4 ms·

Here's a link to the actual papers (and code): (Note that none mentions "spam") http://mscompbio.codeplex.com/wikipage?title=PhyloD http://mscompbio.codeplex.c

Here's a link to the actual papers (and code): (Note that none mentions "spam") http://mscompbio.codeplex.com/wikipage?title=PhyloD http://mscompbio.codeplex.com/wikipage?title=PhyloD Overall it's pretty kickass, and the papers themselves tell why it's HIV in particular: HIV evolves extremely quickly within a specific host, so any general solution needs to be able to account for a virus that can adapt to your specific treatment regimen. And that's the link to spam-fighting: rapidly changing strategies to fool your immune system into thinking it's a good cell that should be let in, which is amenable to similar spam-fighting approaches.

carbocation 15y ago
These are great links, and answer many of the questions that I had. But there must be something more to the story; PhyloD is from 2007 and the news article is from 2011. Tangentially related, the research article that you linked is cited by a paper in PNAS that describes extraordinarily constrained coevolving group of sites in HIV (which appears to be a site of protein-protein interaction in the Gag protein). Such a group is likely a good target for multiple simultaneous therapeutics, as multiple mutations there likely reduce HIV's intrinsic fitness: http://www.pnas.org/content/108/28/11530.full http://www.pnas.org/content/108/28/11530.full
- kevinalexbrown 15y ago
  I was confused about the dates as well. It might be that this specific collaboration is new, but I don't really follow HIV in particular.
- ephermata 15y ago
  Checking David Heckerman's web page shows this paper from October 2011 in the Journal of Virology. I don't know how it relates to the news article specifically but it's interesting if you'd like to follow this stream of work. http://jvi.asm.org/content/early/2011/10/20/JVI.05577-11.abstract http://jvi.asm.org/content/early/2011/10/20/JVI.05577-11.abs... (Disclosure: I work at Microsoft Research, but not on this project.)

carbocation 15y ago

These are great links, and answer many of the questions that I had. But there must be something more to the story; PhyloD is from 2007 and the news article is from 2011. Tangentially related, the research article that you linked is cited by a paper in PNAS that describes extraordinarily constrained coevolving group of sites in HIV (which appears to be a site of protein-protein interaction in the Gag protein). Such a group is likely a good target for multiple simultaneous therapeutics, as multiple mutations there likely reduce HIV's intrinsic fitness: http://www.pnas.org/content/108/28/11530.full http://www.pnas.org/content/108/28/11530.full

kevinalexbrown 15y ago
I was confused about the dates as well. It might be that this specific collaboration is new, but I don't really follow HIV in particular.
ephermata 15y ago
Checking David Heckerman's web page shows this paper from October 2011 in the Journal of Virology. I don't know how it relates to the news article specifically but it's interesting if you'd like to follow this stream of work. http://jvi.asm.org/content/early/2011/10/20/JVI.05577-11.abstract http://jvi.asm.org/content/early/2011/10/20/JVI.05577-11.abs... (Disclosure: I work at Microsoft Research, but not on this project.)