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Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework.Expand
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Genome sequence of Halobacterium species NRC-1.
We report the complete sequence of an extreme halophile, Halobacterium sp. NRC-1, harboring a dynamic 2,571,010-bp genome containing 91 insertion sequences representing 12 families and organized intoExpand
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The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
We present a method (the Inferelator) for deriving genome-wide transcriptional regulatory interactions, and apply the method to predict a large portion of the regulatory network of the archaeonExpand
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Peroxiredoxins are conserved markers of circadian rhythms
Cellular life emerged ∼3.7 billion years ago. With scant exception, terrestrial organisms have evolved under predictable daily cycles owing to the Earth’s rotation. The advantage conferred onExpand
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CTCF physically links cohesin to chromatin
Cohesin is required to prevent premature dissociation of sister chromatids after DNA replication. Although its role in chromatid cohesion is well established, the functional significance of cohesin'sExpand
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Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea.
We report the complete sequence of the 4,274,642-bp genome of Haloarcula marismortui, a halophilic archaeal isolate from the Dead Sea. The genome is organized into nine circular replicons of varyingExpand
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Catabolite control protein A (CcpA) contributes to virulence and regulation of sugar metabolism in Streptococcus pneumoniae.
We characterized the role of catabolite control protein A (ccpA) in the physiology and virulence of Streptococcus pneumoniae. S. pneumoniae has a large percentage of its genome devoted to sugarExpand
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The DNA-binding network of Mycobacterium tuberculosis
Mycobacterium tuberculosis (MTB) infects 30% of all humans and kills someone every 20–30 s. Here we report genome-wide binding for ~80% of all predicted MTB transcription factors (TFs), and assayedExpand
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A systems view of haloarchaeal strategies to withstand stress from transition metals.
Given that transition metals are essential cofactors in central biological processes, misallocation of the wrong metal ion to a metalloprotein can have resounding and often detrimental effects onExpand
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