Identification and characterization of transcription networks in environmentally significant species

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Understanding the regulation of gene expression, transcription regulation in particular, is one of the grand challenges of molecular biology. Transcription regulation is arguably the most important foundation of cellular function, since it exerts the most fundamental control of the abundance of virtually all of a cell's functional macromolecules. Nevertheless, this process, perhaps because of its difficulty, has been the subject of only a limited number of genomic level analyses. We have undertaken bioinformatics projects to address this issue by developing (1) a cross-species comparison method (i.e. phylogenetic footprinting) for the identification of transcription factor binding sites, (2) a Bayesian clustering ... continued below

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Lawrence, Charles E. & McCue, Lee Ann November 30, 2005.

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Description

Understanding the regulation of gene expression, transcription regulation in particular, is one of the grand challenges of molecular biology. Transcription regulation is arguably the most important foundation of cellular function, since it exerts the most fundamental control of the abundance of virtually all of a cell's functional macromolecules. Nevertheless, this process, perhaps because of its difficulty, has been the subject of only a limited number of genomic level analyses. We have undertaken bioinformatics projects to address this issue by developing (1) a cross-species comparison method (i.e. phylogenetic footprinting) for the identification of transcription factor binding sites, (2) a Bayesian clustering method to identify regulons, (3) an improved scanning algorithm that uses a position weight matrix and several related species sequence data to locate transcription factor binding sites, and (4) a method to predict cognate binding sites for transcription factors of unknown specificity. These bioinformatics methods were developed using the model proteobacterium Escherichia coli, with further applications to the genomes of environmentally significant microbes (Rhodopseudomonas palustris, Shewanella oneidensis) in later years of the grant.

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  • Report No.: DOE/ER/63204-1
  • Grant Number: FG02-01ER63204
  • DOI: 10.2172/860762 | External Link
  • Office of Scientific & Technical Information Report Number: 860762
  • Archival Resource Key: ark:/67531/metadc785296

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  • November 30, 2005

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  • Dec. 3, 2015, 9:30 a.m.

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  • Aug. 3, 2016, 8:32 p.m.

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Lawrence, Charles E. & McCue, Lee Ann. Identification and characterization of transcription networks in environmentally significant species, report, November 30, 2005; United States. (digital.library.unt.edu/ark:/67531/metadc785296/: accessed August 21, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.