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STRING: a database of predicted functional associations between proteins
TLDR
STRING contains a unique scoring-framework based on benchmarks of the different types of associations against a common reference set, integrated in a single confidence score per prediction, facilitating the analysis of modularity in biological processes. Expand
STRING: known and predicted protein–protein associations, integrated and transferred across organisms
TLDR
STRING integrates and ranks these associations by benchmarking them against a common reference set, and presents evidence in a consistent and intuitive web interface. Expand
STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene.
TLDR
STRING (search tool for recurring instances of neighbouring genes), a tool to retrieve and display the genes a query gene repeatedly occurs with in clusters on the genome, performs iterative searches and visualises the results in their genomic context. Expand
Deciphering the evolution and metabolism of an anammox bacterium from a community genome
TLDR
This work uses environmental genomics—the reconstruction of genomic data directly from the environment—to assemble the genome of the uncultured anammox bacterium Kuenenia stuttgartiensis from a complex bioreactor community, and identifies candidate genes responsible for ladderane biosynthesis and biological hydrazine metabolism. Expand
Neutral evolution of mutational robustness.
TLDR
The results quantify the extent to which populations evolve mutational robustness-the insensitivity of the phenotype to mutations-and thus reduce genetic load. Expand
Genome phylogeny based on gene content
TLDR
This comprehensive genome phylogeny is independent of phylogenies based on the level of sequence identity of individual genes, and correlates with the standard reference of prokarytic phylogeny based on sequence similarity of 16s rRNA (ref. 4). Expand
Smoothness within ruggedness: the role of neutrality in adaptation.
TLDR
RNA secondary structure folding algorithms predict the existence of connected networks of RNA sequences with identical structure, on which the success of phenotypic adaptation becomes much less sensitive to the initial conditions in genotype space. Expand
Conservation of gene order: a fingerprint of proteins that physically interact.
TLDR
A systematic comparison of nine bacterial and archaeal genomes reveals a low level of gene-order (and operon architecture) conservation, but a number of gene pairs are conserved and appear to interact physically. Expand
Genomes in flux: the evolution of archaeal and proteobacterial gene content.
TLDR
This work reconstructs the gene content of ancestral Archaea and Proteobacteria and quantify the processes connecting them to their present day representatives based on the distribution of genes in completely sequenced genomes. Expand
Benchmarking ortholog identification methods using functional genomics data
TLDR
By combining the sensitivity and the selectivity into an overall score, it is shown that the InParanoid program is the best ortholog identification method in terms of identifying functionally equivalent proteins. Expand
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