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- Name: Oscar Westesson
- Email: oscar.westesson
 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 UCSF Mission Bay
About Oscar
I am a second-year 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 only got into computational biology in 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. Currently I am working on various aspects of viral genomics, ranging from fine-scale quasispecies modeling to evolution of genome structure, particularly with regard to cis-acting structured elements. I'm particularly interested in how short (e.g. within-host) and long (e.g. years, decades) term evolution interact and inform each other.
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Ongoing Projects
- Virus genomics
- Viral quasispecies modeling: Analyzing brand new array-based sequencing data to characterize viral quasispecies evolution. Comparable resolution to UHTS (e.g. 454 Life Sciences (Wikipedia) ), but cheap enough for many many time points. We plan to infect mice with different strains and concentrations and investigate the evolution of the quasispecies (by collecting poo-poo daily: Mouse Experiment). (UPDATE: the array proved problematic, we are migrating towards using Solexa sequencing for this sort of analysis)
- Clade Structure Grammar I'm trying to make reasonable predictions for conserved RNA structures in polio and related viruses (e.g. HRV, FMDV) using various modeling and folding tools. This is somewhat non-trivial since structured RNAs in viruses are both within coding regions and evolve completely differently than in previously studied organisms. The role of structured elements in long-term evolution (e.g. speciation events) as well as short-term (maintenance of population diversity within-host) is unknown, and I hope to address both of these via computational work closely linked with experiments.
- recHMM, a multi-tree HMM for detecting recombination (or rather multiple phylogenetic histories in an alignment). Eventually tying this in to JBrowse. See example plot at right.
- Modeling the fine-scale recombination dynamics, incorporating various genomic factors to account for breakpoint distributions. Initial data at right. Comparing to global distribution and/or synthetic viruses. I'm working on Sanger data from HIV env genes as well as deep sequencing (Illumina/Solexa), (nearly) whole-genome data from poliovirus. It is thought that a small number of 'hot' regions contribute most of the recombination events in poliovirus. Finding, modeling, and destroying these hotspots will provide valuable insights into quasispecies theory (e.g. the effect of recombination on diversity) as well as synthetic vaccine design (e.g. to avoid: Jegouic S, Joffret ML, Blanchard C, Riquet FB, Perret C, Pelletier I, Colbere-Garapin F, Rakoto-Andrianarivelo M, Delpeyroux F. Recombination between polioviruses and co-circulating Coxsackie A viruses: role in the emergence of pathogenic vaccine-derived polioviruses. PLoS Pathog. 2009 May;5(5):e1000412. Epub 2009 May 1. )
Papers
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