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Results: 1 to 20 of 86

1.

Extracting biochemical parameters for cellular modeling: A mean-field approach.

Iafolla MA, McMillen DR.

J Phys Chem B. 2006 Nov 2;110(43):22019-28.

PMID:
17064172
[PubMed - indexed for MEDLINE]
2.

Free RNA polymerase and modeling global transcription in Escherichia coli.

Bremer H, Dennis P, Ehrenberg M.

Biochimie. 2003 Jun;85(6):597-609.

PMID:
12829377
[PubMed - indexed for MEDLINE]
3.

Studying genetic regulatory networks at the molecular level: delayed reaction stochastic models.

Zhu R, Ribeiro AS, Salahub D, Kauffman SA.

J Theor Biol. 2007 Jun 21;246(4):725-45. Epub 2007 Feb 6.

PMID:
17350653
[PubMed - indexed for MEDLINE]
4.
5.

Identifying promoter features of co-regulated genes with similar network motifs.

Harari O, del Val C, Romero-Zaliz R, Shin D, Huang H, Groisman EA, Zwir I.

BMC Bioinformatics. 2009 Apr 29;10 Suppl 4:S1. doi: 10.1186/1471-2105-10-S4-S1.

PMID:
19426448
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Kinetic modeling of ace operon genetic regulation in Escherichia coli.

Peskov K, Goryanin I, Prank K, Tobin F, Demin O.

J Bioinform Comput Biol. 2008 Oct;6(5):933-59.

PMID:
18942160
[PubMed - indexed for MEDLINE]
7.

Modeling feedback loops in the H-NS-mediated regulation of the Escherichia coli bgl operon.

Radde N, Gebert J, Faigle U, Schrader R, Schnetz K.

J Theor Biol. 2008 Jan 21;250(2):298-306. Epub 2007 Nov 5.

PMID:
17981304
[PubMed - indexed for MEDLINE]
8.

Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization.

Thiele I, Jamshidi N, Fleming RM, Palsson BØ.

PLoS Comput Biol. 2009 Mar;5(3):e1000312. doi: 10.1371/journal.pcbi.1000312. Epub 2009 Mar 13.

PMID:
19282977
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Generalized hill function method for modeling molecular processes.

Likhoshvai V, Ratushny A.

J Bioinform Comput Biol. 2007 Apr;5(2B):521-31.

PMID:
17636859
[PubMed - indexed for MEDLINE]
10.

Dynamic change in promoter activation during lysine biosynthesis in Escherichia coli cells.

Ou J, Yamada T, Nagahisa K, Hirasawa T, Furusawa C, Yomo T, Shimizu H.

Mol Biosyst. 2008 Feb;4(2):128-34. doi: 10.1039/b711035a. Epub 2007 Nov 28.

PMID:
18213406
[PubMed - indexed for MEDLINE]
11.

Anatomy of Escherichia coli sigma70 promoters.

Shultzaberger RK, Chen Z, Lewis KA, Schneider TD.

Nucleic Acids Res. 2007;35(3):771-88. Epub 2006 Dec 22.

PMID:
17189297
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

TABASCO: A single molecule, base-pair resolved gene expression simulator.

Kosuri S, Kelly JR, Endy D.

BMC Bioinformatics. 2007 Dec 19;8:480.

PMID:
18093293
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

An experimental and theoretical study of the inhibition of Escherichia coli lac operon gene expression by antigene oligonucleotides.

Cheng B, Fournier RL, Relue PA, Schisler J.

Biotechnol Bioeng. 2001 Aug 5;74(3):220-9.

PMID:
11400095
[PubMed - indexed for MEDLINE]
14.

Catabolite repression in Escherichia coli- a comparison of modelling approaches.

Kremling A, Kremling S, Bettenbrock K.

FEBS J. 2009 Jan;276(2):594-602. doi: 10.1111/j.1742-4658.2008.06810.x. Epub 2008 Dec 11.

PMID:
19087189
[PubMed - indexed for MEDLINE]
15.

Optimizing scaleup yield for protein production: Computationally Optimized DNA Assembly (CODA) and Translation Engineering.

Hatfield GW, Roth DA.

Biotechnol Annu Rev. 2007;13:27-42. Review.

PMID:
17875472
[PubMed - indexed for MEDLINE]
16.

The role of FIS protein in the physiological control of the expression of the Escherichia coli meta-hpa operon.

Galán B, Manso I, Kolb A, García JL, Prieto MA.

Microbiology. 2008 Jul;154(Pt 7):2151-60. doi: 10.1099/mic.0.2007/015578-0.

PMID:
18599842
[PubMed - indexed for MEDLINE]
Free Article
17.

Alternate SlyA and H-NS nucleoprotein complexes control hlyE expression in Escherichia coli K-12.

Lithgow JK, Haider F, Roberts IS, Green J.

Mol Microbiol. 2007 Nov;66(3):685-98. Epub 2007 Sep 24.

PMID:
17892462
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Exploring the antimicrobial action of a carbon monoxide-releasing compound through whole-genome transcription profiling of Escherichia coli.

Nobre LS, Al-Shahrour F, Dopazo J, Saraiva LM.

Microbiology. 2009 Mar;155(Pt 3):813-24. doi: 10.1099/mic.0.023911-0.

PMID:
19246752
[PubMed - indexed for MEDLINE]
Free Article
20.

A hybrid model of anaerobic E. coli GJT001: combination of elementary flux modes and cybernetic variables.

Kim JI, Varner JD, Ramkrishna D.

Biotechnol Prog. 2008 Sep-Oct;24(5):993-1006. doi: 10.1002/btpr.73.

PMID:
19194908
[PubMed - indexed for MEDLINE]

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