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Initial sequencing and analysis of the human genome.
TLDR
The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
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Integration of biological networks and gene expression data using Cytoscape
TLDR
This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest.
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A distinct lineage of CD4 T cells regulates tissue inflammation by producing interleukin 17
TLDR
In vivo, antibody to IL- 17 inhibited chemokine expression in the brain during experimental autoimmune encephalomyelitis, whereas overexpression of IL-17 in lung epithelium caused Chemokine production and leukocyte infiltration, indicating a unique T helper lineage that regulates tissue inflammation.
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The evolution of vertebrate Toll-like receptors.
TLDR
The complete sequences of Takifugu Toll-like receptor (TLR) loci and gene predictions from many draft genomes enable comprehensive molecular phylogenetic analysis and shows that coincidental evolution plays a minor role in TLR evolution.
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Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing
TLDR
Family-based genome analysis enabled us to narrow the candidate genes for both of these Mendelian disorders to only four and demonstrate the value of complete genome sequencing in families.
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Genome sequence of Halobacterium species NRC-1.
TLDR
Analysis of the genome sequence shows the presence of pathways for uptake and utilization of amino acids, active sodium-proton antiporter and potassium uptake systems, sophisticated photosensory and signal transduction pathways, and DNA replication, transcription, and translation systems resembling more complex eukaryotic organisms.
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Circulating microRNAs, potential biomarkers for drug-induced liver injury
TLDR
It is demonstrated that specific microRNA species, such as mir-122 and mir-192, both are enriched in the liver tissue and exhibit dose- and exposure duration-dependent changes in the plasma that parallel serum aminotransferase levels and the histopathology of liver degeneration, but their changes can be detected significantly earlier.
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Integrated genomic and proteomic analyses of a systematically perturbed metabolic network.
TLDR
An integrated approach to build, test, and refine a model of a cellular pathway, in which perturbations to critical pathway components are analyzed using DNA microarrays, quantitative proteomics, and databases of known physical interactions, suggests hypotheses about the regulation of galactose utilization and physical interactions between this and a variety of other metabolic pathways.
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Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes
The compact genome of Fugu rubripes has been sequenced to over 95% coverage, and more than 80% of the assembly is in multigene-sized scaffolds. In this 365-megabase vertebrate genome, repetitive DNA…
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The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
TLDR
The Inferelator uses regression and variable selection to identify transcriptional influences on genes based on the integration of genome annotation and expression data, and successfully predicted Halobacterium's global expression under novel perturbations with predictive power similar to that seen over training data.
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