Transcriptional regulatory networks

Qiu P. Recent advances in computational promoter analysis in understanding the transcriptional regulatory network. Biochem Biophys Res Commun 2003 309 495-501. 

Reconstructed nutrient-controlled transcriptional regulatory network, coupled to GSMM [364]... 

Lee TI, et al. Transcriptional regulatory networks in saccharomyces cerevisiae. Science 2002 298 799-804. 

Banzhaf W. and Kuo P. (2004). Network motifs in artificial and natural transcriptional regulatory network. Journal of Biological Physics and Chemistry. 4, pp 85-92. 

Bolouri, H., and E. H. Davidson. 2002. Modeling transcriptional regulatory networks. BioEs-says 24 1118-29. 

Herrgard, M. J., M. W. Covert, and B. O. Palsson. 2004. Reconstruction of microbial transcriptional regulatory networks. Curr Opin Biotechnol 15 70-7. 

Yamagnchi-Shinozaki, K., and K. Shinozaki. 2006. Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Anna. Rev. Plant Biol. 57 781-803. 

An investigation of transcriptional regulatory networks in Sacch. cerevisiae is reported in [17]. The authors have determined the association of most of the transcriptional regulators with genes across the genome. They use statistical analysis of the measurements to show the presence of network motifs, and then demonstrate that an automated process can use these motifs to assemble a transcriptional regulatory network. For three review articles in this field, see [18-20]. 

A. (2007) The transcriptional regulatory network of the amino acid producer Corynebacterium glutamicum. 

Jensen P, Lutz K, Papin J (2011) Tiger toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks. BMC Syst Biol 5 147 Jevremovic D, Trinh CT, Srienc F, Boley D (2010) On algebraic properties of extreme pathways in metabolic networks. J Comput Biol 17 107-119... 

Blais, A. and B. D. Dynlacht (2005). "Constructing transcriptional regulatory networks."... 

Tuncay, K., L. Ensman, et al. (2007). "Transcriptional regulatory networks via gene ontology and expression data." In Silico Biol 7(1) 21-34. 

Orr et al, 2002, Wuchty et al, 2003). For example, in the E. coli transcription regulatory network, most motifs overlap, in which the specific motifs are no longer clearly separable (Shen-Orr et al., 2002). 

Harris, S.E., Sawhill, B.K., Wuensche, A., Kauffman, S.A. A model of transcriptional regulatory networks based on biases in the observed regulation rules. Complexity 7(4), 23-40 (2001)... 

Ravcheev, D.A., Best, A.A., Sernova, N.V., et al. (2013) Genomic reconstruction of transcriptional regulatory networks in lactic add bactma. BMC Genomics 14,94. 

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