Viruses and Bioinformatics from Virology.uvic.ca
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Viruses and Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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DeNovo: virus-host sequence-based protein–protein interaction prediction

Can we predict protein–protein interactions (PPIs) of a novel virus with its host? Three major problems arise: the lack of known PPIs for that virus to learn from, the cost of learning about its proteins and the sequence dissimilarity among viral families that makes most methods inapplicable or inefficient. We develop DeNovo, a sequence-based negative sampling and machine learning framework that learns from PPIs of different viruses to predict for a novel one, exploiting the shared host proteins. We tested DeNovo on PPIs from different domains to assess generalization.
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BMC Genomics | Abstract | HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions

The HTRIdb is implemented as a relational database PostgreSQL that is connected to a web interface via the JBOSS AS that dynamically generates user-friendly HTML front-end queries using the Apache Tomcat web server. For the network visualization of interactions, HTRIdb uses the web version of the popular Cytoscape visualization tool (Cytoscape Web). The TF-TG interactions data currently present in HTRIdb have been collected from original research articles.

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