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Sökning: WFRF:(Eisen Michael B.)

  • Resultat 11-14 av 14
  • Föregående 1[2]
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11.
  • Kyrpides, Nikos C, et al. (författare)
  • Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.
  • 2014
  • Ingår i: PLoS biology. - 1545-7885. ; 12:8
  • Tidskriftsartikel (refereegranskat)abstract
    • Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.
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12.
  • Misulovin, Ziva, et al. (författare)
  • Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genome
  • 2008
  • Ingår i: Chromosoma. - 0009-5915 .- 1432-0886. ; 117:1, s. 89-102
  • Tidskriftsartikel (refereegranskat)abstract
    • The cohesin complex is a chromosomal component required for sister chromatid cohesion that is conserved from yeast to man. The similarly conserved Nipped-B protein is needed for cohesin to bind to chromosomes. In higher organisms, Nipped-B and cohesin regulate gene expression and development by unknown mechanisms. Using chromatin immunoprecipitation, we find that Nipped-B and cohesin bind to the same sites throughout the entire non-repetitive Drosophila genome. They preferentially bind transcribed regions and overlap with RNA polymerase II. This contrasts sharply with yeast, where cohesin binds almost exclusively between genes. Differences in cohesin and Nipped-B binding between Drosophila cell lines often correlate with differences in gene expression. For example, cohesin and Nipped-B bind the Abd-B homeobox gene in cells in which it is transcribed, but not in cells in which it is silenced. They bind to the Abd-B transcription unit and downstream regulatory region and thus could regulate both transcriptional elongation and activation. We posit that transcription facilitates cohesin binding, perhaps by unfolding chromatin, and that Nipped-B then regulates gene expression by controlling cohesin dynamics. These mechanisms are likely involved in the etiology of Cornelia de Lange syndrome, in which mutation of one copy of the NIPBL gene encoding the human Nipped-B ortholog causes diverse structural and mental birth defects.
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13.
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14.
  • Rübel, Oliver, et al. (författare)
  • Integrating data clustering and visualization for the analysis of 3D gene expression data
  • 2010
  • Ingår i: IEEE/ACM Transactions on Computational Biology & Bioinformatics. - : Institute of Electrical and Electronics Engineers (IEEE). - 1545-5963 .- 1557-9964. ; 7:1, s. 64-79
  • Tidskriftsartikel (refereegranskat)abstract
    • The recent development of methods for extracting precise measurements of spatial gene expression patterns from three-dimensional (3D) image data opens the way for new analyses of the complex gene regulatory networks controlling animal development. We present an integrated visualization and analysis framework that supports user-guided data clustering to aid exploration of these new complex data sets. The interplay of data visualization and clustering-based data classification leads to improved visualization and enables a more detailed analysis than previously possible. We discuss 1) the integration of data clustering and visualization into one framework, 2) the application of data clustering to 3D gene expression data, 3) the evaluation of the number of clusters k in the context of 3D gene expression clustering, and 4) the improvement of overall analysis quality via dedicated postprocessing of clustering results based on visualization. We discuss the use of this framework to objectively define spatial pattern boundaries and temporal profiles of genes and to analyze how mRNA patterns are controlled by their regulatory transcription factors.
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  • Resultat 11-14 av 14
  • Föregående 1[2]
 
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