-
1
-
-
55549134279
-
Energetic contributions to the initiation in E.coli
-
Ramprakash J., Schwarz F.P. Energetic contributions to the initiation in E.coli. Biophys Chem 2008, 138:91-98.
-
(2008)
Biophys Chem
, vol.138
, pp. 91-98
-
-
Ramprakash, J.1
Schwarz, F.P.2
-
2
-
-
33845452240
-
Escherichia coli RNA polymerase enzyme of σ70- dependent promoter requiring a-35 DNA element and an extended-10 TGn motif
-
Hook-Barnard I., Johnson X.B., Hinton D.M. Escherichia coli RNA polymerase enzyme of σ70- dependent promoter requiring a-35 DNA element and an extended-10 TGn motif. JBacteriol 2006, 188:8352-8359.
-
(2006)
JBacteriol
, vol.188
, pp. 8352-8359
-
-
Hook-Barnard, I.1
Johnson, X.B.2
Hinton, D.M.3
-
3
-
-
0036468362
-
Prokaryotic transcription regulators: more than just the helix-turn-helix motif
-
Huffmann J.L., Brennan R.G. Prokaryotic transcription regulators: more than just the helix-turn-helix motif. Curr Opin Struct Biol 2002, 12:98-106.
-
(2002)
Curr Opin Struct Biol
, vol.12
, pp. 98-106
-
-
Huffmann, J.L.1
Brennan, R.G.2
-
4
-
-
39849097831
-
RNA polymerase: the vehicle of transcription
-
Borukhov S., Nudler E. RNA polymerase: the vehicle of transcription. Trends Microbiol 2008, 16(3):126-134.
-
(2008)
Trends Microbiol
, vol.16
, Issue.3
, pp. 126-134
-
-
Borukhov, S.1
Nudler, E.2
-
5
-
-
84891743676
-
Bacterial promoter features description and their application on E. coli in silico prediction and recognition approaches
-
InTech, Rijeka, H. Pérez-Sánchez (Ed.)
-
de Avila Silva S., Echeverrigaray S. Bacterial promoter features description and their application on E. coli in silico prediction and recognition approaches. Bioinformatics 2012, 241-260. InTech, Rijeka. H. Pérez-Sánchez (Ed.).
-
(2012)
Bioinformatics
, pp. 241-260
-
-
de Avila Silva, S.1
Echeverrigaray, S.2
-
7
-
-
36849063165
-
Structure and evolution of gene regulatory networks in microbial genomes
-
Janga S.C., Collado-Vides J. Structure and evolution of gene regulatory networks in microbial genomes. Res Microbiol 2007, 158:787-794.
-
(2007)
Res Microbiol
, vol.158
, pp. 787-794
-
-
Janga, S.C.1
Collado-Vides, J.2
-
8
-
-
33750200659
-
Detection of prokaryotic promoters from the genomic ditribution of hexanucleotides pairs
-
Jacques P.-E., Rodrigue S., Gaudreau L., Goulet J., Brzezinski R. Detection of prokaryotic promoters from the genomic ditribution of hexanucleotides pairs. BMC Bioinform 2006, 7:423.
-
(2006)
BMC Bioinform
, vol.7
, pp. 423
-
-
Jacques, P.-E.1
Rodrigue, S.2
Gaudreau, L.3
Goulet, J.4
Brzezinski, R.5
-
9
-
-
49949117851
-
The cross-species prediction of bacterial promoters using a support vector machine
-
Towsey M., Timms P., Hogan J., Mathews S.A. The cross-species prediction of bacterial promoters using a support vector machine. Comput Biol Chem 2008, 32:359-366.
-
(2008)
Comput Biol Chem
, vol.32
, pp. 359-366
-
-
Towsey, M.1
Timms, P.2
Hogan, J.3
Mathews, S.A.4
-
10
-
-
34250618313
-
Anovel approach to estimation of E.coli promoter gene sequences: combining feature selection and least square support vector machine (FS_LSSVN)
-
Polate K., Günes S. Anovel approach to estimation of E.coli promoter gene sequences: combining feature selection and least square support vector machine (FS_LSSVN). Appl Math Comput 2007, 190:1574-1582.
-
(2007)
Appl Math Comput
, vol.190
, pp. 1574-1582
-
-
Polate, K.1
Günes, S.2
-
11
-
-
33746925662
-
70 promoters in Escherichia coli K-12
-
70 promoters in Escherichia coli K-12. JTheor Biol 2006, 242:135-141.
-
(2006)
JTheor Biol
, vol.242
, pp. 135-141
-
-
Li, Q.-Z.1
Lin, H.2
-
12
-
-
0142241306
-
Sequence alignment for recognition of promoter regions
-
Gordon L., Chervonenkis A., Gammerman A.J., Shahmuradov I.A., Solovyev V.V. Sequence alignment for recognition of promoter regions. Bioinformatics 2003, 19(15):1964-1971.
-
(2003)
Bioinformatics
, vol.19
, Issue.15
, pp. 1964-1971
-
-
Gordon, L.1
Chervonenkis, A.2
Gammerman, A.J.3
Shahmuradov, I.A.4
Solovyev, V.V.5
-
13
-
-
15844412591
-
Improving promoter prediction for the NNPP2.2 algorithm: a case study using Escherichia coli DNA sequences
-
Burden S., Lin Y.-X., Zhang R. Improving promoter prediction for the NNPP2.2 algorithm: a case study using Escherichia coli DNA sequences. Bioinformatics 2005, 21(5):601-607.
-
(2005)
Bioinformatics
, vol.21
, Issue.5
, pp. 601-607
-
-
Burden, S.1
Lin, Y.-X.2
Zhang, R.3
-
14
-
-
80051598704
-
BacPP: bacterial promoter prediction-a tool for accurate sigma-factor specific assignment in enterobacteria
-
de Avila Silva S., Echeverrigaray S., Gerhardt G.J.L. BacPP: bacterial promoter prediction-a tool for accurate sigma-factor specific assignment in enterobacteria. JTheor Biol 2011, 287:92-99.
-
(2011)
JTheor Biol
, vol.287
, pp. 92-99
-
-
de Avila Silva, S.1
Echeverrigaray, S.2
Gerhardt, G.J.L.3
-
15
-
-
0344081940
-
Artificial neural networks for prediction of mycobaterial promoter sequences
-
Kalate R.N., Tambe S.S., Kulkarni B.D. Artificial neural networks for prediction of mycobaterial promoter sequences. Comput Biol Chem 2003, 27:555-564.
-
(2003)
Comput Biol Chem
, vol.27
, pp. 555-564
-
-
Kalate, R.N.1
Tambe, S.S.2
Kulkarni, B.D.3
-
16
-
-
34047173652
-
Analysis of E.coli promoter recognition problem in dinucleotide feature space
-
Rani T.S., Bhavani S.D., Bapi R.S. Analysis of E.coli promoter recognition problem in dinucleotide feature space. Bioinformatics 2007, 23(5):582-588.
-
(2007)
Bioinformatics
, vol.23
, Issue.5
, pp. 582-588
-
-
Rani, T.S.1
Bhavani, S.D.2
Bapi, R.S.3
-
17
-
-
77949497166
-
N4: a precise and highly sensitive promoter predictor using neural network fed by nearest neighbors
-
Askary A., Masoudi-Nejad A., Sharafi R., Mizbani A., Parizi S.N., Purmasjedi M. N4: a precise and highly sensitive promoter predictor using neural network fed by nearest neighbors. Genes Genet Syst 2009, 84(6):425-430.
-
(2009)
Genes Genet Syst
, vol.84
, Issue.6
, pp. 425-430
-
-
Askary, A.1
Masoudi-Nejad, A.2
Sharafi, R.3
Mizbani, A.4
Parizi, S.N.5
Purmasjedi, M.6
-
18
-
-
51049095878
-
Greedy rule generation from discrete data and its use in neural network rule extraction
-
Odajima K., Hayashi Y., Tianxia G., Setiono R. Greedy rule generation from discrete data and its use in neural network rule extraction. Neural Networks 2008, 21:1020-1028.
-
(2008)
Neural Networks
, vol.21
, pp. 1020-1028
-
-
Odajima, K.1
Hayashi, Y.2
Tianxia, G.3
Setiono, R.4
-
19
-
-
0029484103
-
Asurvey and critique of techniques for extracting rules from trained artificial neural networks
-
Andrews R., Diederich J., Tickle A.B. Asurvey and critique of techniques for extracting rules from trained artificial neural networks. Knowledge-Based Syst 1995, 8(6):373-389.
-
(1995)
Knowledge-Based Syst
, vol.8
, Issue.6
, pp. 373-389
-
-
Andrews, R.1
Diederich, J.2
Tickle, A.B.3
-
20
-
-
20344396385
-
Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes
-
Kanhere A., Bansal M. Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes. Nucleic Acids Res 2005, 33(10):3165-3175.
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.10
, pp. 3165-3175
-
-
Kanhere, A.1
Bansal, M.2
-
21
-
-
34548741417
-
Identification and annotation of promoter regions in microbial genome sequences on the basis of DNA stability
-
Rangannan V., Bansal M. Identification and annotation of promoter regions in microbial genome sequences on the basis of DNA stability. JBiosci 2007, 32(5):851-862.
-
(2007)
JBiosci
, vol.32
, Issue.5
, pp. 851-862
-
-
Rangannan, V.1
Bansal, M.2
-
22
-
-
40649114197
-
DNA sequence and structural properties as predictors of human and mouse promoters
-
Akan P., Deloukas P. DNA sequence and structural properties as predictors of human and mouse promoters. Gene 2008, 410(1):165-176.
-
(2008)
Gene
, vol.410
, Issue.1
, pp. 165-176
-
-
Akan, P.1
Deloukas, P.2
-
23
-
-
79957921296
-
Rules extraction from neural networks applied to the prediction and recognition of prokaryotic promoters
-
de Avila Silva S., Gerhardt G.J.L., Echeverrigaray S. Rules extraction from neural networks applied to the prediction and recognition of prokaryotic promoters. Genet Mol Biol 2011, 34(2):353-360.
-
(2011)
Genet Mol Biol
, vol.34
, Issue.2
, pp. 353-360
-
-
de Avila Silva, S.1
Gerhardt, G.J.L.2
Echeverrigaray, S.3
-
24
-
-
0001550068
-
Predicting DNA duplex stability from the base sequence
-
Breslauer K.J., Frank R., Blocker H., Marky L.A. Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci USA 1986, 83:3746-3750.
-
(1986)
Proc Natl Acad Sci USA
, vol.83
, pp. 3746-3750
-
-
Breslauer, K.J.1
Frank, R.2
Blocker, H.3
Marky, L.A.4
-
26
-
-
38549140094
-
RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Text press navigation
-
Gama-Castro S., Jimenez-Jacinto V., Peralta-Gil M., Santos-Zavaleta A., Peñaloza-Spinola M.I., Contreras-Moreira B., et al. RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Text press navigation. Nucleic Acids Research 2008, 36:D120-D124.
-
(2008)
Nucleic Acids Research
, vol.36
-
-
Gama-Castro, S.1
Jimenez-Jacinto, V.2
Peralta-Gil, M.3
Santos-Zavaleta, A.4
Peñaloza-Spinola, M.I.5
Contreras-Moreira, B.6
-
27
-
-
13244287791
-
Anovel method for prokaryotic promoter prediction based on DNA stability
-
Kanhere A., Bansal M. Anovel method for prokaryotic promoter prediction based on DNA stability. BMC Bioinform 2005, 6:1471-2105.
-
(2005)
BMC Bioinform
, vol.6
, pp. 1471-2105
-
-
Kanhere, A.1
Bansal, M.2
-
28
-
-
0000810560
-
Practical implementation of nonlinear time series methods: the TISEAN package
-
Hegger R., Kantz H., Schreiber T. Practical implementation of nonlinear time series methods: the TISEAN package. CHAOS 1999, 9:413-435.
-
(1999)
CHAOS
, vol.9
, pp. 413-435
-
-
Hegger, R.1
Kantz, H.2
Schreiber, T.3
-
29
-
-
22944450849
-
The protein folding problem solved by a fuzzy inference system extracted from an artificial neural network
-
Battistella E., Cechin A.L. The protein folding problem solved by a fuzzy inference system extracted from an artificial neural network. Lecture Notes Comput Sci 2004, 3315:474-483.
-
(2004)
Lecture Notes Comput Sci
, vol.3315
, pp. 474-483
-
-
Battistella, E.1
Cechin, A.L.2
-
30
-
-
19344363436
-
Predictive neural networks for gene expression data analysis
-
Tan Ah.-H., Pan H. Predictive neural networks for gene expression data analysis. Neural Networks 2005, 18:297-306.
-
(2005)
Neural Networks
, vol.18
, pp. 297-306
-
-
Tan, A.-H.1
Pan, H.2
-
31
-
-
5344244656
-
-
R Development Core Team, R Foundation for Statistical Computing, Vienna, Austria, URL:
-
R Development Core Team R: a language and environment for statistical computing 2008, R Foundation for Statistical Computing, Vienna, Austria, URL:. http://www.R-project.org.
-
(2008)
R: a language and environment for statistical computing
-
-
-
32
-
-
65649138430
-
Asystematic analysis of performance measures for classification tasks
-
Sokolova M., Lapalme G. Asystematic analysis of performance measures for classification tasks. Inform Process Manage 2009, 427:427-437.
-
(2009)
Inform Process Manage
, vol.427
, pp. 427-437
-
-
Sokolova, M.1
Lapalme, G.2
-
33
-
-
43149103140
-
ROC analysis: applications to the classification of biological sequences and 3D structures
-
Sonego P., Kocsor A., Pongor S. ROC analysis: applications to the classification of biological sequences and 3D structures. Brief Bioinform 2008, 9(3):198-209.
-
(2008)
Brief Bioinform
, vol.9
, Issue.3
, pp. 198-209
-
-
Sonego, P.1
Kocsor, A.2
Pongor, S.3
-
34
-
-
84856830982
-
Recognition of prokaryotic promoters based on a novel variable-window Z-curve method
-
Song K. Recognition of prokaryotic promoters based on a novel variable-window Z-curve method. Nucleic Acids Res 2012, 40(3):963-971.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.3
, pp. 963-971
-
-
Song, K.1
-
36
-
-
79953328955
-
54-dependent transcription
-
54-dependent transcription. FEMS Microbiol Rev 2011, 35(3):425-440.
-
(2011)
FEMS Microbiol Rev
, vol.35
, Issue.3
, pp. 425-440
-
-
Shingler, V.1
-
37
-
-
84857311371
-
Mechanism of transcription initiation at an activator-dependent promoter defined by single-molecule observation
-
L. J. Friedman, J.Gelles, Mechanism of transcription initiation at an activator-dependent promoter defined by single-molecule observation, Cell 148(4) 679-689.
-
Cell
, vol.148
, Issue.4
, pp. 679-689
-
-
Friedman, L.J.1
Gelles, J.2
-
38
-
-
34249034599
-
Sigma 28 promoter prediction in members of the gammaproteobacteria
-
Song W., Maiste P.J., Naiman D.Q., Ward M.J. Sigma 28 promoter prediction in members of the gammaproteobacteria. FEMS 2007, 271:222-229.
-
(2007)
FEMS
, vol.271
, pp. 222-229
-
-
Song, W.1
Maiste, P.J.2
Naiman, D.Q.3
Ward, M.J.4
-
39
-
-
70350096515
-
Reduced capacity of alternative sigmas to melt promoters ensures stringent promoter recognition
-
Koo B.M., Rhodius V.A., Nonaka G., deHaseth P.L., Gross C.A. Reduced capacity of alternative sigmas to melt promoters ensures stringent promoter recognition. Genes Dev 2009, 23:2426-2436.
-
(2009)
Genes Dev
, vol.23
, pp. 2426-2436
-
-
Koo, B.M.1
Rhodius, V.A.2
Nonaka, G.3
deHaseth, P.L.4
Gross, C.A.5
-
40
-
-
70349327503
-
Mechanisms and evolution of control logic in prokaryotic transcriptional
-
van Hijum S.A.F., Medema M.H., Kuipers O.P. Mechanisms and evolution of control logic in prokaryotic transcriptional. Microbiol Mol Biol Rev 2009, 73(3):481-509.
-
(2009)
Microbiol Mol Biol Rev
, vol.73
, Issue.3
, pp. 481-509
-
-
van Hijum, S.A.F.1
Medema, M.H.2
Kuipers, O.P.3
-
41
-
-
0141758085
-
Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals
-
Huerta A.M., Collado-Vides J. Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals. JMol Biol 2003, 333:261-278.
-
(2003)
JMol Biol
, vol.333
, pp. 261-278
-
-
Huerta, A.M.1
Collado-Vides, J.2
|