determining genome-wide exogenous binding of pathogens to host genome?
The techniques used to do this are ChIP-seq and ChIP-chip.

Basically, you


let the pathogen bind to the (highly replicated) DNA
cut up the DNA into little random pieces by sonication
enrich (“pull down”) the pathogen-bound DNA fragments by using a known antibody which binds to the pathogen
sequence the thus enriched DNA
map the sequenced fragments back to their original location on the genome.


Wikipedia has a nice picture explaining this process in a little more detail: