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We developed Graemlin 2.0, a new multiple network aligner with (1) a novel scoring function that can use arbitrary features of a multiple network alignment, such as protein deletions, protein duplications , protein mutations, and interaction losses; (2) a parameter learning algorithm that uses a training set of known network alignments to learn parameters(More)
The recent proliferation of protein interaction networks has motivated research into network alignment: the cross-species comparison of conserved functional modules. Previous studies have laid the foundations for such comparisons and demonstrated their power on a select set of sparse interaction networks. Recently, however, new computational techniques have(More)
We developed Graemlin 2.0, a new multiple network aligner with (1) a new multi-stage approach to local network alignment; (2) a novel scoring function that can use arbitrary features of a multiple network alignment, such as protein deletions, protein duplications, protein mutations, and interaction losses; (3) a parameter learning algorithm that uses a(More)
We have combined four different types of functional genomic data to create high coverage protein interaction networks for 11 microbes. Our integration algorithm naturally handles statistically dependent predictors and automatically corrects for differing noise levels and data corruption in different evidence sources. We find that many of the predictions in(More)
The collection of multiple genome-scale datasets is now routine, and the frontier of research in systems biology has shifted accordingly. Rather than clustering a single dataset to produce a static map of functional modules, the focus today is on data integration, network alignment, interactive visualization and ontological markup. Because of the intrinsic(More)
We have experimentally and computationally defined a set of genes that form a conserved metabolic module in the alpha-proteobacterium Caulobacter crescentus and used this module to illustrate a schema for the propagation of pathway-level annotation across bacterial genera. Applying comprehensive forward and reverse genetic methods and genome-wide(More)
IOA Freely available online through the Genome Research Open Access option. service Email alerting click here top right corner of the article or Receive free email alerts when new articles cite this article-sign up in the box at the Notes object identifier (DOIs) and date of initial publication. by PubMed from initial publication. Citations to Advance(More)
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