With the talk about computer program and all. I think some of you might find this article interesting.
Joe DeRisi and Don Ganem have developed the Virochip. It is a broad-scale detection tool for identifying unknown pathogens. The chip currently has over approximately 22,000 viral sequences printed on it. DeRisi describest how the chip works like this, "If we are looking at a virus and trying to figure out what it is, we take some DNA and some RNA from a patient and we tag it with a fluorescent dye. Then we put that material onto the virus chip. Because matching genetic sequences stick to each other — the double helix — if there’s a match between what’s on the chip and our biological sample, a particular spot on the chip will glow. That tells us which virus the sample is. And, thanks to computers, we can do this with thousands of viruses at one time." http://www.nytimes.com/2008/10/07/health/research/07conv.html?_r=1&ei=5070&emc=eta1&oref=slogin
Dr. DeRisi is a Stanford alum and "currently an Howard Hughes Medical Institute (HHMI) Investigator and a Professor and Vice Chairman of the Department of Biochemistry and Biophysics at the University of California, San Francisco (UCSF) with a joint appointment at the California Institute for Quantitative Biomedical Research (QB3)." This is straight from Wikipedia, so go there for more info!
More interesting is http://derisilab.ucsf.edu/%20theDeRisi Lab website that showcases the genomic study of infectious disease. There are all sorts of abstracts about the work they are doing... lots of paper topics to be found!