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Regulon inference without arbitrary thresholds: three levels of sensitivity

Reconstruction of transcriptional regulatory networks is one of the major challenges facing the bioinformatics community in view of constantly growing number of complete genomes. The comparative genomics approach has been successfully used for the analysis of the transcriptional regulation of many metabolic systems in various bacteria taxa. The key step in this approach is given a position weight matrix, find an optimal threshold for the search of potential binding sites in genomes. In our previous work we proposed an approach for automatic selection of TFBS score threshold coupled with inference of regulon content. In this study we developed two modifications of this approach providing two additional levels of sensitivity.
Date: November 15, 2010
Creator: Dubchak, Pavel Novichkov, Elena Stavrovskaya, Dmitry Rodionov, Andrey Mironov, Inna; Rodionov, Dmitry; Mironov, Andrey; Dubchak, Inna & Novichkov, P.S.
System: The UNT Digital Library

Reference set of regulons in Desulfovibrionales inferred by comparative genomics approach

in this study, we carried out large-scale comparative genomics analysis of regulatory interactions in Desulfovibrio vulgaris and 12 related genomes from Desulfovibrionales order using our recently developed web server RegPredict (http://regpredict.lbl.gov). An overall reference collection of 26 Desulfovibrionales regulogs can be accessed through RegPrecise database (http://regpredict.lbl.gov).
Date: November 15, 2010
Creator: Kazakov, Alexey E.; Rodionov, Dmitry A.; Price, Morgan N.; Arkin, Adam P.; Dubchak, Inna & Novichkov, Pavel S.
System: The UNT Digital Library

In silico discovery of the dormancy regulons in a number of Actinobacteria genomes

Mycobacterium tuberculosis is a dangerous Actinobacteria infecting nearly one third of the human population. It becomes dormant and phenotypically drug resistant in response to stresses. An important feature of the M. tuberculosis pathogenesis is the prevalence of latent infection without disease, making understanding of the mechanisms used by the bacteria to exist in this state and to switch to metabolically active infectious form a vital problem to consider. M. tuberculosis dormancy is regulated by the three-component regulatory system of two kinases (DosT and DevS) and transcriprional regulator (DevR). DevR activates transcription of a set of genes, which allow the bacteria to survive long periods of anaerobiosis, and may be important for long-term survival within the host during latent infection. The DevR-regulon is studied experimentally in M. tuberculosis and few other phylogenetically close Mycobacteria spp. As many other two-component systems, the devRS operon is autoregulated. However, the mechanism of the dormancy is not completely clear even for these bacteria and there is no data describing the dormancy regulons in other species.
Date: November 16, 2010
Creator: Gerasimova, Anna; Dubchak, Inna; Arkin, Adam & Gelfand, Mikhail
System: The UNT Digital Library

[Concert Poster: The Rolling Stones Project]

Poster advertising a concert by One O'Clock Lab Band with guest artists Bernard Fowler and Tim Ries on November 23, 2010, at Murchison Performing Arts Center.
Date: November 23, 2010
Creator: University of North Texas. College of Music. Division of Jazz Studies.
System: The UNT Digital Library

[Concert Poster: Zebras Fall Concert 2010]

Poster advertising a concert by Zebras on November 22,2010, at Kenton Hall. Poster shows a flamenco dancer in motion wearing a red dress with blue sleeves.
Date: November 22, 2010
Creator: University of North Texas. College of Music. Division of Jazz Studies.
System: The UNT Digital Library