-
1
-
-
34249079154
-
Network motifs: theory and experimental approaches
-
Alon U. Network motifs: theory and experimental approaches. Nat. Rev. Genet. 8 (2007) 450-461
-
(2007)
Nat. Rev. Genet.
, vol.8
, pp. 450-461
-
-
Alon, U.1
-
2
-
-
15944379232
-
The many faces of the helix-turn-helix domain: transcription regulation and beyond
-
Aravind L., Anantharaman V., Balaji S., Babu M.M., and Iyer L.M. The many faces of the helix-turn-helix domain: transcription regulation and beyond. FEMS Microbiol. Rev. 29 (2005) 231-262
-
(2005)
FEMS Microbiol. Rev.
, vol.29
, pp. 231-262
-
-
Aravind, L.1
Anantharaman, V.2
Balaji, S.3
Babu, M.M.4
Iyer, L.M.5
-
3
-
-
0038241770
-
Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli
-
Atkinson M.R., Savageau M.A., Myers J.T., and Ninfa A.J. Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 113 (2003) 597-607
-
(2003)
Cell
, vol.113
, pp. 597-607
-
-
Atkinson, M.R.1
Savageau, M.A.2
Myers, J.T.3
Ninfa, A.J.4
-
4
-
-
20344379457
-
Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli
-
Balazsi G., Barabasi A.L., and Oltvai Z.N. Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 102 (2005) 7841-7846
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 7841-7846
-
-
Balazsi, G.1
Barabasi, A.L.2
Oltvai, Z.N.3
-
5
-
-
0742305866
-
Network biology: understanding the cell's functional organization
-
Barabasi A.L., and Oltvai Z.N. Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 5 (2004) 101-113
-
(2004)
Nat. Rev. Genet.
, vol.5
, pp. 101-113
-
-
Barabasi, A.L.1
Oltvai, Z.N.2
-
6
-
-
0034212551
-
Engineering stability in gene networks by autoregulation
-
Becskei A., and Serrano L. Engineering stability in gene networks by autoregulation. Nature 405 (2000) 590-593
-
(2000)
Nature
, vol.405
, pp. 590-593
-
-
Becskei, A.1
Serrano, L.2
-
7
-
-
0037046560
-
Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)
-
Bentley S.D., Chater K.F., Cerdeno-Tarraga A.M., Challis G.L., Thomson N.R., James K.D., Harris D.E., Quail M.A., Kieser H., Harper D., et al. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417 (2002) 141-147
-
(2002)
Nature
, vol.417
, pp. 141-147
-
-
Bentley, S.D.1
Chater, K.F.2
Cerdeno-Tarraga, A.M.3
Challis, G.L.4
Thomson, N.R.5
James, K.D.6
Harris, D.E.7
Quail, M.A.8
Kieser, H.9
Harper, D.10
-
8
-
-
1842591130
-
The regulation of bacterial transcription initiation
-
Browning D.F., and Busby S.J. The regulation of bacterial transcription initiation. Nat. Rev. Microbiol. 2 (2004) 57-65
-
(2004)
Nat. Rev. Microbiol.
, vol.2
, pp. 57-65
-
-
Browning, D.F.1
Busby, S.J.2
-
9
-
-
0033912262
-
The bacterial enhancer-dependent sigma(54) (sigma(N)) transcription factor
-
Buck M., Gallegos M.T., Studholme D.J., Guo Y., and Gralla J.D. The bacterial enhancer-dependent sigma(54) (sigma(N)) transcription factor. J. Bacteriol. 182 (2000) 4129-4136
-
(2000)
J. Bacteriol.
, vol.182
, pp. 4129-4136
-
-
Buck, M.1
Gallegos, M.T.2
Studholme, D.J.3
Guo, Y.4
Gralla, J.D.5
-
10
-
-
0742333984
-
A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli
-
Bulyk M.L., McGuire A.M., Masuda N., and Church G.M. A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli. Genome Res. 14 (2004) 201-208
-
(2004)
Genome Res.
, vol.14
, pp. 201-208
-
-
Bulyk, M.L.1
McGuire, A.M.2
Masuda, N.3
Church, G.M.4
-
11
-
-
33646877664
-
Modular approaches to expanding the functions of living matter
-
Chin J.W. Modular approaches to expanding the functions of living matter. Nat. Chem. Biol. 2 (2006) 304-311
-
(2006)
Nat. Chem. Biol.
, vol.2
, pp. 304-311
-
-
Chin, J.W.1
-
12
-
-
33748767376
-
Rho-dependent terminators and transcription termination
-
Ciampi M.S. Rho-dependent terminators and transcription termination. Microbiology 152 (2006) 2515-2528
-
(2006)
Microbiology
, vol.152
, pp. 2515-2528
-
-
Ciampi, M.S.1
-
13
-
-
0035931926
-
Massive gene decay in the leprosy bacillus
-
Cole S.T., Eiglmeier K., Parkhill J., James K.D., Thomson N.R., Wheeler P.R., Honore N., Garnier T., Churcher C., Harris D., et al. Massive gene decay in the leprosy bacillus. Nature 409 (2001) 1007-1011
-
(2001)
Nature
, vol.409
, pp. 1007-1011
-
-
Cole, S.T.1
Eiglmeier, K.2
Parkhill, J.3
James, K.D.4
Thomson, N.R.5
Wheeler, P.R.6
Honore, N.7
Garnier, T.8
Churcher, C.9
Harris, D.10
-
14
-
-
0025663103
-
Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures
-
d'Aubenton Carafa Y., Brody E., and Thermes C. Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures. J. Mol. Biol. 216 (1990) 835-858
-
(1990)
J. Mol. Biol.
, vol.216
, pp. 835-858
-
-
d'Aubenton Carafa, Y.1
Brody, E.2
Thermes, C.3
-
15
-
-
55449129670
-
Prediction of transcriptional terminators in Bacillus subtilis and related species
-
de Hoon M.J., Makita Y., Nakai K., and Miyano S. Prediction of transcriptional terminators in Bacillus subtilis and related species. PLoS Comput. Biol. 1 (2005) e25
-
(2005)
PLoS Comput. Biol.
, vol.1
-
-
de Hoon, M.J.1
Makita, Y.2
Nakai, K.3
Miyano, S.4
-
16
-
-
1542741327
-
Molecular biology. When a part is as good as the whole
-
deHaseth P.L., and Nilsen T.W. Molecular biology. When a part is as good as the whole. Science 303 (2004) 1307-1308
-
(2004)
Science
, vol.303
, pp. 1307-1308
-
-
deHaseth, P.L.1
Nilsen, T.W.2
-
17
-
-
2942552376
-
Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network
-
Dobrin R., Beg Q.K., Barabasi A.L., and Oltvai Z.N. Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network. BMC Bioinformatics 5 (2004) 10
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 10
-
-
Dobrin, R.1
Beg, Q.K.2
Barabasi, A.L.3
Oltvai, Z.N.4
-
18
-
-
0034604382
-
Prediction of transcription terminators in bacterial genomes
-
Ermolaeva M.D., Khalak H.G., White O., Smith H.O., and Salzberg S.L. Prediction of transcription terminators in bacterial genomes. J. Mol. Biol. 301 (2000) 27-33
-
(2000)
J. Mol. Biol.
, vol.301
, pp. 27-33
-
-
Ermolaeva, M.D.1
Khalak, H.G.2
White, O.3
Smith, H.O.4
Salzberg, S.L.5
-
20
-
-
27344438594
-
Comparative studies of transcriptional regulation mechanisms in a group of eight gamma-proteobacterial genomes
-
Espinosa V., Gonzalez A.D., Vasconcelos A.T., Huerta A.M., and Collado-Vides J. Comparative studies of transcriptional regulation mechanisms in a group of eight gamma-proteobacterial genomes. J. Mol. Biol. 354 (2005) 184-199
-
(2005)
J. Mol. Biol.
, vol.354
, pp. 184-199
-
-
Espinosa, V.1
Gonzalez, A.D.2
Vasconcelos, A.T.3
Huerta, A.M.4
Collado-Vides, J.5
-
21
-
-
33846400424
-
Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
-
Faith J.J., Hayete B., Thaden J.T., Mogno I., Wierzbowski J., Cottarel G., Kasif S., Collins J.J., and Gardner T.S. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol. 5 (2007) 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
-
22
-
-
0000661051
-
Organization and function of transcription regulatory elements
-
Neidhardt F.C., Curtis III R., Ingraham J., Lin E.C.C., Low K.B., Magasanik B., Reznikoff W., Schaechter M., Umbarger H.E., and Riley M. (Eds), American Society for Microbiology, Washington, DC
-
Gralla J.D., and Collado-Vides J. Organization and function of transcription regulatory elements. In: Neidhardt F.C., Curtis III R., Ingraham J., Lin E.C.C., Low K.B., Magasanik B., Reznikoff W., Schaechter M., Umbarger H.E., and Riley M. (Eds). Cellular and molecular biology: Escherichia coli and Salmonella (1996), American Society for Microbiology, Washington, DC 1232-1245
-
(1996)
Cellular and molecular biology: Escherichia coli and Salmonella
, pp. 1232-1245
-
-
Gralla, J.D.1
Collado-Vides, J.2
-
23
-
-
0242692671
-
Multiple sigma subunits and the partitioning of bacterial transcription space
-
Gruber T.M., and Gross C.A. Multiple sigma subunits and the partitioning of bacterial transcription space. Annu. Rev. Microbiol. 57 (2003) 441-466
-
(2003)
Annu. Rev. Microbiol.
, vol.57
, pp. 441-466
-
-
Gruber, T.M.1
Gross, C.A.2
-
24
-
-
0036578654
-
Topological and causal structure of the yeast transcriptional regulatory network
-
Guelzim N., Bottani S., Bourgine P., and Kepes F. Topological and causal structure of the yeast transcriptional regulatory network. Nat. Genet. 31 (2002) 60-63
-
(2002)
Nat. Genet.
, vol.31
, pp. 60-63
-
-
Guelzim, N.1
Bottani, S.2
Bourgine, P.3
Kepes, F.4
-
25
-
-
0242407438
-
Regulatory network of Escherichia coli: consistency between literature knowledge and microarray profiles
-
Gutierrez-Rios R.M., Rosenblueth D.A., Loza J.A., Huerta A.M., Glasner J.D., Blattner F.R., and Collado-Vides J. Regulatory network of Escherichia coli: consistency between literature knowledge and microarray profiles. Genome Res. 13 (2003) 2435-2443
-
(2003)
Genome Res.
, vol.13
, pp. 2435-2443
-
-
Gutierrez-Rios, R.M.1
Rosenblueth, D.A.2
Loza, J.A.3
Huerta, A.M.4
Glasner, J.D.5
Blattner, F.R.6
Collado-Vides, J.7
-
26
-
-
0035985580
-
The extracytoplasmic function (ECF) sigma factors
-
Helmann J.D. The extracytoplasmic function (ECF) sigma factors. Adv. Microb. Physiol. 46 (2002) 47-110
-
(2002)
Adv. Microb. Physiol.
, vol.46
, pp. 47-110
-
-
Helmann, J.D.1
-
27
-
-
33747357728
-
Co-evolution of transcription factors and their targets depends on mode of regulation
-
Hershberg R., and Margalit H. Co-evolution of transcription factors and their targets depends on mode of regulation. Genome Biol. 7 (2006) R62
-
(2006)
Genome Biol.
, vol.7
-
-
Hershberg, R.1
Margalit, H.2
-
28
-
-
0141758085
-
Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals
-
Huerta A.M., and Collado-Vides J. Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals. J. Mol. Biol. 333 (2003) 261-278
-
(2003)
J. Mol. Biol.
, vol.333
, pp. 261-278
-
-
Huerta, A.M.1
Collado-Vides, J.2
-
29
-
-
33751369021
-
Selection for unequal densities of sigma70 promoter-like signals in different regions of large bacterial genomes
-
Huerta A.M., Francino M.P., Morett E., and Collado-Vides J. Selection for unequal densities of sigma70 promoter-like signals in different regions of large bacterial genomes. PLoS Genet. 2 (2006) e185
-
(2006)
PLoS Genet.
, vol.2
-
-
Huerta, A.M.1
Francino, M.P.2
Morett, E.3
Collado-Vides, J.4
-
30
-
-
0036468362
-
Prokaryotic transcription regulators: more than just the helix-turn-helix motif
-
Huffman J.L., and Brennan R.G. Prokaryotic transcription regulators: more than just the helix-turn-helix motif. Curr. Opin. Struct. Biol. 12 (2002) 98-106
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 98-106
-
-
Huffman, J.L.1
Brennan, R.G.2
-
31
-
-
33748569118
-
The distinctive signatures of promoter regions and operon junctions across prokaryotes
-
Janga S.C., Lamboy W.F., Huerta A.M., and Moreno-Hagelsieb G. The distinctive signatures of promoter regions and operon junctions across prokaryotes. Nucleic Acids Res. 34 (2006) 3980-3987
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 3980-3987
-
-
Janga, S.C.1
Lamboy, W.F.2
Huerta, A.M.3
Moreno-Hagelsieb, G.4
-
32
-
-
13244287791
-
A novel method for prokaryotic promoter prediction based on DNA stability
-
Kanhere A., and Bansal M. A novel method for prokaryotic promoter prediction based on DNA stability. BMC Bioinformatics 6 (2005) 1
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 1
-
-
Kanhere, A.1
Bansal, M.2
-
33
-
-
34447499141
-
Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake
-
Kingsford C.L., Ayanbule K., and Salzberg S.L. Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol. 8 (2007) R22
-
(2007)
Genome Biol.
, vol.8
-
-
Kingsford, C.L.1
Ayanbule, K.2
Salzberg, S.L.3
-
34
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
Lee T.I., Rinaldi N.J., Robert F., Odom D.T., Bar-Joseph Z., Gerber G.K., Hannett N.M., Harbison C.T., Thompson C.M., Simon I., et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298 (2002) 799-804
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
Rinaldi, N.J.2
Robert, F.3
Odom, D.T.4
Bar-Joseph, Z.5
Gerber, G.K.6
Hannett, N.M.7
Harbison, C.T.8
Thompson, C.M.9
Simon, I.10
-
35
-
-
0037015025
-
Identification of the binding sites of regulatory proteins in bacterial genomes
-
Li H., Rhodius V., Gross C., and Siggia E.D. Identification of the binding sites of regulatory proteins in bacterial genomes. Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 11772-11777
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 11772-11777
-
-
Li, H.1
Rhodius, V.2
Gross, C.3
Siggia, E.D.4
-
36
-
-
33746207758
-
Bacterial regulatory networks are extremely flexible in evolution
-
Lozada-Chavez I., Janga S.C., and Collado-Vides J. Bacterial regulatory networks are extremely flexible in evolution. Nucleic Acids Res. 34 (2006) 3434-3445
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 3434-3445
-
-
Lozada-Chavez, I.1
Janga, S.C.2
Collado-Vides, J.3
-
37
-
-
4644326931
-
Genomic analysis of regulatory network dynamics reveals large topological changes
-
Luscombe N.M., Babu M.M., Yu H., Snyder M., Teichmann S.A., and Gerstein M. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431 (2004) 308-312
-
(2004)
Nature
, vol.431
, pp. 308-312
-
-
Luscombe, N.M.1
Babu, M.M.2
Yu, H.3
Snyder, M.4
Teichmann, S.A.5
Gerstein, M.6
-
38
-
-
13244264814
-
Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach
-
Ma H.W., Buer J., and Zeng A.P. Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach. BMC Bioinformatics 5 (2004) 199
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 199
-
-
Ma, H.W.1
Buer, J.2
Zeng, A.P.3
-
39
-
-
0037440734
-
Evolution of transcription factors and the gene regulatory network in Escherichia coli
-
Madan Babu M., and Teichmann S.A. Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res. 31 (2003) 1234-1244
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 1234-1244
-
-
Madan Babu, M.1
Teichmann, S.A.2
-
40
-
-
0037303198
-
Functional determinants of transcription factors in Escherichia coli: protein families and binding sites
-
Madan Babu M., and Teichmann S.A. Functional determinants of transcription factors in Escherichia coli: protein families and binding sites. Trends Genet. 19 (2003) 75-79
-
(2003)
Trends Genet.
, vol.19
, pp. 75-79
-
-
Madan Babu, M.1
Teichmann, S.A.2
-
41
-
-
33646113855
-
Evolutionary dynamics of prokaryotic transcriptional regulatory networks
-
Madan Babu M., Teichmann S.A., and Aravind L. Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J. Mol. Biol. 358 (2006) 614-633
-
(2006)
J. Mol. Biol.
, vol.358
, pp. 614-633
-
-
Madan Babu, M.1
Teichmann, S.A.2
Aravind, L.3
-
42
-
-
0347126296
-
DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics
-
Makita Y., Nakao M., Ogasawara N., and Nakai K. DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics. Nucleic Acids Res. 32 (2004) D75-D77
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Makita, Y.1
Nakao, M.2
Ogasawara, N.3
Nakai, K.4
-
43
-
-
0142027814
-
Structure and function of the feed-forward loop network motif
-
Mangan S., and Alon U. Structure and function of the feed-forward loop network motif. Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 11980-11985
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, pp. 11980-11985
-
-
Mangan, S.1
Alon, U.2
-
44
-
-
32044462728
-
The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli
-
Mangan S., Itzkovitz S., Zaslaver A., and Alon U. The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli. J. Mol. Biol. 356 (2006) 1073-1081
-
(2006)
J. Mol. Biol.
, vol.356
, pp. 1073-1081
-
-
Mangan, S.1
Itzkovitz, S.2
Zaslaver, A.3
Alon, U.4
-
45
-
-
0242364231
-
The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks
-
Mangan S., Zaslaver A., and Alon U. The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks. J. Mol. Biol. 334 (2003) 197-204
-
(2003)
J. Mol. Biol.
, vol.334
, pp. 197-204
-
-
Mangan, S.1
Zaslaver, A.2
Alon, U.3
-
46
-
-
0242386460
-
Identifying global regulators in transcriptional regulatory networks in bacteria
-
Martinez-Antonio A., and Collado-Vides J. Identifying global regulators in transcriptional regulatory networks in bacteria. Curr. Opin. Microbiol. 6 (2003) 482-489
-
(2003)
Curr. Opin. Microbiol.
, vol.6
, pp. 482-489
-
-
Martinez-Antonio, A.1
Collado-Vides, J.2
-
47
-
-
30344484891
-
Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli
-
Martinez-Antonio A., Janga S.C., Salgado H., and Collado-Vides J. Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli. Trends Microbiol. 14 (2006) 22-27
-
(2006)
Trends Microbiol.
, vol.14
, pp. 22-27
-
-
Martinez-Antonio, A.1
Janga, S.C.2
Salgado, H.3
Collado-Vides, J.4
-
48
-
-
0035253676
-
Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes
-
McCue L., Thompson W., Carmack C., Ryan M.P., Liu J.S., Derbyshire V., and Lawrence C.E. Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res. 29 (2001) 774-782
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 774-782
-
-
McCue, L.1
Thompson, W.2
Carmack, C.3
Ryan, M.P.4
Liu, J.S.5
Derbyshire, V.6
Lawrence, C.E.7
-
49
-
-
0141605202
-
Identification and analysis of 'extended-10' promoters in Escherichia coli
-
Mitchell J.E., Zheng D., Busby S.J., and Minchin S.D. Identification and analysis of 'extended-10' promoters in Escherichia coli. Nucleic Acids Res. 31 (2003) 4689-4695
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 4689-4695
-
-
Mitchell, J.E.1
Zheng, D.2
Busby, S.J.3
Minchin, S.D.4
-
50
-
-
22144451439
-
The regional rule for bacterial base composition
-
Mitchison G. The regional rule for bacterial base composition. Trends Genet. 21 (2005) 440-443
-
(2005)
Trends Genet.
, vol.21
, pp. 440-443
-
-
Mitchison, G.1
-
51
-
-
33746599442
-
More robust detection of motifs in coexpressed genes by using phylogenetic information
-
Monsieurs P., Thijs G., Fadda A.A., De Keersmaecker S.C., Vanderleyden J., De Moor B., and Marchal K. More robust detection of motifs in coexpressed genes by using phylogenetic information. BMC Bioinformatics 7 (2006) 160
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 160
-
-
Monsieurs, P.1
Thijs, G.2
Fadda, A.A.3
De Keersmaecker, S.C.4
Vanderleyden, J.5
De Moor, B.6
Marchal, K.7
-
52
-
-
33748679406
-
Identification and analysis of DNA binding transcription factors in Bacillus subtilis and other Firmicutes-a genomic approach
-
Moreno-Campuzano S., Janga S.C., and Perez-Rueda E. Identification and analysis of DNA binding transcription factors in Bacillus subtilis and other Firmicutes-a genomic approach. BMC Genomics 7 (2006) 147
-
(2006)
BMC Genomics
, vol.7
, pp. 147
-
-
Moreno-Campuzano, S.1
Janga, S.C.2
Perez-Rueda, E.3
-
53
-
-
0642340506
-
Genome wide identification of regulatory motifs in Bacillus subtilis
-
Mwangi M.M., and Siggia E.D. Genome wide identification of regulatory motifs in Bacillus subtilis. BMC Bioinformatics 4 (2003) 18
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 18
-
-
Mwangi, M.M.1
Siggia, E.D.2
-
54
-
-
0037261948
-
The sigma70 family of sigma factors
-
Paget M.S., and Helmann J.D. The sigma70 family of sigma factors. Genome Biol. 4 (2003) 203
-
(2003)
Genome Biol.
, vol.4
, pp. 203
-
-
Paget, M.S.1
Helmann, J.D.2
-
55
-
-
0343963178
-
The repertoire of DNA binding transcriptional regulators in Escherichia coli K-12
-
Perez-Rueda E., and Collado-Vides J. The repertoire of DNA binding transcriptional regulators in Escherichia coli K-12. Nucleic Acids Res. 28 (2000) 1838-1847
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 1838-1847
-
-
Perez-Rueda, E.1
Collado-Vides, J.2
-
56
-
-
0036180002
-
The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons
-
Rajewsky N., Socci N.D., Zapotocky M., and Siggia E.D. The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons. Genome Res. 12 (2002) 298-308
-
(2002)
Genome Res.
, vol.12
, pp. 298-308
-
-
Rajewsky, N.1
Socci, N.D.2
Zapotocky, M.3
Siggia, E.D.4
-
57
-
-
13144283679
-
Modular analysis of the transcriptional regulatory network of E. coli
-
Resendis-Antonio O., Freyre-Gonzalez J.A., Menchaca-Mendez R., Gutierrez-Rios R.M., Martinez-Antonio A., Avila-Sanchez C., and Collado-Vides J. Modular analysis of the transcriptional regulatory network of E. coli. Trends Genet. 21 (2005) 16-20
-
(2005)
Trends Genet.
, vol.21
, pp. 16-20
-
-
Resendis-Antonio, O.1
Freyre-Gonzalez, J.A.2
Menchaca-Mendez, R.3
Gutierrez-Rios, R.M.4
Martinez-Antonio, A.5
Avila-Sanchez, C.6
Collado-Vides, J.7
-
58
-
-
33750038239
-
The sigma factors of Mycobacterium tuberculosis
-
Rodrigue S., Provvedi R., Jacques P.E., Gaudreau L., and Manganelli R. The sigma factors of Mycobacterium tuberculosis. FEMS Microbiol. Rev. 30 (2006) 926-941
-
(2006)
FEMS Microbiol. Rev.
, vol.30
, pp. 926-941
-
-
Rodrigue, S.1
Provvedi, R.2
Jacques, P.E.3
Gaudreau, L.4
Manganelli, R.5
-
59
-
-
33644873438
-
RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions
-
Salgado H., Gama-Castro S., Peralta-Gil M., Diaz-Peredo E., Sanchez-Solano F., Santos-Zavaleta A., Martinez-Flores I., Jimenez-Jacinto V., Bonavides-Martinez C., Segura-Salazar J., et al. RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Res. 34 (2006) D394-D397
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Salgado, H.1
Gama-Castro, S.2
Peralta-Gil, M.3
Diaz-Peredo, E.4
Sanchez-Solano, F.5
Santos-Zavaleta, A.6
Martinez-Flores, I.7
Jimenez-Jacinto, V.8
Bonavides-Martinez, C.9
Segura-Salazar, J.10
-
60
-
-
0036578795
-
Network motifs in the transcriptional regulation network of Escherichia coli
-
Shen-Orr S.S., Milo R., Mangan S., and Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 31 (2002) 64-68
-
(2002)
Nat. Genet.
, vol.31
, pp. 64-68
-
-
Shen-Orr, S.S.1
Milo, R.2
Mangan, S.3
Alon, U.4
-
62
-
-
14644388890
-
Making connections between novel transcription factors and their DNA motifs
-
Tan K., McCue L.A., and Stormo G.D. Making connections between novel transcription factors and their DNA motifs. Genome Res. 15 (2005) 312-320
-
(2005)
Genome Res.
, vol.15
, pp. 312-320
-
-
Tan, K.1
McCue, L.A.2
Stormo, G.D.3
-
63
-
-
2442537233
-
Gene regulatory network growth by duplication
-
Teichmann S.A., and Babu M.M. Gene regulatory network growth by duplication. Nat. Genet. 36 (2004) 492-496
-
(2004)
Nat. Genet.
, vol.36
, pp. 492-496
-
-
Teichmann, S.A.1
Babu, M.M.2
-
64
-
-
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
-
65
-
-
0041828241
-
Scaling laws in the functional content of genomes
-
van Nimwegen E. Scaling laws in the functional content of genomes. Trends Genet. 19 (2003) 479-484
-
(2003)
Trends Genet.
, vol.19
, pp. 479-484
-
-
van Nimwegen, E.1
-
66
-
-
33646867391
-
Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress
-
Wang H., and Benham C.J. Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress. BMC Bioinformatics 7 (2006) 248
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 248
-
-
Wang, H.1
Benham, C.J.2
-
67
-
-
0344906814
-
Combining phylogenetic data with co-regulated genes to identify regulatory motifs
-
Wang T., and Stormo G.D. Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics 19 (2003) 2369-2380
-
(2003)
Bioinformatics
, vol.19
, pp. 2369-2380
-
-
Wang, T.1
Stormo, G.D.2
-
68
-
-
33749514099
-
Genomic analysis of the hierarchical structure of regulatory networks
-
Yu H., and Gerstein M. Genomic analysis of the hierarchical structure of regulatory networks. Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 14724-14731
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 14724-14731
-
-
Yu, H.1
Gerstein, M.2
-
69
-
-
33746415885
-
A comprehensive library of fluorescent transcriptional reporters for Escherichia coli
-
Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette M.G., and Alon U. A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 (2006) 623-628
-
(2006)
Nat. Methods
, vol.3
, pp. 623-628
-
-
Zaslaver, A.1
Bren, A.2
Ronen, M.3
Itzkovitz, S.4
Kikoin, I.5
Shavit, S.6
Liebermeister, W.7
Surette, M.G.8
Alon, U.9
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