Mapping the Strategies of Viruses Hijacking Human Host Cells: An Experimental and Computational Comparative Study by Jacques Colinge
Interesting use of tagged proteins with purification and mass spec to analyse the interactions between viral and host proteins. Many viruses target the same proteins, but there is specificity too.
Drilling down on HCV, USP19 is a major target of viral proteins. This protein promotes degradation of misfolded proteins, but it may also be able to detect non-host proteins in general.
Human proteins that are targeted by virusses are much more likely to be hubs of protein/protein interaction networks. As virus are often very small so can only target a small number of proteins, thus targetting the hubs may be efficient (at the cost of specificity of effect).
Multi-task learning for Host-Pathogen protein interactions by Meghana Kshirsagar
Many pathogens will use the same strategies, thus we can learn across different pathogens to find similarities between different host/pathogen pairs. Their working hypothesis is that pathogens will target the same pathways in the host.
This is formalised as a multi-task learning process: loss on the training set is regularized by the difference of pairwise pathway signatures. Technically, this is nice because it can incorporate unlabeled data or missing data (as long as you can compute signatures).