-
1
-
-
0033765113
-
Functional modulation of Escherichia coli RNA polymerase
-
Ishihama, A. 2000, Functional modulation of Escherichia coli RNA polymerase, Annu. Rev. Microbiol., 54, 499-518.
-
(2000)
Annu. Rev. Microbiol.
, vol.54
, pp. 499-518
-
-
Ishihama, A.1
-
2
-
-
1942535726
-
Transcriptional regulation in archaea
-
Ouhammouch, M. 2004, Transcriptional regulation in archaea, Curr. Opin. Genet. Dev., 14, 133-138.
-
(2004)
Curr. Opin. Genet. Dev.
, vol.14
, pp. 133-138
-
-
Ouhammouch, M.1
-
3
-
-
0034671865
-
Arabidopsis transcription factors: Genome-wide comparative analysis among eukaryotes
-
Riechmann, J. L., Heard, J., Martin, G., et al. 2000, Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes, Science, 290, 2105-2110.
-
(2000)
Science
, vol.290
, pp. 2105-2110
-
-
Riechmann, J.L.1
Heard, J.2
Martin, G.3
-
4
-
-
0037440195
-
The phylogenetic diversity of eukaryotic transcription
-
Coulson, R. M. and Ouzounis, C. A. 2003, The phylogenetic diversity of eukaryotic transcription, Nucleic Acids Res., 31, 653-660.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 653-660
-
-
Coulson, R.M.1
Ouzounis, C.A.2
-
5
-
-
0037208166
-
TRANSFAC: Transcriptional regulation, from patterns to profiles
-
Matys, V., Fricke, E., Geffers, R., et al. 2003, TRANSFAC: transcriptional regulation, from patterns to profiles, Nucleic Acids Res., 31, 374-378.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 374-378
-
-
Matys, V.1
Fricke, E.2
Geffers, R.3
-
6
-
-
0343963178
-
The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12
-
Perez-Rueda, E. and Collado-Vides, J. 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
-
7
-
-
0033485460
-
DNA-binding proteins and evolution of transcription regulation in the archaea
-
Aravind, L. and Koonin, E. V. 1999, DNA-binding proteins and evolution of transcription regulation in the archaea, Nucleic Acids Res., 27, 4658-4670.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 4658-4670
-
-
Aravind, L.1
Koonin, E.V.2
-
8
-
-
0033587705
-
Transcription in archaea
-
Kyrpides, N. C. and Ouzounis, C. A. 1999, Transcription in archaea, Proc. Natl Acad. Sci. USA, 96, 8545-8550.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 8545-8550
-
-
Kyrpides, N.C.1
Ouzounis, C.A.2
-
9
-
-
0037665941
-
Transcription regulation and environmental adaptation in bacteria
-
Cases, I., de Lorenzo, V., and Ouzounis, C. A. 2003, Transcription regulation and environmental adaptation in bacteria, Trends Microbiol., 11, 248-253.
-
(2003)
Trends Microbiol.
, vol.11
, pp. 248-253
-
-
Cases, I.1
De Lorenzo, V.2
Ouzounis, C.A.3
-
10
-
-
1042298811
-
Evolution of protein superfamilies and bacterial genome size
-
Ranea, J. A., Buchan, D. W., Thornton, J. M., and Orengo, C. A. 2004, Evolution of protein superfamilies and bacterial genome size, J. Mol. Biol., 336, 871-887.
-
(2004)
J. Mol. Biol.
, vol.336
, pp. 871-887
-
-
Ranea, J.A.1
Buchan, D.W.2
Thornton, J.M.3
Orengo, C.A.4
-
11
-
-
0030777303
-
CATH - A hierarchic classification of protein domain structures
-
Orengo, C. A., Michie, A. D., Jones, S., Jones, D. T., Swindells, M. B., and Thornton, J. M. 1997, CATH - a hierarchic classification of protein domain structures, Structure, 5, 1093-1108.
-
(1997)
Structure
, vol.5
, pp. 1093-1108
-
-
Orengo, C.A.1
Michie, A.D.2
Jones, S.3
Jones, D.T.4
Swindells, M.B.5
Thornton, J.M.6
-
12
-
-
8844258763
-
BacTregulators: A database of transcriptional regulators in bacteria and archaea
-
Martinez-Bueno, M., Molina-Henares, A. J., Pareja, E., Ramos, J. L., and Tobes, R. 2004, BacTregulators: a database of transcriptional regulators in bacteria and archaea, Bioinformatics, 20, 2787-2791.
-
(2004)
Bioinformatics
, vol.20
, pp. 2787-2791
-
-
Martinez-Bueno, M.1
Molina-Henares, A.J.2
Pareja, E.3
Ramos, J.L.4
Tobes, R.5
-
13
-
-
0037440734
-
Evolution of transcription factors and the gene regulatory network in Escherichia coli
-
Babu, M. M. and Teichmann, S. A. 2003, Evolution of transcription factors and the gene regulatory network in Escherichia coli, Nucleic Acids Res., 31, 1234-1244.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 1234-1244
-
-
Babu, M.M.1
Teichmann, S.A.2
-
14
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin, A. G., Brenner, S. E., Hubbard, T., and Chothia, C. 1995, SCOP: a structural classification of proteins database for the investigation of sequences and structures, J. Mol. Biol., 247, 536-540.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
15
-
-
0036084143
-
GTOP: A database of protein structures predicted from genome sequences
-
Kawabata, T., Fukuchi, S., Homma, K., et al. 2002, GTOP: a database of protein structures predicted from genome sequences, Nucleic Acids Res., 30, 294-298.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 294-298
-
-
Kawabata, T.1
Fukuchi, S.2
Homma, K.3
-
16
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S. F., Madden, T. L., Schaffer, A. A., et al. 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.F.1
Madden, T.L.2
Schaffer, A.A.3
-
17
-
-
0033954256
-
The Protein Data Bank
-
Berman, H. M., Westbrook, J., Feng, Z., et al. 2000, The Protein Data Bank, Nucleic Acids Res., 28, 235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
-
18
-
-
13444273448
-
The Universal Protein Resource (UniProt)
-
Bairoch, A., Apweiler, R., Wu, C. H., et al. 2005, The Universal Protein Resource (UniProt), Nucleic Acids Res., 33, D154-D159.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Bairoch, A.1
Apweiler, R.2
Wu, C.H.3
-
19
-
-
0031743421
-
Profile hidden Markov models
-
Eddy, S. R. 1998, Profile hidden Markov models, Bioinformatics, 14, 755-763.
-
(1998)
Bioinformatics
, vol.14
, pp. 755-763
-
-
Eddy, S.R.1
-
20
-
-
9144257886
-
The Pfam protein families database
-
Bateman, A., Coin, L., Durbin, R., et al. 2004, The Pfam protein families database, Nucleic Acids Res., 32, D138-D141.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Bateman, A.1
Coin, L.2
Durbin, R.3
-
21
-
-
0038575389
-
Archaeal chromatin and transcription
-
Reeve, J. N. 2003, Archaeal chromatin and transcription, Mol. Microbiol., 48, 587-598.
-
(2003)
Mol. Microbiol.
, vol.48
, pp. 587-598
-
-
Reeve, J.N.1
-
22
-
-
0141504155
-
Rho factor: Transcription termination in four steps
-
Kaplan, D. L. and O'Donnell, M. 2003, Rho factor: transcription termination in four steps, Curr. Biol., 13, R714-R716.
-
(2003)
Curr. Biol.
, vol.13
-
-
Kaplan, D.L.1
O'Donnell, M.2
-
23
-
-
1942467448
-
Recent developments in bacterial cold-shock response
-
Phadtare, S. 2004, Recent developments in bacterial cold-shock response, Curr. Issues Mol. Biol., 6, 125-36.
-
(2004)
Curr. Issues Mol. Biol.
, vol.6
, pp. 125-136
-
-
Phadtare, S.1
-
24
-
-
14044250534
-
Structure analysis of PH1161 protein, a transcriptional activator TenA homologue from the hyperthermophilic archaeon Pyrococcus horikoshii
-
Itou, H., Yao, M., Watanabe, N., and Tanaka, I. 2004, Structure analysis of PH1161 protein, a transcriptional activator TenA homologue from the hyperthermophilic archaeon Pyrococcus horikoshii, Acta Crystallogr. D Biol. Crystallogr., 60, 1094-1100.
-
(2004)
Acta Crystallogr. D Biol. Crystallogr.
, vol.60
, pp. 1094-1100
-
-
Itou, H.1
Yao, M.2
Watanabe, N.3
Tanaka, I.4
-
25
-
-
0042902833
-
The COG database: An updated version includes eukaryotes
-
Tatusov, R. L., Fedorova, N. D., Jackson, J. D., et al. 2003, The COG database: an updated version includes eukaryotes, BMC Bioinformatics, 4, 41.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 41
-
-
Tatusov, R.L.1
Fedorova, N.D.2
Jackson, J.D.3
-
26
-
-
0842268045
-
Supra-domains: Evolutionary units larger than single protein domains
-
Vogel, C., Berzuini, C., Bashton, M., et al. 2004, Supra-domains: evolutionary units larger than single protein domains, J. Mol. Biol., 336, 809-823.
-
(2004)
J. Mol. Biol.
, vol.336
, pp. 809-823
-
-
Vogel, C.1
Berzuini, C.2
Bashton, M.3
-
27
-
-
0035798398
-
Protein family and fold occurrence in genomes: Power-law behaviour and evolutionary model
-
Qian, J., Luscombe, N. M., and Gerstein, M. 2001, Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model, J. Mol. Biol., 313, 673-681.
-
(2001)
J. Mol. Biol.
, vol.313
, pp. 673-681
-
-
Qian, J.1
Luscombe, N.M.2
Gerstein, M.3
-
28
-
-
0030888558
-
DnaA initiator - Also a transcription factor
-
Messer, W. and Weigel, C. 1997, DnaA initiator - also a transcription factor, Mol. Microbiol., 24, 1-6.
-
(1997)
Mol. Microbiol.
, vol.24
, pp. 1-6
-
-
Messer, W.1
Weigel, C.2
-
29
-
-
0037478650
-
Complete genome sequence of the marine planctomycete Pirellula sp. strain 1
-
Glockner, F. O., Kube, M., Bauer, M., et al. 2003, Complete genome sequence of the marine planctomycete Pirellula sp. strain 1, Proc. Natl Acad. Sci. USA, 100, 8298-8303.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 8298-8303
-
-
Glockner, F.O.1
Kube, M.2
Bauer, M.3
-
30
-
-
0035981243
-
Characterization of genes encoding multi-domain proteins in the genome of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120
-
Ohmori, M., Ikeuchi, M., Sato, N., et al. 2001, Characterization of genes encoding multi-domain proteins in the genome of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120, DNA Res., 8, 271-284.
-
(2001)
DNA Res.
, vol.8
, pp. 271-284
-
-
Ohmori, M.1
Ikeuchi, M.2
Sato, N.3
-
31
-
-
0038349269
-
The Lrp family of transcriptional regulators
-
Brinkman, A. B., Ettema, T. J., de Vos, W. M., and van der Oost, J. 2003, The Lrp family of transcriptional regulators, Mol. Microbiol., 48, 287-294.
-
(2003)
Mol. Microbiol.
, vol.48
, pp. 287-294
-
-
Brinkman, A.B.1
Ettema, T.J.2
De Vos, W.M.3
Van Der Oost, J.4
-
32
-
-
1542267826
-
The archaeal feast/famine regulatory protein: Potential roles of its assembly forms for regulating transcription
-
Koike, H., Ishijima, S. A., Clowney, L., and Suzuki, M. 2004, The archaeal feast/famine regulatory protein: potential roles of its assembly forms for regulating transcription, Proc. Natl Acad. Sci. USA, 101, 2840-2845.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 2840-2845
-
-
Koike, H.1
Ishijima, S.A.2
Clowney, L.3
Suzuki, M.4
-
33
-
-
0035109743
-
Transcription-associated protein families are primarily taxon-specific
-
Coulson, R. M. R., Enright, A. J., and Ouzounis, C. A. 2001, Transcription-associated protein families are primarily taxon-specific, Bioinformatics, 17, 95-97.
-
(2001)
Bioinformatics
, vol.17
, pp. 95-97
-
-
Coulson, R.M.R.1
Enright, A.J.2
Ouzounis, C.A.3
-
34
-
-
0034618559
-
Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS
-
Shigenobu, S., Watanabe, H., Hattori, M., Sakaki, Y., and Ishikawa, H. 2000, Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS, Nature, 407, 81-86.
-
(2000)
Nature
, vol.407
, pp. 81-86
-
-
Shigenobu, S.1
Watanabe, H.2
Hattori, M.3
Sakaki, Y.4
Ishikawa, H.5
-
35
-
-
20444492834
-
Regulation of transcription in a reduced bacterial genome: Nutrient-provisioning genes of the obligate symbiont Buchnera aphidicola
-
Moran, N. A., Dunbar, H. E., and Wilcox, J. L. 2005, Regulation of transcription in a reduced bacterial genome: nutrient-provisioning genes of the obligate symbiont Buchnera aphidicola, J. Bacteriol., 187, 4229-4237.
-
(2005)
J. Bacteriol.
, vol.187
, pp. 4229-4237
-
-
Moran, N.A.1
Dunbar, H.E.2
Wilcox, J.L.3
-
36
-
-
0036225678
-
The genome of M. acetivorans reveals extensive metabolic and physiological diversity
-
Galagan, J. E., Nusbaum, C., Roy, A., et al. 2002, The genome of M. acetivorans reveals extensive metabolic and physiological diversity, Genome Res., 12, 532-542.
-
(2002)
Genome Res.
, vol.12
, pp. 532-542
-
-
Galagan, J.E.1
Nusbaum, C.2
Roy, A.3
-
37
-
-
0031458333
-
The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus
-
Klenk, H. P., Clayton, R. A., Tomb, J. F., et al. 1997, The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus, Nature, 390, 364-370.
-
(1997)
Nature
, vol.390
, pp. 364-370
-
-
Klenk, H.P.1
Clayton, R.A.2
Tomb, J.F.3
-
38
-
-
0037046560
-
Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)
-
Bentley, S. D., Chater, K. F., Cerdeno-Tarraga, A. M., et al. 2002, Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2), Nature, 417, 141-147.
-
(2002)
Nature
, vol.417
, pp. 141-147
-
-
Bentley, S.D.1
Chater, K.F.2
Cerdeno-Tarraga, A.M.3
-
39
-
-
0037195083
-
The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract
-
Schell, M. A., Karmirantzou, M., Snel, B., et al. 2002, The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract, Proc. Natl Acad. Sci. USA, 99, 14422-14427.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 14422-14427
-
-
Schell, M.A.1
Karmirantzou, M.2
Snel, B.3
-
40
-
-
0030731108
-
The complete genome sequence of the gram-positive bacterium Bacillus subtilis
-
Kunst, F., Ogasawara, N., Moszer, I., et al. 1997, The complete genome sequence of the gram-positive bacterium Bacillus subtilis, Nature, 390, 249-256.
-
(1997)
Nature
, vol.390
, pp. 249-256
-
-
Kunst, F.1
Ogasawara, N.2
Moszer, I.3
-
41
-
-
0034902930
-
Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum
-
Nolling, J., Breton, G., Omelchenko, M. V., et al. 2001, Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum, J. Bacteriol., 183, 4823-4838.
-
(2001)
J. Bacteriol.
, vol.183
, pp. 4823-4838
-
-
Nolling, J.1
Breton, G.2
Omelchenko, M.V.3
-
42
-
-
10744220624
-
The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens
-
Duchaud, E., Rusniok, C., Frangeul, L., et al. 2003, The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens, Nat. Biotechnol., 21, 1307-1313.
-
(2003)
Nat. Biotechnol.
, vol.21
, pp. 1307-1313
-
-
Duchaud, E.1
Rusniok, C.2
Frangeul, L.3
-
43
-
-
10744220291
-
The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533
-
Pridmore, R. D., Berger, B., Desiere, F., et al. 2004, The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533, Proc. Natl Acad. Sci. USA, 101, 2512-2517.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 2512-2517
-
-
Pridmore, R.D.1
Berger, B.2
Desiere, F.3
-
44
-
-
0035021812
-
The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403
-
Bolotin, A., Wincker, P., Mauger, S., et al. 2001, The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403, Genome Res., 11, 731-753.
-
(2001)
Genome Res.
, vol.11
, pp. 731-753
-
-
Bolotin, A.1
Wincker, P.2
Mauger, S.3
-
45
-
-
0036206041
-
Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586
-
Kapatral, V., Anderson, I., Ivanova, N., et al. 2002, Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586, J. Bacteriol., 184, 2005-2018.
-
(2002)
J. Bacteriol.
, vol.184
, pp. 2005-2018
-
-
Kapatral, V.1
Anderson, I.2
Ivanova, N.3
-
46
-
-
0348103717
-
Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris
-
Larimer, F. W., Chain, P., Hauser, L., et al. 2004, Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris, Nat. Biotechnol., 22, 55-61.
-
(2004)
Nat. Biotechnol.
, vol.22
, pp. 55-61
-
-
Larimer, F.W.1
Chain, P.2
Hauser, L.3
|