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Items: 1 to 20 of 102

1.

Motif Participation by Genes in E. coli Transcriptional Networks.

Mayo M, Abdelzaher AF, Perkins EJ, Ghosh P.

Front Physiol. 2012 Sep 24;3:357. doi: 10.3389/fphys.2012.00357. eCollection 2012.

2.

Transcriptional Network Growing Models Using Motif-Based Preferential Attachment.

Abdelzaher AF, Al-Musawi AF, Ghosh P, Mayo ML, Perkins EJ.

Front Bioeng Biotechnol. 2015 Oct 12;3:157. doi: 10.3389/fbioe.2015.00157. eCollection 2015. Review.

4.
5.

Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network.

Dobrin R, Beg QK, Barabási AL, Oltvai ZN.

BMC Bioinformatics. 2004 Jan 30;5:10.

6.

Randomization Strategies Affect Motif Significance Analysis in TF-miRNA-Gene Regulatory Networks.

Sadegh S, Nazarieh M, Spaniol C, Helms V.

J Integr Bioinform. 2017 Jul 4. pii: /j/jib.ahead-of-print/jib-2017-0017/jib-2017-0017.xml. doi: 10.1515/jib-2017-0017. [Epub ahead of print]

PMID:
28675749
7.

Predicting transcriptional regulatory interactions with artificial neural networks applied to E. coli multidrug resistance efflux pumps.

Veiga DF, Vicente FF, Nicolás MF, Vasconcelos AT.

BMC Microbiol. 2008 Jun 19;8:101. doi: 10.1186/1471-2180-8-101.

8.

Crosstalk and the Dynamical Modularity of Feed-Forward Loops in Transcriptional Regulatory Networks.

Rowland MA, Abdelzaher A, Ghosh P, Mayo ML.

Biophys J. 2017 Apr 25;112(8):1539-1550. doi: 10.1016/j.bpj.2017.02.044.

9.

Evolvability of feed-forward loop architecture biases its abundance in transcription networks.

Widder S, Solé R, Macía J.

BMC Syst Biol. 2012 Jan 19;6:7. doi: 10.1186/1752-0509-6-7.

10.

An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs.

Ma HW, Kumar B, Ditges U, Gunzer F, Buer J, Zeng AP.

Nucleic Acids Res. 2004 Dec 16;32(22):6643-9. Print 2004.

11.

Cellular automata simulation of topological effects on the dynamics of feed-forward motifs.

Apte AA, Cain JW, Bonchev DG, Fong SS.

J Biol Eng. 2008 Feb 27;2:2. doi: 10.1186/1754-1611-2-2.

12.

Network motifs in the transcriptional regulation network of Escherichia coli.

Shen-Orr SS, Milo R, Mangan S, Alon U.

Nat Genet. 2002 May;31(1):64-8. Epub 2002 Apr 22.

PMID:
11967538
13.

Failure tolerance of motif structure in biological networks.

Mirzasoleiman B, Jalili M.

PLoS One. 2011;6(5):e20512. doi: 10.1371/journal.pone.0020512. Epub 2011 May 26.

14.

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.

15.

The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli.

Mangan S, Itzkovitz S, Zaslaver A, Alon U.

J Mol Biol. 2006 Mar 10;356(5):1073-81. Epub 2005 Dec 19.

PMID:
16406067
16.

Topological generalizations of network motifs.

Kashtan N, Itzkovitz S, Milo R, Alon U.

Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Sep;70(3 Pt 1):031909. Epub 2004 Sep 23.

PMID:
15524551
17.

Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli.

Marr C, Theis FJ, Liebovitch LS, Hütt MT.

PLoS Comput Biol. 2010 Jul 1;6:e1000836. doi: 10.1371/journal.pcbi.1000836.

18.

Top-level dynamics and the regulated gene response of feed-forward loop transcriptional motifs.

Mayo M, Abdelzaher A, Perkins EJ, Ghosh P.

Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Sep;90(3):032706. Epub 2014 Sep 10.

PMID:
25314472
19.

Control of transcriptional variability by overlapping feed-forward regulatory motifs.

Ratushny AV, Ramsey SA, Roda O, Wan Y, Smith JJ, Aitchison JD.

Biophys J. 2008 Oct;95(8):3715-23. doi: 10.1529/biophysj.108.134064. Epub 2008 Jul 11.

20.

Evolutionary modelling of feed forward loops in gene regulatory networks.

Cooper MB, Loose M, Brookfield JF.

Biosystems. 2008 Jan;91(1):231-44. Epub 2007 Oct 5.

PMID:
18082936

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