-
1
-
-
0036668461
-
Transcription termination and anti-termination in E. coli
-
Nudler E., and Gottesman M.E. Transcription termination and anti-termination in E. coli. Genes Cells 7 8 (2002) 755-768
-
(2002)
Genes Cells
, vol.7
, Issue.8
, pp. 755-768
-
-
Nudler, E.1
Gottesman, M.E.2
-
2
-
-
0022555852
-
Transcription termination and the regulation of gene expression
-
Platt T. Transcription termination and the regulation of gene expression. Annu. Rev. Biochem. 55 (1986) 339-372
-
(1986)
Annu. Rev. Biochem.
, vol.55
, pp. 339-372
-
-
Platt, T.1
-
3
-
-
0033597435
-
Mechanism of intrinsic transcription termination and antitermination
-
Yarnell W.S., and Roberts J.W. Mechanism of intrinsic transcription termination and antitermination. Science 284 5414 (1999) 611-615
-
(1999)
Science
, vol.284
, Issue.5414
, pp. 611-615
-
-
Yarnell, W.S.1
Roberts, J.W.2
-
4
-
-
0019877865
-
Rho-independent termination: dyad symmetry in DNA causes RNA polymerase to pause during transcription in vitro
-
Farnham P.J., and Platt T. Rho-independent termination: dyad symmetry in DNA causes RNA polymerase to pause during transcription in vitro. Nucleic Acids Res. 9 3 (1981) 563-577
-
(1981)
Nucleic Acids Res.
, vol.9
, Issue.3
, pp. 563-577
-
-
Farnham, P.J.1
Platt, T.2
-
5
-
-
0030738525
-
Preferential interaction of the his pause RNA hairpin with RNA polymerase beta subunit residues 904-950 correlates with strong transcriptional pausing
-
Wang D., Severinov K., and Landick R. Preferential interaction of the his pause RNA hairpin with RNA polymerase beta subunit residues 904-950 correlates with strong transcriptional pausing. Proc. Natl. Acad. Sci. USA 94 16 (1997) 8433-8438
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, Issue.16
, pp. 8433-8438
-
-
Wang, D.1
Severinov, K.2
Landick, R.3
-
6
-
-
0032190641
-
Interaction of a nascent RNA structure with RNA polymerase is required for hairpin-dependent transcriptional pausing but not for transcript release
-
Artsimovitch I., and Landick R. Interaction of a nascent RNA structure with RNA polymerase is required for hairpin-dependent transcriptional pausing but not for transcript release. Genes Dev. 12 19 (1998) 3110-3122
-
(1998)
Genes Dev.
, vol.12
, Issue.19
, pp. 3110-3122
-
-
Artsimovitch, I.1
Landick, R.2
-
7
-
-
0025294195
-
RNA chain elongation by Escherichia coli RNA polymerase. Factors affecting the stability of elongating ternary complexes
-
Arndt K.M., and Chamberlin M.J. RNA chain elongation by Escherichia coli RNA polymerase. Factors affecting the stability of elongating ternary complexes. J. Mol. Biol. 213 1 (1990) 79-108
-
(1990)
J. Mol. Biol.
, vol.213
, Issue.1
, pp. 79-108
-
-
Arndt, K.M.1
Chamberlin, M.J.2
-
8
-
-
0029073396
-
Transcription termination at intrinsic terminators: the role of the RNA hairpin
-
Wilson K.S., and von Hippel P.H. Transcription termination at intrinsic terminators: the role of the RNA hairpin. Proc. Natl. Acad. Sci. USA 92 19 (1995) 8793-8797
-
(1995)
Proc. Natl. Acad. Sci. USA
, vol.92
, Issue.19
, pp. 8793-8797
-
-
Wilson, K.S.1
von Hippel, P.H.2
-
9
-
-
0023905791
-
Contributions of RNA secondary structure and length of the thymidine tract to transcription termination at the operon attenuator
-
Lynn S.P., Kasper L.M., and Gardner J.F. Contributions of RNA secondary structure and length of the thymidine tract to transcription termination at the operon attenuator. J. Biol. Chem. 263 1 (1988) 472-479
-
(1988)
J. Biol. Chem.
, vol.263
, Issue.1
, pp. 472-479
-
-
Lynn, S.P.1
Kasper, L.M.2
Gardner, J.F.3
-
10
-
-
0019331859
-
DNA-RNA hybrid duplexes containing oligo(dA:rU) sequences are exceptionally unstable and may facilitate termination of transcription
-
Martin F.H., and Tinoco Jr. I. DNA-RNA hybrid duplexes containing oligo(dA:rU) sequences are exceptionally unstable and may facilitate termination of transcription. Nucleic Acids Res. 8 10 (1980) 2295-2299
-
(1980)
Nucleic Acids Res.
, vol.8
, Issue.10
, pp. 2295-2299
-
-
Martin, F.H.1
Tinoco Jr., I.2
-
11
-
-
0021770582
-
A computer algorithm for testing potential prokaryotic terminators
-
Brendel V., and Trifonov E.N. A computer algorithm for testing potential prokaryotic terminators. Nucleic Acids Res. 12 10 (1984) 4411-4427
-
(1984)
Nucleic Acids Res.
, vol.12
, Issue.10
, pp. 4411-4427
-
-
Brendel, V.1
Trifonov, E.N.2
-
12
-
-
0022613406
-
Terminators of transcription with RNA polymerase from Escherichia coli: what they look like and how to find them
-
Brendel V., Hamm G.H., and Trifonov E.N. Terminators of transcription with RNA polymerase from Escherichia coli: what they look like and how to find them. J. Biomol. Struct. Dyn. 3 4 (1986) 705-723
-
(1986)
J. Biomol. Struct. Dyn.
, vol.3
, Issue.4
, pp. 705-723
-
-
Brendel, V.1
Hamm, G.H.2
Trifonov, E.N.3
-
13
-
-
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 4 (1990) 835-858
-
(1990)
J. Mol. Biol.
, vol.216
, Issue.4
, pp. 835-858
-
-
d'Aubenton Carafa, Y.1
Brody, E.2
Thermes, C.3
-
14
-
-
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 1 (2000) 27-33
-
(2000)
J. Mol. Biol.
, vol.301
, Issue.1
, pp. 27-33
-
-
Ermolaeva, M.D.1
Khalak, H.G.2
White, O.3
Smith, H.O.4
Salzberg, S.L.5
-
15
-
-
0035444240
-
Prediction of rho-independent transcriptional terminators in Escherichia coli
-
Lesnik E.A., Sampath R., Levene H.B., Henderson T.J., McNeil J.A., and Ecker D.J. Prediction of rho-independent transcriptional terminators in Escherichia coli. Nucleic Acids Res. 29 17 (2001) 3583-3594
-
(2001)
Nucleic Acids Res.
, vol.29
, Issue.17
, pp. 3583-3594
-
-
Lesnik, E.A.1
Sampath, R.2
Levene, H.B.3
Henderson, T.J.4
McNeil, J.A.5
Ecker, D.J.6
-
16
-
-
0036464509
-
Conserved economics of transcription termination in eubacteria
-
Unniraman S., Prakash R., and Nagaraja V. Conserved economics of transcription termination in eubacteria. Nucleic Acids Res. 30 3 (2002) 675-684
-
(2002)
Nucleic Acids Res.
, vol.30
, Issue.3
, pp. 675-684
-
-
Unniraman, S.1
Prakash, R.2
Nagaraja, V.3
-
17
-
-
0035890840
-
RNAMotif, an RNA secondary structure definition and search algorithm
-
Macke T.J., Ecker D.J., Gutell R.R., Gautheret D., Case D.A., and Sampath R. RNAMotif, an RNA secondary structure definition and search algorithm. Nucleic Acids Res. 29 22 (2001) 4724-4735
-
(2001)
Nucleic Acids Res.
, vol.29
, Issue.22
, pp. 4724-4735
-
-
Macke, T.J.1
Ecker, D.J.2
Gutell, R.R.3
Gautheret, D.4
Case, D.A.5
Sampath, R.6
-
18
-
-
33746533172
-
Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2
-
Livny J., Brencic A., Lory S., and Waldor M.K. Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2. Nucleic Acids Res 34 (2006) 3484-3493
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 3484-3493
-
-
Livny, J.1
Brencic, A.2
Lory, S.3
Waldor, M.K.4
-
19
-
-
33644873202
-
Transterm - extended search facilities and improved integration with other databases
-
Jacobs G.H., Stockwell P.A., Tate W.P., and Brown C.M. Transterm - extended search facilities and improved integration with other databases. Nucleic Acids Res. 34 (2006) D37-D40
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Jacobs, G.H.1
Stockwell, P.A.2
Tate, W.P.3
Brown, C.M.4
-
20
-
-
0036271043
-
A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome
-
Chen S., Lesnik E.A., Hall T.A., Sampath R., Griffey R.H., Ecker D.J., and Blyn L.B. A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome. Biosystems 65 2-3 (2002) 157-177
-
(2002)
Biosystems
, vol.65
, Issue.2-3
, pp. 157-177
-
-
Chen, S.1
Lesnik, E.A.2
Hall, T.A.3
Sampath, R.4
Griffey, R.H.5
Ecker, D.J.6
Blyn, L.B.7
-
21
-
-
0141850376
-
Intergenic sequence inspector: searching and identifying bacterial RNAs
-
Pichon C., and Felden B. Intergenic sequence inspector: searching and identifying bacterial RNAs. Bioinformatics 19 13 (2003) 1707-1709
-
(2003)
Bioinformatics
, vol.19
, Issue.13
, pp. 1707-1709
-
-
Pichon, C.1
Felden, B.2
-
22
-
-
22844436749
-
sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes
-
Livny J., Fogel M.A., Davis B.M., and Waldor M.K. sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes. Nucleic Acids Res. 33 13 (2005) 4096-4105
-
(2005)
Nucleic Acids Res.
, vol.33
, Issue.13
, pp. 4096-4105
-
-
Livny, J.1
Fogel, M.A.2
Davis, B.M.3
Waldor, M.K.4
-
23
-
-
33646029404
-
Prediction of non-coding and antisense RNA genes in Escherichia coli with Gapped Markov Model
-
Yachie N., Numata K., Saito R., Kanai A., and Tomita M. Prediction of non-coding and antisense RNA genes in Escherichia coli with Gapped Markov Model. Gene 372 (2006) 171-181
-
(2006)
Gene
, vol.372
, pp. 171-181
-
-
Yachie, N.1
Numata, K.2
Saito, R.3
Kanai, A.4
Tomita, M.5
-
24
-
-
0022351509
-
A bidirectional rho-independent transcription terminator between the E. coli tonB gene and an opposing gene
-
Postle K., and Good R.F. A bidirectional rho-independent transcription terminator between the E. coli tonB gene and an opposing gene. Cell 41 2 (1985) 577-585
-
(1985)
Cell
, vol.41
, Issue.2
, pp. 577-585
-
-
Postle, K.1
Good, R.F.2
-
25
-
-
0037316319
-
G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining
-
Arakawa K., Mori K., Ikeda K., Matsuzaki T., Kobayashi Y., and Tomita M. G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining. Bioinformatics 19 2 (2003) 305-306
-
(2003)
Bioinformatics
, vol.19
, Issue.2
, pp. 305-306
-
-
Arakawa, K.1
Mori, K.2
Ikeda, K.3
Matsuzaki, T.4
Kobayashi, Y.5
Tomita, M.6
-
26
-
-
33747863519
-
G-language System as a platform for large-scale analysis of high-throughput omics data
-
Arakawa K., and Tomita M. G-language System as a platform for large-scale analysis of high-throughput omics data. J. Pestic. Sci. 31 3 (2006) 282-288
-
(2006)
J. Pestic. Sci.
, vol.31
, Issue.3
, pp. 282-288
-
-
Arakawa, K.1
Tomita, M.2
-
27
-
-
13444262374
-
EcoCyc: a comprehensive database resource for Escherichia coli
-
Keseler I.M., Collado-Vides J., Gama-Castro S., Ingraham J., Paley S., Paulsen I.T., Peralta-Gil M., and Karp P.D. EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res. 33 (2005) D334-D337
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Keseler, I.M.1
Collado-Vides, J.2
Gama-Castro, S.3
Ingraham, J.4
Paley, S.5
Paulsen, I.T.6
Peralta-Gil, M.7
Karp, P.D.8
-
28
-
-
33745209677
-
GPAC: Benchmarking the sensitivity of genome informatics analysis to genome annotation completeness
-
Arakawa K., Nakayama Y., and Tomita M. GPAC: Benchmarking the sensitivity of genome informatics analysis to genome annotation completeness. In Silico Biol. 6 1-2 (2006) 0006
-
(2006)
In Silico Biol.
, vol.6
, Issue.1-2
, pp. 0006
-
-
Arakawa, K.1
Nakayama, Y.2
Tomita, M.3
-
29
-
-
0032401911
-
Analysis of complete genomes suggests that many prokaryotes do not rely on hairpin formation in transcription termination
-
Washio T., Sasayama J., and Tomita M. Analysis of complete genomes suggests that many prokaryotes do not rely on hairpin formation in transcription termination. Nucleic Acids Res. 26 23 (1998) 5456-5463
-
(1998)
Nucleic Acids Res.
, vol.26
, Issue.23
, pp. 5456-5463
-
-
Washio, T.1
Sasayama, J.2
Tomita, M.3
|