Please use this identifier to cite or link to this item: http://hdl.handle.net/1822/32872

TitleGenome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models
Author(s)Faria, J. P.
Overbeek, R.
Xia, F.
Rocha, Miguel
Rocha, I.
Henry, C. S.
Keywordsgenome-scale metabolic (GSM) model
transcriptional regulatory network (TRN)
de novo reverse engineering
integrated metabolic and regulatory models
Issue date2014
PublisherOxford University Press
JournalBriefings in Bioinformatics
CitationFaria, J. P.; Overbeek, R.; Xia, F.; Rocha, Miguel; Rocha, I.; Henry, C. S., Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models. Briefings in Bioinformatics, 15(4), 592-611, 2014
Abstract(s)Advances in sequencing technology are resulting in the rapid emergence of large numbers of complete genome sequences. High throughput annotation and metabolic modeling of these genomes is now a reality. The high throughput reconstruction and analysis of genome-scale transcriptional regulatory networks represents the next frontier in microbial bioinformatics. The fruition of this next frontier will depend upon the integration of numerous data sources relating to mechanisms, components, and behavior of the transcriptional regulatory machinery, as well as the integration of the regulatory machinery into genome-scale cellular models. Here we review existing repositories for different types of transcriptional regulatory data, including expression data, transcription factor data, and binding site locations, and we explore how these data are being used for the reconstruction of new regulatory networks. From template network based methods to de novo reverse engineering from expression data, we discuss how regulatory networks can be reconstructed and integrated with metabolic models to improve model predictions and performance. Finally, we explore the impact these integrated models can have in simulating phenotypes, optimizing the production of compounds of interest or paving the way to a whole-cell model.
TypeArticle
URIhttp://hdl.handle.net/1822/32872
DOI10.1093/bib/bbs071
ISSN1477-4054
e-ISSN1467-5463
Peer-Reviewedyes
AccessOpen access
Appears in Collections:CCTC - Artigos em revistas internacionais
CEB - Publicações em Revistas/Séries Internacionais / Publications in International Journals/Series

Files in This Item:
File Description SizeFormat 
document_14179_1.pdf1,07 MBAdobe PDFView/Open

Partilhe no FacebookPartilhe no TwitterPartilhe no DeliciousPartilhe no LinkedInPartilhe no DiggAdicionar ao Google BookmarksPartilhe no MySpacePartilhe no Orkut
Exporte no formato BibTex mendeley Exporte no formato Endnote Adicione ao seu ORCID