcription activation by the Escherichia coli cyclic AMP receptor protein. Receptors bound in tandem at promoters can interact synergistically
-
Busby, S., D. West, M. Lawes, C. Webster, A. Ishihama, and A. Kolb. 1994. Transcription activation by the Escherichia coli cyclic AMP receptor protein. Receptors bound in tandem at promoters can interact synergistically. J. Mol. Biol. 241:341-352.
-
(1994)
J. Mol. Biol
, vol.241
, pp. 341-352
-
-
Busby, S.1
West, D.2
Lawes, M.3
Webster, C.4
Ishihama, A.5
Kolb, A.6
-
14
-
-
41449103756
-
An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance
-
Casimiro, A. C., S. Vinga, A. T. Freitas, and A. L. Oliveira. 2008. An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance. BMC Bioinform. 9:89.
-
(2008)
BMC Bioinform
, vol.9
, pp. 89
-
-
Casimiro, A.C.1
Vinga, S.2
Freitas, A.T.3
Oliveira, A.L.4
-
15
-
-
5044249735
-
GeConT: Gene context analysis
-
Ciria, R., C. Abreu-Goodger, E. Morett, and E. Merino. 2004. GeConT: gene context analysis. Bioinformatics 20:2307-2308.
-
(2004)
Bioinformatics
, vol.20
, pp. 2307-2308
-
-
Ciria, R.1
Abreu-Goodger, C.2
Morett, E.3
Merino, E.4
-
16
-
-
0026003072
-
Control site location and transcriptional regulation in Escherichia coli
-
Collado-Vides, J., B. Magasanik, and J. D. Gralla. 1991. Control site location and transcriptional regulation in Escherichia coli. Microbiol. Rev. 55: 371-394.
-
(1991)
Microbiol. Rev
, vol.55
, pp. 371-394
-
-
Collado-Vides, J.1
Magasanik, B.2
Gralla, J.D.3
-
17
-
-
36249017917
-
Programming gene expression with combinatorial promoters
-
Cox, R. S., III, M. G. Surette, and M. B. Elowitz. 2007. Programming gene expression with combinatorial promoters. Mol. Syst. Biol. 3:145.
-
(2007)
Mol. Syst. Biol
, vol.3
, pp. 145
-
-
Cox III, R.S.1
Surette, M.G.2
Elowitz, M.B.3
-
18
-
-
52749092937
-
Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences
-
Defrance, M., R. Janky, O. Sand, and J. van Helden. 2008. Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences. Nat. Protoc. 3:1589-1603.
-
(2008)
Nat. Protoc
, vol.3
, pp. 1589-1603
-
-
Defrance, M.1
Janky, R.2
Sand, O.3
van Helden, J.4
-
19
-
-
0034875301
-
DNA microarray-based identification of genes controlled by autoinducer 2-stimulated quorum sensing in Escherichia coli
-
DeLisa, M. P., C. F. Wu, L. Wang, J. J. Valdes, and W. E. Bentley. 2001. DNA microarray-based identification of genes controlled by autoinducer 2-stimulated quorum sensing in Escherichia coli. J. Bacteriol. 183:5239-5247.
-
(2001)
J. Bacteriol
, vol.183
, pp. 5239-5247
-
-
DeLisa, M.P.1
Wu, C.F.2
Wang, L.3
Valdes, J.J.4
Bentley, W.E.5
-
20
-
-
34249932435
-
Probing transcription factor dynamics at the single-molecule level in a living cell
-
Elf, J., G. W. Li, and X. S. Xie. 2007. Probing transcription factor dynamics at the single-molecule level in a living cell. Science 316:1191-1194.
-
(2007)
Science
, vol.316
, pp. 1191-1194
-
-
Elf, J.1
Li, G.W.2
Xie, X.S.3
-
21
-
-
27644434408
-
Phydbac "Gene Function Predictor": A gene annotation tool based on genomic context analysis
-
Enault, F., K. Suhre, and J. M. Claverie. 2005. Phydbac "Gene Function Predictor": a gene annotation tool based on genomic context analysis. BMC Bioinform. 6:247.
-
(2005)
BMC Bioinform
, vol.6
, pp. 247
-
-
Enault, F.1
Suhre, K.2
Claverie, J.M.3
-
22
-
-
33846400424
-
Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
-
Faith, J. J., B. Hayete, J. T. Thaden, I. Mogno, J. Wierzbowski, G. Cottarel, S. Kasif, J. J. Collins, and T. S. Gardner. 2007. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol. 5:e8.
-
(2007)
PLoS Biol
, vol.5
-
-
Faith, J.J.1
Hayete, B.2
Thaden, J.T.3
Mogno, I.4
Wierzbowski, J.5
Cottarel, G.6
Kasif, S.7
Collins, J.J.8
Gardner, T.S.9
-
23
-
-
34250316617
-
The NsrR regulon of Escherichia coli K-12 includes genes encoding the hybrid cluster protein and the periplasmic, respiratory nitrite reductase
-
Filenko, N., S. Spiro, D. F. Browning, D. Squire, T. W. Overton, J. Cole, and C. Constantinidou. 2007. The NsrR regulon of Escherichia coli K-12 includes genes encoding the hybrid cluster protein and the periplasmic, respiratory nitrite reductase. J. Bacteriol. 189:4410-4417.
-
(2007)
J. Bacteriol
, vol.189
, pp. 4410-4417
-
-
Filenko, N.1
Spiro, S.2
Browning, D.F.3
Squire, D.4
Overton, T.W.5
Cole, J.6
Constantinidou, C.7
-
24
-
-
38549098540
-
The Molecular Biology Database Collection: 2008 update
-
Galperin, M. Y. 2008. The Molecular Biology Database Collection: 2008 update. Nucleic Acids Res. 36:D2-D4.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Galperin, M.Y.1
-
25
-
-
38549140094
-
-
Gama-Castro, S, V. Jimenez-Jacinto, M. Peralta-Gil, A. Santos-Zavaleta, M. I. Penaloza-Spinola, B. Contreras-Moreira, J. Segura-Salazar, L. Muniz-Rascado, I. Martinez-Flores, H. Salgado, C. Bonavides-Martinez, C. Abreu-Goodger, C. Rodriguez-Penagos, J. Miranda-Rios, E. Morett, E. Merino, A. M. Huerta, L. Trevino-Quintanilla, and J. Collado-Vides. 2008. RegulonDB (version 6.0, gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res. 36:D120-D124
-
Gama-Castro, S., V. Jimenez-Jacinto, M. Peralta-Gil, A. Santos-Zavaleta, M. I. Penaloza-Spinola, B. Contreras-Moreira, J. Segura-Salazar, L. Muniz-Rascado, I. Martinez-Flores, H. Salgado, C. Bonavides-Martinez, C. Abreu-Goodger, C. Rodriguez-Penagos, J. Miranda-Rios, E. Morett, E. Merino, A. M. Huerta, L. Trevino-Quintanilla, and J. Collado-Vides. 2008. RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res. 36:D120-D124.
-
-
-
-
26
-
-
42449123222
-
Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis. BMC
-
Goelzer, A., F. B. Brikci, I. Martin-Verstraete, P. Noirot, P. Bessieres, S. Aymerich, and V. Fromion. 2008. Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis. BMC Syst. Biol. 2:20.
-
(2008)
Syst. Biol
, vol.2
, pp. 20
-
-
Goelzer, A.1
Brikci, F.B.2
Martin-Verstraete, I.3
Noirot, P.4
Bessieres, P.5
Aymerich, S.6
Fromion, V.7
-
27
-
-
0037562601
-
The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments
-
Gonzalez, V., P. Bustos, M. A. Ramirez-Romero, A. Medrano-Soto, H. Salgado, I. Hernandez-Gonzalez, J. C. Hernandez-Celis, V. Quintero, G. Moreno-Hagelsieb, L. Girard, O. Rodriguez, M. Flores, M. A. Cevallos, J. Collado-Vides, D. Romero, and G. Davila. 2003. The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments. Genome Biol. 4:R36.
-
(2003)
Genome Biol
, vol.4
-
-
Gonzalez, V.1
Bustos, P.2
Ramirez-Romero, M.A.3
Medrano-Soto, A.4
Salgado, H.5
Hernandez-Gonzalez, I.6
Hernandez-Celis, J.C.7
Quintero, V.8
Moreno-Hagelsieb, G.9
Girard, L.10
Rodriguez, O.11
Flores, M.12
Cevallos, M.A.13
Collado-Vides, J.14
Romero, D.15
Davila, G.16
-
28
-
-
32144448660
-
Improved prediction of bacterial transcription start sites
-
Gordon, J. J., M. W. Towsey, J. M. Hogan, S. A. Mathews, and P. Timms. 2006. Improved prediction of bacterial transcription start sites. Bioinformatics 22:142-148.
-
(2006)
Bioinformatics
, vol.22
, pp. 142-148
-
-
Gordon, J.J.1
Towsey, M.W.2
Hogan, J.M.3
Mathews, S.A.4
Timms, P.5
-
29
-
-
0000661051
-
Organization and function of transcription regulatory elements
-
F. C. Neidhardt, R. Curtiss III, J. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. Reznikoff, M. Schaechter, H. E. Umbarger, and M. Riley ed, 2nd ed. ASM Press, Washington, DC
-
Gralla, J. D., and J. Collado-Vides. 1996. Organization and function of transcription regulatory elements, p. 1232-1245. In F. C. Neidhardt, R. Curtiss III, J. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. Reznikoff, M. Schaechter, H. E. Umbarger, and M. Riley (ed.), Cellular and molecular biology: Escherichia coli and Salmonella, 2nd ed. ASM Press, Washington, DC.
-
(1996)
Cellular and molecular biology: Escherichia coli and Salmonella
, pp. 1232-1245
-
-
Gralla, J.D.1
Collado-Vides, J.2
-
30
-
-
0029855802
-
The purB gene of Escherichia coli K-12 is located in an operon
-
Green, S. M., T. Malik, I. G. Giles, and W. T. Drabble. 1996. The purB gene of Escherichia coli K-12 is located in an operon. Microbiology 142:3219-3230.
-
(1996)
Microbiology
, vol.142
, pp. 3219-3230
-
-
Green, S.M.1
Malik, T.2
Giles, I.G.3
Drabble, W.T.4
-
31
-
-
32644439684
-
Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons
-
Harr, B., and C. Schlotterer. 2006. Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons. Nucleic Acids Res. 34:e8.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Harr, B.1
Schlotterer, C.2
-
32
-
-
33749462930
-
Gene expression analysis indicates extensive genotype-specific crosstalk between the conjugative F-plasmid and the E. coli chromosome
-
Harr, B., and C. Schlotterer. 2006. Gene expression analysis indicates extensive genotype-specific crosstalk between the conjugative F-plasmid and the E. coli chromosome. BMC Microbiol. 6:80.
-
(2006)
BMC Microbiol
, vol.6
, pp. 80
-
-
Harr, B.1
Schlotterer, C.2
-
33
-
-
0026436191
-
Escherichia coli purB gene: Cloning, nucleotide sequence, and regulation by purR
-
He, B., J. M. Smith, and H. Zalkin. 1992. Escherichia coli purB gene: cloning, nucleotide sequence, and regulation by purR. J. Bacteriol. 174:130-136.
-
(1992)
J. Bacteriol
, vol.174
, pp. 130-136
-
-
He, B.1
Smith, J.M.2
Zalkin, H.3
-
34
-
-
1242328740
-
Reconstruction of microbial transcriptional regulatory networks
-
Herrgard, M. J., M. W. Covert, and B. O. Palsson. 2004. Reconstruction of microbial transcriptional regulatory networks. Curr. Opin. Biotechnol. 15: 70-77.
-
(2004)
Curr. Opin. Biotechnol
, vol.15
, pp. 70-77
-
-
Herrgard, M.J.1
Covert, M.W.2
Palsson, B.O.3
-
35
-
-
24344447800
-
Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays
-
Herring, C. D., M. Raffaelle, T. E. Allen, E. I. Kanin, R. Landick, A. Z. Ansari, and B. O. Palsson. 2005. Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays. J. Bacteriol. 187:6166-6174.
-
(2005)
J. Bacteriol
, vol.187
, pp. 6166-6174
-
-
Herring, C.D.1
Raffaelle, M.2
Allen, T.E.3
Kanin, E.I.4
Landick, R.5
Ansari, A.Z.6
Palsson, B.O.7
-
36
-
-
33747357728
-
Co-evolution of transcription factors and their targets depends on mode of regulation
-
Hershberg, R., and H. Margalit. 2006. Co-evolution of transcription factors and their targets depends on mode of regulation. Genome Biol. 7:R62.
-
(2006)
Genome Biol
, vol.7
-
-
Hershberg, R.1
Margalit, H.2
-
37
-
-
0032826179
-
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
-
Hertz, G. Z., and G. D. Stormo. 1999. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 15:563-577.
-
(1999)
Bioinformatics
, vol.15
, pp. 563-577
-
-
Hertz, G.Z.1
Stormo, G.D.2
-
38
-
-
0025958130
-
The binding of cyclic AMP receptor protein to two lactose promoter sites is not cooperative in vitro
-
Hudson, J. M., and M. G. Fried. 1991. The binding of cyclic AMP receptor protein to two lactose promoter sites is not cooperative in vitro. J. Bacteriol. 173:59-66.
-
(1991)
J. Bacteriol
, vol.173
, pp. 59-66
-
-
Hudson, J.M.1
Fried, M.G.2
-
39
-
-
0141758085
-
70 promoters in Escherichia coli: Specific transcription in dense regions of overlapping promoter-like signals
-
70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals. J. Mol. Biol. 333:261-278.
-
(2003)
J. Mol. Biol
, vol.333
, pp. 261-278
-
-
Huerta, A.M.1
Collado-Vides, J.2
-
40
-
-
0005316553
-
GETools: Gene expression tool for analysis of transcriptome experiments in E. coli
-
Huerta, A. M., J. D. Glasner, R. M. Gutierrez-Rios, F. R. Blattner, and J. Collado-Vides. 2002. GETools: gene expression tool for analysis of transcriptome experiments in E. coli. Trends Genet. 18:217-218.
-
(2002)
Trends Genet
, vol.18
, pp. 217-218
-
-
Huerta, A.M.1
Glasner, J.D.2
Gutierrez-Rios, R.M.3
Blattner, F.R.4
Collado-Vides, J.5
-
41
-
-
0031811851
-
RegulonDB: A database on transcriptional regulation in Escherichia coli
-
Huerta, A. M., H. Salgado, D. Thieffry, and J. Collado-Vides. 1998. RegulonDB: a database on transcriptional regulation in Escherichia coli. Nucleic Acids Res. 26:55-59.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 55-59
-
-
Huerta, A.M.1
Salgado, H.2
Thieffry, D.3
Collado-Vides, J.4
-
42
-
-
42049108914
-
Protein abundance profiling of the Escherichia coli cytosol
-
Ishihama, Y., T. Schmidt, J. Rappsilber, M. Mann, F. U. Hartl, M. J. Kerner, and D. Frishman. 2008. Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics 9:102.
-
(2008)
BMC Genomics
, vol.9
, pp. 102
-
-
Ishihama, Y.1
Schmidt, T.2
Rappsilber, J.3
Mann, M.4
Hartl, F.U.5
Kerner, M.J.6
Frishman, D.7
-
43
-
-
54249116230
-
Genetic regulatory mechanisms in the synthesis of proteins
-
Jacob, F., and J. Monod. 1961. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3:318-356.
-
(1961)
J. Mol. Biol
, vol.3
, pp. 318-356
-
-
Jacob, F.1
Monod, J.2
-
44
-
-
18244386245
-
Nebulon: A system for the inference of functional relationships of gene products from the rearrangement of predicted operons
-
Janga, S. C., J. Collado-Vides, and G. Moreno-Hagelsieb. 2005. Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons. Nucleic Acids Res. 33:2521-2530.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 2521-2530
-
-
Janga, S.C.1
Collado-Vides, J.2
Moreno-Hagelsieb, G.3
-
45
-
-
2342553864
-
Temperature sensitivity caused by mutant release factor 1 is suppressed by mutations that affect 16S rRNA maturation
-
Kaczanowska, M., and M. Ryden-Aulin. 2004. Temperature sensitivity caused by mutant release factor 1 is suppressed by mutations that affect 16S rRNA maturation. J. Bacteriol. 186:3046-3055.
-
(2004)
J. Bacteriol
, vol.186
, pp. 3046-3055
-
-
Kaczanowska, M.1
Ryden-Aulin, M.2
-
46
-
-
13244289800
-
Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function
-
Kang, Y., K. D. Weber, Y. Qiu, P. J. Kiley, and F. R. Blattner. 2005. Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function. J. Bacteriol. 187:1135-1160.
-
(2005)
J. Bacteriol
, vol.187
, pp. 1135-1160
-
-
Kang, Y.1
Weber, K.D.2
Qiu, Y.3
Kiley, P.J.4
Blattner, F.R.5
-
47
-
-
0345743695
-
Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis
-
Kao, K. C., Y. L. Yang, R. Boscolo, C. Sabatti, V. Roychowdhury, and J. C. Liao. 2004. Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis. Proc. Natl. Acad. Sci.USA 101:641-646.
-
(2004)
Proc. Natl. Acad. Sci.USA
, vol.101
, pp. 641-646
-
-
Kao, K.C.1
Yang, Y.L.2
Boscolo, R.3
Sabatti, C.4
Roychowdhury, V.5
Liao, J.C.6
-
48
-
-
38049007503
-
Multidimensional annotation of the Escherichia coli K-12 genome
-
Karp, P. D., I. M. Keseler, A. Shearer, M. Latendresse, M. Krummenacker, S. M. Paley, I. Paulsen, J. Collado-Vides, S. Gama-Castro, M. Peralta-Gil, A. Santos-Zavaleta, M. I. Penaloza-Spinola, C. Bonavides-Martinez, and J. Ingraham. 2007. Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res. 35:7577-7590.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 7577-7590
-
-
Karp, P.D.1
Keseler, I.M.2
Shearer, A.3
Latendresse, M.4
Krummenacker, M.5
Paley, S.M.6
Paulsen, I.7
Collado-Vides, J.8
Gama-Castro, S.9
Peralta-Gil, M.10
Santos-Zavaleta, A.11
Penaloza-Spinola, M.I.12
Bonavides-Martinez, C.13
Ingraham, J.14
-
50
-
-
6044228192
-
S-dependent genes and identification of their promoter sequences
-
S-dependent genes and identification of their promoter sequences. J. Bacteriol. 186: 7186-7195.
-
(2004)
J. Bacteriol
, vol.186
, pp. 7186-7195
-
-
Lacour, S.1
Landini, P.2
-
51
-
-
41449117761
-
Predicted transcription factor binding sites as predictors of operons in Escherichia coli and Streptomyces coelicolor
-
Laing, E., K. Sidhu, and S. J. Hubbard. 2008. Predicted transcription factor binding sites as predictors of operons in Escherichia coli and Streptomyces coelicolor. BMC Genomics 9:79.
-
(2008)
BMC Genomics
, vol.9
, pp. 79
-
-
Laing, E.1
Sidhu, K.2
Hubbard, S.J.3
-
52
-
-
40449091818
-
The Rcs phosphorelay is a cell envelope stress response activated by peptidoglycan stress and contributes to intrinsic antibiotic resistance
-
Laubacher, M. E., and S. E. Ades. 2008. The Rcs phosphorelay is a cell envelope stress response activated by peptidoglycan stress and contributes to intrinsic antibiotic resistance. J. Bacteriol. 190:2065-2074.
-
(2008)
J. Bacteriol
, vol.190
, pp. 2065-2074
-
-
Laubacher, M.E.1
Ades, S.E.2
-
53
-
-
0033082849
-
Interactions between the Escherichia coli cAMP receptor protein and the C-terminal domain of the alpha subunit of RNA polymerase at class I promoters
-
Law, E. C., N. J. Savery, and S. J. Busby. 1999. Interactions between the Escherichia coli cAMP receptor protein and the C-terminal domain of the alpha subunit of RNA polymerase at class I promoters. Biochem. J. 337: 415-423.
-
(1999)
Biochem. J
, vol.337
, pp. 415-423
-
-
Law, E.C.1
Savery, N.J.2
Busby, S.J.3
-
54
-
-
14644420305
-
Selection-driven transcriptome polymorphism in Escherichia coli/Shigella species
-
Le Gall, T., P. Darlu, P. Escobar-Paramo, B. Picard, and E. Denamur. 2005. Selection-driven transcriptome polymorphism in Escherichia coli/Shigella species. Genome Res. 15:260-268.
-
(2005)
Genome Res
, vol.15
, pp. 260-268
-
-
Le Gall, T.1
Darlu, P.2
Escobar-Paramo, P.3
Picard, B.4
Denamur, E.5
-
55
-
-
0037015025
-
Identification of the binding sites of regulatory proteins in bacterial genomes
-
Li, H., V. Rhodius, C. Gross, and E. D. Siggia. 2002. Identification of the binding sites of regulatory proteins in bacterial genomes. Proc. Natl. Acad. Sci. USA 99:11772-11777.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 11772-11777
-
-
Li, H.1
Rhodius, V.2
Gross, C.3
Siggia, E.D.4
-
56
-
-
33746925662
-
70 promoters in Escherichia coli K-12
-
70 promoters in Escherichia coli K-12. J. Theor. Biol. 242:135-141.
-
(2006)
J. Theor. Biol
, vol.242
, pp. 135-141
-
-
Li, Q.Z.1
Lin, H.2
-
57
-
-
0032519978
-
Spacing requirements for interactions between the C-terminal domain of the alpha subunit of Escherichia coli RNA polymerase and the cAMP receptor protein
-
Lloyd, G. S., S. J. Busby, and N. J. Savery. 1998. Spacing requirements for interactions between the C-terminal domain of the alpha subunit of Escherichia coli RNA polymerase and the cAMP receptor protein. Biochem. J. 330:413-420.
-
(1998)
Biochem. J
, vol.330
, pp. 413-420
-
-
Lloyd, G.S.1
Busby, S.J.2
Savery, N.J.3
-
58
-
-
41749107942
-
Stochasticity and cell fate
-
Losick, R., and C. Desplan. 2008. Stochasticity and cell fate. Science 320: 65-68.
-
(2008)
Science
, vol.320
, pp. 65-68
-
-
Losick, R.1
Desplan, C.2
-
59
-
-
33746207758
-
Bacterial regulatory networks are extremely flexible in evolution
-
Lozada-Chavez, I., S. C. Janga, and J. Collado-Vides. 2006. Bacterial regulatory networks are extremely flexible in evolution. Nucleic Acids Res. 34:3434-3445.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 3434-3445
-
-
Lozada-Chavez, I.1
Janga, S.C.2
Collado-Vides, J.3
-
60
-
-
33646113855
-
Evolutionary dynamics of prokaryotic transcriptional regulatory networks
-
Madan Babu, M., S. A. Teichmann, and L. Aravind. 2006. Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J. Mol. Biol. 358:614-633.
-
(2006)
J. Mol. Biol
, vol.358
, pp. 614-633
-
-
Madan Babu, M.1
Teichmann, S.A.2
Aravind, L.3
-
61
-
-
51849124208
-
Delay-induced transient increase and heterogeneity in gene expression in negatively auto-regulated gene circuits
-
Maithreye, R., R. R. Sarkar, V. K. Parnaik, and S. Sinha. 2008. Delay-induced transient increase and heterogeneity in gene expression in negatively auto-regulated gene circuits. PLoS ONE 3:e2972.
-
(2008)
PLoS ONE
, vol.3
-
-
Maithreye, R.1
Sarkar, R.R.2
Parnaik, V.K.3
Sinha, S.4
-
62
-
-
33744821614
-
Transcript analysis reveals an extended regulon and the importance of protein-protein co-operativity for the Escherichia coli methionine repressor
-
Marincs, F., I. W. Manfield, J. A. Stead, K. J. McDowall, and P. G. Stockley. 2006. Transcript analysis reveals an extended regulon and the importance of protein-protein co-operativity for the Escherichia coli methionine repressor. Biochem. J. 396:227-234.
-
(2006)
Biochem. J
, vol.396
, pp. 227-234
-
-
Marincs, F.1
Manfield, I.W.2
Stead, J.A.3
McDowall, K.J.4
Stockley, P.G.5
-
63
-
-
40649089205
-
Dissecting the logical types of network control in gene expression profiles
-
Marr, C., M. Geertz, M. T. Hutt, and G. Muskhelishvili. 2008. Dissecting the logical types of network control in gene expression profiles. BMC Syst. Biol. 2:18.
-
(2008)
BMC Syst. Biol
, vol.2
, pp. 18
-
-
Marr, C.1
Geertz, M.2
Hutt, M.T.3
Muskhelishvili, G.4
-
64
-
-
33746606073
-
Outer membrane vesicle production by Escherichia coli is independent of membrane instability
-
McBroom, A. J., A. P. Johnson, S. Vemulapalli, and M. J. Kuehn. 2006. Outer membrane vesicle production by Escherichia coli is independent of membrane instability. J. Bacteriol. 188:5385-5392.
-
(2006)
J. Bacteriol
, vol.188
, pp. 5385-5392
-
-
McBroom, A.J.1
Johnson, A.P.2
Vemulapalli, S.3
Kuehn, M.J.4
-
65
-
-
73649152457
-
Allosteric proteins and cellular control systems
-
Monod, J., J. P. Changeux, and F. Jacob. 1963. Allosteric proteins and cellular control systems. J. Mol. Biol. 6:306-329.
-
(1963)
J. Mol. Biol
, vol.6
, pp. 306-329
-
-
Monod, J.1
Changeux, J.P.2
Jacob, F.3
-
66
-
-
0001291140
-
A powerful non-homology method for the prediction of operons in prokaryotes
-
Moreno-Hagelsieb, G., and J. Collado-Vides. 2002. A powerful non-homology method for the prediction of operons in prokaryotes. Bioinformatics 18(Suppl. 1):S329-S336.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Moreno-Hagelsieb, G.1
Collado-Vides, J.2
-
67
-
-
0344710723
-
NifA-dependent in vivo protection demonstrates that the upstream activator sequence of nif promoters is a protein binding site
-
Morett, E., and M. Buck. 1988. NifA-dependent in vivo protection demonstrates that the upstream activator sequence of nif promoters is a protein binding site. Proc. Natl. Acad. Sci. USA 85:9401-9405.
-
(1988)
Proc. Natl. Acad. Sci. USA
, vol.85
, pp. 9401-9405
-
-
Morett, E.1
Buck, M.2
-
68
-
-
14044254746
-
Textpresso: An ontology-based information retrieval and extraction system for biological literature
-
Muller, H. M., E. E. Kenny, and P. W. Sternberg. 2004. Textpresso: an ontology-based information retrieval and extraction system for biological literature. PLoS Biol. 2:e309.
-
(2004)
PLoS Biol
, vol.2
-
-
Muller, H.M.1
Kenny, E.E.2
Sternberg, P.W.3
-
69
-
-
27944453600
-
Virtual Footprint and PRODORIC: An integrative framework for regulon prediction in prokaryotes
-
Munch, R., K. Hiller, A. Grote, M. Scheer, J. Klein, M. Schobert, and D. Jahn. 2005. Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. Bioinformatics 21:4187-4189.
-
(2005)
Bioinformatics
, vol.21
, pp. 4187-4189
-
-
Munch, R.1
Hiller, K.2
Grote, A.3
Scheer, M.4
Klein, J.5
Schobert, M.6
Jahn, D.7
-
70
-
-
33847674425
-
Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli
-
Okuda, S., S. Kawashima, K. Kobayashi, N. Ogasawara, M. Kanehisa, and S. Goto. 2007. Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli. BMC Genomics 8:48.
-
(2007)
BMC Genomics
, vol.8
, pp. 48
-
-
Okuda, S.1
Kawashima, S.2
Kobayashi, K.3
Ogasawara, N.4
Kanehisa, M.5
Goto, S.6
-
71
-
-
0033621407
-
DNA distortion mechanism for transcriptional activation by ZntR, a Zn(II)-responsive MerR homologue in Escherichia coli
-
Outten, C. E., F. W. Outten, and T. V. O'Halloran. 1999. DNA distortion mechanism for transcriptional activation by ZntR, a Zn(II)-responsive MerR homologue in Escherichia coli. J. Biol. Chem. 274:37517- 37524.
-
(1999)
J. Biol. Chem
, vol.274
, pp. 37517-37524
-
-
Outten, C.E.1
Outten, F.W.2
O'Halloran, T.V.3
-
72
-
-
33846073825
-
-
Perez, A. G., V. E. Angarica, A. T. Vasconcelos, and J. Collado-Vides. 2007. Tractor-DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes. Nucleic Acids Res. 35:D132-D136.
-
Perez, A. G., V. E. Angarica, A. T. Vasconcelos, and J. Collado-Vides. 2007. Tractor-DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes. Nucleic Acids Res. 35:D132-D136.
-
-
-
-
73
-
-
0343963178
-
The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12
-
Perez-Rueda, E., and J. Collado-Vides. 2000. The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. Nucleic Acids Res. 28:1838-1847.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 1838-1847
-
-
Perez-Rueda, E.1
Collado-Vides, J.2
-
74
-
-
0024287079
-
Binding of the cyclic AMP receptor protein of Escherichia coli to RNA polymerase
-
Pinkney, M., and J. G. Hoggett. 1988. Binding of the cyclic AMP receptor protein of Escherichia coli to RNA polymerase. Biochem. J. 250:897-902.
-
(1988)
Biochem. J
, vol.250
, pp. 897-902
-
-
Pinkney, M.1
Hoggett, J.G.2
-
75
-
-
0343597687
-
Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter
-
Pribnow, D. 1975. Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter. Proc. Natl. Acad. Sci. USA 72:784-788.
-
(1975)
Proc. Natl. Acad. Sci. USA
, vol.72
, pp. 784-788
-
-
Pribnow, D.1
-
76
-
-
40149098889
-
Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli
-
Price, M. N., P. S. Dehal, and A. P. Arkin. 2008. Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli. Genome Biol. 9:R4.
-
(2008)
Genome Biol
, vol.9
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
77
-
-
34848865681
-
Orthologous transcription factors in bacteria have different functions and regulate different genes
-
Price, M. N., P. S. Dehal, and A. P. Arkin. 2007. Orthologous transcription factors in bacteria have different functions and regulate different genes. PLoS Comput. Biol. 3:1739-1750.
-
(2007)
PLoS Comput. Biol
, vol.3
, pp. 1739-1750
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
78
-
-
0036180002
-
The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons
-
Rajewsky, N., N. D. Socci, M. Zapotocky, and E. D. Siggia. 2002. The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons. Genome Res. 12:298-308.
-
(2002)
Genome Res
, vol.12
, pp. 298-308
-
-
Rajewsky, N.1
Socci, N.D.2
Zapotocky, M.3
Siggia, E.D.4
-
79
-
-
0037199968
-
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
-
80
-
-
0037406843
-
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
-
81
-
-
34548499877
-
Automatic reconstruction of a bacterial regulatory network using Natural Language Processing
-
Rodriguez-Penagos, C., H. Salgado, I. Martinez-Flores, and J. Collado-Vides. 2007. Automatic reconstruction of a bacterial regulatory network using Natural Language Processing. BMC Bioinform. 8:293.
-
(2007)
BMC Bioinform
, vol.8
, pp. 293
-
-
Rodriguez-Penagos, C.1
Salgado, H.2
Martinez-Flores, I.3
Collado-Vides, J.4
-
82
-
-
0036798984
-
Congruent evolution of different classes of non-coding DNA in prokaryotic genomes
-
Rogozin, I. B., K. S. Makarova, D. A. Natale, A. N. Spiridonov, R. L. Tatusov, Y. I. Wolf, J. Yin, and E. V. Koonin. 2002. Congruent evolution of different classes of non-coding DNA in prokaryotic genomes. Nucleic Acids Res. 30:4264-4271.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 4264-4271
-
-
Rogozin, I.B.1
Makarova, K.S.2
Natale, D.A.3
Spiridonov, A.N.4
Tatusov, R.L.5
Wolf, Y.I.6
Yin, J.7
Koonin, E.V.8
-
83
-
-
0031691355
-
Escherichia coli promoters with UP elements of different strengths: Modular structure of bacterial promoters
-
Ross, W., S. E. Aiyar, J. Salomon, and R. L. Gourse. 1998. Escherichia coli promoters with UP elements of different strengths: modular structure of bacterial promoters. J. Bacteriol. 180:5375-5383.
-
(1998)
J. Bacteriol
, vol.180
, pp. 5375-5383
-
-
Ross, W.1
Aiyar, S.E.2
Salomon, J.3
Gourse, R.L.4
-
84
-
-
0034612277
-
Operons in Escherichia coli: Genomic analyses and predictions
-
Salgado, H., G. Moreno-Hagelsieb, T. F. Smith, and J. Collado-Vides. 2000. Operons in Escherichia coli: genomic analyses and predictions. Proc. Natl. Acad. Sci. USA 97:6652-6657.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 6652-6657
-
-
Salgado, H.1
Moreno-Hagelsieb, G.2
Smith, T.F.3
Collado-Vides, J.4
-
85
-
-
33645757123
-
Low degree metabolites explain essential reactions and enhance modularity in biological networks
-
Samal, A., S. Singh, V. Giri, S. Krishna, N. Raghuram, and S. Jain. 2006. Low degree metabolites explain essential reactions and enhance modularity in biological networks. BMC Bioinform. 7:118.
-
(2006)
BMC Bioinform
, vol.7
, pp. 118
-
-
Samal, A.1
Singh, S.2
Giri, V.3
Krishna, S.4
Raghuram, N.5
Jain, S.6
-
86
-
-
33745022557
-
A classification based framework for quantitative description of large-scale microarray data
-
Sangurdekar, D. P., F. Srienc, and A. B. Khodursky. 2006. A classification based framework for quantitative description of large-scale microarray data. Genome Biol. 7:R32.
-
(2006)
Genome Biol
, vol.7
-
-
Sangurdekar, D.P.1
Srienc, F.2
Khodursky, A.B.3
-
87
-
-
0008829420
-
Introduction
-
F. C. Neidhardt, J. Ingraham, K. B. Low, B. Magasanik, M. Schaechter, and H. E. Umbarger ed, 1st ed. ASM Press, Washington, DC
-
Schaechter, M., and F. Neidhardt. 1987. Introduction, p. 1-2. In F. C. Neidhardt, J. Ingraham, K. B. Low, B. Magasanik, M. Schaechter, and H. E. Umbarger (ed.), Cellular and molecular biology: Escherichia coli and Salmonella, 1st ed. ASM Press, Washington, DC.
-
(1987)
Cellular and molecular biology: Escherichia coli and Salmonella
, pp. 1-2
-
-
Schaechter, M.1
Neidhardt, F.2
-
88
-
-
0037315564
-
Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation
-
Selinger, D. W., R. M. Saxena, K. J. Cheung, G. M. Church, and C. Rosenow. 2003. Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. Genome Res. 13:216-223.
-
(2003)
Genome Res
, vol.13
, pp. 216-223
-
-
Selinger, D.W.1
Saxena, R.M.2
Cheung, K.J.3
Church, G.M.4
Rosenow, C.5
-
89
-
-
55849132180
-
-
An assessment of the role of DNA adenine methyltransferase on gene expression regulation in, PLoS ONE
-
Seshasayee, A. S. 2007. An assessment of the role of DNA adenine methyltransferase on gene expression regulation in E. coli. PLoS ONE 2:e273.
-
(2007)
E. coli
, vol.2
-
-
Seshasayee, A.S.1
-
90
-
-
0036578795
-
Network motifs in the transcriptional regulation network of Escherichia coli
-
Shen-Orr, S. S., R. Milo, S. Mangan, and U. Alon. 2002. Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 31: 64-68.
-
(2002)
Nat. Genet
, vol.31
, pp. 64-68
-
-
Shen-Orr, S.S.1
Milo, R.2
Mangan, S.3
Alon, U.4
-
91
-
-
45549084611
-
Large-scale computational and statistical analyses of high transcription potentialities in 32 prokaryotic genomes
-
Sinoquet, C., S. Demey, and F. Braun. 2008. Large-scale computational and statistical analyses of high transcription potentialities in 32 prokaryotic genomes. Nucleic Acids Res. 36:3332-3340.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 3332-3340
-
-
Sinoquet, C.1
Demey, S.2
Braun, F.3
-
92
-
-
0041335300
-
Physiological studies of Escherichia coli strain MG1655: Growth defects and apparent cross-regulation of gene expression
-
Soupene, E., W. C. van Heeswijk, J. Plumbridge, V. Stewart, D. Bertenthal, H. Lee, G. Prasad, O. Paliy, P. Charernnoppakul, and S. Kustu. 2003. Physiological studies of Escherichia coli strain MG1655: growth defects and apparent cross-regulation of gene expression. J. Bacteriol. 185:5611-5626.
-
(2003)
J. Bacteriol
, vol.185
, pp. 5611-5626
-
-
Soupene, E.1
van Heeswijk, W.C.2
Plumbridge, J.3
Stewart, V.4
Bertenthal, D.5
Lee, H.6
Prasad, G.7
Paliy, O.8
Charernnoppakul, P.9
Kustu, S.10
-
93
-
-
0034746567
-
CueR (YbbI) of Escherichia coli is a MerR family regulator controlling expression of the copper exporter CopA
-
Stoyanov, J. V., J. L. Hobman, and N. L. Brown. 2001. CueR (YbbI) of Escherichia coli is a MerR family regulator controlling expression of the copper exporter CopA. Mol. Microbiol. 39:502-511.
-
(2001)
Mol. Microbiol
, vol.39
, pp. 502-511
-
-
Stoyanov, J.V.1
Hobman, J.L.2
Brown, N.L.3
-
94
-
-
28944444766
-
Representations of molecular pathways: An evaluation of SBML, PSI MI and BioPAX
-
Stromback, L., and P. Lambrix. 2005. Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX. Bioinformatics 21: 4401-4407.
-
(2005)
Bioinformatics
, vol.21
, pp. 4401-4407
-
-
Stromback, L.1
Lambrix, P.2
-
95
-
-
0347824672
-
Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: A combined computational approach
-
Strong, M., P. Mallick, M. Pellegrini, M. J. Thompson, and D. Eisenberg. 2003. Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach. Genome Biol. 4:R59.
-
(2003)
Genome Biol
, vol.4
-
-
Strong, M.1
Mallick, P.2
Pellegrini, M.3
Thompson, M.J.4
Eisenberg, D.5
-
96
-
-
0035051602
-
A comparative genomics approach to prediction of new members of regulons
-
Tan, K., G. Moreno-Hagelsieb, J. Collado-Vides, and G. D. Stormo. 2001. A comparative genomics approach to prediction of new members of regulons. Genome Res. 11:566-584.
-
(2001)
Genome Res
, vol.11
, pp. 566-584
-
-
Tan, K.1
Moreno-Hagelsieb, G.2
Collado-Vides, J.3
Stormo, G.D.4
-
97
-
-
2442537233
-
Gene regulatory network growth by duplication
-
Teichmann, S. A., and M. M. Babu. 2004. Gene regulatory network growth by duplication. Nat. Genet. 36:492-496.
-
(2004)
Nat. Genet
, vol.36
, pp. 492-496
-
-
Teichmann, S.A.1
Babu, M.M.2
-
98
-
-
0031827572
-
Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12
-
Thieffry, D., H. Salgado, A. M. Huerta, and J. Collado-Vides. 1998. Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12. Bioinformatics 14:391-400.
-
(1998)
Bioinformatics
, vol.14
, pp. 391-400
-
-
Thieffry, D.1
Salgado, H.2
Huerta, A.M.3
Collado-Vides, J.4
-
99
-
-
48449090922
-
RSAT: Regulatory sequence analysis tools
-
Thomas-Chollier, M., O. Sand, J. V. Turatsinze, R. Janky, M. Defrance, E. Vervisch, S. Brohee, and J. van Helden. 2008. RSAT: regulatory sequence analysis tools. Nucleic Acids Res. 36:W119-W127.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Thomas-Chollier, M.1
Sand, O.2
Turatsinze, J.V.3
Janky, R.4
Defrance, M.5
Vervisch, E.6
Brohee, S.7
van Helden, J.8
-
100
-
-
32144435583
-
An approach for clustering gene expression data with error information
-
Tjaden, B. 2006. An approach for clustering gene expression data with error information. BMC Bioinform. 7:17.
-
(2006)
BMC Bioinform
, vol.7
, pp. 17
-
-
Tjaden, B.1
-
101
-
-
0036713509
-
Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays
-
Tjaden, B., R. M. Saxena, S. Stolyar, D. R. Haynor, E. Kolker, and C. Rosenow. 2002. Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays. Nucleic Acids Res. 30:3732-3738.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 3732-3738
-
-
Tjaden, B.1
Saxena, R.M.2
Stolyar, S.3
Haynor, D.R.4
Kolker, E.5
Rosenow, C.6
-
102
-
-
0036083835
-
AraC-XylS database: A family of positive transcriptional regulators in bacteria
-
Tobes, R., and J. L. Ramos. 2002. AraC-XylS database: a family of positive transcriptional regulators in bacteria. Nucleic Acids Res. 30:318-321.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 318-321
-
-
Tobes, R.1
Ramos, J.L.2
-
103
-
-
33846674939
-
Operon prediction in Pyrococcus furiosus
-
Tran, T. T., P. Dam, Z. Su, F. L. Poole II, M. W. Adams, G. T. Zhou, and Y. Xu. 2007. Operon prediction in Pyrococcus furiosus. Nucleic Acids Res. 35:11-20.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 11-20
-
-
Tran, T.T.1
Dam, P.2
Su, Z.3
Poole II, F.L.4
Adams, M.W.5
Zhou, G.T.6
Xu, Y.7
-
104
-
-
52749097035
-
Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules
-
Turatsinze, J. V., M. Thomas-Chollier, M. Defrance, and J. van Helden. 2008. Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules. Nat. Protoc. 3:1578-1588.
-
(2008)
Nat. Protoc
, vol.3
, pp. 1578-1588
-
-
Turatsinze, J.V.1
Thomas-Chollier, M.2
Defrance, M.3
van Helden, J.4
-
105
-
-
0041620271
-
Regulatory sequence analysis tools
-
van Helden, J. 2003. Regulatory sequence analysis tools. Nucleic Acids Res. 31:3593-3596.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3593-3596
-
-
van Helden, J.1
-
106
-
-
44949236016
-
Inferring the role of transcription factors in regulatory networks
-
Veber, P., C. Guziolowski, M. Le Borgne, O. Radulescu, and A. Siegel. 2008. Inferring the role of transcription factors in regulatory networks. BMC Bioinform. 9:228.
-
(2008)
BMC Bioinform
, vol.9
, pp. 228
-
-
Veber, P.1
Guziolowski, C.2
Le Borgne, M.3
Radulescu, O.4
Siegel, A.5
-
107
-
-
46949104276
-
Predicting transcriptional regulatory interactions with artificial neural networks applied to E. coli multidrug resistance efflux pumps
-
Veiga, D. F., F. F. Vicente, M. F. Nicolas, and A. T. Vasconcelos. 2008. Predicting transcriptional regulatory interactions with artificial neural networks applied to E. coli multidrug resistance efflux pumps. BMC Microbiol. 8:101.
-
(2008)
BMC Microbiol
, vol.8
, pp. 101
-
-
Veiga, D.F.1
Vicente, F.F.2
Nicolas, M.F.3
Vasconcelos, A.T.4
-
108
-
-
33947170439
-
The sugar phosphotransferase system of Vibrio fischeri inhibits both motility and bioluminescence
-
Visick, K. L., T. M. O'Shea, A. H. Klein, K. Geszvain, and A. J. Wolfe. 2007. The sugar phosphotransferase system of Vibrio fischeri inhibits both motility and bioluminescence. J. Bacteriol. 189:2571-2574.
-
(2007)
J. Bacteriol
, vol.189
, pp. 2571-2574
-
-
Visick, K.L.1
O'Shea, T.M.2
Klein, A.H.3
Geszvain, K.4
Wolfe, A.J.5
-
109
-
-
27644580858
-
Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites
-
Wade, J. T., N. B. Reppas, G. M. Church, and K. Struhl. 2005. Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites. Genes Dev. 19:2619-2630.
-
(2005)
Genes Dev
, vol.19
, pp. 2619-2630
-
-
Wade, J.T.1
Reppas, N.B.2
Church, G.M.3
Struhl, K.4
-
111
-
-
0036777602
-
Profiling early osmostress-dependent gene expression in Escherichia coli using DNA microarrays
-
Weber, A., and K. Jung. 2002. Profiling early osmostress-dependent gene expression in Escherichia coli using DNA microarrays. J. Bacteriol. 184: 5502-5507.
-
(2002)
J. Bacteriol
, vol.184
, pp. 5502-5507
-
-
Weber, A.1
Jung, K.2
-
113
-
-
33746348907
-
Operon information improves gene expression estimation for cDNA microarrays
-
Xiao, G., B. Martinez-Vaz, W. Pan, and A. B. Khodursky. 2006. Operon information improves gene expression estimation for cDNA microarrays. BMC Genomics 7:87.
-
(2006)
BMC Genomics
, vol.7
, pp. 87
-
-
Xiao, G.1
Martinez-Vaz, B.2
Pan, W.3
Khodursky, A.B.4
-
114
-
-
33947235074
-
-
Yooseph, S., G. Sutton, D. B. Rusch, A. L. Halpern, S. J. Williamson, K. Remington, J. A. Eisen, K. B. Heidelberg, G. Manning, W. Li, L. Jaroszewski, P. Cieplak, C. S. Miller, H. Li, S. T. Mashiyama, M. P. Joachimiak, C. van Belle, J. M. Chandonia, D. A. Soergel, Y. Zhai, K. Natarajan, S. Lee, B. J. Raphael, V. Bafna, R. Friedman, S. E. Brenner, A. Godzik, D. Eisenberg, J. E. Dixon, S. S. Taylor, R. L. Strausberg, M. Frazier, and J. C. Venter. 2007. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol. 5:e16.
-
Yooseph, S., G. Sutton, D. B. Rusch, A. L. Halpern, S. J. Williamson, K. Remington, J. A. Eisen, K. B. Heidelberg, G. Manning, W. Li, L. Jaroszewski, P. Cieplak, C. S. Miller, H. Li, S. T. Mashiyama, M. P. Joachimiak, C. van Belle, J. M. Chandonia, D. A. Soergel, Y. Zhai, K. Natarajan, S. Lee, B. J. Raphael, V. Bafna, R. Friedman, S. E. Brenner, A. Godzik, D. Eisenberg, J. E. Dixon, S. S. Taylor, R. L. Strausberg, M. Frazier, and J. C. Venter. 2007. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol. 5:e16.
-
-
-
-
115
-
-
7444245668
-
Identification of the CRP regulon using in vitro and in vivo transcriptional profiling
-
Zheng, D., C. Constantinidou, J. L. Hobman, and S. D. Minchin. 2004. Identification of the CRP regulon using in vitro and in vivo transcriptional profiling. Nucleic Acids Res. 32:5874-5893.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 5874-5893
-
-
Zheng, D.1
Constantinidou, C.2
Hobman, J.L.3
Minchin, S.D.4
-
116
-
-
0028109558
-
Characterization of the activating region of Escherichia coli catabolite gene activator protein (CAP). II. Role at class I and class II CAP-dependent promoters
-
Zhou, Y., T. J. Merkel, and R. H. Ebright. 1994. Characterization of the activating region of Escherichia coli catabolite gene activator protein (CAP). II. Role at class I and class II CAP-dependent promoters. J. Mol. Biol. 243:603-610.
-
(1994)
J. Mol. Biol
, vol.243
, pp. 603-610
-
-
Zhou, Y.1
Merkel, T.J.2
Ebright, R.H.3
|