Oscar Westesson

• Name: Oscar Westesson
• Email: oscar.westesson $picture}(10,10)\put(5,5){\circle{10}}\put(2,3){\alpha}\end{picture$ gmail dottt com
• Berkeley Office: 381D Stanley Hall
• UCSF: I can usually be found in the Andino wet lab or the Derisi computational room, both at UCSFMissionBay

I am a bioengineering graduate student interested in computational sequence analysis. I studied mathematics at Univeristy of Rochester and UC Berkeley. Besides computational biology I like climbing, bicycling, harassing my lab-mates, recovering bread, and drinking tea. I used to mostly drink green tea, but in recent years I have shifted towards black tea, especially Chinese teas. Lars Barquist and I keep an impressive selection in the lab, feel free to come by and talk transducers over a cup of Golden Monkey . Though Lars has left, his tea selection remains! I am also a big fan of acronyms, especially inventing and propagating them. If you have any to contribute, please feel free: Acronym List

Interests

Originally I studied math, and became interested in computational biology during a class with Bernd Sturmfels. I am broadly interested in applying mathematical/statistical/algorithmic tools to analyze biological sequence data, particularly from an evolutionary perspective. I find viruses to be an especially interesting venue for this sort of analysis: their small, absurdly complex/sophisticated genomes demand sophisticated modeling, and they evolve so fast that we can watch their genomes evolve in a laboratory setting.

During graduate school I worked on various aspects of viral genomics, modeling recombination, structured RNA, and population mutation distributions. I also worked on more general algorithms for multiple sequence alignment/evolutionary reconstruction and prediction of deleterious SNPs in proteins.

My Ph D research is summarized in my dissertation (25MB PDF).




Papers

• Ovaskainen et al. A probabilistic heirachical taxonomic classifier with applications to fungus in decaying logs. In prep