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REGULATORY ELEMENTS OF MARINE CYANOBACTERIA
Genome Informatics 2007, 2007The free-living, oxyphototroph bacteria of the group of Prochlorococcus populate widely the oceans. Genomic information of nine marine cyanobacteria was used to predict signals essential for regulation. We implemented a pipeline that automatically calculates BLASTp alignments of query genomes, selects a representative subset of orthologs and predicts ...
Szymon M, Kiełbasa +2 more
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RECOGNITION OF CIS-REGULATORY ELEMENTS WITH VOMBAT
Journal of Bioinformatics and Computational Biology, 2007Variable order Markov models and variable order Bayesian trees have been proposed for the recognition of cis-regulatory elements, and it has been demonstrated that they outperform traditional models such as position weight matrices, Markov models, and Bayesian trees for the recognition of binding sites in prokaryotes.
Stefan Posch +5 more
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Unravelling the world of cis-regulatory elements
Medical & Biological Engineering & Computing, 2007Genome-wide comparisons indicate that only studying the coding regions will not be enough for explaining the biological complexity of an organism, while the genetic variants and the epigenetic differences of cis-regulatory elements are crucial to elucidate many complicated biological phenomena. Their various regulatory functions also play indispensable
Zhao Wang +3 more
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Structures of regulatory elements in mRNAs
Current Opinion in Structural Biology, 2006Messenger RNAs often contain structures in their 5'-untranslated region that serve to regulate or promote expression of their gene product. Recent structural studies have revealed that riboswitches, which bind a variety of small molecule metabolites, including purine bases, S-adenosylmethionine, amino acids and cofactors, can contain sophisticated ...
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Prediction of Regulatory Elements
2008Finding the regulatory mechanisms responsible for gene expression remains one of the most important challenges for biomedical research. A major focus in cellular biology is to find functional transcription factor binding sites (TFBS) responsible for the regulation of a downstream gene.
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Regulatory elements and expression profiles
Current Opinion in Structural Biology, 1999There has been steady progress in the computational analysis of transcription control regions, but current methods of predicting the gene regulatory features of noncoding sequences are still not accurate enough to be useful in automatic genome annotation. Therefore, detailed information on the expression patterns of newly sequenced genes is more likely
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In vitro selection of translational regulatory elements
Analytical Biochemistry, 2006Untranslated regions (UTRs) of mRNAs carry various kinds of translational regulatory elements; however, our knowledge of them is still limited. We created an in vitro selection system that allows us to make a systematic enrichment of the sequences that alter translation efficiency (SESTRE) in any given mRNA and translation system.
Issei, Nagao, Junichi, Obokata
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Applied bioinformatics for the identification of regulatory elements
Nature Reviews Genetics, 2004The compilation of multiple metazoan genome sequences and the deluge of large-scale expression data have combined to motivate the maturation of bioinformatics methods for the analysis of sequences that regulate gene transcription. Historically, these bioinformatics methods have been plagued by poor predictive specificity, but new bioinformatics ...
Wyeth W, Wasserman, Albin, Sandelin
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Genomics of Long-Range Regulatory Elements
Annual Review of Genomics and Human Genetics, 2010Transcriptional regulation of gene expression plays a significant role in establishing the diversity of human cell types and biological functions from a common set of genes. The components of regulatory control in the human genome include cis-acting elements that act across immense genomic distances to influence the spatial and temporal distribution ...
James P, Noonan, Andrew S, McCallion
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Transcriptional Regulatory Elements in the Human Genome
Annual Review of Genomics and Human Genetics, 2006The faithful execution of biological processes requires a precise and carefully orchestrated set of steps that depend on the proper spatial and temporal expression of genes. Here we review the various classes of transcriptional regulatory elements (core promoters, proximal promoters, distal enhancers, silencers, insulators/boundary elements, and locus
Glenn A, Maston +2 more
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