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Toward Automatic Reconstruction of a Highly Resolved Tree of Life
We have developed an automatable procedure for reconstructing the tree of life with branch lengths comparable across all three domains. The tree has its basis in a concatenation of 31 orthologsExpand
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Comparative assessment of large-scale data sets of protein–protein interactions
Comprehensive protein–protein interaction maps promise to reveal many aspects of the complex regulatory network underlying cellular function. Recently, large-scale approaches have predicted many newExpand
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The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract
Bifidobacteria are Gram-positive prokaryotes that naturally colonize the human gastrointestinal tract (GIT) and vagina. Although not numerically dominant in the complex intestinal microflora, theyExpand
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STRING: a database of predicted functional associations between proteins
STRING is a precomputed global resource for the exploration and analysis of functional links between proteins that are inferred from genomic associations between the genes that encode them. Expand
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STRING: known and predicted protein–protein associations, integrated and transferred across organisms
A full description of a protein's function requires knowledge of all partner proteins with which it specifically associates. Expand
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STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene.
The repeated occurrence of genes in each other's neighbourhood on genomes has been shown to indicate a functional association between the proteins they encode. Here we introduce STRING (search toolExpand
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STRING 7—recent developments in the integration and prediction of protein interactions
Information on protein–protein interactions is still mostly limited to a small number of model organisms, and originates from a wide variety of experimental and computational techniques. Expand
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Deciphering the evolution and metabolism of an anammox bacterium from a community genome
Anaerobic ammonium oxidation (anammox) has become a main focus in oceanography and wastewater treatment. It is also the nitrogen cycle's major remaining biochemical enigma. Among its features, theExpand
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Genome phylogeny based on gene content
Species phylogenies derived from comparisons of single genes are rarely consistent with each other, due to horizontal gene transfer, unrecognized paralogy and highly variable rates of evolution. TheExpand
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Conservation of gene order: a fingerprint of proteins that physically interact.
A systematic comparison of nine bacterial and archaeal genomes reveals a low level of gene-order (and operon architecture) conservation. Nevertheless, a number of gene pairs are conserved. TheExpand
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