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MOTIVATION It has long been hypothesized that incorporating models of network noise as well as edge directions and known pathway information into the representation of protein-protein interaction (PPI) networks might improve their utility for functional inference. However, a simple way to do this has not been obvious. We find that diffusion state distance(More)
We present an electronic format for exchanging data for HLA and KIR genotyping with extensions for next-generation sequencing (NGS). This format addresses NGS data exchange by refining the Histoimmunogenetics Markup Language (HML) to conform to the proposed Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING) reporting guidelines(More)
Characterizing protein function is a crucial part of understanding biological systems. Here we improve protein function prediction by accounting for data quality issues inherent in protein-protein interaction (PPI) databases. To accomplish this, we incorporate confidence information into the function prediction pipeline. The model pipeline uses weighted(More)
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